Index (EvoLudo: in silico evolution)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

A2 - Static variable in class RungeKutta: More magic numbers from Numerical Recipes in C.
A3 - Static variable in class RungeKutta
A4 - Static variable in class RungeKutta
A5 - Static variable in class RungeKutta
A6 - Static variable in class RungeKutta
About the Mersenne Twister - Section in class org.evoludo.math.MersenneTwister
About this Version - Section in class org.evoludo.math.MersenneTwister
above(double, double) - Method in class Line2D: Check if point (x,y) lies above or below the line.
above(Point2D) - Method in class Line2D: Check if point p lies above or below the line.
abs(double[]) - Static method in class ArrayMath: Element-wise absolute value of double array a.
abs(float[]) - Static method in class ArrayMath: Element-wise absolute value of float array a.
abs(int[]) - Static method in class ArrayMath: Element-wise absolute value of int array a.
absoluteTimeMenu - Variable in class LineGraph: The context menu item to toggle absolute x-axis tick labels.
AbstractGeometry - Class in org.evoludo.simulator.geometries: Abstract implementation of the population interaction and competition structures.
AbstractGeometry(EvoLudo) - Constructor for class AbstractGeometry: Create a new geometry scaffold linked to the given pacemaker.
AbstractGraph<B> - Class in org.evoludo.graphics: Abstract base class for 2D graphs rendered into a Canvas within the UI.
AbstractGraph(AbstractView, Module) - Constructor for class AbstractGraph: Create the base class for graphs.
AbstractGraph.HasLogScaleY - Interface in org.evoludo.graphics: Graphs that support logarithmic scaling on the y-axis should implement this interface.
AbstractGraph.HasTrajectory - Interface in org.evoludo.graphics: Graphs that show trajectories and support exporting their data should implement this interface.
AbstractGraph.MyContext2d - Class in org.evoludo.graphics: Create custom Context2d that admits drawing dashed lines.
AbstractGraph.Shifter - Interface in org.evoludo.graphics: Graphs that support shifting of their view should implement this interface.
AbstractGraph.Shifting - Interface in org.evoludo.graphics: Graphs that support shifting should implement this interface.
AbstractGraph.ZoomCommand - Class in org.evoludo.graphics: The zoom command for the context menu.
AbstractGraph.Zoomer - Interface in org.evoludo.graphics: Graphs that support zooming should implement this interface.
AbstractGraph.Zooming - Interface in org.evoludo.graphics: Graphs that support zooming should implement this interface.
AbstractLattice - Class in org.evoludo.simulator.geometries: Base class for lattice-based geometries providing shared handling of fixed boundary flags and parsing utilities.
AbstractLattice(EvoLudo) - Constructor for class AbstractLattice: Create a lattice geometry scaffold for the given engine.
AbstractNetwork - Class in org.evoludo.simulator.geometries: Base class for geometries constructed from specific degree distributions.
AbstractNetwork(EvoLudo) - Constructor for class AbstractNetwork: Create a network-backed geometry for the provided engine.
AbstractView<G> - Class in org.evoludo.simulator.views: The parent class of all panels that provide graphical representations the state of the current EvoLudo model.
AbstractView(EvoLudoGWT, Data) - Constructor for class AbstractView: The constructor for the abstract view.
AbstractView.ExportCommand - Class in org.evoludo.simulator.views: The export command triggered by the context menu entries.
AbstractView.ExportType - Enum Class in org.evoludo.simulator.views: The available export data types: SVG scalable vector graphics format, svg PDF portable document format, pdf (not yet implemented). EPS encapsulated postscript format, eps (not yet implemented). PNG portable network graphics format, png STAT_DATA statistics data as comma separated list, csv TRAJ_DATA trajectory data as comma separated list, csv (not yet implemented). STATE current state of simulation, plist
accuracy - Variable in class ODE: Desired accuracy to determine whether numerical integration has converged or a population has become monomorphic.
accuracy - Variable in class Network: The desired accuracy of the layouting process.
ACCURACY - Static variable in class RungeKutta: The accuracy required for the integration.
accuTypeScores - Variable in class IBSDPopulation: The array with the total scores for each trait.
action() - Method in class ContextMenuItem: Entry method when context menu item is selected.
activate() - Method in class AbstractGraph: Perform necessary preparations to show the graph in the GUI.
activate() - Method in class GenericPopGraph
activate() - Method in class ParaGraph
activate() - Method in class PopGraph2D
activate() - Method in class PopGraph3D
activate() - Method in class S3Graph
activate() - Method in class AbstractView: Activate the view.
activate() - Method in class Console
active - Variable in class IBSDPopulation: The array indicating which traits are active.
active - Variable in class Module: The array indicating which traits are active.
active - Static variable in class KeyHandler: Controller that currently has priority (typically the popup lab).
activeLinks - Variable in class IBSDPopulation: The array to keep track of all links along which a change in the population composition may occur.
activeModel - Variable in class EvoLudo: The active model
activeModule - Variable in class EvoLudo: The active module.
activeView - Variable in class ViewController: Currently active view.
activeViews - Variable in class ViewController: Registry of active views keyed by name.
add(double[], double) - Static method in class ArrayMath: Add scalar value to each element of double array/vector dst.
add(double[], double[]) - Static method in class ArrayMath: Add double arrays dst and add.
add(double[], double[], double[]) - Static method in class ArrayMath: Non-destructive array addition.
add(double, double) - Method in class Vector2D: Shift the coordinates of this 2D vector dx to the right and dy upwards.
add(double, double, double) - Method in class Vector3D: Shift the coordinates of this 3D vector by dx, dy and dz in the x-, y-, and z-coordinates, respectively.
add(float[], float) - Static method in class ArrayMath: Add scalar value to each element of float array/vector dst.
add(float[], float[]) - Static method in class ArrayMath: Add float arrays dst and add.
add(float[], float[], float[]) - Static method in class ArrayMath: Non-destructive array addition.
add(int[], int) - Static method in class ArrayMath: Add scalar value to each element of integer array/vector dst.
add(int[], int[]) - Static method in class ArrayMath: Add integer arrays dst and add.
add(int[], int[], int[]) - Static method in class ArrayMath: Non-destructive array addition.
add(long[], long) - Static method in class ArrayMath: Add scalar value to each element of long array/vector dst.
add(long[], long[]) - Static method in class ArrayMath: Add long arrays dst and add.
add(long[], long[], long[]) - Static method in class ArrayMath: Non-destructive array addition.
add(FocusPanel, Tooltip.Provider) - Method in class Tooltip: Register a new listener widget for tooltips and associate with the provider of the tooltip.
add(String) - Method in class Console.Log: Add a message to the log buffer.
add(String, ContextMenu) - Method in class ContextMenu: Add new submenu to context menu.
add(Point2D, Point2D) - Method in class Vector2D: Add the 2D vectors a and b and store the result in this vector.
add(Point3D, Point3D) - Method in class Vector3D: Add the 3D vectors a and b and store result in this vector.
add(Vector2D) - Method in class Vector2D: Add the 2D vector add to this vector.
add(Vector3D) - Method in class Vector3D: Add the 3D vector add to this vector.
add(T) - Method in class Module: Add pop to list of species.
add(T) - Method in class RingBuffer.LstItr
addAdvectionContribution(double[], double[], double[], double[]) - Method in class Advection: Adds the advection contribution of a single neighbor (si) to the accumulator adv for the focal site with state sn using precomputed delta = 1 + si - sn.
addAlpha(Color[], int) - Static method in class ColorMap: Utility method to add (or override) the transparency in the array color.
addAlpha(Color, int) - Static method in class ColorMap: Utility method to add (or override) the transparency of color color.
addAnaglyphMenu(ContextMenu) - Method in class Pop3D: Add the menu item to select anaglyph projection of the 3D space for a representation of the graph suitable for colored 3D glasses.
addAnimateMenu(ContextMenu) - Method in class GenericPopGraph: Helper method to process the debug submenu logic for context menu.
addAxesMenu(ContextMenu) - Method in class HistoGraph: Add the axes submenu with autoscale, full-range, and y-axis side controls.
addAxesMenu(ContextMenu) - Method in class LineGraph: Add the axes submenu with autoscale, full-range, log, and side controls.
addAxesMenu(ContextMenu) - Method in class Phase2D: Add the axes submenu with autoscale, full-range, and y-axis side controls.
addBufferSizeMenu(ContextMenu) - Method in class AbstractGraph: Add buffer size menu item to context menu if graph supports historical data.
addCandidate(int, int) - Method in class NetGames.IBSPop: The focal individual with index focal considers acts of cooperation towards the candidate member with index mdl through a probabilistic comparison of their differences in fitness as well as in levels of cooperativity.
addChangeHandler(ChangeHandler) - Method in class Slider
addChangeListener(ChangeListener) - Method in class EvoLudo: Add a change listener to the list of listeners that get notified when the model changes.
addClearMenu(ContextMenu) - Method in class GenericPopGraph: Helper method to process the clear context menu.
addClearMenu(ContextMenu) - Method in class S3Graph: Helper method to process the clear context menu.
addCLO(CLOption) - Method in class CLOParser: Adds option to current list of command line options.
addCLOProvider(CLOProvider) - Method in class CLOController: Register an additional source of command-line options.
addCLOProvider(CLOProvider) - Method in class EvoLudo: Register clo as a provider of command line options.
addCLOProvider(CLOProvider) - Method in class CLOParser: Add provider to the list of providers.
addColors(Color, Color) - Static method in class ColorMap: Utility method for adding the red, green, blue and alpha components of two colors.
addContextMenuHandler(ContextMenuHandler) - Method in class AbstractGraph
addContextMenuHandler(ContextMenuHandler) - Method in class Console.Log
addData(double) - Method in class HistoGraph: Add data point x to histogram.
addData(double[]) - Method in class LineGraph: Add data to the graph.
addData(double, double[]) - Method in class LineGraph: Add data to the graph.
addData(double, double[], boolean) - Method in class ParaGraph: Add data to the graph.
addData(double, double[], boolean) - Method in class S3Graph: Add data to the graph.
addData(int) - Method in class HistoGraph: Add data point to histogram by increasing the count of the bin with index bin by one.
addData(int, double) - Method in class HistoGraph: Add data point to histogram by increasing the count of the bin with index bin by incr.
addDebugSubmenu(ContextMenu, int, int) - Method in class GenericPopGraph: Helper method to process the debug submenu logic for context menu.
addDegreeGraphs(List, int) - Method in class Histogram: Add degree graphs for the given module.
addDirected() - Method in class AbstractGeometry: Add directed links to network.
addDisabledSpeciesName(Module, ContextMenu) - Method in class Phase2D: Add a disabled menu entry used as species header.
addEdgeAt(int, int) - Method in class AbstractGeometry: Add edge (undirected link) by inserting a pair of directed links.
addEventListener(String, EventListener) - Static method in class WindowGlobal: Register a JS event listener on the global window object.
addEvoLudoToDOM(Element, String) - Method in class EvoLudoWeb: Add an EvoLudo lab to the DOM element with the given ID.
addFitnessGraphs(List, int) - Method in class Histogram: Add fitness graphs for the given module.
addFitnessViews(Module, boolean, Map) - Method in class ViewController: Adds fitness-related views based on module capabilities.
addFixationProbabilityGraphs(List, int) - Method in class Histogram: Add fixation probability graphs for the given module.
addFixationTimeGraphs(List, int) - Method in class Histogram: Add fixation time graphs for the given module.
addFullscreenChangeHandler(String, FullscreenChangeHandler) - Static method in class NativeJS: JSNI method: Add a fullscreen change handler.
addFullscreenChangeHandler(FullscreenChangeHandler) - Method in class ContextMenu
addFullscreenChangeHandler(FullscreenChangeHandler) - Method in interface HasFullscreenChangeHandlers: Adds a FullscreenChangeEvent handler.
addFullscreenChangeHandler(FullscreenChangeHandler) - Method in class Tooltip
addGlobalKeyListeners() - Static method in class KeyHandler: Installs JS listeners that route keyboard events to all controllers.
addHeader(String) - Method in class ContextMenu: Add a disabled header item to the context menu.
addInputHandler(InputHandler) - Method in interface HasInputHandlers: Adds a InputEvent handler.
addInputHandler(InputHandler) - Method in class Slider
addKey(String, String) - Method in class CLOption: Add a CLOption.Key to option with name key and description title.
addKey(CLOption.Key) - Method in class CLOption: Add CLOption.Key key to option.
addKeys(Collection) - Method in class CLOption: Add all CLOption.Keys in the collection chain to this option.
addKeys(CLOption.Key[]) - Method in class CLOption: Add all CLOption.Keys in the array chain to this option.
addLifecycleListener(LifecycleListener) - Method in class EvoLudo: Add a lifecycle listener to the list of listeners that get notified when the model reaches lifecycle milestones.
addLineGraph(Module) - Method in class Mean: Create and register the LineGraph(s) for a single module: one graph for the module, and additional graphs for extra traits when the model is continuous.
addLinkAt(int, int) - Method in class AbstractGeometry: Add a directed link from from to to, allocating storage as needed.
addListener(LifecycleListener) - Method in class LifecycleController: Add a lifecycle listener to the list of listeners that get notified when the model reaches lifecycle milestones.
addListener(RunListener) - Method in class RunController: Add a run listener to the list of listeners that get notified about model run state changes.
addListenerWithProvider(ContextMenu.Listener, ContextMenu.Provider) - Method in class ContextMenu: Register a new listener widget for context menu requests and associate with the provider of the context menu.
addLogScaleMenu(ContextMenu) - Method in class AbstractGraph: Add logarithmic scale menu item to context menu if graph supports log scale on y-axis.
addMarker(double[]) - Method in class Markers: Add marker to list of markers.
addMarker(double[], boolean) - Method in class Markers: Add marker to list of markers.
addMarker(double, String, String) - Method in class HistoGraph: Add marker to histogram at x with color color and description descr.
addMarker(double, String, String, int[]) - Method in class HistoGraph: Add marker to histogram at x with color color, description descr, and linestyle linestyle.
addModule(Module) - Method in class EvoLudo: Add module to lookup table of modules using the module's key.
addModuleKey(String, String) - Method in class CLOController: Notify controller that available module keys changed.
addNeighbor(int, int, int, int) - Method in class CubicGeometry: Adds a neighbor if all indices are valid (non-negative).
addProjectionMenu(ContextMenu) - Method in class Pop3D: Add the menu item to select parallel projection of the graph instead of the default perspective projection.
addRunListener(RunListener) - Method in class EvoLudo: Add a run listener to the list of listeners that get notified about model run state changes.
addSampleListener(SampleListener) - Method in class EvoLudo: Add a change listener to the list of listeners that get notified when the model changes.
addscale(double[], double[], double, double[]) - Static method in class ArrayMath: Non-destructive scalar multiplication and array addition.
addSeparator() - Method in class ContextMenu: Add new separator to context menu.
addSetTraitMenu(ContextMenu, int, int) - Method in class S3Graph: Helper method to process the select traits submenu.
addShakeMenu(ContextMenu) - Method in class GenericPopGraph: Helper method to process the debug submenu logic for context menu.
addSixNeighborsFixed(boolean, int, int, int, int) - Method in class CubicGeometry: Adds the six nearest-neighbors with fixed boundary conditions.
addSixNeighborsToroidal(boolean, int, int, int, int) - Method in class CubicGeometry: Adds the six nearest-neighbors with toroidal boundary conditions.
addState(double[]) - Method in class IBSMCPopulation: Adds the traits of all individuals to the array state.
addStationaryGraphs(List, int) - Method in class Histogram: Add stationary distribution graphs for the given module.
addStatisticsViews(Module, Model, Map) - Method in class ViewController: Adds statistics-related views based on model permissions.
addStrategyViews(Module, boolean, Map) - Method in class ViewController: Adds strategy-related views according to module capabilities.
addStructureViews(Module, boolean, Map) - Method in class ViewController: Adds structure-related views when available.
addSwapOrderMenu(ContextMenu, int, int) - Method in class S3Graph: Helper method to process the swap order submenu logic of the context menu.
addTraitGraphs(List) - Method in class Histogram: Add trait histogram for the given module.
addUndirected() - Method in class AbstractGeometry: Add undirected links.
addView(AbstractView, Map) - Method in class ViewController: Registers a view and inserts it into the deck, reusing an existing instance if available.
addVRMenu(ContextMenu) - Method in class Pop3D: Add the menu item to select stereo projection of the 3D space for a virtual reality representation of the graph.
addZoomMenu(ContextMenu) - Method in class AbstractGraph: Add zoom menu items to context menu if graph supports zooming.
adjust(double, double, double, double) - Method in class Rectangle2D: Adjust the position of the origin, the lower left corner (x,y), as well as the dimensions, i.e.
ADJUST_LAYOUT - Enum constant in enum class Network.Status: layout adjustments/improvements requested
adjustBoundaries(AbstractGeometry, int, int, int, boolean) - Static method in class MooreGeometry: Adjust Moore stencils along fixed boundaries.
adjustBoundaries(AbstractGeometry, int, int, int, boolean) - Static method in class SecondNeighbourGeometry: Adjust second-neighbour von Neumann stencils along fixed boundaries.
adjustBoundaries(AbstractGeometry, int, int, int, boolean) - Static method in class VonNeumannGeometry: Adjust von Neumann neighbourhoods when fixed boundaries are requested.
adjustBoundaries(AbstractGeometry, int, int, int, int, boolean) - Static method in class SquareGeometry: Adjust arbitrary-range neighbourhoods along fixed boundaries.
adjustBoundsForLabels() - Method in class AbstractGraph: Adjust bounds to make room for axes labels.
adjustBoundsForTickLabels() - Method in class AbstractGraph: Adjust bounds to make room for tick labels.
adjustBoundsForYSide(double) - Method in class AbstractGraph: Adjust bounds to make room for y-axis decorations on the selected side.
adjustCLO(CLOParser) - Method in class ATBT
adjustCLO(CLOParser) - Method in class CDL
adjustCLO(CLOParser) - Method in class DemesTBT
adjustCLO(CLOParser) - Method in class NetGames
adjustCLO(CLOParser) - Method in class RSP
adjustCLO(CLOParser) - Method in class TBT
adjustCLO(CLOParser) - Method in interface CLOProvider: Providers of command line options may want to remove certain options that other providers provided by overriding this method.
adjustGameScoresAt(int) - Method in class IBSDPopulation: Adjust scores of focal player me and its neighbours (interaction partners).
adjustGameScoresAt(int) - Method in class IBSPopulation: Adjust scores of focal player me and its neighbours (interaction partners).
adjustGameScoresAt(int) - Method in class DemesTBT.IBSPop: Adjust scores of focal player me and its neighbours (interaction partners).
adjustNeighborScores(int[], int, int) - Method in class IBSDPopulation: Adjust the scores of neighboring individuals after a focal individual changed its trait.
adjustOccupiedScoreAt(int[], int, int[], int, int) - Method in class IBSDPopulation: Adjust the score of the neighbours of a focal individual that became occupied.
adjustOpponentScoresAt(int) - Method in class IBSDPopulation: Adjust scores in the opponent population when a trait change happens in an inter-species well-mixed setting.
adjustPairGameScoresAt(int) - Method in class IBSCPopulation: Adjusts scores of focal individual with index me and its neighbors after me changed trait.
adjustPairGameScoresAt(int) - Method in class IBSDPopulation
adjustPairGameScoresAt(int) - Method in class IBSMCPopulation: Adjusts scores of focal individual with index me and its neighbors after me changed trait.
adjustPairGameScoresAt(int) - Method in class IBSPopulation: Adjusts scores of focal individual with index me and its neighbors after me changed trait.
adjustScoreAt(int, double) - Method in class IBSDPopulation
adjustScoreAt(int, double) - Method in class IBSMCPopulation
adjustScoreAt(int, double) - Method in class IBSPopulation: Adjust score of individual with index index by adjust and update all applicable helper variables, e.g.
adjustScoreAt(int, double, double) - Method in class IBSDPopulation
adjustScoreAt(int, double, double) - Method in class IBSMCPopulation
adjustScoreAt(int, double, double) - Method in class IBSPopulation: Adjust score of individual with index index from before to after and update all applicable helper variables, e.g.
adjustScores - Variable in class IBSPopulation: Optimization: Flag to indicate whether adjusting instead of recalculating scores is possible.
adjustVacantScoreAt(int, int, int[], int, int[], int, int) - Method in class IBSDPopulation: Adjust the score of a focal individual that became vacant.
advcoeff - Variable in class Advection: The 2D array of advection coefficients for each trait against all others.
Advection - Class in org.evoludo.simulator.models: Numerical integration of partial differential equations for reaction-diffusion-advection systems based on Euler's method (fixed step size).
Advection(EvoLudo) - Constructor for class Advection: Constructs a new model for the numerical integration of the system of partial differential equations representing the dynamics specified by the Module module using the EvoLudo pacemaker engine to control the numerical evaluations.
AffineTransform - Class in org.evoludo.geom: The AffineTransform class represents a 2D affine transform that performs a linear mapping from 2D coordinates to other 2D coordinates that preserves the "straightness" and "parallelness" of lines.
AffineTransform() - Constructor for class AffineTransform: Constructs a new AffineTransform representing the Identity transformation.
AffineTransform(double[]) - Constructor for class AffineTransform: Constructs a new AffineTransform from an array of double precision values representing either the 4 non-translation entries or the 6 specifiable entries of the 3x3 transformation matrix.
AffineTransform(double, double, double, double, double, double) - Constructor for class AffineTransform: Constructs a new AffineTransform from 6 double precision values representing the 6 specifiable entries of the 3x3 transformation matrix.
AffineTransform(double, double, double, double, double, double, int) - Constructor for class AffineTransform
AffineTransform(AffineTransform) - Constructor for class AffineTransform: Constructs a new AffineTransform that is a copy of the specified AffineTransform object.
ak2 - Variable in class RungeKutta: Temporary variables for intermediate results required to implement the fifth-order Cash-Karp Runge-Kutta method.
ak3 - Variable in class RungeKutta
ak4 - Variable in class RungeKutta
ak5 - Variable in class RungeKutta
ak6 - Variable in class RungeKutta
alert(String) - Static method in class NativeJS: JSNI method: Display javascript alert panel.
ALL - Enum constant in enum class IBSGroup.SamplingType: Sample all neighbours.
ALL - Enum constant in enum class Mutation.Discrete.Type: Mutate to any trait.
alloc() - Method in class AbstractGeometry: Allocate the memory necessary to store the network structure.
allocArrays(boolean) - Method in class ODE: Allocate working arrays for the current dimensionality and payoff mode.
allocateGraphs() - Method in class AbstractView: Allocate all graphs managed by this view.
allocateGraphs() - Method in class Console
allocateGraphs() - Method in class Distribution
allocateGraphs() - Method in class Histogram
allocateGraphs() - Method in class Mean
allocateGraphs() - Method in class Phase2D
allocateGraphs() - Method in class Pop2D
allocateGraphs() - Method in class Pop3D
allocateGraphs() - Method in class S3
allocateIBSGraphs() - Method in class Pop2D: Allocate graphs for individual-based spatial models.
allocateIBSGraphs() - Method in class Pop3D: Allocate graphs for individual-based spatial models.
allocatePDEGraph() - Method in class Pop2D: Allocate graph for PDE models.
allocatePDEGraph() - Method in class Pop3D: Allocate graph for PDE models.
alpha - Variable in class PDE: Helper variable to store the effective diffusion terms.
ambient - Variable in class PopGraph3D: The ambient light source illuminating the scene.
amplification - Variable in class SuperstarGeometry: Amplification factor (length of the linear chain plus additional nodes).
anaglyphMenu - Variable in class Pop3D: The context menu item for selecting anaglyph projection of the 3D space for a reperesentation of the graph suitable for colored 3D glasses.
animate - Variable in class GenericPopGraph: The mode of the animation of the network layouting process.
animateMenu - Variable in class GenericPopGraph: The context menu item for animating the layouting process.
append(boolean[], boolean) - Static method in class ArrayMath: Append element to boolean array array.
append(double[], double) - Static method in class ArrayMath: Append element to double array array.
append(double, double) - Method in class Path2D: Append the point with coordinates (x,y) to this path.
append(int[], int) - Static method in class ArrayMath: Append element to int array array.
append(Path2D.Iterator, boolean) - Method in class Path2D: Appends the geometry of the specified Path2D.Iterator object to the path, possibly connecting the new geometry to the existing path segments with a line segment.
append(T) - Method in class RingBuffer: Append new entry to ring buffer.
append(T[], T) - Static method in class ArrayMath: Append element of type T to array array of the same type.
appendBinTooltip(StringBuilder, int) - Method in class HistoGraph: Append tooltip for bin at mouse coordinates.
appendCategorizedHelp(StringBuilder) - Method in class CLOParser: Appends help text for all options grouped by category.
appendCompNeighborsAt(int, AbstractGeometry, StringBuilder) - Static method in class GenericPop: Append competition neighbours at the given node.
appendFitnessTip(int, Module, StringBuilder) - Method in class GenericPop: Append fitness (and payoffs if the module is using payoff-to-fitness mappings) as well as interaction count for modules implementing the Payoffs interface.
appendFormattedValues(StringBuilder, double[], int, Map2Fitness, boolean) - Method in class GenericPop: Append a comma separated list of values (or '-' for vacant index).
appendInterNeighborsAt(int, AbstractGeometry, StringBuilder) - Static method in class GenericPop: Append interaction neighbours at the given node.
appendLinearTip(int, int, StringBuilder) - Method in class GenericPop: Append tooltip information for linear geometry / time slices.
appendNeighbors(String, int[], int, StringBuilder) - Static method in class GenericPop: Return a formatted string of the neighbourhood structure at the given node.
appendNodeTraitTip(int, int, G, StringBuilder) - Method in class GenericPop: Append node and trait information (with color when appropriate).
appendOppTraitsAt(int, AbstractGeometry, G, StringBuilder) - Method in class GenericPop: Append opponent traits at the given node.
appendOptionsForCategory(StringBuilder, CLOCategory) - Method in class CLOParser: Appends help text for options in the specified category.
appendPDEFitnessTip(int, Module, G, StringBuilder) - Method in class GenericPop: Append fitness and payoff information for PDE models.
appendPDETraitTip(int, Module, G, StringBuilder) - Method in class GenericPop: Append trait and density information for PDE models.
appendProgress(String) - Static method in class MersenneTwister: Append message to buffer (no newline added).
appendTipContinuous(StringBuilder, double[], Color[]) - Method in class LineGraph: Append mean ± sdev row for Continuous modules.
appendTipDegree(StringBuilder, int) - Method in class HistoGraph: Append degree tooltip.
appendTipFixProb(StringBuilder, int) - Method in class HistoGraph: Append fixation probability tooltip.
appendTipFixTime(StringBuilder, int) - Method in class HistoGraph: Append fixation time tooltip.
appendTipHeader(StringBuilder, double, double) - Method in class LineGraph: Build and append the static header rows (label, x and y rows) to the tooltip.
appendTipInterpolation(StringBuilder, double) - Method in class LineGraph: Append interpolated values (either Continuous mean±sdev or trait values) to the tooltip builder using the precomputed interpolation result.
appendTipStationary(StringBuilder, int) - Method in class HistoGraph: Append stationary distribution tooltip.
appendTipTraits(StringBuilder, double[], Color[]) - Method in class LineGraph: Append individual trait rows for non-Continuous modules.
appendUncategorizedHelp(StringBuilder) - Method in class CLOParser: Appends help text for all options without category grouping.
appendY0(double[], int) - Method in class ODEInitialize: Append the provided population initialization vector at the given offset within ODE.y0, resizing as needed.
apply(int, int, double[], double[][]) - Method in class PDEInitialize: Applies the initialization for GeometryType.LINEAR.
apply(int, int, int, double[], double[][]) - Method in class PDEInitialize: Applies the initialization for GeometryType.SQUARE and variants.
apply(int, int, int, int, int, double[], double[][]) - Method in class PDEInitialize: Applies the initialization for GeometryType.CUBE.
APPLY_IDENTITY - Static variable in class AffineTransform: This constant is used for the internal state variable to indicate that no calculations need to be performed and that the source coordinates only need to be copied to their destinations to complete the transformation equation of this transform.
APPLY_SCALE - Static variable in class AffineTransform: This constant is used for the internal state variable to indicate that the scaling components of the matrix (m00 and m11) need to be factored in to complete the transformation equation of this transform.
APPLY_SHEAR - Static variable in class AffineTransform: This constant is used for the internal state variable to indicate that the shearing components of the matrix (m01 and m10) need to be factored in to complete the transformation equation of this transform.
APPLY_TRANSLATE - Static variable in class AffineTransform: This constant is used for the internal state variable to indicate that the translation components of the matrix (m02 and m12) need to be added to complete the transformation equation of this transform.
applyButton - Variable in class SettingsController: Button used to apply or open standalone lab.
applyCLO() - Method in class EvoLudoWeb: Process and apply the command line arguments stored in EvoLudoWeb.evoludoCLO Loads new model (and unloads old one), if necessary, and loads/adjusts the data views as appropriate.
applyCLOFromField() - Method in class EvoLudoWeb: Applies the text currently in the CLO field to the engine.
applyDefaultStyle(GraphStyle) - Method in class Histogram: Apply default style settings to the given graph style.
applyDegreeStyle(HistoGraph, int, int) - Method in class Histogram: Apply style settings for degree histograms.
applyDependentTraits(double[]) - Method in class ODE: Adjust dependent traits for all species in frequency-based dynamics so each species' frequencies sum to one.
applyDependentTraits(double[], int, int, int) - Method in class ODE: Adjust the dependent trait for a single species slice in frequency-based dynamics.
applyFitnessStyle(HistoGraph, int) - Method in class Histogram: Apply style settings for fitness histograms.
applyFixationProbabilityStyle(HistoGraph, int) - Method in class Histogram: Apply style settings for fixation probability histograms.
applyFixationTimeStyle(HistoGraph, int, boolean, boolean) - Method in class Histogram: Apply style settings for fixation time histograms.
applyRanges(double, double, double, double, boolean, boolean) - Method in class ParaGraph: Apply axis ranges with axis-specific constraints.
applyStationaryStyle(HistoGraph, int) - Method in class Histogram: Apply style settings for stationary distribution histograms.
applyStep(int, int, double) - Method in class SDE: Apply an Euler step with zero-clamping to prevent extinct traits from reappearing due to roundoff errors.
applyTraitStyle(HistoGraph, int) - Method in class Histogram: Apply style settings for trait histograms.
applyUiToggles(Runnable) - Method in class SettingsController: Applies the appropriate UI toggles based on the current ePub mode.
applyUpdates(double[], double[], double[]) - Method in class ODE: Apply update dynamics (ecological or player-update) to all species.
applyVisibleRanges(ParaGraph.ViewState) - Method in class ParaGraph: Adjust axis ranges to match the current zoom and shift.
applyXConstraints() - Method in class ParaGraph: Clamp and snap the x-axis range according to axis settings.
applyXDecorations(GraphStyle, boolean, boolean) - Method in class Histogram: Configure x-axis decorations based on group and overall position.
applyYConstraints() - Method in class ParaGraph: Clamp and snap the y-axis range according to axis settings.
args - Variable in class IBS.Statistics: The settings for the statistics.
args - Variable in class IBSC.Init: The array of arguments for the initialization of each trait.
args - Variable in class IBSD.Init: The arguments for the initialization.
Argument() - Constructor for enum class CLOption.Argument
ARRAY_CLOSE - Static variable in class Plist: String constant for closing an array during plist generation.
ARRAY_OPEN - Static variable in class Plist: String constant for opening an array during plist generation.
arrayLength(T) - Method in class RingBuffer: Helper method to deal with entry representing an array.
ArrayMath - Class in org.evoludo.math: Collection of convenience methods for mathematical operations, including array manipulations and statistics.
ArrayMath() - Constructor for class ArrayMath: Ensure non-instantiability with private default constructor
ASYNC - Enum constant in enum class PopulationUpdate.Type: Asynchronous population updates.
ATBT - Class in org.evoludo.simulator.modules: The module for investigating the evolutionary dynamics in asymmetric 2×2 games.
ATBT(EvoLudo) - Constructor for class ATBT: Create a new instance of the module for asymmetric 2×2 games.
ATBT.ATBTMap - Class in org.evoludo.simulator.modules: The class that defines the mapping of asymmetric 2×2 games onto a 2D phase plane: fraction of cooperators along x-axis and fraction of rich patches along y-axis.
ATBT.ATBTPop - Class in org.evoludo.simulator.modules: Extends TBT.TBTPop to take advantage of kaleidoscope initializations.
ATBT.ODE - Class in org.evoludo.simulator.modules: Provide ODE implementation for asymmetric 2×2 games with environmental feedback.
ATBTMap() - Constructor for class ATBT.ATBTMap: Create the 2D projection helper using the surrounding module settings.
ATBTPop(ATBT) - Constructor for class ATBT.ATBTPop: Create a new instance of the IBS model for asymmteric 2×2 games.
attraction - Variable in class Network2D: Helper variable to store intermediate results when considering the potential energy resulting from the attraction between neighbouring nodes.
attraction - Variable in class Network3D: Helper variable to store intermediate results when considering the potential energy resulting from the attraction between neighbouring nodes.
attraction(int) - Method in class Network: Calculate the potential energy based on attraction to its neighbours for the node with index nodeidx.
attraction(int) - Method in class Network2D
attraction(int) - Method in class Network3D
attributes - Variable in class PlistTag: The attributes of tag (or null).
autoClose - Variable in class ContextMenu: true to close sub-menus automatically when pointer exited the sub-menu.
autoDt - Variable in class RungeKutta: true if the adaptive step sizes should be used.
autoHide - Variable in class ContextMenu: true to automatically set timer for hiding context menu after pointer exited context menu.
autoOpen - Variable in class ContextMenu: true to open sub-menus automatically on hovering over the corresponding parent menu item.
autoscale - Static variable in class HistoGraph: The list of thresholds for automatically scaling the y-axis.
autoscale() - Method in class ParaGraph: Automatically adjust the range of autoscaled axes to fit the data in the buffer.
autoscale(boolean, boolean) - Method in class AbstractGraph: Set auto-scaling for horizontal and vertical axes.
autoscaleidx - Variable in class HistoGraph: The index of the current autoscale setting.
autoscaleMenu - Variable in class Phase2D: The context menu item to toggle autoscaling on both axes.
autoscalePoint - Variable in class ParaGraph: Reusable point for autoscale calculations.
autoscaleX - Variable in class GraphStyle: The flag to indicate whether to auto-scale the horizontal axis.
autoscaleY - Variable in class GraphStyle: The flag to indicate whether to auto-scale the vertical axis.
autoscaleYMenu - Variable in class HistoGraph: The context menu item to select autoscaling of the y-axis.
autoscaleYMenu - Variable in class LineGraph: The context menu item to toggle autoscaling of the y-axis.
avgIn - Variable in class GeometryFeatures: The average number of incoming links.
avgOut - Variable in class GeometryFeatures: The average number of outgoing links.
avgScores(double[], double[]) - Method in interface Model.HasDE.DPairs: Calculate the average payoff for the frequency of traits specified in the array state for pairwise interactions.
avgScores(double[], double[]) - Method in class ATBT
avgScores(double[], double[]) - Method in class RSP
avgScores(double[], double[]) - Method in class TBT
avgScores(double[], int, double[]) - Method in interface Model.HasDE.DGroups: Calculate the average payoff for the frequency of traits specified in the array state for interactions in groups of size n.
avgScores(double[], int, double[]) - Method in class CDL: Calculate the average payoff for the frequency of traits specified in the array state for interactions in groups of size n.
avgScores(double[], int, double[]) - Method in class CDLP
avgScores(double[], int, double[]) - Method in class CDLPQ
avgScores(double[], int, double[]) - Method in class EcoPGG
avgTot - Variable in class GeometryFeatures: The average sum of incoming and outgoing links.
axesLabelFont - Variable in class GraphStyle: The font for the axes labels as a CSS string.
axesMenu - Variable in class HistoGraph: The context menu for axis-related options.
axesMenu - Variable in class LineGraph: The context menu for axis-related options.
axesMenu - Variable in class Phase2D: The context menu for axis-related controls.
axis - Variable in class Distribution.TraitCommand: The axis that this command affects.
axis - Variable in class Phase2D.TraitCommand: The axis that this command affects.

B

b - Variable in class Line2D: The y-intercept of the straight line.
b1End - Variable in class scanCSD: The last value of the b1 benefit parameter.
b1Incr - Variable in class scanCSD: The increment of the b1 benefit parameter.
b1Log - Variable in class scanCSD: The flag to indicate whether to use logarithmic increments for the b1 benefit parameter.
b1Start - Variable in class scanCSD: The first value of the b1 benefit parameter.
B21 - Static variable in class RungeKutta
b2End - Variable in class scanCSD: The last value of the b2 benefit parameter.
b2Incr - Variable in class scanCSD: The increment of the b2 benefit parameter.
b2Log - Variable in class scanCSD: The flag to indicate whether to use logarithmic increments for the b2 benefit parameter.
b2Start - Variable in class scanCSD: The first value of the b2 benefit parameter.
B31 - Static variable in class RungeKutta
B32 - Static variable in class RungeKutta
B41 - Static variable in class RungeKutta
B42 - Static variable in class RungeKutta
B43 - Static variable in class RungeKutta
B51 - Static variable in class RungeKutta
B52 - Static variable in class RungeKutta
B53 - Static variable in class RungeKutta
B54 - Static variable in class RungeKutta
B61 - Static variable in class RungeKutta
B62 - Static variable in class RungeKutta
B63 - Static variable in class RungeKutta
B64 - Static variable in class RungeKutta
b64decode(String) - Static method in class NativeJS: JSNI method: decoding of base-64 encoded string.
b64encode(String) - Static method in class NativeJS: JSNI method: base-64 encoding of string.
B65 - Static variable in class RungeKutta
background - Variable in class PDE: The background densities for each trait at initialization.
BarabasiAlbertGeometry - Class in org.evoludo.simulator.geometries: Scale-free network following the Barabási & Albert preferential attachment process.
BarabasiAlbertGeometry(EvoLudo) - Constructor for class BarabasiAlbertGeometry: Create a Barabási-Albert geometry tied to the given engine.
baseline - Variable in class Map2Fitness: Baseline fitness for map.
baseRangeX - Variable in class ParaGraph.ViewState: Cached x-axis range for the base view.
baseRangeY - Variable in class ParaGraph.ViewState: Cached y-axis range for the base view.
baseXMin - Variable in class ParaGraph.ViewState: Cached minimum x-axis value for the base range.
baseYMin - Variable in class ParaGraph.ViewState: Cached minimum y-axis value for the base range.
BasicTooltipProvider - Interface in org.evoludo.simulator.views: Graphs that provide basic tooltips should implement this interface.
BckItr() - Constructor for class RingBuffer.BckItr: Create a backwards iterator starting at the newest element.
becomesVacantAt(int) - Method in class IBSDPopulation
becomesVacantAt(int) - Method in class IBSPopulation: Check if site with index index will become vacant in this time step.
Behavioral notes - Section in class org.evoludo.simulator.views.Distribution
Behavior notes - Section in class org.evoludo.simulator.views.Pop2D
Behavior notes - Section in class org.evoludo.simulator.views.Pop3D
benefit - Variable in class Centipede: The benefit of cooperation, i.e.
benefits - Variable in class Continuous.Traits2Payoff: The array of benefit functions, one for each trait.
benefits(double[], double[]) - Method in class Continuous.Traits2Payoff: Calculate the benefits to the focal individual with traits me when interacting with an opponent with traits you.
benefits(double, double, int) - Method in class Continuous.Traits2Payoff: Calculate the benefits to the focal individual with trait value me in trait with index trait when interacting with an opponent with trait value you.
Benefits(String, String, int) - Constructor for enum class Continuous.Benefits: Create a new type of benefit function with key key and description title as well as nParams parameters.
BEST - Enum constant in enum class PlayerUpdate.Type: best wins (equal - stay)
BEST_RANDOM - Enum constant in enum class PlayerUpdate.Type: best wins (equal - random)
BEST_RESPONSE - Enum constant in enum class PlayerUpdate.Type: best-response
beta - Variable in class Advection: Helper variable to store the effective advection coefficients.
bg - Variable in class ColorMap.GradientND: The background color.
bgColor - Variable in class GraphStyle: The backgorund color of the graph.
bi - Variable in class Continuous.Traits2Payoff: The 2D array of cost function parameters.
bimodality(double[]) - Static method in class Distributions: Bimodality coefficient of data points x[i] stored in double vector x.
bimodality(double[], double) - Static method in class Distributions: Bimodality coefficient of data points x[i] stored in double vector x with known mean m1.
bin - Variable in class HistoGraph.Marker: The index of the marked bin.
BIN_EPSILON - Static variable in class Histogram: Small epsilon to avoid floating point truncation when mapping values to bins.
bin2x(int) - Method in class HistoGraph: Convert the bin index to x-coordinate.
binmarkers - Variable in class HistoGraph: The list of markers for the histogram.
binOf(double) - Method in class ColorMap.Gradient1D: Utility method to calculate the index of the gradient color that corresponds to value.
binOf(double[], int) - Method in class ColorMap.Gradient2D: Utility method to calculate the index of the gradient color that corresponds to value for trait with index trait.
binOf(double, int) - Method in class ColorMap.Gradient2D: Utility method to calculate the index of the gradient color that corresponds to value for trait with index trait.
Binomial(double, int) - Constructor for class RNGDistribution.Binomial: Creates binomial distribution with n trials and success probability p (mean n p) and a new instance of MersenneTwister..
Binomial(MersenneTwister, double, int) - Constructor for class RNGDistribution.Binomial: Creates binomial distribution with n trials and success probability p (mean n p) and the random number generator rng.
bins - Variable in class Distribution: The storage to accommodate the trait histograms.
Bins, range and dynamic resizing - Section in class org.evoludo.graphics.HistoGraph
binSize - Variable in class Histogram: The size of the bins in pixels.
BIRTH_DEATH - Enum constant in enum class IBS.MigrationType: Birth-death migration (fit migrates, random death).
birthRate - Variable in class Module: Per capita birth rate for ecological population updates.
BIT32_MASK - Static variable in class MersenneTwister: Mask used to force results into 32-bit precision.
BLACK - Enum constant in enum class TestEvoLudo.ConsoleColors: Black color.
BLACK - Static variable in class ColorMap3D: The color black.
BLACK_BACKGROUND - Enum constant in enum class TestEvoLudo.ConsoleColors: Black background color.
BLACK_BACKGROUND_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Black high intensity background.
BLACK_BOLD - Enum constant in enum class TestEvoLudo.ConsoleColors: Black color.
BLACK_BOLD_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Black high intensity color.
BLACK_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Black high intensity color.
BLACK_UNDERLINED - Enum constant in enum class TestEvoLudo.ConsoleColors: Black color.
blendColors(Color[], double[]) - Static method in class ColorMap: Utility method for the smooth, component-wise blending of multiple colors with respective weights (includes alpha-channel).
blendColors(Color, Color, double) - Static method in class ColorMap: Utility method for the smooth, component-wise blending of two colors, where color one has weight w1 (and color two has weight (1-w1)) and includes the alpha-channel.
BLUE - Enum constant in enum class TestEvoLudo.ConsoleColors: Blue color.
BLUE_BACKGROUND - Enum constant in enum class TestEvoLudo.ConsoleColors: Blue background color.
BLUE_BACKGROUND_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Blue high intensity background.
BLUE_BOLD - Enum constant in enum class TestEvoLudo.ConsoleColors: Blue color.
BLUE_BOLD_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Blue high intensity color.
BLUE_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Blue high intensity color.
BLUE_UNDERLINED - Enum constant in enum class TestEvoLudo.ConsoleColors: Blue color.
bottom - Variable in class Rectangle2D: The bottom segment of the rectangle.
bounds - Variable in class AbstractGraph: The bounds of the displaying area.
Bounds and layout - Section in class org.evoludo.graphics.AbstractGraph
buffer - Variable in class AbstractGraph: The buffer to store historical data, if applicable.
buffer - Static variable in class MersenneTwister: ChH: for testing on GWT/JRE platforms logging needs to be rewritten
buffer - Variable in class Console.Log: The buffer to store the log messages.
buffer - Variable in class RingBuffer: Array to hold buffer of T objects.
bufferCapacity - Variable in class RingBuffer: Buffer capacity, i.e.
bufferDepth - Variable in class RingBuffer: The depth of a buffer containing arrays.
buffered - Variable in class PlistReader: Buffered tag to return on the next PlistReader.next() call.
Buffering and sampling: - Section in class org.evoludo.graphics.ParaGraph
bufferPtr - Variable in class RingBuffer: Index of most recently added element in buffer.
bufferSizeMenu - Variable in class AbstractGraph: The context menu to set the buffer size for graphs with historical data.
bufferSizeMenu - Variable in class Console: The context menu to set the buffer size for graphs with historical data.
bufferThreshold - Variable in class ParaGraph: Threshold for storing new data point in buffer.
bufferThreshold - Variable in class S3Graph: Threshold for storing new data point in buffer.
buildArgKeys() - Method in class CLOption: Construct the user-facing representation of the argument when keys are defined; mirrors previous loop logic but extracted to reduce complexity.
buildBaseDescription() - Method in class CLOption: Build the base description string, using either the stored description or asking the delegate and appending key descriptions if applicable.
buildConnectedCore(int[], int[], int[]) - Method in class AbstractNetwork: Build a connected core of the network first, excluding leaves.
buildCurrent(StringBuilder, String) - Method in class CLOption: Append the current and default argument description to the provided builder.
buildKey(StringBuilder, CLOption.Key, String[], int) - Method in class CLOption: Append the resolved key value and remaining arguments to the builder.
buildModelStatus(StringBuilder, double[], int, int, int) - Method in class ODE: Build a comma separated status string for one population.
buildTraitMenus(ContextMenu, List, boolean) - Method in class Phase2D: Build or update trait selection sub-menus for the X and Y axes.
BUTTON_APPLY - Static variable in class SettingsController: Label of button to apply parameter settings.
BUTTON_DEBUG - Static variable in class EvoLudoWeb: Label of button to advance model by single microscopic step.
BUTTON_HELP - Static variable in class EvoLudoWeb: Label of button to show help.
BUTTON_INIT - Static variable in class EvoLudoWeb: Label of button to initialize model.
BUTTON_PREV - Static variable in class EvoLudoWeb: Label of button to reverse on step.
BUTTON_RESET - Static variable in class EvoLudoWeb: Label of button to reset model.
BUTTON_SAMPLE - Static variable in class EvoLudoWeb: Label of button to collect one statistics sample.
BUTTON_SETTINGS - Static variable in class EvoLudoWeb: Label of button to show/hide parameter settings.
BUTTON_STANDALONE - Static variable in class SettingsController: Label of button to run in standalone mode.
BUTTON_START - Static variable in class EvoLudoWeb: Label of button to start model.
BUTTON_STEP - Static variable in class EvoLudoWeb: Label of button to advance model by one step.
BUTTON_STOP - Static variable in class EvoLudoWeb: Label of button to stop model.

C

C1 - Static variable in class RungeKutta
c1End - Variable in class scanCSD: The last value of the c1 cost parameter.
c1Incr - Variable in class scanCSD: The increment of the c1 cost parameter.
c1Log - Variable in class scanCSD: The flag to indicate whether to use logarithmic increments for the c1 cost parameter.
c1Start - Variable in class scanCSD: The first value of the c1 cost parameter.
c2End - Variable in class scanCSD: The last value of the c2 cost parameter.
c2Incr - Variable in class scanCSD: The increment of the c2 cost parameter.
c2Log - Variable in class scanCSD: The flag to indicate whether to use logarithmic increments for the c2 cost parameter.
c2Start - Variable in class scanCSD: The first value of the c2 cost parameter.
C3 - Static variable in class RungeKutta
C4 - Static variable in class RungeKutta
C6 - Static variable in class RungeKutta
calcBounds() - Method in class AbstractGraph: Calculate bounds of drawing area.
calcBounds(int, int) - Method in class AbstractGraph: Calculate bounds of drawing area.
calcBounds(int, int) - Method in class LineGraph
calcBounds(int, int) - Method in class ParaGraph
calcBounds(int, int) - Method in class PopGraph2D
calcBounds(int, int) - Method in class PopGraph3D
calcBounds(int, int) - Method in class S3Graph
calcHierarchyUnit(IBSGroup.HierarchyUnit) - Method in class IBSGroup: Calculate hierarchy unit information.
calcInvDeltaX() - Method in class PDE: Helper method to calculate 1 / dx for different lattice geometries.
calcSquareUnit(int) - Method in class HierarchicalGeometry: Calculate the unit size for square-lattice hierarchies, adjusting each level to a perfect square with at least 2x2 units with at least 3x3 individuals each.
calculateType() - Method in class AffineTransform: This is the utility function to calculate the flag bits when they have not been cached.
calcUnitSize() - Method in class HierarchicalGeometry: Process the hierarchy specifications to calculate the number of units and the size of each unit.
cancelHideTimer() - Method in class ContextMenu: Cancel the timer for hiding the context menu.
cancelLayout() - Method in class Network: Abort the layouting process.
canvas - Variable in class AbstractGraph: Handle to the canvas for drawing the graphics.
Canvas & scaling - Section in class org.evoludo.graphics.AbstractGraph
canvas2SVG() - Method in interface Resources: Get the JavaScript file for exporting canvas elements to SVG.
category - Variable in class CLOption: The category of the command line option.
cdf - Variable in class RNGDistribution.Binomial: Cumulative distribution function of binomial probability distribution.
cdf - Variable in class RNGDistribution.Geometric: Cumulative distribution function of geometric probability distribution.
cdf(double, double) - Static method in class RNGDistribution.Exponential: Helper method to calculate the cumulative distribution function, cdf, of the Exponential distribution.
cdf(double, double, double) - Static method in class RNGDistribution.Normal: Helper method to calculate the cumulative distribution function, cdf, of the Normal distribution.
cdf(double, double, double) - Static method in class RNGDistribution.Uniform: Helper method to calculate the cumulative distribution function, cdf, of the Uniform distribution.
CDL - Class in org.evoludo.simulator.modules: Cooperation in voluntary (non-linear) public goods interactions.
CDL(EvoLudo) - Constructor for class CDL: Create a new instance of the module for voluntary public goods games.
CDL.IBSPop - Class in org.evoludo.simulator.modules: The extension for IBS simulations specific to voluntary (non-linear) public goods games.
CDLP - Class in org.evoludo.simulator.modules: Cooperation in voluntary (non-linear) public goods interactions with peer punishment.
CDLP(EvoLudo) - Constructor for class CDLP: Create a new instance of the module for voluntary public goods games with peer punishment.
CDLPQ - Class in org.evoludo.simulator.modules: Cooperation in voluntary (non-linear) public goods interactions with peer and pool punishment.
CDLPQ(EvoLudo) - Constructor for class CDLPQ: Create a new instance of the module for voluntary public goods games with peer and pool punishment.
CentiMap(int) - Constructor for class Centipede.CentiMap: Constructs a new CentiMap instance for the given role.
CentiMutations(Module) - Constructor for class Centipede.CentiMutations: Constructs a new CentiMutations instance to deal with mutations in the Centipede game.
Centipede - Class in org.evoludo.simulator.modules: The Centipede class provides an EvoLudo module for the centipede game.
Centipede(EvoLudo) - Constructor for class Centipede: Constructs a new instance for the Centipede module.
Centipede.CentiMap - Class in org.evoludo.simulator.modules: The CentiMap class provides a mapping of the centipede game to a pair of \(S_3\) simplices for the first mover and second mover roles.
Centipede.CentiMutations - Class in org.evoludo.simulator.modules: The CentiMutations class provides a mutation operator for the centipede game.
centralMoment(double[], double, int) - Static method in class Distributions: m-th centralized moment of data points x[i] stored in double vector x with known mean m1.
centralMoment(double[], int) - Static method in class Distributions: m-th centralized moment of data points x[i] stored in double vector x.
cgroupmodule - Variable in class IBSCPopulation: For group interaction modules module==groupmodule holds and null otherwise.
CHANGE_MODE - Enum constant in enum class ChangeListener.PendingAction: Change execution mode of model.
changeHandler - Variable in class Slider: The change event handler registration.
ChangeListener - Interface in org.evoludo.simulator.models: All ChangeListener's get informed about state changes of the core of EvoLudo models.
ChangeListener.PendingAction - Enum Class in org.evoludo.simulator.models: The GUI or engine can request running models to suspend execution and process a pendingAction.
changeListeners - Variable in class EvoLudo: List of change listeners that get notified when the model changes.
changeRegistration - Variable in class Slider: The change event handler registration.
changeView(AbstractView) - Method in class EvoLudoWeb: Switches to the provided view.
changeViewByName(String) - Method in class ViewController: Change the active view by name.
changeViewTo(AbstractView) - Method in class EvoLudoWeb: Change view of EvoLudo model data.
changeViewTo(AbstractView) - Method in class ViewController: Change the currently active view.
changeViewTo(AbstractView, boolean) - Method in class EvoLudoWeb: Change view of EvoLudo model data.
changeViewTo(AbstractView, boolean) - Method in class ViewController: Change the currently active view.
charge - Variable in class PDESupervisor: The model to manage and supervise its execution.
check() - Method in class AbstractGeometry: Validate geometry parameters and adjust infeasible settings.
check() - Method in class IBS
check() - Method in class IBSDPopulation
check() - Method in class IBSMCPopulation
check() - Method in class IBSPopulation: Check all model parameters for consistency and adjust if necessary (and feasible).
check() - Method in class Model: Check consistency of parameters and adjust if necessary (and possible).
check() - Method in class ODE
check() - Method in class PDE
check() - Method in class RungeKutta
check() - Method in class SDE
check() - Method in class ATBT
check() - Method in class CDL
check() - Method in class Centipede
check() - Method in class Continuous
check() - Method in class DemesTBT.IBSPop
check() - Method in class Module: Check all parameters.
check() - Method in class TBT.IBSPop
checkAdjustScoresConsistency() - Method in class IBSPopulation: Check consistency when not using lookup tables.
checkCompSampling() - Method in class IBSPopulation: Validate competition sampling rules for well-mixed populations and adjust if required.
checkConsistentFitness() - Method in class IBSDPopulation
checkConsistentFitness() - Method in class IBSPopulation: Check consistency of scores and fitness values for modules that implement Payoffs.
checkConvergence() - Method in class IBS: For asynchronous updates, updates the scores for all populations, checks convergence across all species and returns the total update rate.
checkConvergence() - Method in class IBSDPopulation
checkConvergence() - Method in class IBSMCPopulation
checkConvergence() - Method in class IBSPopulation: Check if population has converged.
checkConvergence() - Method in class DemesTBT.IBSPop
checkConvergence() - Method in class SIR.IBSPop
checkConvergence(double) - Method in class ODE: Helper method to check whether the squared distance dist2 qualifies to signal convergence.
checkConvergence(double) - Method in class SDE: Helper method to check whether the squared distance dist2 qualifies to signal convergence.
checkDt() - Method in class Advection
checkDt() - Method in class PDE: Helper method to check whether the time increment, ODE.dt, is acceptable.
checkFitnessSum(double) - Method in class IBSPopulation: Check consistency of total fitness.
checkGeometry() - Method in class IBSPopulation: Check the interaction and competition geometries for consistency and adjust if necessary (and feasible).
checkGeometryRewire() - Method in class IBSPopulation: Rewire the interaction and competition geometries if requested.
checkIndividualConsistency(int) - Method in class IBSPopulation: Check consistency of scores for a single individual.
checkInOut() - Method in class AbstractGeometry: Check consistency of in- and out-connections.
checkInteractions(int) - Method in class IBSDPopulation
checkInteractions(int) - Method in class IBSPopulation: Validate interaction structures and adjust incompatible settings.
checkLookupTable(int, boolean) - Method in class IBSPopulation: Check whether lookup tables for scores and fitness can be used.
checkLookupTableConsistency() - Method in class IBSPopulation: Check consistency of scores when using lookup tables.
checkMigration() - Method in class IBSPopulation: Check consistency of migration settings and adjust if necessary (and feasible).
checkMultiple(int[], int[][], String) - Method in class AbstractGeometry: Check for multiple connections in the given links.
checkNoAdjustScoresConsistency() - Method in class IBSPopulation: Check consistency when scores are not adjusted.
checkNoLookupTable(boolean) - Method in class IBSPopulation: Free memory used for lookup tables and allocate arrays for scores, fitness and interactions.
checkOptimizations() - Method in class IBSDPopulation
checkOptimizations() - Method in class IBSPopulation: Check whether optimizations for homogeneous states can be used.
checkPayoffs(int) - Method in class IBSPopulation: Check settings for modules implementing Payoffs.
checkReference(File, Plist, String) - Method in class TestEvoLudo: Search for reference file with the name base refbasename (no SHA, no extensions) in directory references.
checkRegular() - Method in class AbstractGeometry: Check regularity of the graph.
checkRounding(Double, Double) - Method in class Plist: Check if the difference between ref and check is due to rounding errors.
checkRounding(Double, Double, Integer) - Method in class Plist: Check if the difference between ref and check is due to rounding errors.
checkSelfing() - Method in class AbstractGeometry: Check for self-connections (loops).
checkSettings() - Method in class AbstractGeometry: Hook for subclasses to implement geometry specific checks.
checkSettings() - Method in class CompleteGeometry
checkSettings() - Method in class CubicGeometry
checkSettings() - Method in class DesarguesGeometry
checkSettings() - Method in class DodekahedronGeometry
checkSettings() - Method in class FranklinGeometry
checkSettings() - Method in class FruchtGeometry
checkSettings() - Method in class HeawoodGeometry
checkSettings() - Method in class HexagonalGeometry
checkSettings() - Method in class HierarchicalGeometry
checkSettings() - Method in class IcosahedronGeometry
checkSettings() - Method in class LinearGeometry
checkSettings() - Method in class MooreGeometry
checkSettings() - Method in class RandomDirectedGeometry
checkSettings() - Method in class RandomGeometry
checkSettings() - Method in class RandomRegularGeometry
checkSettings() - Method in class ScalefreeGeometry
checkSettings() - Method in class SecondNeighbourGeometry
checkSettings() - Method in class SquareGeometry
checkSettings() - Method in class StarGeometry
checkSettings() - Method in class StrongAmplifierGeometry
checkSettings() - Method in class StrongSuppressorGeometry
checkSettings() - Method in class SuperstarGeometry
checkSettings() - Method in class TietzeGeometry
checkSettings() - Method in class TriangularGeometry
checkSettings() - Method in class VonNeumannGeometry
checkSettings() - Method in class WheelGeometry
checkTraitScores(double[], double[]) - Method in class IBSPopulation: Check consistency of scores for all traits.
checkUndirected() - Method in class AbstractGeometry: Check undirected structure of the graph.
childMenu - Variable in class ContextMenu: Reference to current child menu or null if no child menu is visible.
childMenu - Variable in class ContextMenuItem: Reference to submenu if this menu item controls one and null otherwise.
ci - Variable in class Continuous.Traits2Payoff: The 2D array of cost function parameters.
CIRCLE - Enum constant in enum class PDEInitialize.Type: Circle in the center with uniform densities <d1,...dn>.
circles() - Method in interface Resources: Get decorations for GWT GUI elements.
CLabour - Class in org.evoludo.simulator.modules: The module for the evolution of two behavioural traits.
CLabour(EvoLudo) - Constructor for class CLabour: Constructs a new EvoLudo module for the evolution of two behavioural traits.
clampLogMin(double) - Method in class ParaGraph: Clamp the minimum of a log-scaled axis.
clampLogRange() - Method in class LineGraph: Clamp the y-axis range for logarithmic scaling.
clampPercentMax(double) - Method in class ParaGraph: Clamp the maximum of a percent axis.
clampPercentMin(double) - Method in class ParaGraph: Clamp the minimum of a percent axis.
clampProbability(double) - Method in class KlemmEguiluzGeometry: Clamp the probability parameter into the range [0,1].
clampViewCorner(ParaGraph.ViewState) - Method in class ParaGraph: Clamp the current view corner to keep the visible range inside the domain.
clampViewX(double, double, double, double) - Method in class ParaGraph: Clamp a horizontal view corner to keep the visible range inside the domain.
clampViewY(double, double, double, double) - Method in class ParaGraph: Clamp a vertical view corner to keep the visible range inside the domain.
clear() - Method in class Network
clear() - Method in class Console.Log: Clear the log buffer and the display.
clear() - Method in class RingBuffer: Remove all entries from ring buffer.
clearCanvas() - Method in class AbstractGraph: Clear the canvas.
clearCLO() - Method in class CLOParser: Clears current collection of options.
clearCommandLineOptions() - Method in class EvoLudoWeb: Clear the command line option field in the GUI.
clearData() - Method in class HistoGraph: Clear the histrogram data.
clearGraph() - Method in class AbstractGraph: Clear the graph.
clearHistory() - Method in class AbstractGraph: Clear the history of the graph (if there is one).
clearHistory() - Method in class ParaGraph
clearKeys() - Method in class CLOption: Clear all keys from the option.
clearLinksFrom(int) - Method in class AbstractGeometry: Remove all outgoing links from node idx.
clearLinksTo(int) - Method in class AbstractGeometry: Remove all incoming links to node idx.
clearLog() - Method in class Console: Clear the console log.
clearMarkers() - Method in class HistoGraph: Clear all markers from the histogram.
clearMenu - Variable in class GenericPopGraph: The context menu item to clear the canvas.
clearMenu - Variable in class LineGraph: The context menu item to clear the graph.
clearMenu - Variable in class ParaGraph: The context menu item to clear the canvas.
clearMenu - Variable in class S3Graph: The context menu item to clear the canvas.
clearMenu - Variable in class Console: The context menu item to clear the console.
clearMenu - Variable in class Histogram: The clear context menu.
clearMessage() - Method in class AbstractGraph: Clear the message.
clearMessage() - Method in class HistoGraph
clearMessage() - Method in class PopGraph3D
clearSeed() - Method in class RNGDistribution: Clear seed for random number generator.
clearSnapshotMarker() - Method in class EvoLudoWeb: Remove the temporary DOM marker indicating that a snapshot is ready.
cli - Variable in class AbstractGeometry: Optional trimmed CLI string used to create this geometry.
clickHandler - Variable in class ContextMenuItem: The handler of click events.
clickRegistration - Variable in class Slider: The click event handler registration.
clo - Variable in class CLOController: Cached command-line string that should be applied when parsing.
clo - Variable in class EvoLudo: The command line options (raw string provided in URL, HTML tag, TextArea or command line)
clo - Variable in class IBS.Statistics: Command line option to customize statistics settings.
clo - Variable in class IBSC.Init: Command line option to set the type of initial configuration.
clo - Variable in class IBSD.Init: Command line option to set the type of initial configuration.
clo - Variable in class Markers: Command line option to mark points on graphs (ParaGraph, S3Graph, LineGraph and HistoGraph).
clo - Variable in class PopulationUpdate: Command line option to set the method for updating the population(s).
clo - Variable in class Map2Fitness: Command line option to set the payoff/score to fitness map.
clo - Variable in class Mutation.Continuous: Command line option to set the type of player updates.
clo - Variable in class Mutation.Discrete: Command line option to set the type of player updates.
clo - Variable in class PlayerUpdate: Command line option to set the type of player updates.
clo - Variable in class SpeciesUpdate: Command line option to set the method for updating the population(s).
cloAccumulatedScores - Variable in class IBS: Command line option to set whether player scores from interactions are accumulated or averaged (default).
cloAdjustedDynamics - Variable in class ODE: Command line option to activate adjusted replicator dynamics (if possible) in ODE models.
cloAsymmetry - Variable in class ATBT: Command line option to set the origin of asymmetries to differences in genotype or in the environment.
cloB1 - Variable in class scanCSD: Command line option to set the benefit parameter b1, or its range or its range to scan.
cloB2 - Variable in class scanCSD: Command line option to set the benefit parameter b2, or its range or its range to scan.
cloBasin - Variable in class simCDLP: Command line option to determine the basin of attraction of punishers and cooperators.
cloBenefit - Variable in class Centipede: Command line option to set the benefit of cooperation, i.e.
cloBenefits - Variable in class Continuous: Command line option to set the benefit function(s) for continuous traits.
cloBins - Variable in class scanCSD: Command line option to set the number of bins for the distribution (histogram).
cloBirthRate - Variable in class Module: Command line option to set the birth rate uninfected hosts.
cloC1 - Variable in class scanCSD: Command line option to set the cost parameter c1, or its range or its range to scan.
cloC2 - Variable in class scanCSD: Command line option to set the cost parameter c2, or its range or its range to scan.
CLOCategory - Class in org.evoludo.util: Handle different categories of options.
CLOCategory(String) - Constructor for class CLOCategory: Create a new category with the header header.
CLOCategory(String, int) - Constructor for class CLOCategory: Create a new category with header and priority.
cloColors - Variable in class NetGames: Command line option to set the colors for altruists, fair players, and egoists.
cloCompRate - Variable in class Module: Command line option to set the competition rate for ecological population updates.
cloConsistency - Variable in class IBS: Command line option to enable consistency checks.
cloController - Variable in class EvoLudo: Controller for command line option parsing.
CLOController - Class in org.evoludo.simulator: Encapsulates command line option setup, preprocessing, and parsing for EvoLudo.
CLOController(EvoLudo) - Constructor for class CLOController: Create a controller bound to the supplied engine.
cloCost - Variable in class CDL: Command line option to set the cost of cooperation, i.e.
cloCost - Variable in class Centipede: Command line option to set the cost of cooperation, i.e.
cloCost - Variable in class EcoPGG: Command line option to set the cost of cooperation, i.e.
cloCostPoolPunish - Variable in class CDLPQ: Command line option to set the cost of pool punishment.
cloCostPunish - Variable in class CDLP: Command line option to set the cost of peer punishment.
cloCosts - Variable in class Continuous: Command line option to set the cost function(s) for continuous traits.
cloDEAccuracy - Variable in class ODE: Command line option to set the desired accuracy of ODE calculations as criteria for convergence and whether population is monomorphic.
cloDeathRate - Variable in class Module: Command line option to set death rate for ecological population updates.
cloDEdt - Variable in class ODE: Command line option to set the time increment dt in DE models.
cloDelay - Variable in class CLOController: Command line option to set the delay between subsequent updates.
CLODelegate - Interface in org.evoludo.util: Interface to process command line arguments
cloDistribution - Variable in class scanCSD: The command line option to print the trait distribution.
cloEmulate - Variable in class SettingsController: Command line option to mimic ePub modes and to disable device capabilities.
cloEnvironment - Variable in class ATBT: Command line option to set the environmental values of the two different patch types.
cloFeedback - Variable in class ATBT: Command line option to set the feedback between traits and patch quality.
cloField - Variable in class SettingsController: Label displaying the current command-line options.
cloFitness - Variable in class Moran: Command line option to set the fitness values for residents and mutants.
cloGeometry - Variable in class Module: Command line option to set the geometry (interaction and competition graphs identical).
cloGeometryAddwire - Variable in class IBS: Command line option to set the fraction of links to add.
cloGeometryCompetition - Variable in class IBS: Command line option to set the competition geometry.
cloGeometryInteraction - Variable in class IBS: Command line option to set the interaction geometry.
cloGeometryRewire - Variable in class IBS: Command line option to set the fraction of links to rewire.
cloHelp - Variable in class CLOController: Command line option to print help message for available command line options.
cloHistogram - Variable in class simCDLP: Command line option to generate a histogram of states visited.
cloIncidence - Variable in class SIR: Command line option to set the incidence rates for S → I.
cloInfect - Variable in class SIR: Command line option to set the transition probability for S → I.
cloInit - Variable in class ODE: Command line option to set the initial configuration in ODE/SDE models.
cloInteractions - Variable in class IBS: Command line option to set whether players interact with all their neighbours or a random subsample.
cloInterest - Variable in class CDL: Command line option to set the multiplication factor for public good interactions.
cloInterest - Variable in class EcoPGG: Command line option to set the multiplication factor for public good interactions.
cloLeniencyCooperators - Variable in class CDLP: Command line option to set the leniency of peer punishers towards cooperators, provided the composition of the interaction group reveals them as second-order free riders.
cloLeniencyLoners - Variable in class CDLP: Command line option to set the leniency of peer punishers towards loners.
cloLoneCooperator - Variable in class CDL: Command line option to set the payoff to cooperators that failed to find any interaction partners.
cloLoneCooperator - Variable in class EcoPGG: Command line option to set the payoff to cooperators that failed to find any interaction partners.
cloLoneDefector - Variable in class CDL: Command line option to set the payoff to defectors that failed to find any interaction partners.
cloLoneDefector - Variable in class EcoPGG: Command line option to set the payoff to defectors that failed to find any interaction partners.
cloLoner - Variable in class CDL: Command line option to set the payoff to loners that refuse to participate in the public goods interaction.
cloMigration - Variable in class IBS: Command line option to set the migration types and probabilities of players.
cloMinTime - Variable in class simTraits: Command line option to set the minimal measurement time.
cloModel - Static variable in class Module: Command line option to set the type of model (see ModelType).
cloModule - Variable in class CLOController: Command line option to set module.
cloMonoStop - Variable in class Discrete: Command line option to request that models stop execution when reaching monomorphic population states.
clone() - Method in class MersenneTwister: Clone this MersenneTwister to ensure both objects return identical sequences of random numbers.
clone() - Method in class RNGDistribution.Binomial
clone() - Method in class RNGDistribution: Clone this RNGDistribution to ensure both objects return identical sequences of random numbers.
clone() - Method in class RNGDistribution.Exponential
clone() - Method in class RNGDistribution.Geometric
clone() - Method in class RNGDistribution.Gillespie
clone() - Method in class RNGDistribution.Normal
clone() - Method in class RNGDistribution.Uniform
clone() - Method in class AbstractGeometry: Clone geometry.
clone() - Method in class AbstractLattice
clone() - Method in class HierarchicalGeometry
clone() - Method in class KlemmEguiluzGeometry
clone() - Method in class LinearGeometry
clone() - Method in class ScalefreeGeometry
clone() - Method in class SuperstarGeometry
clone(boolean[]) - Static method in class ArrayMath: GWT has an aversion to clone()ing - provide alternatives.
clone(double[]) - Static method in class ArrayMath: GWT has an aversion to clone()ing - provide alternatives.
clone(double[][]) - Static method in class ArrayMath: GWT has an aversion to clone()ing - provide alternatives.
clone(int[]) - Static method in class ArrayMath: GWT has an aversion to clone()ing - provide alternatives.
clone(RNGDistribution) - Method in class RNGDistribution: Copy settings of this to clone.
cloneCoordsDouble(AffineTransform) - Method in class Path2D
cloNGroup - Variable in class Module: Command line option to set the size of interaction groups.
cloNodes - Variable in class Centipede: Command line option to set the maximum number of decision nodes for the centipede game.
cloNPopulation - Variable in class Module: Command line option to set the population size.
cloNPopulations - Variable in class simTraits: Command line option to specify the population sizes.
cloNSteps - Variable in class simCDL: Command line option to set the number of steps for initial frequencies.
cloOptimize - Variable in class IBSD: Command line option to request optimizations.
cloOthers - Variable in class CDL: Command line option to set whether contributors get a share of the benefits generated by their own contributions.
CLOParser - Class in org.evoludo.util: Parser for command line options.
CLOParser(Set) - Constructor for class CLOParser: New command line option parser.
CLOParser(CLOProvider) - Constructor for class CLOParser: New command line option parser.
cloPayoff - Variable in class RSP: Command line option to set the payoff matrix.
cloPayoffs - Variable in class TBT: Command line option to set the 2×2 payoff matrix for interactions between cooperators and defectors.
cloPayoffs4x4 - Variable in class ATBT: Command line option to set the 2×2 payoff matrix for interactions between cooperators and defectors or the (generic) 4×4 payoff matrix for arbitrary interactions between four traits.
cloPdeAdvection - Variable in class Advection: Command line option to set the advection coefficients of every trait against all others.
cloPdeDiffusion - Variable in class PDE: Command line option to set the diffusion coefficients.
cloPdeL - Variable in class PDE: Command line option to set the linear extension.
cloPdeN - Variable in class PDE: Command line option to set the discretization as the total number of spatial units to use for the numerical integration of the PDE.
cloPdeSymmetric - Variable in class PDE: Command line option to request preservation of symmetry.
cloPhase2DAxes - Variable in class Module: Command line option to set the traits on phase plane axes.
cloPoolPunish - Variable in class CDLPQ: Command line option to set the fine of pool punishment for non-contributors.
cloProgress - Variable in class scanCSD: Command line option to show the simulation progress.
cloProgress - Variable in class simCDL: Command line option to show the simulation progress.
cloProgress - Variable in class simMoran: Command line option to show the simulation progress.
cloProgress - Variable in class simTBT: Command line option to show the simulation progress.
cloProgress - Variable in class simTraits: Command line option to show the simulation progress.
CLOProvider - Interface in org.evoludo.util: Interface for classes that that to provide command line options for configurable parameters.
CLOption - Class in org.evoludo.util: Command line option and argument.
CLOption(String, String, String, CLODelegate) - Constructor for class CLOption: Creates command line option with the name name (with required argument), which defaults to defaultArg, and brief description description as well as the delegate delegate to process the argument and optionally retrieve the description.
CLOption(String, String, CLOCategory, String, CLODelegate) - Constructor for class CLOption: Creates command line option with the name name (with required argument), which defaults to defaultArg, of catgeory category and brief description description as well as the delegate delegate to process the argument and optionally retrieve the description.
CLOption(String, String, CLODelegate) - Constructor for class CLOption: Creates command line option with the name name (no arguments) and short description description as well as the delegate delegate to process the argument and optionally retrieve the description.
CLOption(String, String, CLOption.Argument, String, CLODelegate) - Constructor for class CLOption: Creates command line option with the name name of type type, which defaults to defaultArg, and brief description description as well as the delegate delegate to process the argument and optionally retrieve the description.
CLOption(String, String, CLOption.Argument, CLOCategory, String, CLODelegate) - Constructor for class CLOption: Creates command line option with the name name of type type, which defaults to defaultArg, in category category and brief description description as well as the delegate delegate to process the argument and optionally retrieve the description.
CLOption(String, String, CLOption.Argument, CLOCategory, CLODelegate) - Constructor for class CLOption: Creates command line option with the name name of type type, which defaults to defaultArg, and catgeory category as well as the delegate delegate to process the argument and retrieve the description.
CLOption(String, String, CLOption.Argument, CLODelegate) - Constructor for class CLOption: Creates command line option with the name name of type type, which defaults to defaultArg, as well as the delegate delegate to process the argument and retrieve the description.
CLOption(String, CLOCategory, String, CLODelegate) - Constructor for class CLOption: Creates command line option with the name name (no arguments) with category category and brief description description as well as the delegate delegate to process the argument and optionally retrieve the description.
CLOption(String, CLOCategory, CLODelegate) - Constructor for class CLOption: Creates command line option with the name name (no arguments) with category category and the delegate to process the argument and retrieve the description.
CLOption(String, CLODelegate) - Constructor for class CLOption: Creates command line option with the name name and the delegate to process the argument and provide the description.
CLOption.Argument - Enum Class in org.evoludo.util: Types of command line options: REQUIRED required argument.
CLOption.Key - Interface in org.evoludo.util: The interface for keys of command line options.
CLOption.SimpleKey - Class in org.evoludo.util: Simple key for command line options.
cloPunishment - Variable in class CDLP: Command line option to set the fine of peer punishment for non-contributors.
cloRatio - Variable in class NetGames: Command line option to set the cost-to-benefit ratio of cooperation.
cloRecover - Variable in class SIR: Command line option to set the transition probability for I → R.
cloReferences - Variable in class IBS: Command line option to set the method for choosing references/models among the neighbours of a player for updating their trait.
cloRun - Variable in class CLOController: Command line option to request that the EvoLudo model immediately starts running after loading.
cloRun - Variable in class EvoLudo: Command-line option controlling the number of model runs.
cloRuns - Variable in class simTBT: Command line option to set the number of runs.
cloSamples - Variable in class Model: Command line option to set the number of samples to take for statistical measurements.
cloScanDG - Variable in class simTBT: Command line option to scan the donation game.
cloScanNL - Variable in class simCDL: Command line option to set the range and increments for scanning non-linearities.
cloScanST - Variable in class simTBT: Command line option to scan the S-T-plane.
cloScoringType - Variable in class IBS: Command line option to set method for resetting the scores of individuals.
close() - Method in class EvoLudoWeb.EvoLogHandler: Nothing to close in GWT.
close() - Method in class EvoLudoTrigger.LightboxPanel: Close the overlay.
close() - Method in class ContextMenu: Close submenu or context menu if this is the top level.
close() - Method in class ContextMenuItem: Set timer to close submenu, if there is one, otherwise close this context menu without delay.
close() - Method in class Tooltip: Close tooltip now.
closeAll() - Method in class ContextMenu: Recursively close hierarchy of context submenus, including the top level context menu.
closeChildMenu() - Method in class ContextMenu: Close submenu, if one is showing.
cloSeed - Variable in class CLOController: Command line option to set seed of random number generator.
cloSeed - Variable in class EvoLudo: Command-line option controlling the RNG seed.
cloSelection - Variable in class NetGames: Command line option to set the cost-to-benefit ratio of cooperation.
closeNow() - Method in class ContextMenuItem: Close submenu without delay.
closePath() - Method in class Path2D: Closes the current subpath by drawing a straight line back to the coordinates of the last moveTo.
closePath(boolean) - Method in class AbstractGraph: Helper method to close the path and draw (or fill) it.
closePopup() - Method in class EvoLudoWeb: Closes the overlay containing this EvoLudo lab, if any.
closestCorner(double, double) - Method in class S3Graph: Find the corner closest to the point (x, y).
closestEdge(double, double) - Method in class S3Graph: Find the edge closest to the point (x, y).
cloSize - Variable in class FSController: Command line option to set the size of the GUI or enter fullscreen.
cloSnap - Variable in class EvoLudoGWT: Command line option to request that the EvoLudo model signals the completion of of the layouting procedure for taking snapshots, e.g.
cloSnapInterval - Variable in class scanCSD: The command line option to set the interval for snapshots.
cloSnapInterval - Variable in class simCDLPQ: Command line option to set the interval for taking snapshots.
cloSnapInterval - Variable in class simTBT: Command line option to set the interval for taking snapshots.
cloSnapPrefix - Variable in class simTBT: Command line option to set the prefix for snapshot filenames.
cloSolo - Variable in class CDL: Command line option to set whether a single contributor suffices to generate the public good.
cloSuscept - Variable in class SIR: Command line option to set the transition probability for R → S.
cloThreshold - Variable in class simCDLP: Command line option to set the threshold for corner states.
cloTime2Punish - Variable in class simCDLP: Command line option to determine the time to reach the threshold of punishers.
cloTimeRelax - Variable in class Model: Command line option to set the number of generations to relax the model from the initial configuration.
cloTimeReversed - Variable in class ODE: Command line option to set the number of generations between reports for EvoLudo.modelNext().
cloTimeStep - Variable in class Model: Command line option to set the number of generations between reports for EvoLudo.modelNext().
cloTimeStop - Variable in class Model: Command line option to set the number of generations after which to stop the model calculations.
cloTraitColors - Variable in class Module: Command line option to set the color of traits.
cloTraitColorScheme - Variable in class Continuous: Command line option to set color scheme for coloring continuous traits.
cloTraitDisable - Variable in class Module: Command line option to disable individual traits.
cloTraitNames - Variable in class Module: Command line option to assign trait names.
cloTraitRange - Variable in class Continuous: Command line option to set the minimum value of each trait.
cloTrajectoryColor - Variable in class CLOController: Command line option to set the color for trajectories.
cloVerbose - Variable in class CLOController: Command line option to set verbosity level of logging.
cloView - Variable in class ViewController: CLO option controlling the initial view selection.
cmd - Variable in class ContextMenuItem: Command that gets executed when selecting this menu item and null if this menu item controls a submenu.
CModel - Interface in org.evoludo.simulator.models: Common interface for all models with continuous traits.
code - Variable in enum class TestEvoLudo.ConsoleColors: The style code.
Collaborators - Section in class org.evoludo.simulator.views.Distribution
collectCLO(CLOParser) - Method in class EvoLudoWeb
collectCLO(CLOParser) - Method in class CLOController: Register all built-in CLOs with the supplied parser.
collectCLO(CLOParser) - Method in class EvoLudo: All providers of command line options must implement this method to collect their options.
collectCLO(CLOParser) - Method in class EvoLudoGWT
collectCLO(CLOParser) - Method in class scanCSD
collectCLO(CLOParser) - Method in class simCDL
collectCLO(CLOParser) - Method in class simCDLP
collectCLO(CLOParser) - Method in class simCDLPQ
collectCLO(CLOParser) - Method in class simMoran
collectCLO(CLOParser) - Method in class simTBT
collectCLO(CLOParser) - Method in class simTraits
collectCLO(CLOParser) - Method in class Advection
collectCLO(CLOParser) - Method in class IBS
collectCLO(CLOParser) - Method in class IBSC
collectCLO(CLOParser) - Method in class IBSD
collectCLO(CLOParser) - Method in class Model
collectCLO(CLOParser) - Method in class ODE
collectCLO(CLOParser) - Method in class PDE
collectCLO(CLOParser) - Method in class SDE
collectCLO(CLOParser) - Method in class ATBT
collectCLO(CLOParser) - Method in class CDL
collectCLO(CLOParser) - Method in class CDLP
collectCLO(CLOParser) - Method in class CDLPQ
collectCLO(CLOParser) - Method in class Centipede
collectCLO(CLOParser) - Method in class Continuous
collectCLO(CLOParser) - Method in class Discrete
collectCLO(CLOParser) - Method in class EcoPGG
collectCLO(CLOParser) - Method in class Module
collectCLO(CLOParser) - Method in class Moran
collectCLO(CLOParser) - Method in class NetGames
collectCLO(CLOParser) - Method in class RSP
collectCLO(CLOParser) - Method in class SIR
collectCLO(CLOParser) - Method in class TBT
collectCLO(CLOParser) - Method in interface CLOProvider: All providers of command line options must implement this method to collect their options.
color - Variable in class HistoGraph.Marker: The color of the marker.
COLOR_KEYS - Static variable in class CLOParser: Lookup table for predefined colors.
color2Color(Color) - Method in class ColorMap: Utility method to convert the color into a color object of type T.
color2Color(Color) - Method in class ColorMap3D.Gradient1D
color2Color(Color) - Method in class ColorMap3D.Gradient2D
color2Color(Color) - Method in class ColorMap3D.GradientND
color2Color(Color) - Method in class ColorMap3D.Hue
color2Color(Color) - Method in class ColorMap3D.Index
color2Color(Color) - Method in class ColorMapCSS.Gradient1D
color2Color(Color) - Method in class ColorMapCSS.Gradient2D
color2Color(Color) - Method in class ColorMapCSS.GradientND
color2Color(Color) - Method in class ColorMapCSS.Hue
color2Color(Color) - Method in class ColorMapCSS.Index
Color2Color(double, double, double) - Static method in class ColorMap3D: Convert red, green, blue to a WebGL Color object.
Color2Color(Color) - Static method in class ColorMap3D: Convert a java.awt.Color object to a Color object.
Color2Css(Color) - Static method in class ColorMapCSS: Convert Color to CSS style string.
Color2Css(Color[]) - Static method in class ColorMapCSS: Convert an array of Color's to an array of CSS style strings.
Color2Material(double, double, double, double) - Static method in class ColorMap3D: Convert red, green, blue and transparency values (RGBA) to a WebGL Material object.
Color2Material(Color) - Static method in class ColorMap3D: Convert a java.awt.Color to a WebGL Material object.
colorMap - Variable in class GenericPopGraph: The map for translating discrete traits into colors.
ColorMap<T> - Class in org.evoludo.simulator: Interface for mapping data to colors.
ColorMap() - Constructor for class ColorMap: Protected constructor to restrict instantiation to subclasses.
ColorMap.Gradient<T> - Class in org.evoludo.simulator: Abstract super class for color maps following a gradient.
ColorMap.Gradient1D<T> - Class in org.evoludo.simulator: One dimensional color gradient spanning two or more colors
ColorMap.Gradient2D<T> - Class in org.evoludo.simulator: Two dimensional color gradient with one color for each dimension.
ColorMap.GradientND<T> - Class in org.evoludo.simulator: Color gradient for N dimensional data with one color for each dimension.
ColorMap.Hue<T> - Class in org.evoludo.simulator: Color gradient following the hue.
ColorMap.Index<T> - Class in org.evoludo.simulator: Associates integer indices with colors.
ColorMap3D - Class in org.evoludo.simulator: Coloring3D is a wrapper class for different schemes to map data onto colors for 3D visualization using WebGL.
ColorMap3D() - Constructor for class ColorMap3D: Protected constructor to restrict instantiation to subclasses.
ColorMap3D.Gradient1D - Class in org.evoludo.simulator: One dimensional color gradient spanning two or more colors
ColorMap3D.Gradient2D - Class in org.evoludo.simulator: Two dimensional color gradient with one color for each dimension.
ColorMap3D.GradientND - Class in org.evoludo.simulator: N dimensional color gradient with one color for each dimension.
ColorMap3D.Hue - Class in org.evoludo.simulator: Color gradient following the hue.
ColorMap3D.Index - Class in org.evoludo.simulator: Associates integer indices with colors.
ColorMapCSS - Class in org.evoludo.simulator: Coloring is a wrapper class for different schemes to map data onto colors for 2D visualizations using the HTML5 canvas element.
ColorMapCSS() - Constructor for class ColorMapCSS: Protected constructor to restrict instantiation to subclasses.
ColorMapCSS.Gradient1D - Class in org.evoludo.simulator: One dimensional color gradient spanning two or more colors
ColorMapCSS.Gradient2D - Class in org.evoludo.simulator: Two dimensional color gradient with one color for each dimension.
ColorMapCSS.GradientND - Class in org.evoludo.simulator: N dimensional color gradient with one color for each dimension.
ColorMapCSS.Hue - Class in org.evoludo.simulator: Color gradient following the hue.
ColorMapCSS.Index - Class in org.evoludo.simulator: Associates integer indices with colors.
colorModelType - Variable in class Continuous: The coloring method type.
ColorModelType(String, String) - Constructor for enum class Continuous.ColorModelType: Create a new color model type.
colors - Variable in class AbstractGraph: The array of colors used for drawing the graph.
colors - Variable in class ColorMap.Index: Array of generic colors T.
colors - Variable in class S3Map: The colors of the traits.
combinationFrac(int, int, int) - Static method in class Combinatorics: Efficient calculation of \[\dfrac{\binom{n}{k}}{\binom{m}{k}}=\frac{n!(m-k)!}{m!(n-k)!},\] or Binomial[n,k]/Binomial[m,k] for Mathematica, while reducing the risk of numerical overflow.
combinations(int, int) - Static method in class Combinatorics: Combinations: number of ways to draw k elements from pool of size n.
combinations(long, long) - Static method in class Combinatorics: Combinations: number of ways to draw k elements from pool of size n.
Combinatorics - Class in org.evoludo.math: Collection of convenience methods for mathematical operations dealing with combinatorics.
Combinatorics() - Constructor for class Combinatorics: Ensure non-instantiability with private default constructor
Command-Line Options (CLO) - Section in class org.evoludo.EvoLudoWeb
commitTraitAt(int) - Method in class IBSCPopulation
commitTraitAt(int) - Method in class IBSDPopulation
commitTraitAt(int) - Method in class IBSMCPopulation
commitTraitAt(int) - Method in class IBSPopulation: The change of a trait of the player at index is stored in a temporary variable and must be committed before proceeding.
commitTraitAt(int) - Method in class DemesTBT.IBSPop
commitTraitAt(int) - Method in class NetGames.IBSPop
commitTraits() - Method in class IBSDPopulation: After a synchronous update step the new state must be copied back to become the current state.
commitTraits() - Method in class IBSMCPopulation
commitTraits() - Method in class IBSPopulation: After a synchronous update step the new state must be copied back to become the current state.
commitTraits() - Method in class DemesTBT.IBSPop
commitTraits() - Method in class NetGames.IBSPop
compare(double[][], double[][]) - Static method in class ArrayMath: Compares the two specified double[][] arrays.
compare(double[], double[]) - Static method in class ArrayMath: Compares the two specified double[] arrays.
compare(int[][], int[][]) - Static method in class ArrayMath: Compares the two specified int[][] arrays.
compare(int[], int[]) - Static method in class ArrayMath: Compares the two specified int[] arrays.
compareData(double[], double[]) - Method in class LineGraph: Compare two data arrays based on their minimum value (ignoring first entry, time).
compareRuns(File, Plist, Plist) - Method in class TestEvoLudo: Compare reference output reference with the output of the test replicate and generate a report if differences are found.
compareTo(CLOption) - Method in class CLOption
competition - Variable in class IBSPopulation: The geometry of the competition graph.
competitionRate - Variable in class Module: Competition rate with kin for ecological population updates.
competitionRates - Variable in class Module: Competition rates for multi-species ecological population updates.
compGroup - Variable in class IBSPopulation: Reference to the competition/reference/model group.
COMPLETE - Enum constant in enum class GeometryType: Complete graph, connectivity \(k=N-1\).
CompleteGeometry - Class in org.evoludo.simulator.geometries: Geometry implementation for complete graphs where every node connects to every other node.
CompleteGeometry(EvoLudo) - Constructor for class CompleteGeometry: Create a complete-graph geometry for the given engine.
computeEffRates(Module, int, double[], double[]) - Method in class ODE: Compute effective birth and death rates, including competition adjustments.
computeFitness(double[], double[]) - Method in class ODE: Compute fitness values for all species based on the current state.
computeLinearDigits(double, double, int, boolean, boolean) - Method in class AbstractGraph: Compute the number of decimal digits needed for linear labels so consecutive ticks remain distinct.
computeMinZoom(double, double) - Method in class ParaGraph: Compute minimum zoom factor for a base range and domain width.
computeNormBounds(double[], double[]) - Method in class HistoGraph: Compute min/max from per-bin normalization row; returns {yMin, yMax}.
computeTotalTraits(List, boolean) - Method in class Phase2D: Compute total number of trait entries that will appear in the trait menus.
computeYRange() - Method in class AbstractGraph: Compute the (possibly logarithmic) y-range for tick computations.
computeYScale(double) - Method in class LineGraph: Compute y-axis scale info: [ymin, yrange, yScale]
computeYVal(int, double, double, double) - Method in class AbstractGraph: Compute the y-value for tick number n.
computeZoom(double) - Method in class ParaGraph.ViewState: Compute per-axis zoom factors after applying domain constraints.
concatenate(AffineTransform) - Method in class AffineTransform: Concatenates an AffineTransform Tx to this AffineTransform Cx in the most commonly useful way to provide a new user space that is mapped to the former user space by Tx.
Concepts and data layout: - Section in class org.evoludo.graphics.LineGraph
Concepts and inputs - Section in class org.evoludo.simulator.models.PDEInitialize
Concurrency and Threading - Section in class org.evoludo.EvoLudoWeb
configGUI() - Method in class EvoLudoWeb: Helper method to update the views after the command line options have been applied.
configureGraph(PopGraph2D) - Method in class Pop2D: Configure the graph's style according to its geometry.
connect - Variable in class Model: Flag to indicate whether the current data point belongs to the same time series.
connectCorePairs(int[], int[], int[], int) - Method in class AbstractNetwork: Connect pairs of nodes from the core until no unmatched nodes remain or no further progress can be made.
connectivity - Variable in class AbstractGeometry: Connectivity (average number of neighbors).
consistencyCheckRequested - Variable in class IBSPopulation: The flag to indicate whether consistency checks on the state of the IBS model are requested.
console - Variable in class EvoLudoWeb.EvoLogHandler: The GUI console (or null).
console - Variable in class ViewController: Console view that is always present.
Console - Class in org.evoludo.simulator.views: The view to display the console log.
Console(EvoLudoGWT) - Constructor for class Console: Create a new console log.
Console.Log - Class in org.evoludo.simulator.views: The console log widget.
ConsoleColors(String) - Constructor for enum class TestEvoLudo.ConsoleColors: Constructor for ConsoleColors.
contains(double, double) - Method in class Rectangle2D: Check if the rectangle contains the point (px, py).
contains(int, int) - Method in class AbstractGraph: Checks if the (browser) coordinates (x, y) are inside this graph.
contains(Object) - Method in class Network
contains(Point2D) - Method in class Rectangle2D: Check if the rectangle contains the point p.
contains(Point2D, Point2D, Point2D) - Static method in class Segment2D: For the three collinear points p,q,x, check if the point x lies on the line segment p-q.
containsHelpOption(String[]) - Method in class CLOController: Check whether the --help option was provided.
containsView(AbstractView) - Method in class ViewController: Checks whether the supplied view is managed by this controller.
contextMenu - Variable in class AbstractGraph: The reference to the (shared) context menu.
contextMenu - Variable in class Console: The context menu for the console.
contextMenu - Static variable in class ContextMenu: Shared instance of context menu.
ContextMenu - Class in org.evoludo.ui: Context menu extension to GWT's user interface.
ContextMenu() - Constructor for class ContextMenu: Create new context menu.
ContextMenu(ContextMenu) - Constructor for class ContextMenu: Create new context submenu for parent menu.
ContextMenu(ContextMenu, String) - Constructor for class ContextMenu: Create new context submenu for parent menu with a header.
ContextMenu.Listener - Interface in org.evoludo.ui: Listener interface for widgets that offer context menus.
ContextMenu.Provider - Interface in org.evoludo.ui: Provider interface for classes that are responsible for supplying the contents of the context menu.
ContextMenu.Registration - Class in org.evoludo.ui: Manage registrations of listener widgets, their context menu providers and the corresponding event handlers.
ContextMenu.TouchTimer - Class in org.evoludo.ui: Timer for handling touch events triggering the context menu.
Context menu and UI interactions - Section in class org.evoludo.graphics.S3Graph
ContextMenuCheckBoxItem - Class in org.evoludo.ui: Component of the context menu extension to GWT's user interface.
ContextMenuCheckBoxItem(String, Scheduler.ScheduledCommand) - Constructor for class ContextMenuCheckBoxItem: Create new menu item with check box and the title text.
contextMenuHandler - Variable in class ContextMenu.Registration: The reference to the context menu event handler.
contextMenuHandler - Variable in class ContextMenuItem: The handler of context menu events.
ContextMenuHeader - Class in org.evoludo.ui: Component of the context menu extension to GWT's user interface.
ContextMenuHeader(String) - Constructor for class ContextMenuHeader: Create a new context menu header with the given title.
ContextMenuItem - Class in org.evoludo.ui: Component of the context menu extension to GWT's user interface.
ContextMenuItem(String, Scheduler.ScheduledCommand) - Constructor for class ContextMenuItem: Create a new context menu item with the title name and triggers the command cmd when selected.
ContextMenuItem(String, ContextMenu) - Constructor for class ContextMenuItem: Create a new context menu item with the title name that controls the submenu child.
ContextMenuSeparator - Class in org.evoludo.ui: Component of the context menu extension to GWT's user interface.
ContextMenuSeparator() - Constructor for class ContextMenuSeparator: Creates a new separator to structure entries in context menus.
Continuous - Class in org.evoludo.simulator.modules: Parent class of all EvoLudo modules with one or more continuous traits.
Continuous(EvoLudo) - Constructor for class Continuous: Create new module with continuous traits.
Continuous(EvoLudo, Continuous) - Constructor for class Continuous: Create a new module with continuous traits for pacemaker engine and interactions with module partner.
Continuous(Continuous) - Constructor for class Continuous: Create another module with continuous traits.
Continuous(Module) - Constructor for class Mutation.Continuous: Construct mutator for continuous traits.
Continuous.Benefits - Enum Class in org.evoludo.simulator.modules: Selected benefit functions to translate continuous traits into payoffs.
Continuous.ColorModelType - Enum Class in org.evoludo.simulator.modules: Coloring methods for multiple continuous traits.
Continuous.Costs - Enum Class in org.evoludo.simulator.modules: Selected cost functions to translate continuous traits into payoffs.
Continuous.Traits2Payoff - Class in org.evoludo.simulator.modules: Translate continuous traits into payoffs based on configurable cost and benefit functions.
control - Variable in class PopGraph3D.Pop3DScene: The control for rotating and zooming the scene.
converged - Variable in class Model: Flag to indicate whether the model has converged.
convertToScaledCoordinates(int, int) - Method in class AbstractGraph: Convert the (browser) coordinates (x, y) to scaled coordinates in \([0,1]^2\).
convertToScaledCoordinates(int, int, Point2D) - Method in class AbstractGraph: Convert the (browser) coordinates (x, y) to scaled coordinates in \([0,1]^2\) and store in dest.
CONVEX - Enum constant in enum class Map2Fitness.Map: convex combination of baseline fitness and scores, \(fit = b(1-w)+w*score\)
COOPERATE - Static variable in class CDL: The trait (and index) value of cooperators.
COOPERATE - Static variable in class EcoPGG: The trait (and index) value of cooperators.
COOPERATE - Static variable in class TBT: The trait (and index) value of cooperators.
COOPERATE_POOR - Static variable in class ATBT: The trait (and index) value of poor cooperators.
COOPERATE_RICH - Static variable in class ATBT: The trait (and index) value of rich cooperators.
copy(double[][], double[][]) - Static method in class ArrayMath: Copy the double 2D array/matrix src to dst.
copy(double[], double[]) - Static method in class ArrayMath: Copy the double 2D array/matrix src to dst.
copy(int[][], int[][]) - Static method in class ArrayMath: Copy the integer 2D array/matrix src to dst.
copy(int[], double[]) - Static method in class ArrayMath: Element-wise copy of integer array/vector src to double array/vector dst.
copy(int[], int[]) - Static method in class ArrayMath: Copy the integer array/vector src to dst.
COPYRIGHT - Static variable in class EvoLudo: The copyright string.
corner() - Method in interface Resources: Get decorations for GWT GUI elements.
CORNER_LEFT - Static variable in interface HasS3: The index of the bottom left corner.
CORNER_RIGHT - Static variable in interface HasS3: The index of the bottom right corner.
CORNER_TOP - Static variable in interface HasS3: The index of the top corner.
correlation(double[], double[]) - Static method in class Distributions: Pearson correlation coefficient between data points x[i], y[i] stored in double vectors x and y using one-pass algorithm based on Welford's algorithm.
correlation(double[], double, double, double[], double, double) - Static method in class Distributions: Pearson correlation coefficient between data points x[i], y[i] stored in double vectors x and y with known means meanx, meany and variances varx, vary.
cost - Variable in class Centipede: The cost of cooperation, i.e.
cost - Variable in class EcoPGG: The cost of cooperation or the individual contribution to the public good.
costCoop - Variable in class CDL: The cost of cooperation or the individual contribution to the public good.
costPeerPunish - Variable in class CDLP: The cost of peer punishment of non-contributors.
costPoolPunish - Variable in class CDLPQ: The cost of pool punishment.
costs - Variable in class Continuous.Traits2Payoff: The array of cost functions, one for each trait.
costs(double[], double[]) - Method in class Continuous.Traits2Payoff: Calculate the costs to the focal individual with traits me when interacting with an opponent with traits you.
costs(double, double, int) - Method in class Continuous.Traits2Payoff: Calculate the costs to the focal individual with trait value me in trait with index trait when interacting with an opponent with trait value you.
Costs(String, String, int) - Constructor for enum class Continuous.Costs: Create a new type of cost function with key key and description title as well as nParams parameters.
countGraphs() - Method in class Histogram: Count how many graphs are required based on current Data type and module settings.
countTraits(int[], int[], int, int) - Method in class IBSDPopulation: Count the number of each trait in the array traits starting at offset for len individuals.
covariance(double[], double[]) - Static method in class Distributions: Sample covariance of data points x[i], y[i] stored in double vectors x and y using one-pass algorithm based on Welford's algorithm.
covariance(double[], double, double[], double) - Static method in class Distributions: Sample covariance of data points x[i], y[i] stored in double vectors x and y with known means meanx and meany.
cpairmodule - Variable in class IBSCPopulation: For pairwise interaction modules module==pairmodule holds and null otherwise.
cpop - Variable in class scanCSD: The population with continuous traits.
cProbs - Variable in class IBSPopulation: Conveninece variable to store cumulative probability distributions for replicator updating.
cpu - Variable in class RunController: Starting time of CPU sampling (negative if not sampling).
cpuMean - Variable in class RunController: Mean time of CPU sampling.
cpuSamples - Variable in class RunController: Number of CPU time samples.
cpuVar - Variable in class RunController: Variance of time of CPU sampling.
create(EvoLudo, String) - Static method in class AbstractGeometry: Instantiate the requested geometry based on cli.
create(EvoLudo, String, AbstractGeometry) - Static method in class AbstractGeometry: Instantiate the requested geometry based on cli if it differs from current.
create(EvoLudo, GeometryType) - Static method in class AbstractGeometry: Factory method for creating geometry instances by type.
createColorMap(Module) - Method in class Pop2D: Create the ColorMap for a given module/graph based on the current data type and model settings.
createColorMap(Module) - Method in class Pop3D: Create the ColorMap for a given module/graph based on the current data type and model settings.
createEvoLudoLab(String, String) - Static method in class EvoLudoWeb: Expose method for creating EvoLudo labs (EvoLudoWeb objects) to javascript
createEvoLudoTrigger(String) - Static method in class EvoLudoWeb: Expose method for creating EvoLudoTriggers to javascript.
createFitnessColorMap(Module) - Method in class Pop2D: Helper to create color map for fitness data.
createFitnessColorMap(Module) - Method in class Pop3D: Helper to create color map for fitness data.
createGeometry(int) - Method in class Distribution: Create a geometry for the given number of traits.
createGraphs(int) - Method in class Histogram: Create and configure graphs for all species.
createIBS() - Method in interface Model.HasIBS: Provides opportunity for module to supply custom implementation of individual based simulations, IBS.
createIBSPopulation() - Method in class simCDL
createIBSPopulation() - Method in class ATBT
createIBSPopulation() - Method in class CDL
createIBSPopulation() - Method in class CDLP: Opportunity to supply custom individual based simulations.
createIBSPopulation() - Method in class DemesTBT
createIBSPopulation() - Method in class LV
createIBSPopulation() - Method in class Module: Opportunity to supply custom individual based simulations.
createIBSPopulation() - Method in class NetGames
createIBSPopulation() - Method in class Predator
createIBSPopulation() - Method in class RSP
createIBSPopulation() - Method in class SIR
createIBSPopulation() - Method in class TBT
createIBSPopulation(Module) - Method in class IBS: Factory method to create an IBSPopulation instance for the provided module type.
createInverse() - Method in class AffineTransform: Returns an AffineTransform object representing the inverse transformation.
createModel(ModelType) - Method in class ATBT
createModel(ModelType) - Method in class Continuous
createModel(ModelType) - Method in class Discrete
createModel(ModelType) - Method in class LV
createModel(ModelType) - Method in class Module: Creates a model of type type for module.
createModel(ModelType) - Method in class SIR
createNetwork2D(AbstractGeometry) - Method in class EvoLudo: Generate 2D network.
createNetwork2D(AbstractGeometry) - Method in class EvoLudoGWT
createNetwork3D(AbstractGeometry) - Method in class EvoLudo: Generate 3D network.
createNetwork3D(AbstractGeometry) - Method in class EvoLudoGWT
createPolygon2D(double[], double[]) - Static method in class Path2D: Construct a polygon from array of x- and y coordinates.
createS3Graph(Module, int) - Method in class S3: Helper method to create and configure an S3Graph for a given role.
createSVGContext(int, int) - Static method in class NativeJS: JSNI method: Create a SVG context for exporting the view.
createTraitColorMapContinuous(Module) - Method in class Pop2D: Helper for continuous trait color maps.
createTraitColorMapContinuous(Module) - Method in class Pop3D: Helper for continuous trait color maps.
createTraitColorMapDiscreteOrPDE(Module) - Method in class Pop2D: Helper for discrete and PDE trait color maps.
createTraitColorMapDiscreteOrPDE(Module) - Method in class Pop3D: Helper for discrete and PDE trait color maps.
createTransformedShape(Path2D) - Method in class AffineTransform: Returns a new Path2D object defined by the geometry of the specified Path2D after it has been transformed by this transform.
cross(Vector3D) - Method in class Vector3D: Calculate the cross product of the 3D vector d and this vector.
cross(Vector3D, Vector3D) - Method in class Vector3D: Calculate the cross product of two 3D vectors a, b and store result in this vector.
CSD - Class in org.evoludo.simulator.modules: The module for investigating the evolutionary dynamics of the continuous snowdrift game, or more generally, interactions among pairs of individuals with continuous traits.
CSD(EvoLudo) - Constructor for class CSD: Create a new instance of the module for continuous games.
css() - Method in interface Resources: Get the GSS style file for the GWT EvoLudo GUI.
CSS_CURSOR_MOVE_VIEW - Static variable in class AbstractGraph: The CSS class name for the view movement cursor.
CSS_CURSOR_MOVE_VIEW - Static variable in class TrackballControls: CSS class name for changing the cursor while panning the view.
CSS_CURSOR_ROTATE_VIEW - Static variable in class TrackballControls: CSS class name for changing the cursor while rotating the view.
CSS Style Rules - Section in class org.evoludo.ui.ContextMenu
CSS Style Rules - Section in class org.evoludo.ui.ContextMenuCheckBoxItem
CSS Style Rules - Section in class org.evoludo.ui.ContextMenuItem
CSS Style Rules - Section in class org.evoludo.ui.Slider
CSS Style Rules - Section in class org.evoludo.ui.Tooltip
CSS Style Rules - Section in class org.evoludo.ui.TrackballControls
CSS Style Rules - Section in org.evoludo.graphics.AbstractGraph.onMouseMove(MouseMoveEvent)
CSS Style Rules - Section in org.evoludo.graphics.AbstractGraph.onMouseMove(MouseMoveEvent)
CSS Style Rules - Section in org.evoludo.graphics.AbstractGraph.onMouseUp(MouseUpEvent)
CSS Style Rules - Section in org.evoludo.graphics.AbstractGraph.onMouseUp(MouseUpEvent)
CSS Style Rules - Section in org.evoludo.graphics.AbstractGraph.onMouseUp(MouseUpEvent)
CSS Style Rules - Section in org.evoludo.graphics.AbstractGraph.onMouseWheel(MouseWheelEvent)
CSS Style Rules - Section in org.evoludo.graphics.PopGraph2D.PopGraph2D(AbstractView, Module)
CSS Style Rules - Section in org.evoludo.graphics.PopGraph2D.onMouseDown(MouseDownEvent)
CSS Style Rules - Section in org.evoludo.graphics.PopGraph2D.onMouseMove(MouseMoveEvent)
CSS Style Rules - Section in org.evoludo.graphics.PopGraph3D.PopGraph3D(Pop3D, Module)
CSV_MEAN - Enum constant in enum class AbstractView.ExportType: Mean state data as a comma separated list, csv (not yet implemented).
CSV_STAT - Enum constant in enum class AbstractView.ExportType: Statistics data as a comma separated list, csv
CSV_TRAJ - Enum constant in enum class AbstractView.ExportType: Trajectory data as a comma separated list, csv (not yet implemented).
CUBE - Enum constant in enum class GeometryType: Cubic lattice, 3D.
CubicGeometry - Class in org.evoludo.simulator.geometries: Cubic lattice geometry (3D) with optional fixed boundaries.
CubicGeometry(EvoLudo) - Constructor for class CubicGeometry: Create a cubic-lattice geometry tied to the given engine.
current - Variable in class Tooltip: Reference to current provider of tooltips and null if no provider available.
currentSegment(double[]) - Method in class Path2D.Iterator: Returns the coordinates and type of the current path segment in the iteration.
currentSegment(double[]) - Method in interface PathIterator: Returns the coordinates and type of the current path segment in the iteration.
currentViewState() - Method in class ParaGraph: Update and return the cached view state for the current axis ranges.
cursor - Variable in class RingBuffer.BckItr: Index of current element in Iterator.
cursor - Variable in class RingBuffer.FwdItr: Index of current element in Iterator.
CURSOR_GRAB_NODE_CLASS - Static variable in class AbstractGraph: CSS class applied when the user is grabbing a node.
CURSOR_MOVE_NODE_CLASS - Static variable in class AbstractGraph: CSS class applied when the user is dragging a node.
CURSOR_ZOOM_IN_CLASS - Static variable in class AbstractGraph: CSS class applied when the user is zooming in.
CURSOR_ZOOM_OUT_CLASS - Static variable in class AbstractGraph: CSS class applied when the user is zooming out.
cursorRotate() - Method in interface Resources: Get the rotate cursor.
curvecoords - Static variable in class Path2D.Iterator
curveTo(double, double, double, double, double, double) - Method in class Path2D: Adds a curved segment, defined by three new points, to the path by drawing a Bézier curve that intersects both the current coordinates and the specified coordinates (x3,y3), using the specified points (x1,y1) and (x2,y2) as Bézier control points.
customLevelColor - Variable in class GraphStyle: The color of the custom levels.
customXLevels - Variable in class GraphStyle: The array with x-values to draw custom vertical levels.
customYLevels - Variable in class GraphStyle: The array with y-values to draw custom horizontal levels.
cxMaxMonoScore - Variable in class Continuous: The maximum score in a monomorphic population.
cxMaxScore - Variable in class Continuous: The absolute maximum score.
cxMinMonoScore - Variable in class Continuous: The minimum score in a monomorphic population.
cxMinScore - Variable in class Continuous: The absolute minimum score.
CYAN - Enum constant in enum class TestEvoLudo.ConsoleColors: Cyan color.
CYAN_BACKGROUND - Enum constant in enum class TestEvoLudo.ConsoleColors: Cyan background color.
CYAN_BACKGROUND_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Cyan high intensity background.
CYAN_BOLD - Enum constant in enum class TestEvoLudo.ConsoleColors: Cyan color.
CYAN_BOLD_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Cyan high intensity color.
CYAN_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Cyan high intensity color.
CYAN_UNDERLINED - Enum constant in enum class TestEvoLudo.ConsoleColors: Cyan color.

D

dashedLine - Variable in class GraphStyle: The dashing pattern for a dashed line.
data - Variable in class GenericPopGraph: The array to store the data for drawing the population structure.
data - Variable in class HistoGraph: The data array backing the histogram.
Data - Enum Class in org.evoludo.simulator.models: Data types that are handled by the model.
Data(String) - Constructor for enum class Data: Construct an enum for the type of data.
data2Phase(double[], Point2D) - Method in class TraitMap
data2Phase(double[], Point2D) - Method in class ATBT.ATBTMap
data2Phase(double[], Point2D) - Method in class EcoPGG.EcoPGGMap
data2Phase(double[], Point2D) - Method in interface HasPhase2D.Data2Phase: Convert data array to point on phase plane.
data2S3(double[], Point2D) - Method in class Centipede.CentiMap
data2S3(double[], Point2D) - Method in class S3Map: Convert the data array to cartesian coordinates of point on simplex.
data2S3(double, double, double, Point2D) - Method in class S3Map: Convert data triplet to cartesian coordinates of point on simplex.
Data model and normalization - Section in class org.evoludo.graphics.HistoGraph
dataXFromLocal(double) - Method in class ParaGraph.ViewState: Convert a local x-coordinate into data coordinates.
dataYFromLocal(double) - Method in class ParaGraph.ViewState: Convert a local y-coordinate into data coordinates.
DC1 - Static variable in class RungeKutta
DC3 - Static variable in class RungeKutta
DC4 - Static variable in class RungeKutta
DC5 - Static variable in class RungeKutta
DC6 - Static variable in class RungeKutta
deactivate() - Method in class AbstractGraph: The graph is removed from the GUI.
deactivate() - Method in class PopGraph3D
deactivate() - Method in class AbstractView: Deactivate the view.
DEATH_BIRTH - Enum constant in enum class IBS.MigrationType: Death-birth migration (random death, fit migrates).
deathRate - Variable in class Module: Death rate for ecological population updates.
debug() - Method in class EvoLudo: Advances the EvoLudo model by a single debugging step.
debug() - Method in class RunController: Advances the EvoLudo model by a single debugging step.
debugFocal - Variable in class IBSPopulation: Helper variable to store index of focal individual (birth) that got updated during debug step.
debugFocalSpecies - Variable in class IBS: Pointer to focal species for debugging.
debugMarkChange() - Method in class IBSDPopulation
debugMarkChange() - Method in class IBSPopulation: Override in subclass for example to mark those individuals in the GUI that were involved in the debug step.
debugModel - Variable in class IBSPopulation: Helper variable to store index of target individual (death) that got updated during debug step.
debugModels - Variable in class IBSPopulation: Helper variable to store array of indices of individual that served as models during debug step.
debugNModels - Variable in class IBSPopulation: Helper variable to number of individual that served as models during debug step.
debugNodeMenu - Variable in class GenericPopGraph: The context menu item for updating the current node.
debugSame - Variable in class IBSPopulation: Helper flag to indicate an actual trait change during debug step.
debugScores(double) - Method in class IBSPopulation: Log report if picking failed to shed better light on what might be the root cause for the failure.
debugStep() - Method in class IBS
debugStep() - Method in class Model: Perform single debug step in models that allow it.
debugSubmenu - Variable in class GenericPopGraph: The context menu for visually exploring (or debugging) the updating process.
debugSubmenuTrigger - Variable in class GenericPopGraph: The context menu item for attaching the debug submenu.
debugUpdate(int, int, double, double, double) - Method in class IBSPopulation: Log report if updating failed to shed better light on what might be the root cause for the failure.
debugUpdatePopulationAt(int) - Method in class IBSPopulation: Update focal individual with index focal for debugging.
deck - Variable in class ViewController: Deck widget hosting the views.
decode(String) - Static method in class XMLCoder: Decode XML string.
decodeGeometry(Plist) - Method in class AbstractGeometry: Decode the geometry from the plist.
decreaseDelay() - Method in class EvoLudo: Decrease delay between subsequent updates by fixed factor.
decreaseDelay() - Method in class RunController: Decrease delay between updates.
DEFAULT - Enum constant in enum class Continuous.ColorModelType: Default coloring type.
DEFAULT_BUFFER_SIZE - Static variable in class AbstractGraph: The default buffer size.
DEFAULT_CAPACITY - Static variable in class Console.Log: The default capacity of the log buffer.
DEFAULT_OFFSET_X - Static variable in class ContextMenu: Default horizontal offset of context menu relative to the coordinates of the context menu triggering event.
DEFAULT_OFFSET_X - Static variable in class Tooltip: Default horizontal offset of tooltip relative to the coordinates of the pointer (or the tap that triggered the tooltip).
DEFAULT_OFFSET_Y - Static variable in class ContextMenu: Default vertical offset of context menu relative to the coordinates of the context menu triggering event.
DEFAULT_OFFSET_Y - Static variable in class Tooltip: Default vertical offset of tooltip relative to the coordinates of the pointer (or the tap that triggered the tooltip).
DEFAULT_STEPS - Static variable in class LineGraph: The default number of steps along the x-axis.
defaultArg - Variable in class CLOption: The default argument for option (if applicable).
defaultButton - Variable in class SettingsController: Button used to reset parameters to default values.
defaultColor - Static variable in class Module: The array with default colors for traits.
DEFECT - Static variable in class CDL: The trait (and index) value of defectors.
DEFECT - Static variable in class EcoPGG: The trait (and index) value of defectors.
DEFECT - Static variable in class TBT: The trait (and index) value of defectors.
DEFECT_POOR - Static variable in class ATBT: The trait (and index) value of poor defectors.
DEFECT_RICH - Static variable in class ATBT: The trait (and index) value of rich defectors.
deferStatusThresholdReset - Variable in class EvoLudoWeb: Defer resetting the status threshold until after the loading sequence completes.
DEGREE - Enum constant in enum class Data: Degree: the data represents degrees of the network structure.
degreeProcessed - Variable in class Histogram: The flag to indicate whether the properties of the gemetric structure have been processed.
delay - Variable in class RunController: Delay between subsequent updates in milliseconds when model is running.
DELAY_HIDE - Static variable in class ContextMenu: Default delay before hiding the context (sub)menu (in milliseconds) after the pointer has exited the context (sub)menu.
DELAY_INCR - Static variable in class EvoLudo: Delay decrement for speed slider Slider
DELAY_INIT - Static variable in class EvoLudo: Initial delay between subsequent updates for speed slider Slider
DELAY_MAX - Static variable in class EvoLudo: Maximum delay between subsequent updates for speed slider Slider
DELAY_MIN - Static variable in class EvoLudo: Minimum delay between subsequent updates for speed slider Slider
delayHide - Variable in class ContextMenu: Delay before hiding the context (sub)menu (in milliseconds) after the pointer has exited the context (sub)menu.
delayHide - Variable in class Tooltip: Time until tooltip expires and closes (in milliseconds).
delayHideTimer - Variable in class Tooltip: Timer for handling the timeout after which the tooltip is closed.
delayShow - Variable in class Tooltip: Delay before showing the tooltip (in milliseconds) after the pointer started to hover over (part of) element that supplies tooltip.
delayShowTimer - Variable in class Tooltip: Timer for handling the delay in showing tooltips.
delegate - Variable in class CLOption: The delegate for parsing arguments, reporting settings and retrieving customized descriptions.
deltaTraits(int, int) - Method in class IBSMCPopulation: Measure the (Cartesian) distance between traits at a and b
deltaTransform(double[], int, double[], int, int) - Method in class AffineTransform: Transforms an array of relative distance vectors by this transform.
deltaTransform(Point2D, Point2D) - Method in class AffineTransform: Transforms the relative distance vector specified by ptSrc and stores the result in ptDst.
DemesTBT - Class in org.evoludo.simulator.modules: Simulations of 2x2 games in deme structured populations.
DemesTBT(EvoLudo) - Constructor for class DemesTBT: Create a new instance of the DemesTBT module.
DemesTBT.IBSPop - Class in org.evoludo.simulator.modules: Custom implemenation for individual based simulations in deme structured populations.
demeTypeCount - Variable in class DemesTBT.IBSPop: The number of traits in each deme.
density - Variable in class PDE: Density distribution of traits as a 2D array.
DENSITY - Enum constant in enum class ODEInitialize.InitType: Set initial densities as specified.
dependent - Variable in class PDE: The index of the dependent trait.
dependents - Variable in class ODE: Array containing the indices of the dependent trait in each species.
deriveCompetitionGeometry() - Method in class AbstractGeometry: Derive competition geometry from current (interaction) geometry for inter-species interactions with isSingle == true.
derivedId - Variable in class AbstractGeometry: Identifier of the geometry this one was derived from, or -1 if this geometry was not derived.
DESARGUES - Enum constant in enum class GeometryType: Desargues graph, size \(N=20\), connectivity \(k=3\).
DesarguesGeometry - Class in org.evoludo.simulator.geometries: Geometry implementation for the Desargues (Truncated Petersen) graph.
DesarguesGeometry(EvoLudo) - Constructor for class DesarguesGeometry: Create a Desargues geometry tied to the given engine.
descr - Variable in class HistoGraph.Marker: The description of the marker.
description - Variable in enum class GeometryType: Optional long description of geometry type for help display.
description - Variable in class CLOption: the short description of the command line option.
Design notes and behavior: - Section in class org.evoludo.graphics.GenericPopGraph
deStep(double) - Method in class ODE: Attempts a numerical integration step of size step with step size adjustment.
deStep(double) - Method in class RungeKutta: Attempts a numerical integration step of size step with step size adjustment.
deStep(double) - Method in class SDE: Attempts a numerical integration step of size step with step size adjustment.
destination - Variable in class IBSDPopulation.Link: The index of the individual at the head of the link.
destroyGraphs() - Method in class AbstractView: Destroy all graphs in this view and free up resources.
destroyGraphs() - Method in class GenericPop
detectFeatures() - Method in class SettingsController: Detects the capabilities of the current ePub host and updates the shared settings accordingly.
dh - Variable in class PopGraph2D: The height of a node for lattices.
dh3 - Variable in class PopGraph2D: Convenience variable.
diff(Plist) - Method in class Plist: Compare this plist to plist.
diff(Plist, Collection) - Method in class Plist: Compare this plist to plist but ignore keys in clo.
DIFF_KEY - Static variable in class Plist: String constant for reporting differences in keys.
diffArray(String, int) - Method in class Plist: Helper method for formatting output of differences in arrays.
diffArray(List, List, Collection) - Method in class Plist: Helper method to compare two plist-arrays.
diffcoeff - Variable in class PDE: The array of diffusion coefficients for each (independent) trait.
diffDict(Plist, Plist, Collection) - Method in class Plist: Helper method to compare two plist-dictionaries.
differAt(String, String) - Static method in class CLOption: Compare two strings and return the index of the first character that differs.
diffMeRef(Object, Object) - Method in class Plist: Helper method for formatting output of differences in plists.
diffMeRefDelta(Double, Double) - Method in class Plist: Helper method for formatting output of differences in plists optimized for Double to also show the numerical difference.
diffuse() - Method in class PDESupervisor: Perform the diffusion step.
diffuse(int, int) - Method in class Advection: / GWT.log("react: meanDensity="+meanDensity);
diffuse(int, int) - Method in class PDE: Diffusion step.
diffuseStandard(int, int, double[], double[], double[]) - Method in class PDE: Standard (non-symmetric) diffusion for the provided index range; extracts work from the original diffuse method to reduce its cognitive complexity.
diffuseStandard(int, int, double[], double[], double[], double[], double[]) - Method in class Advection: Process sites in the general (asymmetric) case.
diffuseSymmetric(int, int, double[], double[], double[]) - Method in class PDE: Symmetric diffusion for the provided index range; extracts work from the original diffuse method to reduce its cognitive complexity.
diffuseSymmetric(int, int, double[], double[], double[], double[], double[]) - Method in class Advection: Process sites in the symmetric case (neighbour ordering must be sorted).
DIFFUSION - Enum constant in enum class IBS.MigrationType: Diffusive migration (exchange of neighbors).
dim - Variable in class GenericPop: The type of data to display.
DIRECTED - Static variable in class ColorMap3D: The baseline color of directed links.
DIRECTED_DST - Static variable in class ColorMap3D: The color of directed links at the destination.
DIRECTED_SRC - Static variable in class ColorMap3D: The color of directed links at the origin.
Discrete - Class in org.evoludo.simulator.modules: Parent class of all EvoLudo modules with discrete sets of traits.
Discrete(EvoLudo) - Constructor for class Discrete: Create new module with a discrete set of traits.
Discrete(EvoLudo, Discrete) - Constructor for class Discrete: Create a new module with a discrete set of traits with pacemaker engine and interactions with module partner.
Discrete(Discrete) - Constructor for class Discrete: Create another module with a discrete set of traits.
Discrete(Module) - Constructor for class Mutation.Discrete: Construct mutator for discrete traits.
discretization - Variable in class PDE: Discretization of space as the total number of spatial units.
Discussions/extensions - Section in org.evoludo.simulator.models.IBSDPopulation.reset()
Discussions/extensions - Section in org.evoludo.simulator.models.IBSDPopulation.reset()
Discussions/extensions - Section in org.evoludo.simulator.models.IBSPopulation.step()
Discussions/extensions - Section in org.evoludo.simulator.models.IBSPopulation.step()
Discussions/extensions: - Section in org.evoludo.simulator.models.IBSPopulation.pickFitFocalIndividual()
Discussions/extensions: - Section in org.evoludo.simulator.models.IBSPopulation.resetScoreAt(int)
Discussions/extensions: - Section in org.evoludo.simulator.models.IBSPopulation.resetScoreAt(int)
Discussions/extensions: - Section in org.evoludo.simulator.models.IBSPopulation.updateEffScoreRange(int, double, double)
dispatch(FullscreenChangeHandler) - Method in class FullscreenChangeEvent
dispatch(InputHandler) - Method in class InputEvent
dispatchKeyDown(String) - Static method in class KeyHandler: Dispatches keydown events first to the active controller, then to others.
dispatchKeyUp(String) - Static method in class KeyHandler: Dispatches keyup events first to the active controller, then to others.
displayMessage(String) - Method in class AbstractGraph: Display message msg on the graph (no HTML formatting).
displayMessage(String) - Method in class PopGraph3D
displaySingle(AbstractGeometry, AbstractGeometry) - Static method in class AbstractGeometry: Checks whether a single graphical representation can be used for the interaction and competition graphs.
displayStatus(String) - Method in class EvoLudoWeb: Displays a message in the status line of the EvoLudo GUI with the default level Level.INFO.
displayStatus(String, int) - Method in class EvoLudoWeb: Displays a message in the status line of the EvoLudo GUI with the severity level.
displayStatusThresholdLevel - Variable in class EvoLudoWeb: Threshold level for overriding status message.
dist(double[], double[]) - Static method in class ArrayMath: Distance of two double arrays a and b given by the square root of the sum over (a[i]-b[i])^2.
dist(int[], int[]) - Static method in class ArrayMath: Distance of two integer arrays a and b given by the square root of the sum over (a[i]-b[i])^2.
distance() - Method in class Point2D: Calculate the distance from the origin (0,0): \(\sqrt{x^2+y^2}\).
distance() - Method in class Point3D: Calculate distance from the origin (0,0,0): \(\sqrt{x^2+y^2+z^2}\).
distance(Node2D) - Method in class Node2D: Calculate the distance between this 2D node n and node m.
distance(Node3D) - Method in class Node3D: Calculate the distance between this 3D node n and node m.
distance(Point2D) - Method in class Line2D: Calculate the distance between point p and the line.
distance(Point2D) - Method in class Point2D: Calculate the distance between the two 2D points p and q: \(\sqrt{(p.x-q.x)^2+(p.y-q.y)^2}\).
distance(Point2D) - Method in class Segment2D
distance(Point3D) - Method in class Point3D: Calculate the distance between the two 3D points p and q: \(\sqrt{(p.x-q.x)^2+(p.y-q.y)^2+(p.z-q.z)^2}\).
DISTANCE - Enum constant in enum class Continuous.ColorModelType: Color the traits according to their (Euclidian) distance from the origin.
distance2() - Method in class Point2D: Calculate the distance squared from the origin (0,0): \(x^2+y^2\).
distance2() - Method in class Point3D: Calculate the distance squared from the origin (0,0,0): \(x^2+y^2+z^2\).
distance2(Line2D, Point2D) - Static method in class Line2D: Calculate the squared distance between point p and the line l.
distance2(Node2D) - Method in class Node2D: Calculate the distance squared between this 2D node n and node m.
distance2(Node3D) - Method in class Node3D: Calculate the distance squared between this 3D node n and node m.
distance2(Point2D) - Method in class Line2D: Calculate the squared distance between point p and the line.
distance2(Point2D) - Method in class Point2D: Calculate the distance squared between the two 2D points p and q: \((p.x-q.x)^2+(p.y-q.y)^2\).
distance2(Point2D) - Method in class Segment2D
distance2(Point2D, Point2D, Point2D) - Static method in class Segment2D: Find the square distance of the point p from the segment, specified by the two points s1 and s2.
distance2(Point3D) - Method in class Point3D: Calculate the distance squared between the two 3D points p and q: \((p.x-q.x)^2+(p.y-q.y)^2+(p.z-q.z)^2\).
distance2(Segment2D, Point2D) - Static method in class Segment2D: Find the square distance of the point p from the segment s.
distrCentralMoment(double[], int) - Static method in class Distributions: m-th central moment of probability distribution with weights w[i] stored in double vector w.
distrCentralMoment(double[], int, double) - Static method in class Distributions: m-th central moment of probability distribution with weights w[i] stored in double vector w with known mean m1.
Distribution - Class in org.evoludo.simulator.views: View component that renders the distribution of continuous traits for one or more species in the EvoLudo simulation.
Distribution(EvoLudoGWT, Data) - Constructor for class Distribution: Construct a new view to display the distribution of continuous traits of the current EvoLudo model.
Distribution.TraitCommand - Class in org.evoludo.simulator.views: Command to toggle the inclusion of a trait on the phase plane axes.
Distributions - Class in org.evoludo.math: Collection of convenience methods for mathematical operations dealing with distributions.
Distributions() - Constructor for class Distributions: Ensure non-instantiability with private default constructor
distrMean(double[]) - Static method in class Distributions: Mean of probability distribution with weights w[i] stored in double vector w.
distrMigrants - Variable in class IBSPopulation: The distribution to determine the number of migrants.
distrMigration - Variable in class DemesTBT.IBSPop: The distribution for migration events.
distrMoment(double[], int) - Static method in class Distributions: m-th moment of probability distribution with weights w[i] stored in double vector w.
distrMutationMigration - Variable in class DemesTBT.IBSPop: The distribution for mutant-migration events.
distrStdev(double[]) - Static method in class Distributions: Standard deviation of probability distribution with weights w[i] stored in double vector w.
distrStdev(double[], double) - Static method in class Distributions: Standard deviation of probability distribution with weights w[i] stored in double vector w with known mean m1.
distrVariance(double[]) - Static method in class Distributions: Variance of probability distribution with weights w[i] stored in double vector w.
distrVariance(double[], double) - Static method in class Distributions: Variance of probability distribution with weights w[i] stored in double vector w with known mean m1.
distSq(double[], double[]) - Method in class ParaGraph: Helper method to calculate the distance squared between two vectors.
distSq(double[], double[]) - Method in class S3Graph: Helper method to calculate the distance squared between two vectors.
distSq(double[], double[]) - Static method in class ArrayMath: Squared distance of two double arrays a and b given by the sum over (a[i]-b[i])^2.
distSq(int[], int[]) - Static method in class ArrayMath: Squared distance of two integer arrays a and b given by the sum over (a[i]-b[i])^2.
DModel - Interface in org.evoludo.simulator.models: Common interface for all models with discrete sets of traits.
doAdjustScores() - Method in class IBSDPopulation
doAdjustScores() - Method in class IBSMCPopulation
doAdjustScores() - Method in class IBSPopulation: Check if scores can be adjusted rather than recalculated after an individual changed its trait.
doAdvection - Variable in class Advection: The flag to indicate whether advection coefficients are non-vanishing.
doBasin - Variable in class simCDLP: Generate the basins of attraction.
doBirthDeathMigration() - Method in class IBSPopulation: Perform a birth-death migration, where a focal individual (selected proportional to fitness) produces a migrant offspring, which replaces another member of the population uniformly at random.
DOCTYPE_TAG - Static variable in class PlistReader: Tag identifying DOCTYPE declaration.
doDeathBirthMigration() - Method in class IBSPopulation: Perform a death-birth migration, where a member of the population (selected uniformly at random) dies and the remaining individuals compete to repopulate the vacant site.
doDeathBirthMigration() - Method in class DemesTBT.IBSPop: Perform a death-birth migration, where a member of the population (selected uniformly at random) dies and the remaining individuals compete to repopulate the vacant site.
DODEKAHEDRON - Enum constant in enum class GeometryType: Dodekahedron graph, size \(N=20\), connectivity \(k=3\).
DodekahedronGeometry - Class in org.evoludo.simulator.geometries: Geometry implementation for the dodecahedral graph.
DodekahedronGeometry(EvoLudo) - Constructor for class DodekahedronGeometry: Create a dodecahedral geometry tied to the given engine.
doDiffusionMigration() - Method in class IBSPopulation: Perform diffusion migration, which is implemented as two players swap their locations while leaving their respective neighbourhood structure untouched.
doDiffusionMigration() - Method in class DemesTBT.IBSPop: Perform diffusion migration, which is implemented as two players swap their locations while leaving their respective neighbourhood structure untouched.
doEuler - Variable in class RungeKutta: true to resort to the traditional Euler's method with fixed step size.
doFixtimeDistr(Module) - Method in class Histogram: Helper method to check whether to show the fixation time distribution or the fixation times for each node.
doLayout(Network.LayoutListener) - Method in class Network2DGWT
doLayout(Network.LayoutListener) - Method in class Network3DGWT
doLayout(Network.LayoutListener) - Method in class Network: Start the layouting process.
doLayoutPrep() - Method in class Network: Prepare for the layouting process.
doLayoutStep() - Method in class Network2DGWT: Perform a single step in the layouting process by relaxing nodes sequentially.
doLayoutStep() - Method in class Network3DGWT: Perform a single step in the layouting process by relaxing nodes sequentially.
doLocation - Variable in class simCDLP: Generate a histogram of states visited.
DOM_DATA_CLO - Static variable in class EvoLudoWeb: Attribute name for command line options in DOM elements.
domain - Variable in class ParaGraph: Reusable rectangle for the domain bounds.
doMigration() - Method in class IBSPopulation: Perform asynchronous migration.
doMutate() - Method in class Mutation.Continuous
doMutate() - Method in class Mutation.Discrete
doMutate() - Method in class Mutation: Check if a mutation arises.
done - Variable in class PlistReader: true if done reading the plist-string.
doPan - Variable in class TrackballControls: true if panning is pending.
doPrev - Variable in class RunController: Flag to indicate if a backstep is in progress.
doRotate - Variable in class TrackballControls: true if rotation is pending.
doShow() - Method in class Tooltip: Helper method: show tooltip now and set timeout timer.
doSolo - Variable in class CDL: The flag to indicate whether the public good gets created even with a single participant.
doSyncMigration() - Method in class IBSPopulation: Perform synchronous migration.
dot(double[], double[]) - Static method in class ArrayMath: Dot product of two double arrays a and b given by the sum over a[i]*b[i].
dot(float[], float[]) - Static method in class ArrayMath: Dot product of two float arrays a and b given by the sum over a[i]*b[i].
dot(int[], int[]) - Static method in class ArrayMath: Dot product of two integer arrays a and b given by the sum over a[i]*b[i].
dot(long[], long[]) - Static method in class ArrayMath: Dot product of two long arrays a and b given by the sum over a[i]*b[i].
dot(Vector2D) - Method in class Vector2D: Calculate the dot product of 2D vector d and this vector.
dot(Vector3D) - Method in class Vector3D: Calculate the dot product of 3D vector d and this vector.
dottedLine - Variable in class GraphStyle: The dashing pattern for a dotted line.
doubleClickHandler - Variable in class AbstractGraph: The handler for DoubleClickEvents.
doubleCoords - Variable in class Path2D
doubleCoords - Variable in class Path2D.Iterator
doubleMaxRange() - Method in class HistoGraph: Double the range of the histogram by increasing the maximum value.
doubleMinRange() - Method in class HistoGraph: Double the range of the histogram by lowering the minimum value.
doUpdate(FocusPanel) - Method in class Tooltip: Helper method: remember current provider of tooltips for future use and update tooltip.
doUpdateStatus(boolean) - Method in class AbstractView: Check if enough time has elapsed to compute a status update.
doUpdateView(boolean) - Method in class AbstractView: Check if enough time has elapsed to perform a view update.
doZoom - Variable in class TrackballControls: true if zooming is pending.
dR - Variable in class PopGraph2D: The diameter of nodes for networks.
Drag-and-Drop and State Restore - Section in class org.evoludo.EvoLudoWeb
dragEnterHandler - Variable in class EvoLudoWeb: Reference to registration of drag'n'drop handlers.
dragLeaveHandler - Variable in class EvoLudoWeb: Reference to registration of drag'n'drop handlers.
drawBars(double[], double[], double, double, double) - Method in class HistoGraph: Draw bars for the histogram using either per-bin normalization row or global normalization flag.
drawCornerLabels(double, double) - Method in class S3Graph: Draw the corner labels of the simplex in their respective colours.
drawCustomMarkers(double, double) - Method in class S3Graph: Draw any additional markers stored in markers.
drawCustomMarkers(Point2D, double, double) - Method in class ParaGraph: Draw custom markers stored in AbstractGraph.markers.
drawCustomXLevels(double, double) - Method in class AbstractGraph: Draw vertical guide lines at custom x positions.
drawCustomYLevels(double, double) - Method in class AbstractGraph: Draw horizontal guide lines at custom y positions.
drawFrame(int) - Method in class S3Graph: Draws the frame of the simplex.
drawFrame(int, int) - Method in class AbstractGraph: Draw the frame of the graph including axes labels, ticks and tick marks, as applicable.
drawFrame(int, int, double) - Method in class AbstractGraph: Draw the frame of the graph including axes labels, ticks and tick marks, as applicable, after scaling the canvas by gscale.
drawFrameBorder(double, double) - Method in class AbstractGraph: Draw the bounding box of the graph frame.
drawFrameForView(ParaGraph.ViewState, int, int) - Method in class ParaGraph: Draw the frame using the visible ranges implied by the current zoom and shift.
drawGraphLabel(double) - Method in class AbstractGraph: Draw the label shown inside the graph canvas.
drawHoneycomb() - Method in class PopGraph2D: Draw honeycomb lattice.
drawLatestMarkers(double, double[], int) - Method in class LineGraph: Draw markers for the newest sample (extracted helper).
drawLattice() - Method in class GenericPopGraph: Draws structures with static layout of lattices.
drawLattice() - Method in class PopGraph2D
drawLattice() - Method in class PopGraph3D
drawLinearLattice() - Method in class PopGraph2D: Draw linear lattice with history.
drawLines(double, double[], int) - Method in class LineGraph: Draw the line plots.
drawMarkerCircle(Point2D, double, double, boolean, double) - Method in class ParaGraph: Draw a marker circle in screen coordinates to avoid distortion from scaling.
drawMarkers() - Method in class HistoGraph: Draw the marked bins.
drawMarkers(double, double, int) - Method in class LineGraph: Draw horizontal marker lines (if any) using the same y transform.
drawNetwork() - Method in class GenericPopGraph: Draws the network.
drawNetwork() - Method in class PopGraph2D
drawNetwork() - Method in class PopGraph3D
drawOutline() - Method in class S3Graph: Draw the outline of the simplex.
drawS3Levels(int, double, double) - Method in class S3Graph: Draw the subdivision levels of the simplex.
drawS3Ticks(int, double, double) - Method in class S3Graph: Draw the ticks along the boundaries of the simplex.
drawSegmentClipped(double, double, double[], double[], int, double[], double) - Method in class LineGraph: Draw a historical segment between 'start' and 'end', handling clipping against the visible window (-w ..
drawSquareLattice() - Method in class PopGraph2D: Draw square (hierarchical) lattice (SQUARE, SQUARE_MOORE, SQUARE_NEUMANN).
drawSquareNeumann2nd() - Method in class PopGraph2D: Draw the special SQUARE_NEUMANN_2ND lattice.
drawStartEndMarkers(double, double) - Method in class S3Graph: Draw start and end markers for the trajectory.
drawStartEndMarkers(Point2D, double, double) - Method in class ParaGraph: Draw start and end markers for the trajectory.
drawTrajectory(double, double) - Method in class S3Graph: Draw the trajectory stored in the buffer.
drawTrajectory(Point2D, Point2D, double, double) - Method in class ParaGraph: Draw the trajectory stored in the buffer.
drawTriangular() - Method in class PopGraph2D: Draw triangular lattice.
drawUniverse() - Method in class PopGraph3D: Adds the nodes, links, lights and camera to the scene.
drawXAxisLabel(double, double) - Method in class AbstractGraph: Draw the x-axis label.
drawXLevels(int, double, double) - Method in class AbstractGraph: Draw regular vertical guide lines, ticks, and labels.
drawYAxisLabel(double, double) - Method in class AbstractGraph: Draw the y-axis label, including positioning logic based on tick labels.
drawYLevels(int, double, double) - Method in class AbstractGraph: Draw the y-levels including ticks and tick labels.
drawYTickLabel(double, double, int, double, int) - Method in class AbstractGraph: Draw the y-axis tick label at the specified screen level.
drop(boolean[], int) - Static method in class ArrayMath: Drop the element at index from the array array of type boolean[].
drop(boolean[], int, int) - Static method in class ArrayMath: Drop a range of elements starting with index from to index to from the boolean[] array array.
drop(double[], int) - Static method in class ArrayMath: Drop the element at index from the array array of type double[].
drop(double[], int, int) - Static method in class ArrayMath: Drop a range of elements starting with index from to index to from the double[] array array.
drop(int[], int) - Static method in class ArrayMath: Drop the element at index from the array array of type int[].
drop(int[], int, int) - Static method in class ArrayMath: Drop a range of elements starting with index from to index to from the int[] array array.
drop(T[], int) - Static method in class ArrayMath: Drop the element at index from the array array of type T.
drop(T[], int, int) - Static method in class ArrayMath: Drop a range of elements starting with index from to index to from the array array of type T.
dstate - Variable in class ODE: Pointer to temporarily store a reference to the current state yt.
dt - Variable in class ODE: Discretization of time increment for continuous time models.
dtTaken - Variable in class ODE: The size of step taken by integrator.
dtTry - Variable in class ODE: The attempted size of next step to take.
dumpMinor - Variable in class TestEvoLudo: The flag to indicate whether to dump differences for minor failures.
dw - Variable in class PopGraph2D: The width of a node for lattices.
dw2 - Variable in class PopGraph2D: Convenience variable.
DYNAMIC - Enum constant in enum class GeometryType: Dynamically changing network structure.
dynamicDampingFactor - Variable in class TrackballControls: Factor for dynamic damping of changes to the view.
DynamicGeometry - Class in org.evoludo.simulator.geometries: Geometry wrapper representing dynamically changing structures provided by the simulation modules.
DynamicGeometry(EvoLudo) - Constructor for class DynamicGeometry: Create a dynamic geometry placeholder controlled by the provided engine.
DYNAMICS - Enum constant in enum class Mode: Dynamics: follow the time series of the model.
dyt - Variable in class ODE: The frequency/density increments of the ODE between the current state ODE.yt and the previous state ODE.yout.

E

e0 - Variable in class S3Graph: The lower left corner of the simplex.
e1 - Variable in class S3Graph: The lower right corner of the simplex.
e2 - Variable in class S3Graph: The upper corner of the simplex.
ECOLOGY - Enum constant in enum class PopulationUpdate.Type: Asynchronous updates (non-constant population size).
EcoPGG - Class in org.evoludo.simulator.modules: Cooperation in ecological public goods interactions.
EcoPGG(EvoLudo) - Constructor for class EcoPGG: Create a new instance of the module for ecological public goods games.
EcoPGG.EcoPGGMap - Class in org.evoludo.simulator.modules: Map translating ecological public goods data to a 2D phase plane and tooltip content.
EcoPGGMap() - Constructor for class EcoPGG.EcoPGGMap: Create the 2D projection helper using the surrounding module settings.
EDGE_BOTTOM - Static variable in interface HasS3: The index of the bottom edge.
EDGE_LEFT - Static variable in interface HasS3: The index of the left edge.
EDGE_RIGHT - Static variable in interface HasS3: The index of the right edge.
effect - Variable in class PopGraph3D: Helper variable for additional effects on the 3D view.
effRate - Variable in class ODE: Reusable scratch space for effective rates used by single-threaded ODE and SDE models.
elapsedTime - Variable in class EvoLudoGWT: Create timer to measure execution times since instantiation.
elapsedTimeMsec() - Method in interface MersenneTwister.Chronometer: Calculate elapsed time since instantiation in milliseconds.
elapsedTimeMsec() - Method in class MersenneTwister.StopWatch
elapsedTimeMsec() - Method in class EvoLudoGWT: Calculate elapsed time since instantiation in milliseconds.
element - Variable in class AbstractGraph: Handle to the object's underlying DOM element.
elementID - Variable in class EvoLudoWeb: ID of element in DOM that contains the EvoLudo lab.
EM - Enum constant in enum class ModelType: Euler method for ordinary differential equation models.
empty - Static variable in class IBSGroup: Shared empty group returned when no neighbours are sampled.
EMPTY_LINKS - Static variable in class AbstractGeometry: Empty link arrays used for well-mixed geometries and while allocating networks lazily.
enableAutoscaleYMenu - Variable in class HistoGraph: The flag to indicate whether the autoscale y-axis menu is enabled.
enableAutoscaleYMenu(boolean) - Method in class HistoGraph: Enable or disable the autoscale y-axis menu.
encode(String) - Static method in class XMLCoder: Encode string as XML.
ENCODE_MT - Static variable in class MersenneTwister: Constants for encoding and restoring state in plist.
ENCODE_MTI - Static variable in class MersenneTwister: Key used when encoding MersenneTwister.mti.
ENCODE_NEXT_GAUSSIAN - Static variable in class MersenneTwister: Key used when encoding MersenneTwister.nextGaussian.
encodeArray(double[]) - Static method in class Plist: Helper method to encode double array
encodeArray(double[][]) - Static method in class Plist: Helper method to encode double matrix
encodeArray(double[], int) - Static method in class Plist: Helper method to encode first len elements of double array
encodeArray(int[]) - Static method in class Plist: Helper method to encode int array
encodeArray(int[], int) - Static method in class Plist: Helper method to encode first len elements of int array
encodeArray(String[]) - Static method in class Plist: Helper method to encode String array
encodeArray(String[], int) - Static method in class Plist: Helper method to encode first len elements of String array
encodeFitness(StringBuilder) - Method in class IBSPopulation: Encode the fitness of all individuals in the IBS model in a plist inspired XML string.
encodeFitness(StringBuilder) - Method in class ODE: Encodes the fitness of the model in the form of a plist string.
encodeFitness(StringBuilder) - Method in class PDE
encodeGeometry() - Method in class AbstractGeometry: Encode geometry as a plist string fragment.
encodeGeometry(StringBuilder) - Method in class IBSPopulation: Encode the interaction and competition structures of the IBS model in a plist inspired XML string.
encodeGeometry(StringBuilder) - Method in class PDE: Encodes the geometry of the spatial structure for this PDE in the form of a plist string.
encodeInteractions(StringBuilder) - Method in class IBSPopulation: Encode the interactions of all individuals in the IBS model in a plist inspired XML string.
encodeKey(String, boolean) - Static method in class Plist: Utility method to encode boolean with tag key.
encodeKey(String, double) - Static method in class Plist: Utility method to encode double with tag key.
encodeKey(String, double[]) - Static method in class Plist: Utility method to encode double array with tag key.
encodeKey(String, double[][]) - Static method in class Plist: Utility method to encode double matrix with tag key.
encodeKey(String, double[], int) - Static method in class Plist: Utility method to encode first len entries of double array with tag key.
encodeKey(String, int) - Static method in class Plist: Utility method to encode int with tag key.
encodeKey(String, int[]) - Static method in class Plist: Utility method to encode int array with tag key.
encodeKey(String, int[], int) - Static method in class Plist: Utility method to encode first len entries of int array with tag key.
encodeKey(String, String) - Static method in class Plist: Utility method to encode String with tag key.
encodeKey(String, String[]) - Static method in class Plist: Utility method to encode String array with tag key.
encodeKey(String, String[], int) - Static method in class Plist: Utility method to encode first len entries of String array with tag key.
encodeState() - Method in class MersenneTwister: Encode state of random number generator as plist for saving.
encodeState() - Method in class EvoLudo: Encode current state of EvoLudo model as XML string (plist format).
encodeState() - Method in class StateEncoder: Encode current state of EvoLudo model as XML string (plist format).
encodeState(StringBuilder) - Method in class IBS
encodeState(StringBuilder) - Method in class Model: Encode the state of the model in a plist inspired XML string.
encodeState(StringBuilder) - Method in class ODE
encodeState(StringBuilder) - Method in class PDE
encodeTraits(StringBuilder) - Method in class IBSDPopulation
encodeTraits(StringBuilder) - Method in class IBSMCPopulation
encodeTraits(StringBuilder) - Method in class IBSPopulation: Encode the traits of all individuals in the IBS model in a plist inspired XML string.
encodeTraits(StringBuilder) - Method in class ODE: Encodes state of the model in the form of a plist string.
encodeTraits(StringBuilder) - Method in class PDE
endColor - Variable in class GraphStyle: The color to mark end of trajectory.
endCPUSample() - Method in class RunController: Complete a CPU sampling measurement and log aggregated statistics.
enforceEqualAxisScale() - Method in class ParaGraph: Enforce equal units-per-pixel scale on both axes for linear plots.
enforceSize(int) - Method in class AbstractGeometry: Ensure the geometry uses at least requiredSize nodes.
engine - Variable in class EvoLudoWeb: Controller.
engine - Variable in class CLOController: Owning EvoLudo engine coordinating models and modules.
engine - Variable in class TestEvoLudo: Pointer to engine.
engine - Variable in class AbstractGeometry: The pacemaker of all models.
engine - Variable in class LifecycleController: Owning engine used to query modules and dispatch events.
engine - Variable in class IBSPopulation: The pacemaker of all models.
engine - Variable in class Model: The pacemaker of all models.
engine - Variable in class PDESupervisor: The pacemaker of all models.
engine - Variable in class Module: The pacemaker of all models.
engine - Variable in class Network: The pacemaker of all models.
engine - Variable in class RunController: Engine whose execution is coordinated by this controller.
engine - Variable in class StateEncoder: Owning runtime whose state will be encoded.
engine - Variable in class FSController: Reference to the engine so fullscreen requests propagate to the core.
engine - Variable in class ViewController: EvoLudo engine powering the views.
engine - Variable in class WebListener: The associated EvoLudo engine.
engine - Variable in class AbstractView: The reference to the EvoLudo engine that manages the simulation.
ensureAutoscaleVisible() - Method in class ParaGraph: Shift the view corner to keep the latest autoscale point visible without shrinking the current ranges.
ensureDegreeData(HistoGraph, AbstractGeometry, AbstractGeometry, double[][]) - Method in class Histogram: Ensure the provided data buffer is sized appropriately for the given interaction/competition geometries, update the histogram data and set axis limits on the graph; returns the (possibly new) data buffer.
ensureSquareSize(boolean) - Method in class AbstractLattice: Enforce square lattice size and optionally even side lengths.
ensureWellmixed(AbstractGeometry, int) - Method in class IBSPopulation: Ensure a well-mixed geometry instance is available, sized, and initialized.
environment - Variable in class ATBT: The array of environmental values for rich and poor sites.
environmentalAsymmetry - Variable in class ATBT: The flag indicating the type of environmental asymmetry.
EPHEMERAL - Enum constant in enum class IBS.ScoringType: Determine payoffs/fitness calculated only for updating.
ephrng - Variable in class IBS: The random number generator to display states with ephemeral payoffs.
EPS - Enum constant in enum class AbstractView.ExportType: Encapsulated postscript format, eps (not yet implemented).
ePub Behaviour - Section in class org.evoludo.EvoLudoWeb
ePubReaderHasFeature(String) - Static method in class NativeJS: JSNI method: test if ePub reader supports feature.
equals(Object) - Method in class AffineTransform: Returns true if this AffineTransform represents the same affine coordinate transform as the specified argument.
equals(Object) - Method in class Network2DGWT
equals(Object) - Method in class Network3DGWT
equals(Object) - Method in class AbstractGeometry
equals(Object) - Method in class AbstractLattice
equals(Object) - Method in class GeometryFeatures
equals(Object) - Method in class HierarchicalGeometry
equals(Object) - Method in class KlemmEguiluzGeometry
equals(Object) - Method in class LinearGeometry
equals(Object) - Method in class ScalefreeGeometry
equals(Object) - Method in class SuperstarGeometry
equals(Object) - Method in class Network
equals(Object) - Method in class Network2D
equals(Object) - Method in class Network3D
equals(Object) - Method in class CLOption
equals(Object) - Method in class Plist: Override equals for consistency with hashCode.
erf(double) - Static method in class RNGDistribution.Normal: Numerical approximation of error function erf(x) from Abramowitz & Stegun.
ERRCON - Static variable in class RungeKutta: The maximum error in a single step.
error - Variable in class PlayerUpdate: The probability of an error during the updating of the trait.
estimateVacantFrequency(int) - Method in class IBSDPopulation: Helper method to determine the frequency of vacant sites based on an estimate of the carrying capacity.
evaluateSpecies() - Method in class ODE: Validate modules and derive aggregate state vector dimensions and scaling factors.
Event() - Constructor for enum class IBS.Event
EventListener - Interface in org.evoludo.ui: JavaScript-compatible callback interface used to hook browser events.
EvoLogHandler(Console) - Constructor for class EvoLudoWeb.EvoLogHandler: Construct new log handler that reports to the EvoLudo console (if one is present) and the EvoLudo status line.
EvoLudo - Class in org.evoludo.simulator: Interface with the outside world.
EvoLudo() - Constructor for class EvoLudo: Create an instance of the EvoLudo controller.
EVOLUDO_CURSOR_NODE - Static variable in class GenericPopGraph: The CSS class name for changing the cursor when hovering over a node.
EvoLudo.Directive - Interface in org.evoludo.simulator: The interface to execute commands in a manner that is agnostic to the implementation details regarding GWT or JRE environments.
evoludoApply - Variable in class EvoLudoWeb: The 'Apply' button ('Standalone' in ePubs)
evoludoCLO - Variable in class EvoLudoWeb: The text field containing the command line options for the EvoLudo model.
evoludoCLOPanel - Variable in class EvoLudoWeb: Panel containing all elements to change/view parameters.
evoludoDeck - Variable in class EvoLudoWeb: Panel containing all the canvas elements to display the EvoLudo model's data.
evoludoDefault - Variable in class EvoLudoWeb: The 'Default' button
EvoLudoGWT - Class in org.evoludo.simulator: GWT specific implementation of EvoLudo controller.
EvoLudoGWT(EvoLudoWeb) - Constructor for class EvoLudoGWT: Construct EvoLudo controller for GWT applications (web or ePub).
evoludoHelp - Variable in class EvoLudoWeb: The 'Help' button
evoludoInitReset - Variable in class EvoLudoWeb: The 'Init'/'Reset' button
evoludoLayout - Variable in class EvoLudoWeb: Basic layout of EvoLudo model GUI with header (for time display, EvoLudoWeb.evoludoTime, and view selector EvoLudoWeb.evoludoViews), footer (for delay slider EvoLudoWeb.evoludoSlider, control buttons EvoLudoWeb.evoludoSettings, EvoLudoWeb.evoludoInitReset, EvoLudoWeb.evoludoStartStop, EvoLudoWeb.evoludoStep and status line EvoLudoWeb.evoludoStatus plus possibly parameters EvoLudoWeb.evoludoCLOPanel) as well as the main content area (for different canvases, EvoLudoWeb.evoludoDeck).
evoludoOverlay - Variable in class EvoLudoWeb: Overlay for drag'n'drop operations
evoludoPanel - Variable in class EvoLudoWeb: Outermost panel containing the EvoLudo GUI.
evoludoResize - Variable in class EvoLudoWeb: Panel implementing the ability to resize the GUI of EvoLudo models (only possible in browser or standalone mode in ePubs).
evoludoSettings - Variable in class EvoLudoWeb: 'Settings' button
evoludoSlider - Variable in class EvoLudoWeb: Slider adjusting the delay between updates.
evoludoStartStop - Variable in class EvoLudoWeb: The 'Start'/'Stop' button
evoludoStatus - Variable in class EvoLudoWeb: Status line of EvoLudo model GUI.
evoludoStep - Variable in class EvoLudoWeb: The 'Step' button
evoludoTime - Variable in class EvoLudoWeb: Label to display elapsed generations (time).
EvoLudoTrigger - Class in org.evoludo.simulator: Create button to launch an EvoLudo lab in a semi-transparent overlay.
EvoLudoTrigger(String) - Constructor for class EvoLudoTrigger: Create a new EvoLudo trigger button for the HTML element with ID id.
EvoLudoTrigger.LightboxPanel - Class in org.evoludo.simulator: The panel to provide a transparent overlay over the entire page and displays the EvoLudo lab.
evoludoViews - Variable in class EvoLudoWeb: Selector for all graphical representations to visualize the state of the EvoLudo model.
EvoLudoWeb - Section in class org.evoludo.EvoLudoWeb
EvoLudoWeb - Class in org.evoludo: EvoLudoWeb
EvoLudoWeb() - Constructor for class EvoLudoWeb: Note: empty default constructor seems to be required by GWT.
EvoLudoWeb(String, String) - Constructor for class EvoLudoWeb: Main constructor for EvoLudo labs.
EvoLudoWeb(String, EvoLudoTrigger.LightboxPanel) - Constructor for class EvoLudoWeb: Constructor restricted to trigger buttons that create an overlay displaying an EvoLudo lab.
EvoLudoWeb.EvoLogHandler - Class in org.evoludo: Custom handler for logging system.
EvoLudoWeb.EvoLudoWebBinder - Interface in org.evoludo: GWT magic to define GUI elements (see EvoLudoWeb.ui.xml).
EvoLudoWeb.GUIState - Class in org.evoludo: Helper structure to store the current state of the GUI.
Example - Section in class org.evoludo.ui.Slider
Examples: - Section in org.evoludo.simulator.geometries.AbstractGeometry.displaySingle(AbstractGeometry, AbstractGeometry)
exclSize - Variable in class IBSGroup.HierarchyUnit: Size of the excluded neighborhood from previous level.
execute() - Method in class AbstractGraph.ZoomCommand
execute() - Method in interface EvoLudo.Directive: The command to execute.
execute() - Method in class AbstractView.ExportCommand
execute() - Method in class Distribution.TraitCommand
execute() - Method in class Phase2D.TraitCommand: Toggle the inclusion of the trait on the axis.
execute(EvoLudo.Directive) - Method in class EvoLudo: Execute directive in JRE or GWT environments.
execute(EvoLudo.Directive) - Method in class EvoLudoGWT
exitFullscreen() - Static method in class NativeJS: JSNI method: Exit fullscreen mode.
EXPAND_MAX - Static variable in class Path2D
EXPAND_MAX_COORDS - Static variable in class Path2D
EXPAND_MIN - Static variable in class Path2D
expandCoords(double[], int) - Static method in class Path2D
expandPointTypes(byte[], int) - Static method in class Path2D
Exponential() - Constructor for class RNGDistribution.Exponential: Creates exponential distribution with mean==1 and a new instance of MersenneTwister.
Exponential(double) - Constructor for class RNGDistribution.Exponential: Creates exponential distribution with mean and a new instance of MersenneTwister.
Exponential(MersenneTwister, double) - Constructor for class RNGDistribution.Exponential: Creates exponential distribution with mean and random number generator rng.
EXPONENTIAL - Enum constant in enum class Map2Fitness.Map: exponential mapping of scores to fitness, \(fit = b*\exp(w*score)\)
export(String, String) - Static method in class NativeJS: JSNI method: encourage browser to download dataURL as a file named filename.
export(AbstractGraph.MyContext2d) - Method in class AbstractGraph: Export the graphical context ctx.
export(AbstractGraph.MyContext2d) - Method in class HistoGraph
export(AbstractGraph.MyContext2d) - Method in class LineGraph
export(AbstractGraph.MyContext2d) - Method in class ParaGraph
export(AbstractGraph.MyContext2d) - Method in class PopGraph2D
export(AbstractGraph.MyContext2d) - Method in class PopGraph3D
export(AbstractGraph.MyContext2d) - Method in class S3Graph
export(AbstractGraph.MyContext2d, int) - Method in class AbstractView: Export each graph in this view.
export(AbstractView.ExportType) - Method in class AbstractView: Export the data of the view.
Export and context menu - Section in class org.evoludo.simulator.views.Histogram
ExportCommand(AbstractView.ExportType) - Constructor for class AbstractView.ExportCommand: The constructor for the export command.
exportCreateEvoLudoLab() - Static method in class EvoLudoWeb: JSNI method: create EvoLudo labs directly from javascript.
exportCreateEvoLudoTrigger() - Static method in class EvoLudoWeb: JSNI method: create EvoLudo lab trigger buttons directly from javascript.
exportDataHeader() - Method in class AbstractView: The header for data exports.
exportInsertEPubEvoLudoLab() - Static method in class EvoLudoWeb: JSNI method: expose method for inserting EvoLudo models into ePub to javascript.
exportInsertEvoLudoLab() - Static method in class EvoLudoWeb: JSNI method: expose method for inserting EvoLudo models into HTML to javascript.
exportMeanData() - Method in class AbstractView: Export the mean data.
exportPNG() - Method in class AbstractView: Export the view as a PNG image.
Exports - Section in class org.evoludo.simulator.views.Mean
exportStatData() - Method in class AbstractView: Export the statistics data.
exportStatData() - Method in class Histogram
exportState() - Method in class EvoLudo: Export the current state of the engine using the appropriate means available in the current environment (GWT/JRE).
exportState() - Method in class EvoLudoGWT: Export the current state of the engine using the appropriate means available in the current environment (GWT/JRE).
exportSubmenu - Variable in class AbstractView: The field to store the export context submenu.
exportSubmenuTrigger - Variable in class AbstractView: The field to store the export submenu trigger.
Export support - Section in class org.evoludo.simulator.views.Phase2D
exportSVG() - Method in class AbstractView: Export the view as a SVG image.
exportSVG(Context2d) - Static method in class NativeJS: JSNI method: Export the SVG context.
exportTrajData() - Method in class AbstractView: Export the trajectories.
exportTrajectory(StringBuilder) - Method in interface AbstractGraph.HasTrajectory: Export the trajectory of the graph to export.
exportTrajectory(StringBuilder) - Method in class ParaGraph
exportTrajectory(StringBuilder) - Method in class S3Graph
exportType - Variable in class AbstractView.ExportCommand: The type of data to export.
ExportType(String) - Constructor for enum class AbstractView.ExportType: The constructor for the export type.
exportTypes() - Method in class AbstractView: Return the list of export types that are acceptable for _all_ graphs in this view.
exportTypes() - Method in class Distribution
exportTypes() - Method in class Histogram
exportTypes() - Method in class Mean
exportTypes() - Method in class Phase2D
exportTypes() - Method in class Pop2D
exportTypes() - Method in class Pop3D
exportTypes() - Method in class S3
Extensibility: - Section in class org.evoludo.graphics.GenericPopGraph
Extensibility & Limitations - Section in class org.evoludo.graphics.PopGraph2D
Extension Points - Section in class org.evoludo.EvoLudoWeb
extremalScoresSet - Variable in class Continuous: The flag that indicates whether maximal and minimal scores have already been calculated.
eye - Variable in class TrackballControls: Location of eye.

F

FACTOR - Static variable in class ColorMap3D: Helper constant: the factor to derive darker shades of a color.
failfast() - Method in class Plist: Check if in fail-fast mode.
failfast(boolean) - Method in class Plist: Set the fail-fast mode to stop comparisons after the first issue encountered.
failFast - Variable in class Plist: The flag to indicate if the comparison should fail fast, i.e.
fatal(String) - Method in class EvoLudo: Report error and stop model execution, if running.
features - Variable in class AbstractGeometry: Lazily computed summary statistics for the geometry.
Features - Interface in org.evoludo.simulator.modules: Interface to query features of the Module.
Features.Groups - Interface in org.evoludo.simulator.modules: All modules that admit interactions in larger groups (as opposed to interactions in pairs) should implement this interface.
Features.Multispecies - Interface in org.evoludo.simulator.modules: All modules that admit multiple species should implement this interface.
Features.Pairs - Interface in org.evoludo.simulator.modules: All modules that admit interactions in pairs (as opposed to larger groups) should implement this interface.
Features.Payoffs - Interface in org.evoludo.simulator.modules: Interface that all modules with frequency dependent fitness/payoffs should implement.
Features.Static - Interface in org.evoludo.simulator.modules: Interface that all modules with static fitness/payoffs should implement.
feedback - Variable in class ATBT: The array with environmental feedback rates.
Fields of interest (summary): - Section in class org.evoludo.graphics.LineGraph
fill(Path2D) - Method in class AbstractGraph: Fill the path path.
fillCircle(double, double, double) - Method in class AbstractGraph: Fill the circle with the center at (x,y) and radius radius.
fillCircle(Node2D) - Method in class AbstractGraph: Draw the filled 2D node.
fillCircle(Point2D, double) - Method in class AbstractGraph: Draw a filled circle at point with radius.
fillEvenIRows(int, boolean, int, int, boolean, int) - Method in class HexagonalGeometry: Populate even-index rows for the hexagonal lattice, respecting boundary conditions.
fillOddIRows(int, boolean, int, int, int, boolean) - Method in class HexagonalGeometry: Populate odd-index rows for the hexagonal lattice, respecting boundary conditions.
fillRect(double, double, double, double) - Method in class AbstractGraph: Fill the rectangle with origin at (x,y), width w and height h.
fillStripe(int, int, int) - Method in class IBSDPopulation: Helper method to initialize lattice structures with homogeneous stripes of each trait.
fillTextVertical(String, double, double) - Method in class AbstractGraph: Draw filled text vertically starting at point (x,y)
findExtrema(double[], double[], int[], int[], double[][], double[][], double[], double[], int[], int[], double, int, double) - Method in class Continuous: Helper method to find the minimum or maximum payoff.
findExtrema(double[], int[], double[][], double[], int[], double, int, double) - Method in class Continuous: Helper method to find the minimum or maximum payoff for monomorphic populations.
findExtremalMonoScore(boolean) - Method in class Continuous: Helper method to find the minimum or maximum payoff for monomorphic populations.
findExtremalScore(boolean) - Method in class Continuous: Helper method to determine the minimum or maximum payoff.
findHoneycombNode(int, int) - Method in class PopGraph2D: Find the index of the node at the location with coordinates (x, y) in a honeycomb lattice.
findInterpolationForMouse(double) - Method in class LineGraph: Scan the buffer and determine the two surrounding samples and the interpolation factor for the supplied mouse time.
findLinearNode(int, int) - Method in class PopGraph2D: Find the index of the node at the location with coordinates (x, y) in a linear lattice.
findMax(RingBuffer, int[]) - Method in class TraitMap: Find the maximum value of the data in the buffer accross all the indices in idxs.
findMin(RingBuffer, int[]) - Method in class TraitMap: Find the minimum value of the data in the buffer accross all the indices in idxs.
findMinMaxCoords(double[], int) - Static method in class Path2D: Helper method to find min/max x and y coordinates in the array.
findNetworkNode(int, int) - Method in class PopGraph2D: Locate the node under the given screen coordinates for general network layouts.
findNextCategory(int) - Method in class CLOParser: Finds the next category with highest priority less than the given priority.
findNodeAt(int, int) - Method in class GenericPopGraph: Find the index of the node at the location with coordinates (x, y).
findNodeAt(int, int) - Method in class PopGraph2D: Find the index of the node at the location with coordinates (x, y).
findNodeAt(int, int) - Method in class PopGraph3D
FINDNODEAT_OUT_OF_BOUNDS - Static variable in class GenericPopGraph: Return value if GenericPopGraph.findNodeAt(int, int) couldn't find a node at the mouse position.
FINDNODEAT_UNIMPLEMENTED - Static variable in class GenericPopGraph: Return value if GenericPopGraph.findNodeAt(int, int) isn't implemented for the particular backing geometry.
findQ(int, double, double) - Method in class simCDLP: Find the interior fixed point Q for the CDL model.
findSquareNode(int, int) - Method in class PopGraph2D: Find the index of the node at the location with coordinates (x, y) in a (hierarchical) square lattice.
findTriangularNode(int, int) - Method in class PopGraph2D: Find the index of the node at the location with coordinates (x, y) in a triangular lattice.
finePeerPunish - Variable in class CDLP: The fine for peer punishment of non-contributors.
finePoolPunish - Variable in class CDLPQ: The pool punishment fine for non-contributors.
finishGraphSetup(LineGraph, boolean) - Method in class Mean: Finalize the setup of a graph (x-label, x-range, module label).
finishLayout() - Method in class Network: Add the finishing touches to the graph layout: shift center of mass into origin rescale size of graph find number of links
finishLayout() - Method in class Network2D
finishLayout() - Method in class Network3D: Prepare graph for display: shift center of mass into origin rescale size of graph find number of links
fireModelChanged() - Method in class EvoLudo: Called whenever the state of the model has changed.
fireModelInit() - Method in class EvoLudo: Called after the model has been re-initialized.
fireModelInit() - Method in class RunController: Called after the model has been re-initialized.
fireModelLoaded() - Method in class EvoLudo: Called whenever a new model has finished loading.
fireModelLoaded() - Method in class LifecycleController: Called whenever a new model has finished loading.
fireModelRelaxed() - Method in class EvoLudo: Called after the model completed its relaxation.
fireModelRelaxed() - Method in class RunController: Called after the model completed its relaxation.
fireModelReset() - Method in class EvoLudo: Called after the model has been reset.
fireModelReset() - Method in class RunController: Called after the model has been reset.
fireModelRunning() - Method in class EvoLudo: Called whenever the model starts its calculations.
fireModelRunning() - Method in class RunController: Called whenever the model starts its calculations.
fireModelSample(boolean) - Method in class EvoLudo: Called after the population has reached an absorbing state (or has converged to an equilibrium state).
fireModelStopped() - Method in class EvoLudo: Called after the population has reached an absorbing state (or has converged to an equilibrium state).
fireModelStopped() - Method in class EvoLudoGWT
fireModelStopped() - Method in class RunController: Called after the population has reached an absorbing state (or has converged to an equilibrium state).
fireModelUnloaded() - Method in class EvoLudo: Called whenever a new model has finished loading.
fireModelUnloaded() - Method in class LifecycleController: Called whenever a new model has finished loading.
fireModuleLoaded() - Method in class EvoLudo: Called whenever a new module has finished loading.
fireModuleLoaded() - Method in class LifecycleController: Called whenever a new module has finished loading.
fireModuleRestored() - Method in class EvoLudo: Called after the state of the model has been restored either through drag'n'drop with the GWT GUI or through the --restore command line argument.
fireModuleRestored() - Method in class LifecycleController: Called after the state of the model has been restored either through drag'n'drop with the GWT GUI or through the --restore command line argument.
fireModuleUnloaded() - Method in class EvoLudo: Called whenever the current module has finished unloading.
fireModuleUnloaded() - Method in class EvoLudoGWT
fireModuleUnloaded() - Method in class LifecycleController: Called whenever the current module has finished unloading.
fireSettingsChanged() - Method in class EvoLudo: Called whenever the settings of the model have changed.
fireSettingsChanged() - Method in class RunController: Called whenever the settings of the model have changed.
first() - Method in class RingBuffer: Return first/oldest buffer entry.
first(double[], double) - Static method in class ArrayMath: Find the first occurence of the element b in the array double[] a.
first(int[], int) - Static method in class ArrayMath: Find the first occurence of the element b in the array int[] a.
fitness - Variable in class IBSDPopulation.Link: The fitness of the individual at the tail end (for fitness based picking of individuals).
fitness - Variable in class IBSPopulation: The array of individual fitness values.
fitness - Variable in class PDE: Fitness distribution of traits as a 2D array.
FITNESS - Enum constant in enum class Data: Fitness: the data represents payoffs/scores/fitness.
FITNESS - Enum constant in enum class SpeciesUpdate.Type: Pick focal species based on population fitness.
FixationData - Class in org.evoludo.simulator.models: EXPERIMENTAL: should mature into data structure useful for statistics
FixationData() - Constructor for class FixationData: Default constructor for FixationData.
Fixation statistics - Section in class org.evoludo.simulator.views.Histogram
fixData - Variable in class Model: The container for collecting statistics samples.
fixedBoundary - Variable in class AbstractLattice: Flag indicating whether boundaries are fixed or periodic (default).
fLinks - Variable in class Network: The fraction of links in the network to be drawn.
flush() - Method in class EvoLudoWeb.EvoLogHandler: Nothing to flush in GWT.
focal - Variable in class IBSGroup: The index of the focal individual.
focusOn(Element) - Static method in class NativeJS: JSNI method: focus on element.
format(double[][], int) - Static method in class Formatter: Format array/matrix of doubles aMatrix as String.
format(double[], int) - Static method in class Formatter: Format array/vector of doubles aVector as String.
format(double, int) - Static method in class Formatter: Format double aDouble as String with at most digits decimal places (trailing zeroes are suppressed).
format(float[][], int) - Static method in class Formatter: Format array/matrix of floats aMatrix as String.
format(float[], int) - Static method in class Formatter: Format array/vector of floats aVector as String.
format(int) - Static method in class Formatter: Format integer anInteger as String
format(int[]) - Static method in class Formatter: Format integer array/vector aVector as String.
format(int[][]) - Static method in class Formatter: Format array/matrix of integers aMatrix as String.
format(int, double...) - Static method in class Formatter: Format an arbitrary number of doubles as String formatted as an array of with at most digits decimal places (trailing zeroes are suppressed).
format(LogRecord) - Method in class XMLLogFormatter
format(T[]) - Static method in class Formatter: Format the vector aVector of type T as String with elements separated by '", "'.
format(T[], String) - Static method in class Formatter: Format the vector aVector of type T as a String with elements separated by delimiter string.
formatBenefits(int) - Method in class Continuous.Traits2Payoff: Return formatted string of the benefit function of trait index idx.
formatCosts(int) - Method in class Continuous.Traits2Payoff: Return formatted string of the cost function of trait index idx.
formatDistributionMean(double[], GraphStyle) - Method in class Histogram: Format mean ± sdev for a distribution stored in data (assumed normalized counts).
formatFix(double[][], int) - Static method in class Formatter: Format array/matrix of doubles aMatrix as String.
formatFix(double[], int) - Static method in class Formatter: Format array/vector of doubles aVector as String.
formatFix(double, int) - Static method in class Formatter: Format double aDouble as String with digits decimal places (trailing zeroes are included).
formatInfoAt(int, int) - Method in class IBSPopulation: Helper method to format information about updating the focal individual at index focal using the model individual with index model.
formatPercent(double, int) - Static method in class Formatter: Format double aDouble as percent String with digits decimal places (trailing zeroes are included).
formatPretty(double, int) - Static method in class Formatter: Same as Formatter.formatSci(double, int) but formatting of exponent 'prettyfied' using HTML.
formatSci(double[][], int) - Static method in class Formatter: Format array/matrix of doubles aMatrix as String.
formatSci(double[], int) - Static method in class Formatter: Format array/vector of doubles aVector as String.
formatSci(double, int) - Static method in class Formatter: Format double aDouble as String with up to digits decimal places (trailing zeroes are suppressed) forcing scientific formatting including exponent (separated by 'E').
Formatter - Class in org.evoludo.util: Collection of convenience methods for formatting numbers, vectors and matrices as Strings.
Formatter() - Constructor for class Formatter: Ensure non-instantiability with private default constructor
formatWeightedMean(double[], double[]) - Method in class Histogram: Compute weighted mean ± sdev from node-wise times (dat) and sample counts (sam).
forward - Variable in class ODE: The flag is true if the numerical integration moves forward in time.
frameColor - Variable in class GraphStyle: The color of the frame.
frameWidth - Variable in class GraphStyle: The stroke width of the frame.
FRANKLIN - Enum constant in enum class GeometryType: Franklin graph, size \(N=12\), connectivity \(k=3\).
FranklinGeometry - Class in org.evoludo.simulator.geometries: Geometry implementation for the Franklin graph (a 12-node cubic cage).
FranklinGeometry(EvoLudo) - Constructor for class FranklinGeometry: Create a Franklin geometry tied to the given engine.
FREQUENCY - Enum constant in enum class IBSD.Init.Type: Random distribution of traits with frequencies <f1,..,fd> (default).
FREQUENCY - Enum constant in enum class ODEInitialize.InitType: Set initial frequencies as specified.
FRUCHT - Enum constant in enum class GeometryType: Frucht graph, size \(N=12\), connectivity \(k=3\).
FruchtGeometry - Class in org.evoludo.simulator.geometries: Frucht graph implementation.
FruchtGeometry(EvoLudo) - Constructor for class FruchtGeometry: Create a Frucht-graph geometry coordinated by the supplied engine.
fsController - Variable in class EvoLudoWeb: Controller handling fullscreen and --size option.
FSController - Class in org.evoludo.simulator.ui: Manages fullscreen handling and GUI sizing for EvoLudoWeb instances.
FSController(EvoLudoGWT, Widget) - Constructor for class FSController: Create a new controller for the given engine.
ft - Variable in class ODE: The current fitness of all traits in the ODE.
ftmp - Variable in class RungeKutta
fullRangeMenu - Variable in class HistoGraph: The context menu item to reset percent axes to full range.
fullRangeMenu - Variable in class Phase2D: The context menu item to set the full frequency range.
FULLSCREEN - Static variable in class FullscreenChangeEvent: Name of fullscreenchange event with prefix added if needed.
FullscreenChangeEvent - Class in org.evoludo.ui: Represents a native fullscreenchange event.
FullscreenChangeEvent() - Constructor for class FullscreenChangeEvent: Protected constructor, use DomEvent.fireNativeEvent(com.google.gwt.dom.client.NativeEvent, com.google.gwt.event.shared.HasHandlers) to fire fullscreenchange events.
fullscreenChangeEventName() - Static method in class NativeJS: JSNI method: Determine name of the fullscreen change event in current web browser.
fullscreenChangeHandler - Variable in class ContextMenu: Reference to fullscreen change handler.
FullscreenChangeHandler - Interface in org.evoludo.ui: Handler interface for FullscreenChangeEvent events.
fullscreenElement - Variable in class EvoLudoGWT: The reference to the fullscreen element.
fullscreenHandler - Variable in class FSController: Registration for the native fullscreen change handler.
fullscreenHandler - Variable in class Tooltip: Reference to fullscreen change handler.
fullscreenMenu - Variable in class EvoLudoGWT: The field to store the fullscreen context menu.
fullscreenWidget - Variable in class FSController: Widget whose size/fullscreen state is controlled (typically the lab container).
fullXRangeMenu - Variable in class LineGraph: The context menu item to show the full x-range of the buffer.
fullYRangeMenu - Variable in class LineGraph: The context menu item to reset percent axes to full range.
func(double, int, double) - Method in class simCDLP: The function \(F(z)\) for the interior fixed point \(Q\).
Functions - Class in org.evoludo.math: Collection of mathematical functions.
Functions() - Constructor for class Functions: Ensure non-instantiability with private default constructor
FwdItr() - Constructor for class RingBuffer.FwdItr: Create a forward iterator starting at the oldest element.

G

g - Variable in class AbstractGraph: Handle to the graphical context for drawing on the canvas.
game - Variable in class ATBT: The 2×2 payoff matrix for interactions between cooperators and defectors.
gatherPlayers(IBSGroup) - Method in class IBSMCPopulation: Gather the traits of all individuals in the interaction group group.
GAUSSIAN - Enum constant in enum class IBSC.Init.Type: Gaussian distribution of traits with mean mi and standard deviation si.
GAUSSIAN - Enum constant in enum class PDEInitialize.Type: Gaussian density distribution in the center.
GAUSSIAN - Enum constant in enum class Mutation.Continuous.Type: Gaussian distributed mutations around parental trait.
gCols - Variable in class AbstractView: The number of columns of graphs in this view.
generate() - Method in class TestEvoLudo: Generate test cases from generator file or directory.
generate(File) - Method in class TestEvoLudo: Generate test cases from generator file clo.
generateBasename(String, int) - Method in class TestEvoLudo: Generate the base name for tests from command line options clo and index idx.
generator - Variable in class TestEvoLudo: Directory with generator scripts for tests.
Generic parameter - Section in class org.evoludo.graphics.AbstractGraph
GenericPop<T,N,G> - Class in org.evoludo.simulator.views: Abstract base view for rendering population-related data (traits or fitness) for EvoLudo models that expose spatial/graph structure (IBS and PDE models).
GenericPop(EvoLudoGWT, Data) - Constructor for class GenericPop: Construct a new view to display the configuration of the current state of the EvoLudo model in 2D or 3D.
GenericPopGraph<T,N> - Class in org.evoludo.graphics: Abstract base class for visualizing a population as a graph.
GenericPopGraph(AbstractView, Module) - Constructor for class GenericPopGraph: Create the base class for population graphs.
Geometric(double) - Constructor for class RNGDistribution.Geometric: Creates geometric distribution with success probability p (mean 1/p) and a new instance of MersenneTwister.
Geometric(MersenneTwister, double) - Constructor for class RNGDistribution.Geometric: Creates geometric distribution with success probability p (mean 1/p) and the random number generator rng.
geometry - Variable in class GenericPopGraph: The structure of the population.
geometry - Variable in class IBSGroup: The geometry associated with this group.
geometry - Variable in class Network: The structure of the population.
GeometryFeatures - Class in org.evoludo.simulator.geometries: Encapsulates frequently used geometry statistics such as minimal or maximal degrees.
GeometryFeatures(AbstractGeometry) - Constructor for class GeometryFeatures: Evaluate geometry features for the given geometry.
GeometryFeatures(GeometryFeatures) - Constructor for class GeometryFeatures: Copy constructor to duplicate cached geometry metrics.
geometryId - Variable in class AbstractGeometry: Identifier for this geometry instance.
GeometryType - Enum Class in org.evoludo.simulator.geometries: The types of graph geometries.
GeometryType(String, String) - Constructor for enum class GeometryType: Instantiate new type of geometry.
GeometryType(String, String, String) - Constructor for enum class GeometryType: Instantiate new geometry type.
get(int) - Method in class Network2D
get(int) - Method in class Network3D
get(int) - Method in class RingBuffer: Retrieve buffer entry at position index (without removing it).
get2DTraitHistogramData(double[], int, int) - Method in class IBSMCPopulation: Creates 2D histogram for traits trait1 and trait2.
get2DTraitHistogramData(int, double[], int, int) - Method in interface CModel: Gets the histogram of the trait distribution for the traits of the Module.
get2DTraitHistogramData(int, double[], int, int) - Method in class IBSC
getAbsoluteLeft() - Method in interface ContextMenu.Listener: Get the absolute left positioning of the widget requesting the context menu.
getAbsoluteTop() - Method in interface ContextMenu.Listener: Get the absolute top positioning of the widget requesting the context menu.
getAccuracy() - Method in class ODE: Gets the numerical accuracy for determining convergence.
getActiveElement() - Static method in class NativeJS: JSNI method: return the currently focused element in the document.
getActiveTraits() - Method in class Module: Gets an array indicating which traits are active.
getActiveView() - Method in class EvoLudoWeb: Return the currently active view.
getActiveView() - Method in class ViewController: Retrieves the currently active view.
getActiveViewIndex() - Method in class EvoLudoWeb: Return the index of the currently active view in the list of active views.
getActiveViewIndex() - Method in class ViewController: Reports the index of the active view inside the deck.
getActiveViews() - Method in class EvoLudoWeb: Return the list of all active views.
getActiveViews() - Method in class ViewController: Provides a snapshot of all active views, including the console.
getAddwire() - Method in class AbstractGeometry: Get the probability used when adding new links.
getAdvection() - Method in class Advection: Gets the 2D advection array for the advection coefficients of each trait against every other one.
getAltruistColor() - Method in class NetGames: Get the color of pure altruists (only help others, don't receive any help from others).
getArg() - Method in class CLOption: Get the option argument.
getArgs() - Method in class IBS.Statistics: Get the settings for the statistics.
getArgs() - Method in class IBSC.Init: Get the arguments of this initialization type.
getArgs() - Method in class IBSD.Init: Get the arguments of this initialization type.
getAssociatedType() - Method in class FullscreenChangeEvent
getAssociatedType() - Method in class InputEvent
getAttributes() - Method in class PlistTag: Get the attributes of this plist entry.
getAuthors() - Method in class ATBT
getAuthors() - Method in class CDL
getAuthors() - Method in class CDLP
getAuthors() - Method in class CDLPQ
getAuthors() - Method in class Centipede
getAuthors() - Method in class CLabour
getAuthors() - Method in class CSD
getAuthors() - Method in class DemesTBT
getAuthors() - Method in class EcoPGG
getAuthors() - Method in class LV
getAuthors() - Method in class Module: Returns a string with information about the authors of the module.
getAuthors() - Method in class Moran
getAuthors() - Method in class NetGames
getAuthors() - Method in class RSP
getAuthors() - Method in class SIR
getAuthors() - Method in class TBT
getAutoDt() - Method in class RungeKutta: Gets whether adaptive step sizes are used.
getBaseline() - Method in class Map2Fitness: Gets the baseline fitness of the map.
getBenefit() - Method in class Centipede: Get the benefit of cooperation, i.e.
getBenefitFunction(int) - Method in class Continuous.Traits2Payoff: Get the benefit function for trait index.
getBenefitFunctions() - Method in class Continuous.Traits2Payoff: Get the array of benefit functions for each trait.
getBenefitParameters() - Method in class Continuous.Traits2Payoff: Get the 2D array of benefit function parameters.
getBenefitParameters(int) - Method in class Continuous.Traits2Payoff: Get the array of benefit function parameters for trait with index idx.
getBinAt(int, int) - Method in class HistoGraph: Get the index of the bin at (x, y).
getBirthRate() - Method in class Module: Get the per capita birth rate for ecological population updates.
getBounds2D() - Method in class Path2D: Returns a high precision and more accurate bounding box of the Path2D than the getBounds method.
getBuffer() - Method in class AbstractGraph: Return the RingBuffer<double[]> containing historical data, if applicable.
getCanvas() - Method in class PopGraph3D.Pop3DScene
getCanvasElement() - Method in class PopGraph3D: Get the canvas element.
getCapacity() - Method in class RingBuffer: Get the capacity of the ring buffer.
getCLI() - Method in class AbstractGeometry: Get the trimmed CLI string that created this geometry (if available).
getCLO() - Method in class CLOController: Return the cached command-line string awaiting parsing.
getCLO() - Method in class EvoLudo: Get the raw command line options, as provided in URL, HTML tag, settings TextArea or command line.
getCLO() - Method in class CLOParser: Return String containing all currently set command line options.
getCLO(String) - Method in class CLOParser: Return option with name from current list of command line options.
getCLOElement() - Method in class EvoLudoWeb: Obtain the DOM element that backs the CLO label for direct manipulation.
getCloEmulate() - Method in class SettingsController: Returns the --emulate command-line option.
getCLOFromURL() - Method in class EvoLudoWeb: Extract command line options from URL parameter clo.
getCLOHelp() - Method in class CLOController: Build a help string summarizing all available options for the active module and model.
getCLOHelp() - Method in class EvoLudo: Format, encode and output help on command line options.
getCloModuleOption() - Method in class EvoLudo: Access the module command line option.
getCLOptions() - Method in class CLOParser: Get the current list of command line options.
getCloSize() - Method in class FSController: Return the CLO option controlling fullscreen/sizing.
getCloView() - Method in class ViewController: Returns the CLO option controlling the initial view displayed in the GUI.
getColorMap() - Method in class GenericPopGraph: Get the map for translating trait values into colors.
getColorModelType() - Method in class Continuous: Get the type of color model for translating continuous traits into colors.
getColors() - Method in class ColorMap.Index: Get the array of colors tha backs this color map.
getColors() - Method in class Centipede.CentiMap
getColors() - Method in class S3Map: Get the colors of the traits.
getCompetitionGeometry() - Method in class IBSPopulation: Gets the competition geometry.
getCompetitionRate() - Method in class Module: Gets the competition rate for ecological population updates.
getCompetitionRates() - Method in class Module: Gets the competition rate for ecological population updates.
getCompGroup() - Method in class IBSPopulation: Gets the competition/reference/model group.
getConnectivity() - Method in class AbstractGeometry: Get the average node degree (connectivity) configured for the geometry.
getConsoleView() - Method in class ViewController: Provides access to the console view.
getCooperativityDiff(int, int) - Method in class NetGames.IBSPop: Calculate the difference in cooperativity of individual index focal as compared to the model individual with index mdl.
getCost() - Method in class Centipede: Get the cost of cooperation, i.e.
getCostCoop() - Method in class CDL: Get the cost of cooperation.
getCostCoop() - Method in class EcoPGG: Get the cost of cooperation.
getCostFunction(int) - Method in class Continuous.Traits2Payoff: Get the cost function for trait index.
getCostFunctions() - Method in class Continuous.Traits2Payoff: Get the array of cost functions, one for each trait.
getCostParameters() - Method in class Continuous.Traits2Payoff: Get the 2D array of cost function parameters.
getCostParameters(int) - Method in class Continuous.Traits2Payoff: Get the array of cost function parameters for trait with index idx.
getCounter() - Method in class IBS
getCounter() - Method in class Model: Gets a formatted string summarizing the elapsed time.
getCSSColorAt(int) - Method in class GenericPopGraph: Get the color of the node at index node as a CSS color string.
getCSSColorAt(int) - Method in class PopGraph2D: Get the color of the node at index node as a CSS color string.
getCSSColorAt(int) - Method in class PopGraph3D: Get the color of the node at index node as a CSS color string.
getCurrentPoint() - Method in class Path2D: Returns the coordinates most recently added to the end of the path as a Point2D object.
getCustomLevels(Data, int) - Method in class Moran
getCustomLevels(Data, int) - Method in interface HasHistogram: Some models may provide reference values for histograms as a horizontal line marking a particular value.
getData() - Method in class GenericPopGraph: Get the color data for all nodes as an array.
getData() - Method in class HistoGraph: Get the data for the histogram.
getData(int) - Method in class HistoGraph: Get the data for the histogram in bin with index idx.
getDeathRate() - Method in class Module: Gets the death rate for ecological population updates.
getDefault() - Method in class CLOption: Return the default argument for command line option.
getDegreeBins(AbstractGeometry, AbstractGeometry) - Method in class Histogram: Determine the number of bins required for the degree distributions of the interaction and competition geometries.
getDegreeGraphs(AbstractGeometry, AbstractGeometry) - Method in class Histogram: Determine the number of histograms required for the degree distributions of the interaction and competition geometries.
getDegreeHistogramData(double[][], AbstractGeometry, int, double) - Method in class Histogram: Generate the degree histogram data for the given geometry.
getDegreeHistogramData(double[][], AbstractGeometry, AbstractGeometry) - Method in class Histogram: Generate the degree histogram data for the given interaction and competition geometries.
getDegreeLabels(int, boolean) - Method in class Histogram: Get the labels for the degree distributions of the interaction and competition geometries.
getDelay() - Method in class EvoLudo: Get delay between subsequent updates.
getDelay() - Method in class RunController: Get current delay between updates.
getDependent() - Method in interface Model.HasDE: For replicator dynamics the frequencies of all traits must sum up to one.
getDependent() - Method in class ATBT
getDependent() - Method in class CDL
getDependent() - Method in class EcoPGG
getDependent() - Method in class LV
getDependent() - Method in class Moran
getDependent() - Method in class Predator
getDependent() - Method in class RSP
getDependent() - Method in class SIR
getDependent() - Method in class TBT
getDepth() - Method in class RingBuffer: Get the depth of array entries.
getDerivatives(double, double[], double[], double) - Method in class SIR: The SIR model is defined by the following equations:
getDerivatives(double, double[], double[], double[]) - Method in class ODE: Calculate the rates of change for all species in state at time given the fitness fitness and returned in change.
getDerivatives(double, double[], double[], double[]) - Method in class ATBT.ODE
getDerivatives(double, double[], double[], double[]) - Method in class SIR.ODE
getDerivatives(double, double[], double[], double[]) - Method in class SIR.PDE
getDerivatives(double, double[], double[], double[]) - Method in class SIR.SDE
getDescription() - Method in enum class GeometryType
getDescription() - Method in interface CLODelegate: If settings for option are not known upon initialization, an up-to-date description is requested when needed (e.g.
getDescription() - Method in class CLOption: Retrieve short description of option and include the default as well as the current arguments.
getDescription() - Method in interface CLOption.Key: Optional: long description of purpose of this key.
getDescriptionKey() - Method in class CLOption: Get the description of all keys of this option.
getDescriptionKey(String) - Method in class CLOption: Get the description of the key with name aKey.
getDeterminant() - Method in class AffineTransform: Returns the determinant of the matrix representation of the transform.
getDevicePixelRatio() - Static method in class NativeJS: JSNI method: return the pixel ratio of the current device.
getDiffusion() - Method in class PDE: Gets the diffusion coefficients for all traits as an array.
getDiscretization() - Method in class PDE: Gets the number of units used to discretize the spatial dimensions for numerical integration of the PDE.
getDt() - Method in class ODE: Gets the discretization of time increments in continuous time models.
getEffectiveNoise(Module, int) - Method in class SDE: Helper method to determine the effective demographic noise for a given module based on the current population size.
getEgoistColor() - Method in class NetGames: Get the color of pure egoists (only receive help from others, don't provide any help to others).
getEncodeKey() - Method in class AbstractGeometry: Retrieve the name of the key for storing geometry in plist.
getEngine() - Method in class EvoLudoWeb: Return the engine that controls the EvoLudo modules.
getEnvironment() - Method in class ATBT: Get the environmental values or patch qualities for rich and poor sites.
getEnvironmentalAsymmetry() - Method in class ATBT: Check whether asymmetries are due to environmental differences, i.e.
getEPubReader() - Static method in class NativeJS: JSNI method: Retrieve string identifying the ePub reading system: web browser: null iBooks: iBooks, Apple Books Adobe Digital Editions 4.5.8 (macOS): RMSDK Readium: no JS (and no display equations!) TEA Ebook 1.5.0 (macOS): no JS (and issues with MathML) calibre: calibre-desktop (supports JS and MathML but appears unstable) Note: nonlinear content in Apple Books on iOS does not report as an ePub reading system (at least on the iPad).
getError() - Method in class PlayerUpdate: Get the error of the updating process.
getFairColor() - Method in class NetGames: Get the color of fair individuals (help the same number of individuals as help them, regardless of any potential reciprocity).
getFeatures() - Method in class AbstractGeometry: Evaluate geometry.
getFeedback() - Method in class ATBT: Get the array with feedback rates/probabilities.
getFirstView() - Method in class ViewController: Returns the first available view in the registry.
getFitness() - Method in class Moran: Get the array of fitness values for residents and mutants.
getFitness(int) - Method in class IBSPopulation: Gets the fitness of all individuals with precision digits.
getFitness(int) - Method in class Moran: Get the fitness value for trait aType.
getFitnessAt(int) - Method in class IBSDPopulation
getFitnessAt(int) - Method in class IBSPopulation: Gets the fitness of the individual with index idx.
getFitnessData(int, T[], ColorMap.Gradient1D) - Method in class IBS
getFitnessData(int, T[], ColorMap.Gradient1D) - Method in class Model: Translates fitness data into colors using ColorMap colorMap.
getFitnessData(int, T[], ColorMap.Gradient1D) - Method in class ODE
getFitnessData(int, T[], ColorMap.Gradient1D) - Method in class PDE
getFitnessData(T[], ColorMap.Gradient1D) - Method in class IBSPopulation: Returns the fitness of all individuals in this population coded as colors in the array colors using the map colorMap.
getFitnessData(T[], ColorMap.Gradient1D) - Method in class NetGames.IBSPop
getFitnessDiff(int, int) - Method in class NetGames.IBSPop: Calculate the difference in fitness of individual with index focal as compared to the model individual with index mdl.
getFitnessHistogramData(double[][]) - Method in class IBSDPopulation
getFitnessHistogramData(double[][]) - Method in class IBSPopulation: Generates a histogram of the fitness distribution in this population.
getFitnessHistogramData(double[][]) - Method in class NetGames.IBSPop
getFitnessHistogramData(int, double[][]) - Method in class IBS
getFitnessHistogramData(int, double[][]) - Method in class Model: Generates a histogram of fitness data and returns the result in the provided array bins.
getFitnessHistogramData(int, double[][]) - Method in class ODE
getFitnessHistogramData(int, double[][]) - Method in class PDE
getFitnessNameAt(int) - Method in class IBSPopulation: Gets the formatted and prettyfied fitness of the individual with index idx as a string.
getFitnessNameAt(int, boolean) - Method in class IBSPopulation: Gets the formatted fitness of the individual with index idx as a string.
getFitnessNameAt(int, int) - Method in class IBS
getFitnessNameAt(int, int) - Method in class Model: Gets the fitness at location idx for species with ID id as a formatted string.
getFitnessNameAt(int, int) - Method in class PDE
getFixationData() - Method in class Model: Gets the statistics sample of the fixation data.
getFixationProbabilityStatus() - Method in class Histogram: Build status string for fixation probabilities.
getFixationTimeStatus() - Method in class Histogram: Build status string for fixation times.
getFocal() - Method in class IBSGroup: Gets the index of the focal individual.
getFullscreenElement() - Static method in class NativeJS: JSNI method: Gets fullscreen element if in fullscreen mode or null if not in fullscreen or fullscreen not supported by web browser.
getGeometry() - Method in class GenericPopGraph: Get the geometry backing the graph.
getGeometry() - Method in class PDE: Gets the geometry representing the spatial structure of this PDE.
getGeometry() - Method in class Module: Gets the geometry of the population.
getGeometry() - Method in class Network: Get the geometry that is backing this network.
getGit() - Method in class EvoLudo: Gets current git version of code base.
getGit() - Method in class EvoLudoGWT
getGitDate() - Method in class EvoLudo: Gets the compilation date of the current git version.
getGitDate() - Method in class EvoLudoGWT
getGraphAt(int, int) - Method in class AbstractView: Get the graph at the coordinates (x,y).
getGroup() - Method in class IBSGroup: Gets the array of indices of the interaction/reference group members.
getHeader() - Method in class CLOCategory: Get the header of category for help display.
getHeight() - Method in class Rectangle2D: Get the height of the rectangle.
getHierarchyLevels() - Method in class HierarchicalGeometry: Retrieve a copy of the processed hierarchy definition (levels plus individuals per deme).
getHierarchyWeight() - Method in class HierarchicalGeometry: Report the weight applied to inter-level interactions.
getIBSDPopulation(int) - Method in class IBSD: Helper routine to retrieve the IBSDPopulation associated with module with id.
getIBSMCPopulation(int) - Method in class IBSC: Helper routine to retrieve the IBSPopulation associated with module with id.
getIBSPopulation() - Method in class Module: Gets the IBSPopulation that represents this module in individual based simulations or null for all other types of models.
getIBSPopulation(int) - Method in class IBS: Helper routine to retrieve the IBSPopulation associated with module with id.
getId() - Method in class Module: Gets unique identifier ID of species.
getInit() - Method in class IBSDPopulation: Gets the type of the initial configuration and its arguments.
getInit() - Method in class IBSMCPopulation: Gets the type of the initial configuration and its arguments.
getInitialTraits(double[]) - Method in interface DModel: Collect and return initial trait values for all species.
getInitialTraits(double[]) - Method in class IBSD
getInitialTraits(double[]) - Method in class IBSDPopulation: Returns the initial trait(s) of this population in the array init.
getInitialTraits(double[]) - Method in class ODE
getInitialTraits(int, double[]) - Method in interface DModel: Return initial trait values for species with ID id.
getInitialTraits(int, double[]) - Method in class IBSD
getInitialTraits(int, double[]) - Method in class ODE
getInputElement() - Method in class Slider: Get the input element underlying the slider.
getInteractionGeometry() - Method in class IBSPopulation: Gets the interaction geometry.
getInteractionsAt(int) - Method in class IBSPopulation: Gets the number of interactions of the individual with index idx.
getInteractionsAt(int) - Method in class NetGames.IBSPop
getInteractionsAt(int, int) - Method in class IBS: Gets the number of interactions at location idx for species with ID id.
getInterest() - Method in class CDL: Get the interest rate in linear public goods games, or, for a single contributor in non-linear public goods games, i.e.
getInterest() - Method in class EcoPGG: Get the multiplication factor of the linear public goods game.
getInterGroup() - Method in class IBSPopulation: Gets the interaction group.
getJavaVersion() - Method in class EvoLudo: Get version of JRE (if not running in browser).
getKey() - Method in enum class GeometryType
getKey() - Method in enum class IBS.MigrationType
getKey() - Method in enum class IBS.ScoringType
getKey() - Method in enum class IBS.Statistics.Type
getKey() - Method in enum class IBSC.Init.Type
getKey() - Method in enum class IBSD.Init.Type
getKey() - Method in enum class IBSD.OptimizationType
getKey() - Method in enum class IBSGroup.SamplingType
getKey() - Method in enum class ModelType
getKey() - Method in enum class ODEInitialize.InitType
getKey() - Method in enum class PDEInitialize.Type
getKey() - Method in enum class PopulationUpdate.Type
getKey() - Method in class ATBT
getKey() - Method in class Centipede
getKey() - Method in class CLabour
getKey() - Method in enum class Continuous.Benefits
getKey() - Method in enum class Continuous.ColorModelType
getKey() - Method in enum class Continuous.Costs
getKey() - Method in class CSD
getKey() - Method in class DemesTBT
getKey() - Method in class EcoPGG
getKey() - Method in enum class Map2Fitness.Map
getKey() - Method in class Module: Returns identifier of the active module.
getKey() - Method in enum class Mutation.Continuous.Type
getKey() - Method in enum class Mutation.Discrete.Type
getKey() - Method in class NetGames
getKey() - Method in enum class PlayerUpdate.Type
getKey() - Method in enum class SpeciesUpdate.Type
getKey() - Method in class TBT
getKey() - Method in interface CLOption.Key: Return key of in this collection.
getKey() - Method in class CLOption.SimpleKey
getKey(String) - Method in class CLOption: Get the key with name aKey.
getKeyPos() - Method in interface CLODelegate: Optional: position of key in the list of arguments.
getKeys() - Method in class CLOption: Gets all keys of this option.
getLabel() - Method in class AbstractGeometry: Compose a human readable prefix for log messages.
getLabel() - Method in class S3Map: Get the name of the map.
getLayoutTimout() - Method in class Network: Get the timeout for layout calculations.
getLeafColor(T, ColorMap) - Method in class NetGames.IBSPop: Utility method to determine the color of leaves in the network.
getLeniencyCoop() - Method in class CDLP: Get the leniency towards cooperators, provided the composition of the interaction group reveals them as second-order free riders.
getLeniencyLoner() - Method in class CDLP: Get the leniency towards loners.
getLine() - Method in class PlistReader: Return line number of last line read.
getLinearAsymmetry() - Method in class LinearGeometry: Get the current left-right neighbour difference.
getLinearExtension() - Method in class PDE: Gets the linear extension of the lattice.
getLinks() - Method in class Network3DGWT: Get the links of this 3D network representation.
getLinks() - Method in class Network2D: Get the links in this network for the GUI to draw.
getListener() - Method in class ContextMenu.Registration: Get the listener widget for context menu events.
getLogger() - Method in class EvoLudo: Note: Instead of sharing logging system, EvoLudo could implement helper routines for logging notifications.
getLogger() - Method in class Model: Return the logger for reporting information.
getLogger() - Method in class AbstractView: Get the logger for returning progress, problems and messages to user.
getMap() - Method in class ParaGraph: Get the map for converting data to phase plane coordinates.
getMap() - Method in class S3Graph: Get the map for converting data to simplex coordinates.
getMap2Fitness() - Method in interface Features.Payoffs: Gets the score/payoff to fitness map.
getMap2Fitness() - Method in class Module: Default implementation of Payoffs interface.
getMarkers() - Method in class Markers: Get the list of markers.
getMarkers() - Method in class Model: Get the list of markers.
getMatrix(double[]) - Method in class AffineTransform: Retrieves the 6 specifiable values in the 3x3 affine transformation matrix and places them into an array of double precisions values.
getMax() - Method in class RNGDistribution.Uniform: Get the upper bound of the uniform distribution (exclusive).
getMax() - Method in class Slider: Get the maximum value of the slider.
getMaxBins() - Method in class HistoGraph: Calculate the maximum number of bins for the histogram with a width of at least MIN_BIN_WIDTH.
getMaxFitness(int) - Method in class IBS
getMaxFitness(int) - Method in class Model: Calculates and returns the absolute fitness maximum.
getMaxFitness(int) - Method in class ODE
getMaxMonoPayoff() - Method in class Continuous: Default implementation of Features.Payoffs.getMaxMonoPayoff().
getMaxMonoPayoff() - Method in class Discrete: Default implementation of Features.Payoffs.getMaxMonoPayoff().
getMaxMonoPayoff() - Method in interface Features.Payoffs: Calculates and returns the maximum payoff/score of individuals in monomorphic populations.
getMaxMonoScore(int) - Method in interface CModel: Calculates and returns maximum score in monomorphic population.
getMaxMonoScore(int) - Method in class IBSC
getMaxPayoff() - Method in class CDL
getMaxPayoff() - Method in class Centipede
getMaxPayoff() - Method in class Continuous: Default implementation of Features.Payoffs.getMaxPayoff().
getMaxPayoff() - Method in class EcoPGG
getMaxPayoff() - Method in interface Features.Payoffs: Calculates and returns the maximum payoff/score of an individual.
getMaxPayoff() - Method in class Moran
getMaxPayoff() - Method in class NetGames
getMaxPayoff() - Method in class RSP
getMaxPayoff() - Method in class TBT
getMaxScore() - Method in class IBSPopulation: Returns the maximum score min in this population, taking the population structure and payoff accounting into account.
getMaxScore() - Method in class NetGames.IBSPop
getMaxScore(int) - Method in class IBS
getMaxScore(int) - Method in class Model: Returns the maximum score that individuals of species with ID id can achieve in this model.
getMaxScore(int) - Method in class ODE
getMaxTraits() - Method in class IBSMCPopulation: Gets the maximal value of each trait in the population and stores it in the array max.
getMaxTraits(double[]) - Method in class IBSMCPopulation: Gets the maximal value of each trait in the population and stores it in the array max.
getMaxX(RingBuffer) - Method in class TraitMap
getMaxX(RingBuffer) - Method in interface HasPhase2D.Data2Phase: Return maximum value for x-axis.
getMaxY(RingBuffer) - Method in class TraitMap
getMaxY(RingBuffer) - Method in interface HasPhase2D.Data2Phase: Return maximum value for y-axis.
getMean() - Method in class RNGDistribution.Exponential: Get the mean of the exponential distribution.
getMean() - Method in class RNGDistribution.Normal: Get the mean of the Normal distribution.
getMeanColors() - Method in class Module: Gets the colors for the mean values of traits.
getMeanColors() - Method in class TBT
getMeanFitness(double[]) - Method in class IBS
getMeanFitness(double[]) - Method in class IBSDPopulation
getMeanFitness(double[]) - Method in class IBSMCPopulation: Returns the mean fitness of this population in the array mean.
getMeanFitness(double[]) - Method in class IBSPopulation: Returns the mean fitness of this population in the array mean.
getMeanFitness(double[]) - Method in class Model: Gets the mean fitness values for traits in all species.
getMeanFitness(double[]) - Method in class ODE
getMeanFitness(double[]) - Method in class NetGames.IBSPop
getMeanFitness(double[]) - Method in class TBT.IBSPop
getMeanFitness(int, double[]) - Method in class IBS
getMeanFitness(int, double[]) - Method in class Model: Gets the mean fitness values for species with ID id.
getMeanFitness(int, double[]) - Method in class ODE
getMeanFitness(int, double[]) - Method in class PDE
getMeanFitnessAt(int, int) - Method in class Model: Gets the mean fitness(es) of this model at location idx.
getMeanFitnessAt(int, int) - Method in class PDE
getMeanName(int) - Method in class Model: Return the name of the mean trait with index index or null if index is invalid.
getMeanNames() - Method in class Model: Return the names of the mean traits of this model.
getMeanTraitAt(int, int) - Method in class Model: Return mean trait values at location idx for species with ID id.
getMeanTraitAt(int, int) - Method in class PDE
getMeanTraits(double[]) - Method in class IBS
getMeanTraits(double[]) - Method in class IBSDPopulation
getMeanTraits(double[]) - Method in class IBSMCPopulation: Returns the mean trait(s) of this population in the array mean.
getMeanTraits(double[]) - Method in class IBSPopulation: Returns the mean trait(s) of this population in the array mean.
getMeanTraits(double[]) - Method in class Model: Collect and return mean trait values for all species.
getMeanTraits(double[]) - Method in class ODE
getMeanTraits(double[]) - Method in class PDE
getMeanTraits(double[]) - Method in class NetGames.IBSPop
getMeanTraits(double[]) - Method in class TBT.IBSPop
getMeanTraits(int, double[]) - Method in class IBS
getMeanTraits(int, double[]) - Method in class Model: Return mean trait values for species with ID id.
getMeanTraits(int, double[]) - Method in class ODE
getMeanTraits(int, double[]) - Method in class PDE
getMigrationProb() - Method in class IBSPopulation: Gets the migration probability.
getMigrationType() - Method in class IBSPopulation: Gets the type of migrations.
getMin() - Method in class RNGDistribution.Uniform: Get the lower bound of the uniform distribution (inclusive).
getMin() - Method in class Slider: Get the minimum value of the slider.
getMinFitness(int) - Method in class IBS
getMinFitness(int) - Method in class Model: Calculates and returns the absolute fitness minimum.
getMinFitness(int) - Method in class ODE
getMinMonoPayoff() - Method in class Continuous: Default implementation of Features.Payoffs.getMinMonoPayoff().
getMinMonoPayoff() - Method in class Discrete: Default implementation of Features.Payoffs.getMinMonoPayoff().
getMinMonoPayoff() - Method in interface Features.Payoffs: Calculates and returns the minimum payoff/score of individuals in monomorphic populations.
getMinMonoScore(int) - Method in interface CModel: Calculates and returns minimum score in monomorphic population.
getMinMonoScore(int) - Method in class IBSC
getMinPayoff() - Method in class CDL
getMinPayoff() - Method in class CDLP
getMinPayoff() - Method in class CDLPQ
getMinPayoff() - Method in class Centipede
getMinPayoff() - Method in class Continuous: Default implementation of Features.Payoffs.getMinPayoff().
getMinPayoff() - Method in class EcoPGG
getMinPayoff() - Method in interface Features.Payoffs: Calculates and returns the minimum payoff/score of an individual.
getMinPayoff() - Method in class Moran
getMinPayoff() - Method in class NetGames
getMinPayoff() - Method in class RSP
getMinPayoff() - Method in class TBT
getMinScore() - Method in class IBSPopulation: Returns the minimum score min in this population, taking the population structure and payoff accounting into account.
getMinScore() - Method in class NetGames.IBSPop
getMinScore(int) - Method in class IBS
getMinScore(int) - Method in class Model: Returns the minimum score that individuals of species with ID id can achieve in this model.
getMinScore(int) - Method in class ODE
getMinTraits() - Method in class IBSMCPopulation: Gets the minimal value of each trait in the population and stores it in the array min.
getMinTraits(double[]) - Method in class IBSMCPopulation: Gets the minimal value of each trait in the population and stores it in the array min.
getMinX(RingBuffer) - Method in class TraitMap
getMinX(RingBuffer) - Method in interface HasPhase2D.Data2Phase: Return minimum value for x-axis.
getMinY(RingBuffer) - Method in class TraitMap
getMinY(RingBuffer) - Method in interface HasPhase2D.Data2Phase: Return minimum value for y-axis.
getMode() - Method in enum class ChangeListener.PendingAction: Return the requested execution mode.
getMode() - Method in enum class Data: Returns the appropriate mode for the model based on the data type.
getMode() - Method in class Model: Gets the Mode of the model.
getMode() - Method in class AbstractView: Get the mode required by this view.
getMode() - Method in class Histogram
getModel() - Method in class EvoLudo: Get the active model.
getModel() - Method in class AbstractView: Get the type of the model supplying the data visualized on the graph.
getModelType() - Method in class Module: Gets the type of the current model or ModelType.NONE if no model is loaded.
getModelType() - Method in class AbstractView: Gets the type of the current model or ModelType.NONE if no model is loaded.
getModelTypes() - Method in class simMoran
getModelTypes() - Method in class DemesTBT: Return array of Model types that this Module supports.
getModelTypes() - Method in class Module: Return array of Model types that this Module supports.
getModule() - Method in class AbstractGraph: Get the module that backs the graph.
getModule() - Method in class EvoLudo: Gets the active Module.
getModule() - Method in class IBSPopulation: Gets the module associated with this population.
getMonoPayoff(int) - Method in class CDL
getMonoPayoff(int) - Method in class CDLP: Calculate and return the payoff/score of individuals in monomorphic populations with trait type.
getMonoPayoff(int) - Method in class CDLPQ: Calculate and return the payoff/score of individuals in monomorphic populations with trait type.
getMonoPayoff(int) - Method in class Centipede
getMonoPayoff(int) - Method in class Discrete: Calculate and return the payoff/score of individuals in monomorphic populations with trait type.
getMonoPayoff(int) - Method in class EcoPGG
getMonoPayoff(int) - Method in class Moran
getMonoPayoff(int) - Method in class RSP
getMonoPayoff(int) - Method in class TBT
getMonoScore(int) - Method in class IBSDPopulation: Gets the score of individuals in a population that is monomorphic in trait type.
getMonoScore(int, int) - Method in interface DModel: Calculate and return the payoff/score of individuals in monomorphic populations with trait idx but also deals with payoff accounting (averaged versus accumulated).
getMonoScore(int, int) - Method in class IBSD
getMonoScore(int, int) - Method in class ODE
getMonoStop() - Method in class Discrete: Get the flag which indicates whether models stop once a monomorphic state has been reached.
getMouseOnScreen(int, int) - Method in class TrackballControls: Re-scale pointer coordinates to [0, 1]².
getMouseProjectionOnBall(int, int) - Method in class TrackballControls: Convert pointer coordinates to coordinates on (virtual) trackball (unit sphere).
getMutation() - Method in class Centipede
getMutation() - Method in class Continuous
getMutation() - Method in class Discrete
getMutation() - Method in class Module: Gets the mutation type.
getNActive() - Method in class Module: Gets the number of active traits.
getName() - Method in class AbstractGeometry: Retrieve the display name of the geometry (sans trailing structural suffixes such as ": Structure").
getName() - Method in class Map2Fitness: Gets the name/key of the current map.
getName() - Method in class Module: Gets the name of this species
getName() - Method in class AbstractView: Get the name of this view.
getName() - Method in class Console
getName() - Method in class Distribution
getName() - Method in class GenericPop
getName() - Method in class Histogram
getName() - Method in class Mean
getName() - Method in class Phase2D
getName() - Method in class S3
getName() - Method in class CLOption: Get the name of the option.
getName(int) - Method in class S3Map: Get the name of the traits at the corner with index idx.
getNames() - Method in class Centipede.CentiMap
getNames() - Method in class S3Map: Get the names of the traits.
getNDemes() - Method in class DemesTBT: Return the number of demes.
getNetwork() - Method in class GenericPopGraph: Get the network representation of the graph represented by the geometry.
getNetwork2D() - Method in class AbstractGeometry: Retrieve (and lazily create) the 2D representation associated with this geometry.
getNetwork3D() - Method in class AbstractGeometry: Retrieve (and lazily create) the 3D representation associated with this geometry.
getNextHalt() - Method in class Model: Gets the next generation for which stopping the model execution has been requested.
getNGroup() - Method in interface Features.Groups: Get the interaction group size.
getNGroup() - Method in class Module: Gets the interaction group size.
getNIssues() - Method in class Plist: Get the number of issues found.
getNLines() - Method in class LineGraph: Get the number of lines plotted in this graph.
getNLinks() - Method in class Network: Get the number of links in the network.
getNMajor() - Method in class Plist: Get the number of major issues found.
getNMean() - Method in class IBS
getNMean() - Method in class IBSPopulation: Return the number of mean values for this population (for traits or fitness).
getNMean() - Method in class Model: Return the number of mean values for this model including all species (for traits or fitness).
getNMean() - Method in class ODE
getNMean() - Method in class TBT.IBSPop
getNMean(int) - Method in class IBS
getNMean(int) - Method in class Model: Return the number of mean trait values for species with ID id.
getNMean(int) - Method in class ODE
getNMinor() - Method in class Plist: Get the number of minor issues found (most likely numerical).
getNMixedInteractions(int) - Method in class IBSPopulation: Determine the number of interactions in well-mixed populations with lookup tables.
getNodes() - Method in class Centipede: Get the number of decision nodes for the centipede game.
getNoise() - Method in class PlayerUpdate: Get the noise of the updating process.
getNoteAt(int) - Method in class HistoGraph: Get the description of the marker at bin bin or null if no marker is set.
getNPopulation() - Method in class Module: Gets the population size.
getNRoles() - Method in class Centipede
getNRoles() - Method in class Module: Gets the number of roles that an individual can adopt.
getNSampled() - Method in class IBSGroup: Get the number of interactions with random neighbours.
getNSamples() - Method in class IBSGroup: Get the number of interactions with random neighbours.
getNSamples() - Method in class Model: Gets the number of statistical samples after which the active Model is halted.
getNSpecies() - Method in class Model: Return the number of species in this model.
getNSpecies() - Method in class Module: Gets the number of different species in this module.
getNStatisticsFailed() - Method in class Model: Gets the number of failed statistics samples.
getNStatisticsSamples() - Method in class Model: Gets the number of statistics samples collected so far.
getNTraits() - Method in class Module: Gets the number of traits in this Module.
getNTraits() - Method in interface HasDistribution: Gets the number of traits in the Modules.
getNTraits() - Method in interface HasHistogram: Get the number of traits in the Modules.
getOccupiedDensity(int, double[]) - Method in class ODE: Compute the occupied density (sum over non-vacant traits) for a species.
getOppCompGraph(G) - Method in class GenericPop: Get the competition graph of the opponent of the module associated with the given graph.
getOppInterGraph(G) - Method in class GenericPop: Get the interaction graph of the opponent of the module associated with the given graph.
getOpponent() - Method in class Module: Gets the opponent of this module/population.
getOrder() - Method in class S3Map: Get the indices of the traits that span the simplex.
getOthersOnly() - Method in class CDL: Get the flag whether the return of the public good is split among all members of the group or only all other's, i.e.
getParentMenu() - Method in class ContextMenu: Get the parent menu.
getParser() - Method in class CLOController: Return the underlying parser used to register CLOs.
getParserCLO() - Method in class CLOController: Get the raw command-line string currently stored in the parser.
getPathIterator() - Method in class Path2D: Returns an iterator object that iterates along this path.
getPayFirst(int, int) - Method in class Centipede: Returns the payoff for the first mover.
getPayLoneCoop() - Method in class CDL: Get the payoff to lone cooperators.
getPayLoneCoop() - Method in class EcoPGG: Get the payoff to lone cooperators.
getPayLoneDefect() - Method in class CDL: Get the payoff to lone defectors.
getPayLoneDefect() - Method in class EcoPGG: Get the payoff to lone defectors.
getPayLoner() - Method in class CDL: Set the payoff of loners.
getPayoff(int, int) - Method in class TBT: Get the payoff for type me against type you.
getPayoffs() - Method in class RSP: Get the payoff matrix.
getPayoffs() - Method in class TBT: Get the payoffs as a 2×2 matrix.
getPaySecond(int, int) - Method in class Centipede: Returns the payoff for the second mover.
getPhase2DMap() - Method in class ATBT
getPhase2DMap() - Method in class EcoPGG
getPhase2DMap() - Method in interface HasPhase2D: Get the map that transforms the data of the module to a 2D phase plane (projection).
getPlayerScoreAveraged() - Method in class IBSPopulation: Gets whether player scores are averaged (as opposed to accumulated).
getPlayerScoring() - Method in class IBSPopulation: Gets the type for managing scores of individuals.
getPlayerUpdate() - Method in class Module: Gets the score/payoff to fitness map.
getPoint(int) - Method in class Path2D: Return the point in the Path2D with the specified index.
getPoolPunishCost() - Method in class CDLPQ: Get the cost of pool punishment.
getPoolPunishFine() - Method in class CDLPQ: Get the fine for pool punishment.
getPopulationSize() - Method in class IBSDPopulation
getPopulationSize() - Method in class IBSPopulation: Gets current population size.
getPopulationUpdate() - Method in class IBSPopulation: Gets the population update.
getPriority() - Method in class CLOCategory: Get the priority of this category.
getProbability() - Method in class RNGDistribution.Binomial: Get the probability of success p of a single trial for the binomial distribution.
getProbability() - Method in class RNGDistribution.Geometric: Get the success probability of a single trial.
getProbability() - Method in class Mutation: Get the probability of mutations.
getProbability(double) - Method in class NetGames.IBSPop: Converts the difference z into a probability following the Fermi function \[p = 1/(1+\exp(-w z)),\] where \(w\) denotes the selection strength.
getProvider() - Method in class ContextMenu.Registration: Get the provider of entries of context menu for this listener widget.
getPunishCost() - Method in class CDLP: Get the cost of peer punishment of non-contributors.
getPunishFine() - Method in class CDLP: Get the peer punishment fine to non-contributors.
getQuadrantRotateInstance(int) - Static method in class AffineTransform: Returns a transform that rotates coordinates by the specified number of quadrants.
getQuadrantRotateInstance(int, double, double) - Static method in class AffineTransform: Returns a transform that rotates coordinates by the specified number of quadrants around the specified anchor point.
getR() - Method in class Node2D: Get the radius r of this 2D node.
getR() - Method in class Node3D: Get the radius r of this 3D node.
getRadius() - Method in class Network: Get the radius of the network.
getRandomSampleProb() - Method in class NetGames: Get the probability of picking a random model for comparison.
getRange() - Method in class RNGDistribution.Uniform: Get the range of the uniform distribution.
getRatio() - Method in class NetGames: Get the cost-to-benefit ratio of cooperation.
getReferenceProb(int) - Method in class Moran: Helper method to retrieve the reference fixation probabilities for trait trait for the initial number of mutants according to init.
getReferenceTime(int) - Method in class Moran: Helper method to retrieve the reference fixation times for trait trait for the initial number of mutants according to init.
getRenderer() - Method in class PopGraph3D.Pop3DScene
getRewire() - Method in class AbstractGeometry: Get the probability used when rewiring existing links.
getRNG() - Method in class RNGDistribution: Get random number generator of this distribution.
getRNG() - Method in class EvoLudo: Get the shared random number generator to ensure the reproducibility of results.
getRole() - Method in class S3Map: Get the role of the map.
getRotateInstance(double) - Static method in class AffineTransform: Returns a transform representing a rotation transformation.
getRotateInstance(double, double) - Static method in class AffineTransform: Returns a transform that rotates coordinates according to a rotation vector.
getRotateInstance(double, double, double) - Static method in class AffineTransform: Returns a transform that rotates coordinates around an anchor point.
getRotateInstance(double, double, double, double) - Static method in class AffineTransform: Returns a transform that rotates coordinates around an anchor point according to a rotation vector.
getS3Map(int) - Method in class Centipede
getS3Map(int) - Method in interface HasS3: Get the map that transforms the data of the model to a 2D phase plane (projection).
getSamples() - Method in class HistoGraph: Get the number of samples for this histogram.
getSamples(int) - Method in class HistoGraph: Get the total number of samples in bin with index idx.
getSampling() - Method in class IBSGroup: Gets the type of sampling of interaction/reference groups.
getScaleInstance(double, double) - Static method in class AffineTransform: Returns a transform representing a scaling transformation.
getScaleX() - Method in class AffineTransform: Returns the m00 element of the 3x3 affine transformation matrix.
getScaleY() - Method in class AffineTransform: Returns the m11 element of the 3x3 affine transformation matrix.
getScoreAt(int) - Method in class IBSDPopulation
getScoreAt(int) - Method in class IBSPopulation: Gets the score of the individual with index idx.
getScoreNameAt(int) - Method in class IBSPopulation: Gets the formatted score of the individual with index idx.
getScoreNameAt(int, int) - Method in class IBS
getScoreNameAt(int, int) - Method in class Model: Gets the score at location idx for species with ID id as a formatted string.
getScores(int) - Method in class IBSPopulation: Gets the scores of all individuals with precision digits.
getSeed() - Method in class MersenneTwister: Returns the seed of the random number generator.
getSeed() - Method in class RNGDistribution: Retrieve seed of random number generator in [0, 2³³-1].
getSelection() - Method in class Map2Fitness: Gets the selection strength of the map.
getSelection() - Method in class NetGames: Get the selection strength on differences in payoffs and cooperativity.
getSelf() - Method in class IBSGroup: Gets whether random sampling includes the focal individual or not.
getShearInstance(double, double) - Static method in class AffineTransform: Returns a transform representing a shearing transformation.
getShearX() - Method in class AffineTransform: Returns the X coordinate shearing element (m01) of the 3x3 affine transformation matrix.
getShearY() - Method in class AffineTransform: Returns the Y coordinate shearing element (m10) of the 3x3 affine transformation matrix.
getSize() - Method in class AbstractGeometry: Report the current number of nodes contained in the geometry.
getSize() - Method in class RingBuffer: Get the number of entries in the ring buffer.
getSizeDemes() - Method in class DemesTBT: Return the size of each demes.
getSlope(double, double, double, double) - Static method in class Line2D: Calculate the slope of a line running through points (x1,y1) and (x2,y2).
getSlope(Point2D, Point2D) - Static method in class Line2D: Calculate the slope of a line running through points p1 and p2.
getSnapLayoutTimeout() - Method in class EvoLudo: Gets the timeout for the layout process of snapshots in msec.
getSolo() - Method in class CDL: Get whether a single contributor is enough to generate the public good.
getSpecies() - Method in class Module: Gets list with all species.
getSpecies(int) - Method in class Model: Return the species with ID id.
getSpecies(int) - Method in class Module: Gets module of species at index idx.
getSpeciesUpdate() - Method in class IBS: Get species update type.
getSpeciesUpdateRate() - Method in class IBSDPopulation
getSpeciesUpdateRate() - Method in class IBSPopulation: Gets the update rate of this species.
getSpecs() - Method in class AbstractGeometry: Get the CLI specification string that configured this geometry.
getSplitCLO() - Method in class CLOController: Return the cached command-line string split on option boundaries.
getSplitCLO() - Method in class EvoLudo: Get the command line options split into an array with option names followed by their arguments (if applicable).
getStaticScores() - Method in interface Features.Static: Gets the static scores for the different types.
getStaticScores() - Method in class Moran
getStatus() - Method in class IBS
getStatus() - Method in class IBSDPopulation
getStatus() - Method in class IBSMCPopulation
getStatus() - Method in class IBSPopulation: Gets the status of the as a formatted string.
getStatus() - Method in class Model: Returns status message from model.
getStatus() - Method in class ODE
getStatus() - Method in class PDE
getStatus() - Method in class DemesTBT.IBSPop
getStatus() - Method in class NetGames.IBSPop
getStatus() - Method in class TBT.IBSPop
getStatus() - Method in class Network: Get the status of the layouting process.
getStatus() - Method in class AbstractView: Get the status of this view.
getStatus(boolean) - Method in class AbstractView: Get the status of this view.
getStatus(boolean) - Method in class Histogram
getStatus(double[]) - Method in class ODE: Returns a string representation of the current state of the model.
getStdev() - Method in class RNGDistribution.Normal: Get the standard deviation of the Normal distribution.
getSteps() - Method in class LineGraph: Get the number of steps along the x-axis.
getStyle() - Method in class AbstractGraph: Get the graph style.
getSubType() - Method in class HierarchicalGeometry: Retrieve the geometry used within each hierarchy level (e.g.
getSymmetric() - Method in class PDE: Gets whether preservation of symmetry was requested.
getSyncFraction() - Method in class IBSPopulation: Get the fraction of the population that gets updated in synchronous updates.
getTag() - Method in class PlistTag: The <key>, name of this plist entry.
getTagAt(int) - Method in class IBSPopulation: Gets the tag of the individual with index idx.
getTagData(T[], ColorMap) - Method in class IBSPopulation: Returns the tags of all individuals in this population coded as colors in the array colors using the map colorMap.
getTagNameAt(int) - Method in class IBSPopulation: Gets the formatted tag of the individual with index idx as string.
getTagNameAt(int) - Method in class NetGames.IBSPop
getTagNameAt(int, int) - Method in class IBS: Gets formatted tag of individual at location idx for species with ID id.
getTags(double[]) - Method in class IBSPopulation: Copies the tags of all individuals in the population and returns them in the array mem.
getTarget() - Method in class TrackballControls: Get the target point where the eye is looking.
getTime() - Method in class IBS
getTime() - Method in class Model: Returns the elapsed time measured in terms of the rates at which events happen.
getTimeRelax() - Method in class Model: Gets the number of generations to relax the initial configuration of the active Model.
getTimestamp() - Method in class Network: Get the timestamp of the last time the layouting process has completed.
getTimeStep() - Method in class Model: Get the interval between subsequent reports to the GUI or the simulation controller measured in generations (or fractions thereof).
getTimeStop() - Method in class Model: Gets the number of generations after which the active Model is halted.
getTitle() - Method in enum class GeometryType
getTitle() - Method in enum class IBS.MigrationType
getTitle() - Method in enum class IBS.ScoringType
getTitle() - Method in enum class IBS.Statistics.Type
getTitle() - Method in enum class IBSC.Init.Type
getTitle() - Method in enum class IBSD.Init.Type
getTitle() - Method in enum class IBSD.OptimizationType
getTitle() - Method in enum class IBSGroup.SamplingType
getTitle() - Method in enum class ModelType
getTitle() - Method in enum class ODEInitialize.InitType
getTitle() - Method in enum class PDEInitialize.Type
getTitle() - Method in enum class PopulationUpdate.Type
getTitle() - Method in class ATBT
getTitle() - Method in class CDL
getTitle() - Method in class CDLP
getTitle() - Method in class CDLPQ
getTitle() - Method in class Centipede
getTitle() - Method in class CLabour
getTitle() - Method in enum class Continuous.Benefits
getTitle() - Method in enum class Continuous.ColorModelType
getTitle() - Method in enum class Continuous.Costs
getTitle() - Method in class CSD
getTitle() - Method in class DemesTBT
getTitle() - Method in class EcoPGG
getTitle() - Method in interface Features: Returns title of active module, e.g.
getTitle() - Method in interface Features.Multispecies
getTitle() - Method in class LV
getTitle() - Method in class Map2Fitness: Gets the brief description of the current map.
getTitle() - Method in enum class Map2Fitness.Map
getTitle() - Method in class Moran
getTitle() - Method in enum class Mutation.Continuous.Type
getTitle() - Method in enum class Mutation.Discrete.Type
getTitle() - Method in class NetGames
getTitle() - Method in enum class PlayerUpdate.Type
getTitle() - Method in class RSP
getTitle() - Method in class SIR
getTitle() - Method in enum class SpeciesUpdate.Type
getTitle() - Method in class TBT
getTitle() - Method in interface CLOption.Key: Brief description of purpose of this key.
getTitle() - Method in class CLOption.SimpleKey
getTooltipAt(double, double) - Method in class LineGraph
getTooltipAt(double, double) - Method in class TraitMap
getTooltipAt(double, double) - Method in class ATBT.ATBTMap
getTooltipAt(double, double) - Method in class EcoPGG.EcoPGGMap
getTooltipAt(double, double) - Method in interface BasicTooltipProvider: Get the tooltip at the scaled coordinates (x,y) with the origin in the lower left corner of the graph.
getTooltipAt(double, double) - Method in class S3Map
getTooltipAt(int) - Method in class HistoGraph
getTooltipAt(int) - Method in interface BasicTooltipProvider: Get the tooltip for the location with index index.
getTooltipAt(int, int) - Method in class GenericPopGraph
getTooltipAt(int, int) - Method in class HistoGraph
getTooltipAt(int, int) - Method in class LineGraph
getTooltipAt(int, int) - Method in class ParaGraph
getTooltipAt(int, int) - Method in class S3Graph
getTooltipAt(int, int) - Method in interface Tooltip.Provider: Get the tooltip information for the location with coordinates (x, y).
getTooltipAt(AbstractGraph, int) - Method in interface TooltipProvider.Index: Get the tooltip for the location with index index.
getTooltipAt(AbstractGraph, int) - Method in class Distribution
getTooltipAt(AbstractGraph, int) - Method in class GenericPop
getTooltipAt(ParaGraph, double, double) - Method in interface TooltipProvider.Parametric: Get the tooltip for the parametric plot graph at the scaled coordinates (x,y) with the origin in the lower left corner of the phase plane.
getTooltipAt(S3Graph, double, double) - Method in interface TooltipProvider.Simplex: Get the tooltip for the simplex graph at the scaled coordinates (x,y) with the origin in the lower left corner of the simplex.
getTotalFitness() - Method in class IBSPopulation: Gets the total fitness of the population.
getTraitAt(int) - Method in class IBSDPopulation: Gets the trait of the individual with index idx.
getTraitAt(int) - Method in class IBSMCPopulation: Get the trait of individual with index idx.
getTraitAt(int, int) - Method in class IBSMCPopulation: Get trait d of individual with index idx.
getTraitColor(int) - Method in class Module: Gets the color for the trait with index trait.
getTraitColors() - Method in class Module: Gets the colors for all traits.
getTraitColors() - Method in interface HasHistogram: Get the colors for the different trait histograms.
getTraitData(int, T[], ColorMap) - Method in class IBS
getTraitData(int, T[], ColorMap) - Method in class Model: Gets the trait data for species with ID id and translates them into colors using the colorMap.
getTraitData(int, T[], ColorMap) - Method in class ODE: Unused interface method.
getTraitData(int, T[], ColorMap) - Method in class PDE
getTraitData(T[], ColorMap) - Method in class IBSDPopulation
getTraitData(T[], ColorMap) - Method in class IBSMCPopulation
getTraitData(T[], ColorMap) - Method in class IBSPopulation: Returns the traits of all individuals in this population coded as colors in the array colors using the map colorMap.
getTraitData(T[], ColorMap) - Method in class NetGames.IBSPop: Returns the traits of all individuals in this population coded as colors in the array colors using the map colorMap.
getTraitHistogramData(double[]) - Method in class IBSCPopulation: Creates a histogram for trait and returns the result in the array bins.
getTraitHistogramData(double[][]) - Method in class IBSMCPopulation: Creates a histogram for each trait separately (if there are multiple) and returns the result in the array bins where the first index denotes the trait and the second refers to the bin.
getTraitHistogramData(double[], int) - Method in class IBSMCPopulation: Creates a histogram for the trait with index trait and returns the result in the array bins.
getTraitHistogramData(int, double[][]) - Method in interface CModel: Gets the histogram of the trait distributions and returns the data in an array bins, where the first index denotes the trait (in case there are multiple) and the second index refers to the bins in the histogram.
getTraitHistogramData(int, double[][]) - Method in class IBSC
getTraitMax() - Method in class Continuous: Get the maxima for all traits.
getTraitMin() - Method in class Continuous: Get the minima for all traits.
getTraitName(int) - Method in class Module: Gets the name of the trait with index trait.
getTraitName(int) - Method in class TBT
getTraitName(int) - Method in interface HasDistribution: Gets the name of the trait with index idx.
getTraitName(int) - Method in class Phase2D: Get the name of the trait with index idx.
getTraitNameAt(int) - Method in class IBSDPopulation
getTraitNameAt(int) - Method in class IBSMCPopulation
getTraitNameAt(int) - Method in class IBSPopulation: Gets the formatted name of the trait of the individual at site index.
getTraitNameAt(int) - Method in class NetGames.IBSPop
getTraitNameAt(int) - Method in class TBT.IBSPop
getTraitNameAt(int, int) - Method in class IBS
getTraitNameAt(int, int) - Method in class Model: Gets the formatted trait names at location idx for species with ID id.
getTraitNameAt(int, int) - Method in class PDE
getTraitNames() - Method in class Module: Gets the names of all traits.
getTraitRangeMax() - Method in class IBSMCPopulation: Get the maxima for all traits.
getTraitRangeMax(int) - Method in interface CModel: Gets the maximum trait values in this module.
getTraitRangeMax(int) - Method in class IBSC
getTraitRangeMin() - Method in class IBSMCPopulation: Get the minima for all traits.
getTraitRangeMin(int) - Method in interface CModel: Gets the minimum trait values in this module.
getTraitRangeMin(int) - Method in class IBSC
getTraits() - Method in class IBSDPopulation: Gets the traits of all individuals as indices.
getTraits(int) - Method in class IBSMCPopulation: Gets all traits of all individuals.
getTraitsAt(int) - Method in class IBSMCPopulation: Get the trait array of individual with index idx.
getTraitsAt(int, double[]) - Method in class IBSMCPopulation: Get the trait array of individual with index idx.
getTraitsCount() - Method in class IBSDPopulation: Gets the count of each trait.
getTraitsX() - Method in class TraitMap
getTraitsX() - Method in interface HasPhase2D.Data2Phase: Get the array of indices of traits displayed on the horizontal axis of the phase plane.
getTraitsY() - Method in class TraitMap
getTraitsY() - Method in interface HasPhase2D.Data2Phase: Get the array of indices of traits displayed on the vertical axis of the phase plane.
getTrajectoryColor() - Method in class Module: Gets the color of trajectories.
getTranslateInstance(double, double) - Static method in class AffineTransform: Returns a transform representing a translation transformation.
getTranslateX() - Method in class AffineTransform: Returns the X coordinate of the translation element (m02) of the 3x3 affine transformation matrix.
getTranslateY() - Method in class AffineTransform: Returns the Y coordinate of the translation element (m12) of the 3x3 affine transformation matrix.
getTrials() - Method in class RNGDistribution.Binomial: Get the number of trials n for the binomial distribution.
getType() - Method in class AffineTransform: Retrieves the flag bits describing the conversion properties of this transform.
getType() - Method in class AbstractGeometry: Get the current GeometryType that defines this structure.
getType() - Method in class Model: Gets the type of the model.
getType() - Method in class PopulationUpdate: Gets the population update type.
getType() - Method in class PlayerUpdate: Gets the player update type.
getType() - Method in class SpeciesUpdate: Gets the population update type.
getType() - Method in class AbstractView: Get the type of data visualized on the graph.
getType() - Static method in class FullscreenChangeEvent: Gets the event type associated with fullscreenchange events.
getType() - Static method in class InputEvent: Gets the event type associated with input events.
getType() - Method in class CLOption: Get the type of the option.
getUpdates() - Method in class IBS
getUpdates() - Method in class Model: Gets the elapsed time in model.
getVacantIdx() - Method in class Module: Get the index for the vacant type or -1 if Module does not admit empty sites.
getValue() - Method in class Slider: Get the value of slider taking its linear or logarithmic scaling into account.
getValue() - Method in class PlistTag: The value of this plist entry.
getVersion() - Method in class EvoLudo: Return version string of current model.
getVersion() - Method in class StateEncoder: Return version string of current model.
getViewByName(String) - Method in class ViewController: Finds a view by name.
getWidth() - Method in class Rectangle2D: Get the width of the rectangle.
getWindingRule() - Method in class Path2D: Returns the fill style winding rule.
getWindingRule() - Method in class Path2D.Iterator: Returns the winding rule for determining the interior of the path.
getWindingRule() - Method in interface PathIterator: Returns the winding rule for determining the interior of the path.
getWorldView() - Method in class Network3DGWT: Get the visual perspective of this network.
getX() - Method in class Point2D: Get the x-coordinate of this 2D point.
getX() - Method in class Point3D: Get the x-coordinate of this 3D point.
getX() - Method in class Rectangle2D: Get the x-coordinate of the lower left corner of the rectangle.
getXAxisLabel() - Method in class ATBT.ATBTMap
getXAxisLabel() - Method in class EcoPGG.EcoPGGMap
getXAxisLabel() - Method in interface HasPhase2D.Data2Phase: Return custom label for x-axis
getXAxisLabel() - Method in class Phase2D: Get the label of the horizontal axis.
getXDecorationHeight(GraphStyle) - Method in class Histogram: Return the vertical space used by x-axis decorations in pixels.
getY() - Method in class Point2D: Get the y-coordinate of this 2D point.
getY() - Method in class Point3D: Get the y-coordinate of this 3D point.
getY() - Method in class Rectangle2D: Get the y-coordinate of the lower left corner of the rectangle.
getYAxisLabel() - Method in class ATBT.ATBTMap
getYAxisLabel() - Method in class EcoPGG.EcoPGGMap
getYAxisLabel() - Method in interface HasPhase2D.Data2Phase: Return custom label for y-axis
getYAxisLabel() - Method in class Phase2D: Get the label of the vertical axis.
getYIntercept(double, double, double, double) - Static method in class Line2D: Calculate the slope of a line running through points p1 and p2.
getYIntercept(Point2D, Point2D) - Static method in class Line2D: Calculate the slope of a line running through points p1 and p2.
getZ() - Method in class Point3D: Get the z-coordinate of this 3D point.
Gillespie() - Constructor for class RNGDistribution.Gillespie: Creates a weighted distribution over intergers using the Gillespie algorithm and a new instance of MersenneTwister.
Gillespie(MersenneTwister) - Constructor for class RNGDistribution.Gillespie: Creates a weighted distribution over intergers using the Gillespie algorithm using the random number generator rng.
GILLESPIE_OPTIMIZATION_THRESHOLD - Static variable in class IBSPopulation: Threshold population size for using the Gillespie optimization for picking individuals proportional to fitness.
Git - Interface in org.evoludo.simulator: The interface to provide access to the Git.properties file.
gitDate() - Method in interface Git: Returns the time of the last git commit formatted as a string.
gitVersion() - Method in interface Git: Returns the id (short SHA hash) of the last git commit formatted as a string.
Global - Static variable in class CLOCategory: The category for global options.
GOOD_SEED - Static variable in class MersenneTwister: A good initial seed (of int size, though stored in a long)
gradient - Variable in class ColorMap.Gradient1D: Reference to pre-allocated gradient colors.
gradient - Variable in class ColorMap.Gradient2D: Reference to pre-allocated gradient colors.
Gradient() - Constructor for class ColorMap.Gradient: Protected constructor to restrict instantiation to subclasses.
Gradient1D(Color[], int) - Constructor for class ColorMap3D.Gradient1D: Construct color gradient running through all the colors in the array colors.
Gradient1D(Color[], int) - Constructor for class ColorMapCSS.Gradient1D: Construct color gradient running through all the colors in the array colors.
Gradient1D(Color[], int, int) - Constructor for class ColorMapCSS.Gradient1D: Construct color gradient running through all the colors in the array colors.
Gradient1D(Color[], int, T[]) - Constructor for class ColorMap.Gradient1D: For internal use only.
Gradient1D(Color, Color, int) - Constructor for class ColorMap3D.Gradient1D: Construct color gradient ranging from color start to color end and interpolate with steps-1 intermediate colors.
Gradient1D(Color, Color, int) - Constructor for class ColorMapCSS.Gradient1D: Construct color gradient ranging from color start to color end and interpolate with steps-1 intermediate colors.
Gradient1D(Color, Color, int, int) - Constructor for class ColorMapCSS.Gradient1D: Construct color gradient ranging from color start to color end and interpolate with steps-1 intermediate colors.
Gradient1D(T[]) - Constructor for class ColorMap.Gradient1D: For internal use only.
Gradient1D(T[], int) - Constructor for class ColorMap.Gradient1D: For internal use only.
Gradient2D(int, int) - Constructor for class ColorMap.Gradient2D: For internal use only.
Gradient2D(Color[], int) - Constructor for class ColorMap3D.Gradient2D: Construct two dimensional color gradient to represent two dimensional data values.
Gradient2D(Color[], int) - Constructor for class ColorMapCSS.Gradient2D: Construct two dimensional color gradient to represent two dimensional data values.
Gradient2D(Color[], int, int) - Constructor for class ColorMap3D.Gradient2D: Construct two dimensional color gradient to represent three dimensional data values where one data value is dependent on the other two.
Gradient2D(Color[], int, int) - Constructor for class ColorMapCSS.Gradient2D: Construct two dimensional color gradient to represent three dimensional data values where one data value is dependent on the other two.
Gradient2D(Color[], int, T[][]) - Constructor for class ColorMap.Gradient2D: Construct a 2D color gradient.
GradientND(int) - Constructor for class ColorMap.GradientND: For internal use only.
GradientND(Color[]) - Constructor for class ColorMap.GradientND: Construct N dimensional color gradient to represent N dimensional data values.
GradientND(Color[]) - Constructor for class ColorMap3D.GradientND: Construct N dimensional color gradient to represent N dimensional data values.
GradientND(Color[]) - Constructor for class ColorMapCSS.GradientND: Construct N dimensional color gradient to represent N dimensional data values.
GradientND(Color[], int) - Constructor for class ColorMap.GradientND: Construct N dimensional color gradient to represent N+1 dimensional data values where one data value is dependent on the other two.
GradientND(Color[], int) - Constructor for class ColorMap3D.GradientND: Construct N dimensional color gradient to represent N+1 dimensional data values where one data value is dependent on the other two.
GradientND(Color[], int) - Constructor for class ColorMapCSS.GradientND: Construct N dimensional color gradient to represent N+1 dimensional data values where one data value is dependent on the other two.
GradientND(Color[], Color) - Constructor for class ColorMap.GradientND: Construct N dimensional color gradient to represent N dimensional data with a background color other than black, or, to represent N+1 dimensional data values where one data value is dependent on the other N.
GradientND(Color[], Color) - Constructor for class ColorMap3D.GradientND: Construct N dimensional color gradient to represent N dimensional data with a background color other than black, or, to represent N+1 dimensional data values where one data value is dependent on the other N.
GradientND(Color[], Color) - Constructor for class ColorMapCSS.GradientND: Construct N dimensional color gradient to represent N dimensional data with a background color other than black, or, to represent N+1 dimensional data values where one data value is dependent on the other N.
graph - Variable in class Phase2D: The graph that displays the trajectory in a 2D phase plane.
graph3DCamera - Variable in class PopGraph3D: The camera of the 3D graph.
graph3DPanel - Variable in class PopGraph3D: The panel for rendering the 3D graph.
graph3DScene - Variable in class PopGraph3D: The 3D scene of the graph.
graphColor - Variable in class GraphStyle: The color for drawing the graph.
graphs - Variable in class AbstractView: The list of graphs that are displayed in this view.
GraphStyle - Class in org.evoludo.graphics: The style features for graphs.
GraphStyle() - Constructor for class GraphStyle: Create a style with the default set of axis, label, and tick options.
GREEN - Enum constant in enum class TestEvoLudo.ConsoleColors: Green color.
GREEN_BACKGROUND - Enum constant in enum class TestEvoLudo.ConsoleColors: Green background color.
GREEN_BACKGROUND_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Green high intensity background.
GREEN_BOLD - Enum constant in enum class TestEvoLudo.ConsoleColors: Green color.
GREEN_BOLD_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Green high intensity color.
GREEN_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Green high intensity color.
GREEN_UNDERLINED - Enum constant in enum class TestEvoLudo.ConsoleColors: Green color.
group - Variable in class IBSGroup: Reference to the indices of the members of the group.
groupmodule - Variable in class IBSDPopulation: For group interaction modules module==groupmodule holds and null otherwise.
groupmodule - Variable in class IBSMCPopulation: For group interaction modules module==groupmodule holds and null otherwise.
groupScores - Variable in class IBSPopulation: Array to hold scores of individuals during payoff calculations.
groupScores(double[], double[], int, double[]) - Method in interface Model.HasIBS.MCGroups: Calculate the payoff/score for modules with interactions in groups and multiple single continuous traits.
groupScores(double, double[], int, double[]) - Method in interface Model.HasIBS.CGroups: Calculate the payoff/score for modules with interactions in groups and a single continuous trait.
groupScores(int[], double[]) - Method in interface Model.HasIBS.DGroups: Calculate the payoff/score for interactions in groups consisting of traits with respective numbers given in the array traitCount.
groupScores(int[], double[]) - Method in class CDL
groupScores(int[], double[]) - Method in class CDLP
groupScores(int[], double[]) - Method in class CDLPQ
groupScores(int[], double[]) - Method in class EcoPGG
growBuffer(int) - Method in class RingBuffer: Grow buffer to capacity.
gRows - Variable in class AbstractView: The number of rows of graphs in this view.
gui - Variable in class EvoLudoGWT: The reference to the GUI.
gui - Variable in class KeyHandler: The EvoLudoWeb instance that owns this controller.
gui - Variable in class WebListener: The associated EvoLudoWeb instance.
GUI - Static variable in class CLOCategory: The category for user interface specific options.
guiReady() - Method in class EvoLudoGWT: Called when the GUI has finished loading and the dimensions of all elements are known.
guiState - Variable in class EvoLudoWeb: Field to store the current state of the GUI while applying a new set of parameters.
GUIState() - Constructor for class EvoLudoWeb.GUIState: Create an empty GUI state snapshot.
gwtHalt - Variable in class PDE: The generation when the model execution is halted next.

H

h - Variable in class ParaGraph.ViewState: Cached frame height in pixels.
H2(int, int, int, int) - Static method in class Combinatorics: Efficient calculation of the hypergeometric probability distribution H<sub>2</sub>(X,x,Y,y) for sampling x individuals from pool of size X and y individuals from pool of size Y.
handleCLOActiveKeys(String) - Method in class KeyHandler: Handles key events when the command line options field is active.
handleConsoleToggle() - Method in class KeyHandler: Handles toggling the console view.
handleDEGraph(HistoGraph, ModelType, Module) - Method in class Histogram: Handle messaging for DE/PDE models; returns true if a message was set on the graph and further processing should be skipped.
handleDeleteKeys() - Method in class KeyHandler: Handles the Delete and Backspace key functionality.
handleDnD(JavaScriptObject, EvoLudoWeb) - Static method in class NativeJS: JSNI method: the HTML5 File API enables reading of files.
handleEmptyBuffer(double, double[]) - Method in class ParaGraph: Handle the case that the buffer is empty.
handleEmptyBuffer(double, double[]) - Method in class S3Graph: Handle the case that the buffer is empty.
handleEscapeKey() - Method in class KeyHandler: Handles the Escape key functionality.
handleEvent(Object) - Method in interface EventListener: Callback receiving DOM events exposed via JSNI.
handleExport() - Method in class KeyHandler: Handles exporting the current model state.
handleFullscreen() - Method in class KeyHandler: Handles toggling fullscreen mode.
handleGlobalKeys(String) - Method in class KeyHandler: Handles global key events.
handleHoneycomb(int, int) - Method in class PopGraph2D: Handle honeycomb lattice geometry.
handleLargeYMax(double, double[]) - Method in class HistoGraph: Handle the case where yMax > 1.0 by rounding the maximum up if necessary and determining/rounding yMin when applicable.
handleLinear(int, int) - Method in class PopGraph2D: Handle linear lattice geometry with history.
handleModelDidReset() - Method in class EvoLudoWeb: Handle model reset event.
handleModuleOption(String[], boolean) - Method in class CLOController: Process the --module option (loading modules early if needed).
handleNaNTime(double[], double) - Method in class S3Graph: Handle the case that the time t is NaN.
handleNaNTime(double, double, double[], int) - Method in class ParaGraph: Handle the case that the time t is NaN.
handleNetwork(int, int) - Method in class PopGraph2D: Handle generic network geometry.
handleNoRepresentation(GeometryType) - Method in class PopGraph2D: Handle geometries without graphical representation.
handleNumericViewSwitch(String) - Method in class KeyHandler: Handles numeric view switching for keys 1-9.
handleSingleUnmatched(int, int[]) - Method in class AbstractNetwork: Handle the case where a single node remains unmatched by breaking an existing edge and reconnecting both endpoints to that final node.
handleSmallYMax(double) - Method in class HistoGraph: Handle the case where yMax <= 1.0 by selecting an autoscale index and updating GraphStyle.yMax.
handleSquare(int, int) - Method in class PopGraph2D: Handle square lattice geometry.
handleTriangular(int, int) - Method in class PopGraph2D: Handle triangular lattice geometry.
handleVerboseOption(String[]) - Method in class CLOController: Process the --verbose option and update logger state.
Handling 90-Degree Rotations - Section in class org.evoludo.geom.AffineTransform
HAS_LAYOUT - Enum constant in enum class Network.Status: layout completed
HAS_MESSAGE - Enum constant in enum class Network.Status: message displayed instead of network
hasAnimatedLayout() - Method in class GenericPopGraph: Check whether the layout of the graph is animated.
hasAttributes() - Method in class PlistTag: Check if this plist entry has attributes.
hasConverged() - Method in class Model: Checks if model has converged.
HasDistribution - Interface in org.evoludo.simulator.views: Modules that implement the HasDistribution interface request a graphical view to visualize the density distribution of data in multiple dimensions in their GUI: Distribution for GWT and MVCDistr, MVC2Distr for JRE modules with one or two continuous traits, respectively.
HasDistribution.Strategy - Interface in org.evoludo.simulator.views: Modules that implement the HasDistribution.Strategy interface include a graphical view that depicts the density distribution of strategic traits over time in their GUI.
hasExportType(AbstractView.ExportType) - Method in class AbstractView: Checks if the view supports the export type type.
hasFixedAxes - Variable in class TraitMap: Flag indicating whether the axes are fixed.
hasFixedAxes() - Method in class TraitMap
hasFixedAxes() - Method in interface HasPhase2D.Data2Phase: Return whether axes of the phase plane are customizable.
hasFocus() - Static method in class NativeJS: JSNI method: Check if document has focus.
HasFullscreenChangeHandlers - Interface in org.evoludo.ui: A widget that implements this interface provides registration for FullscreenChangeHandler instances.
hashCode() - Method in class AffineTransform: Returns the hashcode for this transform.
hashCode() - Method in class Network2DGWT
hashCode() - Method in class Network3DGWT
hashCode() - Method in class AbstractGeometry
hashCode() - Method in class AbstractLattice
hashCode() - Method in class GeometryFeatures
hashCode() - Method in class HierarchicalGeometry
hashCode() - Method in class KlemmEguiluzGeometry
hashCode() - Method in class LinearGeometry
hashCode() - Method in class ScalefreeGeometry
hashCode() - Method in class SuperstarGeometry
hashCode() - Method in class Network
hashCode() - Method in class Network2D
hashCode() - Method in class Network3D
hashCode() - Method in class CLOption
hashCode() - Method in class Plist: Override hashCode to only use the actual plist content (HashMap entries).
HasHistogram - Interface in org.evoludo.simulator.views: Modules that implement the HasHistogram interface request a graphical view to depicts a histogram of data in their GUI: Histogram in GWT and MVCTraitHistogram, MVFitHistogram in JRE for a single continuous trait or the fitness distribution, respectively.
HasHistogram.Degree - Interface in org.evoludo.simulator.views: Modules that implement the HasHistogram.Degree interface include histograms of the degree distribution of the population geometry.
HasHistogram.Fitness - Interface in org.evoludo.simulator.views: Modules that implement the HasHistogram.Fitness interface include histograms of fitness distributions.
HasHistogram.StatisticsProbability - Interface in org.evoludo.simulator.views: Modules that implement the HasHistogram.StatisticsProbability interface must be capable of running statistics over multiple runs and include histograms of fixation probabilities.
HasHistogram.StatisticsStationary - Interface in org.evoludo.simulator.views: Modules that implement the HasHistogram.StatisticsStationary interface must be capable of generate histograms of the number of times particular configurations (frequencies of strategies) are visited, which eventually converges to a stationary distributions in ergodic settings.
HasHistogram.StatisticsTime - Interface in org.evoludo.simulator.views: Modules that implement the HasHistogram.StatisticsTime interface must be capable of running statistics over multiple runs and include histograms of fixation times.
HasHistogram.Strategy - Interface in org.evoludo.simulator.views: Modules that implement the HasHistogram.Strategy interface include histograms of strategy distributions.
hasHistory() - Method in class AbstractGraph: Check whether the graph entertains a buffer with historical data.
hashSHA256(Object) - Static method in class TestEvoLudo: Compute SHA-256 hash of serializable object obj.
HasInputHandlers - Interface in org.evoludo.ui: A widget that implements this interface provides registration for InputHandler instances.
hasKeys - Variable in class SettingsController.Settings: true if the reader exposes keyboard events.
hasKeys() - Method in class SettingsController: Reports whether the ePub reader exposes keyboard input.
hasKeys() - Static method in class NativeJS: JSNI method: Check if execution environment supports keyboard events.
hasLayout() - Method in class AbstractView: Check if the view has finished layouting its graphs.
hasLayout() - Method in class GenericPop
hasLookupTable - Variable in class IBSPopulation: Optimization: Flag to indicate whether lookup tables can be used.
HasMean - Interface in org.evoludo.simulator.views: Modules that implement the HasMean interface request a graphical view to visualize the mean state of the population as a function of time in their GUI: Mean for GWT and MVDMean, MVCMean for JRE.
HasMean.Fitness - Interface in org.evoludo.simulator.views: Modules that implement this interface request a LineGraph that depicts the mean fitness of the population.
HasMean.Traits - Interface in org.evoludo.simulator.views: Modules that implement this interface request a LineGraph that depicts the mean traits of the population.
hasMessage - Variable in class AbstractGraph: Flag to indicate whether the graph displays a message.
hasMessage() - Method in class AbstractGraph: Check if the graph displays a message.
hasMessage() - Method in class GenericPopGraph
hasMouse - Variable in class SettingsController.Settings: true if the reader exposes mouse events.
hasMouse() - Method in class SettingsController: Reports whether the ePub reader exposes mouse input.
hasMouse() - Static method in class NativeJS: JSNI method: Check if execution environment supports mouse events.
hasMultitrait() - Method in class TraitMap
hasMultitrait() - Method in interface HasPhase2D.Data2Phase: Return whether multiple traits can be selected for each axis of the phase plane.
hasNeigh(int, int, int[], int, String) - Method in class AbstractGeometry: Helper that checks whether neighs contains src and logs an error if it does not.
hasNext() - Method in class Network
hasNext() - Method in class PlistReader
hasNext() - Method in class RingBuffer.BckItr
hasNext() - Method in class RingBuffer.FwdItr
hasPan - Variable in class TrackballControls: Flag indicating whether panning is enabled.
HasPhase2D - Interface in org.evoludo.simulator.views: Modules that implement the HasPhase2D interface request a graphical view to visualize the mean state of the population in a 2D (projection) of the phase plane as a function of time in their GUI: Phase2D for GWT and MVDPhase2D for JRE.
HasPhase2D.Data2Phase - Interface in org.evoludo.simulator.views: Interface for providing custom mappings from data to 2D phase plane projections.
HasPop2D - Interface in org.evoludo.simulator.views: Modules that implement the HasPop2D interface request a graphical view to visualize a 2D representation of the geomtery of the population in their GUI: Pop2D for GWT and MVPop2D for JRE.
HasPop2D.Fitness - Interface in org.evoludo.simulator.views: Modules that implement the HasPop2D.Fitness interface include 2D graphical visualizations of the geometry of the population where nodes display the color coded fitness of each individual.
HasPop2D.Traits - Interface in org.evoludo.simulator.views: Modules that implement the HasPop2D.Traits interface include 2D graphical visualizations of the geometry of the population where nodes display the color coded trait of each individual.
HasPop3D - Interface in org.evoludo.simulator.views: Modules that implement the HasPop3D interface request a graphical view to visualize a 3D representation of the geomtery of the population in their GUI: Pop3D for GWT and none for JRE (java3d has long been retired).
HasPop3D.Fitness - Interface in org.evoludo.simulator.views: Modules that implement the HasPop3D.Traits interface include 3D graphical visualizations of the geometry of the population where nodes display the color coded fitness of each individual.
HasPop3D.Traits - Interface in org.evoludo.simulator.views: Modules that implement the HasPop3D.Traits interface include 2D graphical visualizations of the geometry of the population where nodes display the color coded trait of each individual.
hasPopup() - Method in class EvoLudoWeb: Check if this lab owns a popup overlay.
hasPrevious() - Method in class RingBuffer.LstItr
hasRotate - Variable in class TrackballControls: Flag indicating whether rotation is enabled.
HasS3 - Interface in org.evoludo.simulator.views: Modules that implement the HasS3 interface request a graphical view to visualize the mean state of the population in the simplex \(S_3\) as a function of time in their GUI: S3 for GWT and MVDS3 for JRE.
hasSetTraits() - Method in interface HasPhase2D.Data2Phase: Modules may probe whether setTraits is implemented.
hasStaticLayout() - Method in class GenericPopGraph: Check whether the layout of the graph is static, i.e.
hasSubmenu() - Method in class ContextMenuItem: Check if context menu item controls a submenu.
hasSVGjs - Static variable in class AbstractView: The flag to indicate whether the script for exporting SVG has been injected.
hasTouch - Variable in class SettingsController.Settings: true if the reader exposes touch events.
hasTouch() - Method in class SettingsController: Reports whether the ePub reader exposes touch input.
hasTouch() - Static method in class NativeJS: JSNI method: Check if execution environment supports touch events.
hasVacant() - Method in class Module: Check if module admits vacant type (empty sites).
hasZipJs - Static variable in class EvoLudoWeb: The helper variable to indicate JavaScript for dealing with zip archives has already been loaded.
hasZoom - Variable in class AbstractGraph: The flag to indicate whether the graph supports zoom.
hasZoom - Variable in class TrackballControls: Flag indicating whether zooming is enabled.
haveSameTrait(int, int) - Method in class IBSCPopulation
haveSameTrait(int, int) - Method in class IBSDPopulation
haveSameTrait(int, int) - Method in class IBSMCPopulation
haveSameTrait(int, int) - Method in class IBSPopulation: Check if individuals with index a and index b have the same traits.
haveSameTrait(int, int) - Method in class NetGames.IBSPop
hBorder() - Method in interface Resources: Get the horizontal border for GWT GUI elements.
header - Variable in class CLOCategory: The brief category description.
HEAWOOD - Enum constant in enum class GeometryType: Heawood graph, size \(N=14\), connectivity \(k=3\).
HeawoodGeometry - Class in org.evoludo.simulator.geometries: Geometry implementation for the Heawood graph (14-node cubic symmetric graph).
HeawoodGeometry(EvoLudo) - Constructor for class HeawoodGeometry: Create a Heawood geometry tied to the given engine.
height - Variable in class Rectangle2D: The height of the rectangle.
help() - Method in class TestEvoLudo: Print help screen.
helpButton - Variable in class SettingsController: Button used to open help for command-line options.
helpCLO - Variable in class CLOController: Replacement command line option for serious parsing failures to display help screen.
helpCLO(boolean) - Method in class CLOParser: Returns a short description of every command line option in the options list, including its default value as well as the current setting (if different).
HEXAGONAL - Enum constant in enum class GeometryType: Hexagonal (honeycomb) lattice, connectivity \(k=6\).
HexagonalGeometry - Class in org.evoludo.simulator.geometries: Honeycomb/hexagonal lattice geometry with optional fixed boundaries.
HexagonalGeometry(EvoLudo) - Constructor for class HexagonalGeometry: Create a hexagonal (honeycomb) geometry tied to the given engine.
hgeom - Variable in class IBSGroup.HierarchyUnit: Cached hierarchy geometry to avoid repeated casts.
HI_IDENTITY - Static variable in class AffineTransform
HI_SCALE - Static variable in class AffineTransform
HI_SHEAR - Static variable in class AffineTransform
HI_SHIFT - Static variable in class AffineTransform
HI_TRANSLATE - Static variable in class AffineTransform
hideAltModeFromTouch() - Method in class KeyHandler: Hides the touch-activated Alt mode and restores the original labels.
hideContextMenuTimer - Variable in class ContextMenu: Timer for closing the context menu after a fixed delay.
Hierarchical - Interface in org.evoludo.simulator.geometries: Narrow contract for geometries that can initialize demes inside a hierarchical meta-population.
HierarchicalGeometry - Class in org.evoludo.simulator.geometries: Hierarchical meta-population structure implementation.
HierarchicalGeometry(EvoLudo) - Constructor for class HierarchicalGeometry: Create a hierarchical geometry tied to the given engine.
hierarchy - Variable in class HierarchicalGeometry: The number of units at each hierarchical level.
HIERARCHY - Enum constant in enum class GeometryType: Hierarchical (meta-)populations.
HIERARCHY_GAP - Static variable in class PopGraph2D: Convenience variable.
hierarchyGapAt(int) - Method in class PopGraph2D: Compute number of hierarchy gaps that occur before the given index.
HierarchyUnit() - Constructor for class IBSGroup.HierarchyUnit: Private constructor for the HierarchyUnit class.
hierarchyWeight - Variable in class HierarchicalGeometry: Coupling strength between hierarchical levels.
hirePDESupervisor(PDE) - Method in class EvoLudo: Hire supervisor for managing PDE calculations.
hirePDESupervisor(PDE) - Method in class EvoLudoGWT
Histogram - Class in org.evoludo.simulator.views: Histogram view for displaying binned distributions of model quantities.
Histogram(EvoLudoGWT, Data) - Constructor for class Histogram: Construct a new view to display the histogram of various quantities.
HistoGraph - Class in org.evoludo.graphics: A histogram graph used to render and interact with binned data.
HistoGraph(Histogram, Module, int) - Constructor for class HistoGraph: Create new histogram graph for module running in view.
HistoGraph.Marker - Class in org.evoludo.graphics: Marker for highlighting a specific bin in the histogram.
History & buffering - Section in class org.evoludo.graphics.AbstractGraph
hitDragged - Variable in class PopGraph2D: The flag to indicate whether GenericPopGraph.hitNode is being dragged.
hitNode - Variable in class GenericPopGraph: The index of the node that was hit by the mouse or a tap.
hitNode - Variable in class GenericPop: The index of the node that was hit by the mouse.
hLevels - Variable in class PopGraph2D: Convenience variable.
HOMO - Enum constant in enum class IBSD.OptimizationType: Skip homogeneous states by introducing a mutant and advancing the time according to an exponential distribution for an event happening with probability Module#getMutationProb().
homoDemes() - Method in class DemesTBT.IBSPop: Determine the number of homogeneous demes in trait A, provided that all demes are homogeneous.
hPeriods - Variable in class PopGraph2D: Convenience variable.
html - Variable in class Slider: Reference to slider.
HTMLDecode - Static variable in class XMLCoder: Lookup table for decoding HTML strings.
Hue(double, double, boolean, T[]) - Constructor for class ColorMap.Hue: Construct a new Hue color map, starting at a hue of 0.0 (red) up to hue 1.0 (red, again) and interpolate with steps-1 intermediate colors.
Hue(double, double, int) - Constructor for class ColorMap3D.Hue: Construct a new Hue color map, starting at hue start up to hue end (both in [0.0, 1.0]) and interpolate with steps-1 intermediate colors.
Hue(double, double, int) - Constructor for class ColorMapCSS.Hue: Construct a new Hue color map, starting at hue start up to hue end (both in [0.0, 1.0]) and interpolate with steps-1 intermediate colors.
Hue(int) - Constructor for class ColorMap3D.Hue: Construct a new Hue color map, starting at a hue of 0.0 (red) up to hue 1.0 (red, again) and interpolate with steps-1 intermediate colors.
Hue(int) - Constructor for class ColorMapCSS.Hue: Construct a new Hue color map, starting at a hue of 0.0 (red) up to hue 1.0 (red, again) and interpolate with steps-1 intermediate colors.

I

I - Static variable in class SIR: The index of the infected trait/cohort.
ibs - Variable in class simTBT: The two player, two trait model.
ibs - Variable in class simTraits: The IBS model.
ibs - Variable in class IBS.Statistics: The model that is using the statistics settings.
ibs - Variable in class IBSC.Init: The model that is using this initialization.
ibs - Variable in class IBSD.Init: The model that is using this initialization.
ibs - Variable in class PopulationUpdate: The model that is using this population update.
ibs - Variable in class SIR.IBSPop: The individual based simulation model for SIR.
IBS - Class in org.evoludo.simulator.models: Base class for individual based simulation models, IBS.
IBS - Enum constant in enum class ModelType: Individual based simulation model.
IBS(EvoLudo) - Constructor for class IBS: Creates a population of individuals for IBS simulations.
IBS.Event - Enum Class in org.evoludo.simulator.models: Enumeration of possible events in focal population.
IBS.MigrationType - Enum Class in org.evoludo.simulator.models: Types of species updates (only relevant for multi-species models): none no migration D diffusive migration (exchange of neighbors) B birth-death migration (fit migrates, random death). d death-birth migration (random death, fit migrates).
IBS.ScoringType - Enum Class in org.evoludo.simulator.models: Schedules for resetting individual payoffs/fitness: onchange Reset when changing trait (only after updating from reference model with a different trait) onupdate Reset when updating from reference individual (not necessarily a change in trait) ephemeral Determine payoffs/fitness calculated only for updating
IBS.Statistics - Class in org.evoludo.simulator.models: The class managing the settings for statistics mode.
IBS.Statistics.Type - Enum Class in org.evoludo.simulator.models: Type of statistics.
IBSC - Class in org.evoludo.simulator.models: Base class for individual based simulation models, IBS, with a single or multiple continuous traits.
IBSC(EvoLudo) - Constructor for class IBSC: Creates a population of individuals for IBS simulations with continuous traits.
IBSC.Init - Class in org.evoludo.simulator.models: The initialization of populations with continuous traits.
IBSC.Init.Type - Enum Class in org.evoludo.simulator.models: Type of initial density distribution of traits.
IBSCPopulation - Class in org.evoludo.simulator.models: The core class for individual based simulations with a single continuous trait.
IBSCPopulation(EvoLudo, Continuous) - Constructor for class IBSCPopulation: Creates a population of individuals with a single continuous trait for IBS simulations.
IBSD - Class in org.evoludo.simulator.models: Base class for individual based simulation models, IBS, with discrete traits.
IBSD(EvoLudo) - Constructor for class IBSD: Creates a population of individuals for IBS simulations with discrete traits.
IBSD.Init - Class in org.evoludo.simulator.models: The initialization of populations with discrete traits.
IBSD.Init.Type - Enum Class in org.evoludo.simulator.models: Type of initial density distribution.
IBSD.OptimizationType - Enum Class in org.evoludo.simulator.models: Type of optimizations.
IBSDPopulation - Class in org.evoludo.simulator.models: The core class for individual based simulations with discrete traits.
IBSDPopulation(EvoLudo, Discrete) - Constructor for class IBSDPopulation: Creates a population of individuals with discrete traits for IBS simulations.
IBSDPopulation.Link - Class in org.evoludo.simulator.models: A minimalstic helper class (or data structure) to represent a single directed link in the network structure.
IBSGroup - Class in org.evoludo.simulator.models: Interaction and reference groups in IBS models.
IBSGroup(RNGDistribution) - Constructor for class IBSGroup: Create a new interaction or competition group.
IBSGroup.HierarchyUnit - Class in org.evoludo.simulator.models: Internal class to store hierarchy unit information.
IBSGroup.SamplingType - Enum Class in org.evoludo.simulator.models: Types of sampling of groups for interactions or references: none no interactions all interact with all neighbours random interact with n random neighbours
IBSMCPopulation - Class in org.evoludo.simulator.models: The core class for individual based simulations with multiple continuous traits.
IBSMCPopulation(EvoLudo, Continuous) - Constructor for class IBSMCPopulation: Creates a population of individuals with multiple continuous traits for IBS simulations.
ibspop - Variable in class Module: The field point to the IBSPopulation that represents this module in individual based simulations.
IBSPop - Class in org.evoludo.simulator.modules: Individual based simulation implementation of the Lotka-Volterra model.
IBSPop() - Constructor for class SIR.IBSPop: Constructor for SIR population.
IBSPop(EvoLudo, CDL) - Constructor for class CDL.IBSPop: Create a new instance of the IBS model for voluntary (non-linear) public goods games.
IBSPop(EvoLudo, DemesTBT) - Constructor for class DemesTBT.IBSPop: Create a new instance of the IBSPop class.
IBSPop(EvoLudo, Discrete) - Constructor for class IBSPop: Create a new custom implementation for IBS simulations.
IBSPop(EvoLudo, NetGames) - Constructor for class NetGames.IBSPop: Create a new instance of the IBS model for cooperative actions on dynamical networks.
IBSPop(EvoLudo, RSP) - Constructor for class RSP.IBSPop: Create a new instance of the IBS model for 3×3 games.
IBSPop(EvoLudo, TBT) - Constructor for class TBT.IBSPop: Create a new instance of the IBS model for 2×2 games.
IBSPopulation<M,P> - Class in org.evoludo.simulator.models: The core class for individual based simulations.
IBSPopulation(EvoLudo, M) - Constructor for class IBSPopulation: Creates a population of individuals for IBS simulations.
ibsStep(double) - Method in class IBS: Advances the IBS model by a step of size stepDt.
ibsStepAsync(double) - Method in class IBS: Advances the IBS model by a step of size stepDt.
ibsStepSync(double) - Method in class IBS: Advances the IBS model by a step of size stepDt.
ICOSAHEDRON - Enum constant in enum class GeometryType: Icosahedron graph, size \(N=12\), connectivity \(k=5\).
IcosahedronGeometry - Class in org.evoludo.simulator.geometries: Geometry implementation for the icosahedral graph (12 nodes, degree 5).
IcosahedronGeometry(EvoLudo) - Constructor for class IcosahedronGeometry: Create an icosahedral geometry tied to the given engine.
id - Variable in enum class Data: Identifying id of the type of data.
id - Variable in enum class Mode: Identifying id of the type of mode.
id - Variable in class Module: In multi-species modules each species is represented by a Module, see Module.species.
ID - Variable in class EvoLudo: Unique ID of EvoLudo instance.
IDcounter - Static variable in class EvoLudo: The loggers of each EvoLudo lab instance need to have unique names to keep the logs separate.
idx - Variable in class Network: Counter for the iterator over all nodes.
idx - Variable in class Distribution.TraitCommand: The index of the trait to show on the axis.
idxSpecies - Variable in class ODE: Array containing indices that delimit individual species in the ODE state variables.
IllegalPathStateException - Exception Class in org.evoludo.geom: The IllegalPathStateException represents an exception that is thrown if an operation is performed on a path that is in an illegal state with respect to the particular operation being performed, such as appending a path segment to a GeneralPath without an initial moveto.
IllegalPathStateException() - Constructor for exception class IllegalPathStateException: Constructs an IllegalPathStateException with no detail message.
IllegalPathStateException(String) - Constructor for exception class IllegalPathStateException: Constructs an IllegalPathStateException with the specified detail message.
IMITATE - Enum constant in enum class PlayerUpdate.Type: imitate/replicate (linear)
IMITATE_BETTER - Enum constant in enum class PlayerUpdate.Type: imitate/replicate (better only)
Implementation details - Section in class org.evoludo.simulator.views.Histogram
Implementation details - Section in class org.evoludo.simulator.views.Pop2D
Implementation details - Section in class org.evoludo.simulator.views.Pop3D
Implementation note: - Section in org.evoludo.graphics.AbstractGraph.clearCanvas()
Implementation note: - Section in org.evoludo.graphics.AbstractGraph.displayMessage(String)
Implementation note: - Section in org.evoludo.graphics.AbstractGraph.displayMessage(String)
Implementation note: - Section in org.evoludo.simulator.EvoLudo.unloadModule()
Implementation note: - Section in org.evoludo.simulator.LifecycleController.unloadModule()
Implementation Note: - Section in org.evoludo.graphics.AbstractGraph.drawFrame(int, int)
Implementation Note: - Section in org.evoludo.graphics.AbstractGraph.drawFrame(int, int, double)
Implementation notes: - Section in org.evoludo.graphics.AbstractGraph.sketch(Path2D, boolean)
Implementation notes: - Section in org.evoludo.simulator.modules.Continuous.findExtrema(double[], double[], int[], int[], double[][], double[][], double[], double[], int[], int[], double, int, double)
Implementation notes: - Section in org.evoludo.simulator.modules.Continuous.findExtrema(double[], int[], double[][], double[], int[], double, int, double)
Implementation notes: - Section in org.evoludo.simulator.modules.Continuous.findExtremalMonoScore(boolean)
Implementation notes: - Section in org.evoludo.simulator.modules.Continuous.findExtremalScore(boolean)
Implementation Notes: - Section in org.evoludo.math.Functions.tanh(double)
Implementation Notes: - Section in org.evoludo.math.MersenneTwister.setSeed(long)
Implementation Notes: - Section in org.evoludo.simulator.models.ODE.checkConvergence(double)
Implementation Notes: - Section in org.evoludo.simulator.models.ODE.checkConvergence(double)
Implementation Notes: - Section in org.evoludo.simulator.models.ODE.next()
Implementation Notes: - Section in org.evoludo.simulator.models.ODE.next()
Implementation Notes: - Section in org.evoludo.simulator.models.ODE.next()
Implementation Notes: - Section in org.evoludo.simulator.models.RungeKutta.deStep(double)
Implementation Notes: - Section in org.evoludo.simulator.models.RungeKutta.rkck(double)
Implementation Notes: - Section in org.evoludo.simulator.models.SDE.deStep(double)
Implementation Notes: - Section in org.evoludo.simulator.ui.KeyHandler.onKeyDown(String)
Implementation Notes: - Section in org.evoludo.simulator.ui.KeyHandler.onKeyUp(String)
Important - Section in interface org.evoludo.simulator.views.BasicTooltipProvider
Important: - Section in org.evoludo.simulator.models.IBSPopulation.updatePlayerBestResponse(int, int[], int)
Important: - Section in org.evoludo.simulator.models.IBSPopulation.updatePlayerBestResponse(int, int[], int)
Important: - Section in org.evoludo.simulator.models.IBSPopulation.updatePlayerBestResponse(int, int[], int)
Important: - Section in org.evoludo.simulator.models.IBSPopulation.updateScoreAt(int, double, int)
Important: - Section in org.evoludo.simulator.models.IBSPopulation.updateScoreAt(int, double, int)
Important: - Section in org.evoludo.simulator.models.Model.HasIBS.CGroups.groupScores(double, double[], int, double[])
Important: - Section in org.evoludo.simulator.models.Model.HasIBS.CPairs.pairScores(double, double[], int, double[])
Important: - Section in org.evoludo.simulator.models.Model.HasIBS.CPairs.pairScores(double, double[], int, double[])
Important: - Section in org.evoludo.simulator.models.Model.HasIBS.DGroups.mixedScores(int[], int, double[])
Important: - Section in org.evoludo.simulator.models.Model.HasIBS.DGroups.mixedScores(int[], int, double[])
Important: - Section in org.evoludo.simulator.models.Model.HasIBS.DGroups.mixedScores(int[], int, double[])
Important: - Section in org.evoludo.simulator.models.Model.HasIBS.DGroups.mixedScores(int[], int, double[])
Important: - Section in org.evoludo.simulator.models.Model.HasIBS.DGroups.mixedScores(int[], int, double[])
Important: - Section in org.evoludo.simulator.models.Model.HasIBS.MCGroups.groupScores(double[], double[], int, double[])
Important: - Section in org.evoludo.simulator.models.Model.HasIBS.MCPairs.pairScores(double[], double[], int, double[])
Important: - Section in org.evoludo.simulator.models.Model.HasIBS.MCPairs.pairScores(double[], double[], int, double[])
Important: - Section in org.evoludo.simulator.models.Model.HasIBS.MCPairs.pairScores(double[], double[], int, double[])
Important: - Section in org.evoludo.simulator.modules.Module.species
Important: - Section in org.evoludo.util.RingBuffer.append(T)
Important: - Section in org.evoludo.util.RingBuffer.replace(T)
Important: - Section in org.evoludo.util.RingBuffer.replace(int, T)
Important behavior notes - Section in class org.evoludo.graphics.S3Graph
Important fields and conventions referenced by subclasses: - Section in class org.evoludo.graphics.GenericPopGraph
Important implementation notes and caveats: - Section in class org.evoludo.graphics.LineGraph
in - Variable in class AbstractGeometry: The array storing the neighbourhood of each node by listing the indices of nodes that connect to this one.
incidence - Variable in class SIR: The incidence power {p, q} for infected and susceptible density, I^p S^q in S → I.
increaseDelay() - Method in class EvoLudo: Increase delay between subsequent updates by fixed factor.
increaseDelay() - Method in class RunController: Increase delay between updates.
incrementTime(double) - Method in class PDE: Increments time by incr.
Index(int) - Constructor for class ColorMap.Index: Constructs a new index color map.
Index(Color[]) - Constructor for class ColorMap3D.Index: Construct a new Index color map.
Index(Color[]) - Constructor for class ColorMapCSS.Index: Construct a new Index color map.
Index(Color[], int) - Constructor for class ColorMap3D.Index: Construct a new Index color map with transparency where \(\alpha\in[0,255]\) with \(0\) fully transparent and \(255\) fully opaque.
Index(Color[], int) - Constructor for class ColorMapCSS.Index: Construct a new Index color map with transparency where \(\alpha\in[0,255]\) with \(0\) fully transparent and \(255\) fully opaque.
Index(Color[], int, T[]) - Constructor for class ColorMap.Index: Constructs a new index color map with transparency alpha.
indexOf(Object) - Method in class Network
inheritedKeys - Variable in class CLOption: The flag to indicate if keys were inherited from another option.
inheritKeysFrom(CLOption) - Method in class CLOption: Inherit keys from another option.
init - Variable in class ParaGraph: The starting point of the most recent trajectory.
init - Variable in class S3Graph: The starting point of the most recent trajectory.
init - Variable in class IBSDPopulation: Type of initial configuration.
init - Variable in class IBSMCPopulation: Type of initial configuration.
init - Variable in class Slider: Initial value of slider.
init() - Method in class AbstractGraph: Initialize the graph.
init() - Method in class simCDL.simCDLIBS
init() - Method in class AbstractGeometry: Initialise the geometry.
init() - Method in class BarabasiAlbertGeometry: Generates a connected undirected scale-free network following the Barabási–Albert preferential attachment model.
init() - Method in class CompleteGeometry: Generates a complete graph where every node is connected to every other node.
init() - Method in class CubicGeometry: Generates a cubic (3D) regular lattice.
init() - Method in class DesarguesGeometry: Generates the Desargues graph (also known as the Truncated Petersen graph), a symmetric cubic graph with \(20\) nodes.
init() - Method in class DodekahedronGeometry: Generates a dodecahedron graph: a cubic symmetric graph with \(20\) nodes.
init() - Method in class DynamicGeometry
init() - Method in class FranklinGeometry: Generates the Franklin graph, a cubic cage with \(12\) nodes discovered by Philip Franklin.
init() - Method in class FruchtGeometry: Generates the Frucht graph, the smallest regular graph without any symmetries (a cubic graph with \(12\) nodes and no automorphisms apart from the identity).
init() - Method in class HeawoodGeometry: Generates the Heawood graph, a cubic symmetric graph with \(14\) nodes that is the point-line incidence graph of the Fano plane.
init() - Method in class HexagonalGeometry: Generates a hexagonal (honeycomb) regular lattice with degree \(6\) (or optional self-links when connectivity is set to 1).
init() - Method in class HierarchicalGeometry: Initialise the geometry.
init() - Method in class IcosahedronGeometry: Generates an icosahedron graph: a symmetric graph with \(12\) nodes and degree \(5\).
init() - Method in class KlemmEguiluzGeometry: Generates a connected undirected scale-free/small-world network following the Klemm & Eguíluz growth process.
init() - Method in class LinearGeometry: Generates a linear chain (1D lattice).
init() - Method in class MooreGeometry
init() - Method in class RandomDirectedGeometry: Generates a connected directed random graph by first creating a spanning tree and then adding remaining edges uniformly at random.
init() - Method in class RandomGeometry: Generates a connected undirected random graph.
init() - Method in class RandomRegularGeometry: Generates a connected undirected random regular graph with degree equal to the requested connectivity, retrying construction if necessary.
init() - Method in class ScalefreeGeometry: Generates a connected undirected scale-free network by sampling degrees from a power-law distribution and then constructing a matching graph.
init() - Method in class SecondNeighbourGeometry
init() - Method in class SquareGeometry: Generates square regular lattices with arbitrary neighbourhood sizes.
init() - Method in class StarGeometry: Generates a star geometry with a hub in the middle that is connected to all other nodes (leaves).
init() - Method in class StrongAmplifierGeometry: Generates a strong undirected amplifier of selection as described by Giakkoupis (2016).
init() - Method in class StrongSuppressorGeometry: Generates a strong undirected suppressor of selection.
init() - Method in class SuperstarGeometry: Generates a superstar geometry, i.e.
init() - Method in class TietzeGeometry: Generates Tietze's graph, a cubic graph with \(12\) nodes and automorphisms corresponding to the symmetries of a hexagon.
init() - Method in class TriangularGeometry: Generates a triangular regular lattice (degree \(3\))—sometimes called a hexagonal tiling when interpreted as dual to the honeycomb lattice.
init() - Method in class VonNeumannGeometry
init() - Method in class WellmixedGeometry: Generates a well-mixed graph, also termed mean-field network or unstructured population.
init() - Method in class WheelGeometry: Generates a wheel geometry, i.e.
init() - Method in class IBS
init() - Method in class IBSDPopulation
init() - Method in class IBSMCPopulation
init() - Method in class IBSPopulation: Initialize the model.
init() - Method in class Model: Milestone: Initialize this model
init() - Method in class ODE
init() - Method in class PDE
init() - Method in class DemesTBT.IBSPop
init() - Method in class Module: Initialize Module based on current parameters.
init() - Method in class NetGames.IBSPop
init(boolean) - Method in class IBS: Initializes the IBS model.
init(boolean) - Method in class ODE: Helper method to set the intital state of the model.
init(boolean) - Method in class ODEInitialize: Initialize the model state vectors, optionally randomizing species flagged with ODEInitialize.InitType.RANDOM.
init(double[][]) - Method in class PDEInitialize: Initialize the density array according to the configured type.
init(RenderingPanel, AnimatedScene.AnimationUpdateHandler) - Method in class PopGraph3D.Pop3DScene
Init(IBS) - Constructor for class IBSD.Init: Instantiate new initialization for use in IBS models.
Init(IBS, int) - Constructor for class IBSC.Init: Instantiate new initialization for use in IBS models.
INIT - Enum constant in enum class ChangeListener.PendingAction: Initialize model (re-initialize traits, stop execution).
INIT_SIZE - Static variable in class Path2D
init4x4 - Variable in class ATBT: The flag to indicate whether a generic 4×4 was provided to for the interactions among the four traits.
initCLO() - Method in class CLOParser: Initializes parser.
initcount - Variable in class simCDL: The initial counts for the different traits.
initCount - Variable in class IBSDPopulation: The array with the initial number of individuals of each trait.
initCubeKaleidoscope() - Method in class CDL.IBSPop: Initialize the cube kaleidoscope pattern for cubic geometries.
initCubeKaleidoscope() - Method in class TBT.IBSPop: Initialize kaleidoscope on cubic lattice.
initCubeKaleidoscopeCinD(int, int) - Method in class TBT.IBSPop: Initialize kaleidoscope on cubic lattice with cooperators in center.
initCubeKaleidoscopeDinC(int, int) - Method in class TBT.IBSPop: Initialize kaleidoscope on cubic lattice with defectors in center.
initDiffusion(double) - Method in class Advection
initDiffusion(double) - Method in class PDE: Helper method to initialize the effective rate of diffusion for the time increment dt.
initFixed(int, int) - Method in class CubicGeometry: Populate the lattice with a larger interaction range than the von-Neumann stencil, with fixed boundaries.
initFrequency() - Method in class IBSDPopulation: Initial configuration with trait frequencies as specified in arguments.
initFunction(double[][], double[], AbstractGeometry) - Method in class PDEInitialize: Dispatch initialization based on the dimensionality of the geometry.
initFunction1D(double[][], double[], AbstractGeometry) - Method in class PDEInitialize: Initialization for GeometryType.LINEAR geometries extracted to reduce complexity.
initFunction2D(double[][], double[], AbstractGeometry) - Method in class PDEInitialize: Initialization for square/triangular/hexagonal lattice geometries extracted to reduce cognitive complexity.
initFunction3D(double[][], double[], AbstractGeometry) - Method in class PDEInitialize: Initialization for GeometryType.CUBE geometries extracted to reduce complexity.
initGaussian() - Method in class IBSMCPopulation: Initialize traits by sampling from a (possibly truncated) Gaussian distribution per trait.
initGeometryDegreeDistr(int[]) - Method in class AbstractNetwork: Utility method to generate a network that realises the requested degree sequence.
initHierarchicalComplete(AbstractGeometry, int, int, int, boolean) - Static method in class CompleteGeometry: Initialize one hierarchical complete-graph deme inside a host geometry.
initHierarchicalDeme(AbstractGeometry, int, int, int, boolean) - Method in interface Hierarchical: Initialize one deme inside a host geometry.
initHierarchicalMoore(AbstractGeometry, int, int, int, boolean) - Static method in class MooreGeometry: Initialize one hierarchical Moore square deme using population and deme sizes.
initHierarchicalSecondNeighbour(AbstractGeometry, int, int, int, boolean) - Static method in class SecondNeighbourGeometry: Initialize one hierarchical second-neighbour square deme using population and deme sizes.
initHierarchicalSquare(AbstractGeometry, int, int, int, boolean) - Static method in class SquareGeometry: Initialize one hierarchical square deme using population and deme sizes.
initHierarchicalVonNeumann(AbstractGeometry, int, int, int, boolean) - Static method in class VonNeumannGeometry: Initialize one hierarchical von Neumann square deme using population and deme sizes.
initHierarchy(int, int) - Method in class HierarchicalGeometry: Utility method to generate hierarchical graphs.
initialDistance - Variable in class TrackballControls: Initial eye distance.
initialize(Line2D, double, double) - Static method in class Line2D: Initialize the line with the given slope and y-intercept.
initialize(Rectangle2D, double, double, double, double) - Static method in class Rectangle2D: Helper method to prevent this-escape warnings.
initialize(RNGDistribution.Binomial, double, int) - Static method in class RNGDistribution.Binomial: Helper method to prevent this-escape warnings.
initialize(RNGDistribution.Geometric, double) - Static method in class RNGDistribution.Geometric: Helper method to prevent this-escape warnings.
initializeCore() - Method in class AbstractNetwork: Initialize the core array with all node indices.
initializer - Variable in class ODE: Helper responsible for parsing and initializing ODE state vectors.
initializer - Variable in class PDE: Helper responsible for parsing and applying PDE initialization options.
initializeWithArray(MersenneTwister, int[]) - Static method in class MersenneTwister: Static helper method to initialize a MersenneTwister with an array seed.
initializeWithSeed(MersenneTwister, long) - Static method in class MersenneTwister: Static helper method to initialize a MersenneTwister with a long seed.
initialView - Variable in class ViewController: Initial view specification (index or name with optional args).
initInQ - Variable in class simCDLP: The flag to indicate whether the initial configuration is given by the interior fixed point Q (for CDL only).
initInterest() - Method in class CDL: Helper method to initialize the array with nonlinear interest rates for group size 1,2,3,...,N, where N is the maximum interaction group size based on the interest rate for groups with a single cooperator r1 and groups of all cooperators rN.
initK1() - Method in class HexagonalGeometry: Initialize the lattice with self-links only (connectivity 1).
initKaleidoscope() - Method in class IBSDPopulation: Initial configuration that generates evolutionary kaleidoscopes for deterministic update rules.
initKaleidoscope() - Method in class CDL.IBSPop
initKaleidoscope() - Method in class RSP.IBSPop
initKaleidoscope() - Method in class TBT.IBSPop
initMono() - Method in class IBSDPopulation: Monomorphic initial configuration with specified trait (and frequency in modules that allow empty sites).
initMono() - Method in class IBSMCPopulation: Initialize all individuals with the same (monomorphic) trait value.
initMono(int) - Method in class IBSDPopulation: Initialize monomorphic population with trait monoType.
initMono(int, double) - Method in class IBSDPopulation: Initialize monomorphic population with trait monoType.
initMoore(AbstractGeometry, int, int, int, boolean) - Static method in class MooreGeometry: Initialize a Moore square lattice.
initMutant() - Method in class IBSDPopulation: Monomorphic initial configuration with a single mutant placed in a location chosen uniformly at random (uniform initialization, cosmic rays).
initMutant() - Method in class IBSMCPopulation: Initialize a monomorphic resident population with a single mutant.
initNodes(double, double, double) - Method in class Network: Generate the initial placement of all nodes.
initNodes(double, double, double) - Method in class Network2D
initNodes(double, double, double) - Method in class Network3D
initPerturbation(double[][], double[], AbstractGeometry) - Method in class PDEInitialize: Initialize a uniform background with a single perturbed site at the center.
initRandom(double[][], double[], AbstractGeometry) - Method in class PDEInitialize: Initialize each site independently at random (normalized if needed).
initRange(int, int) - Method in class CubicGeometry: Populate the lattice with a larger interaction range than the von-Neumann stencil, optionally with toroidal wrapping.
initReset() - Method in class EvoLudoWeb: Initialize or reset EvoLudo model.
initRRGCore(RNGDistribution, int, int, int) - Method in class StrongAmplifierGeometry: Initialise the random-regular core subgraph.
initSecondNeighbour(AbstractGeometry, int, int, int, boolean) - Static method in class SecondNeighbourGeometry: Initialize a second-neighbour square lattice.
initSelf(int, int) - Method in class CubicGeometry: Connect each node exclusively to itself (used when connectivity is 1).
initSixNeighbors(int, int) - Method in class CubicGeometry: Populate the lattice with von-Neumann (6-neighbour) connectivity, respecting the configured boundary conditions.
initSquare(AbstractGeometry, int, int, int, boolean) - Static method in class SquareGeometry: Initialize a square lattice with arbitrary (odd) neighbourhood sizes.
initSquareSelf(AbstractGeometry, int, int, int) - Static method in class SquareGeometry: Initialize a square lattice that only connects nodes to themselves (used when connectivity equals one).
initStatisticsFailed() - Method in class Model: Clear statistics sample and get ready to collect next sample.
initStatisticsSample() - Method in class Model: Clear statistics sample and get ready to collect next sample.
initStripes() - Method in class IBSDPopulation: Initial configuration with monomorphic stripes of each type to investigate invasion properties of one trait into another with at least one instance of all possible pairings.
initTemperature() - Method in class IBSDPopulation: Monomorphic initial configuration with a single mutant placed in a random location chosen with probability proprtional to the number of incoming links (temperature initialization, errors in reproduction).
initToroidal(int, int) - Method in class CubicGeometry: Populate the lattice with a larger interaction range than the von-Neumann stencil, with toroidal wrapping.
initType - Variable in class ODE: Type of initial configuration for each species.
initType - Variable in class PDE: Type of initial configuration for each species.
InitType(String, String) - Constructor for enum class ODEInitialize.InitType: Instantiate new initialization type.
initUniform() - Method in class IBSDPopulation: Initial configuration with uniform trait frequencies of all active traits.
initUniform() - Method in class IBSMCPopulation: Initialize each trait uniformly at random in its allowed range.
initUniform(double[][], double[], AbstractGeometry) - Method in class PDEInitialize: Initialize every lattice point with the same state.
initUniverse(Geometry) - Method in class PopGraph3D: Initialize the universe of the 3D graph.
initVonNeumann(AbstractGeometry, int, int, int, boolean) - Static method in class VonNeumannGeometry: Initialize a von Neumann square lattice.
initWithVacant(int) - Method in class IBSDPopulation: Initialize monomorphic resident population with vacant sites and return location of a random resident to be changed to a mutant.
inProgress - Variable in class PDESupervisorGWT: true if calculations are already in progress.
INPUT - Static variable in class InputEvent: Name of input event.
InputEvent - Class in org.evoludo.ui: Represents a native input event.
InputEvent() - Constructor for class InputEvent: Protected constructor, use DomEvent.fireNativeEvent(com.google.gwt.dom.client.NativeEvent, com.google.gwt.event.shared.HasHandlers) to fire input events.
InputHandler - Interface in org.evoludo.ui: Handler interface for InputEvent events.
Input Handling and Shortcuts - Section in class org.evoludo.EvoLudoWeb
inputRegistration - Variable in class Slider: The input event handler registration.
insert(boolean[], boolean, int) - Static method in class ArrayMath: Insert element element of type boolean into array array of the same type at index.
insert(double[], double, int) - Static method in class ArrayMath: Insert element element of type double into array array of the same type at index.
insert(int[], int, int) - Static method in class ArrayMath: Insert element element of type int into array array of the same type at index.
insert(T[], T, int) - Static method in class ArrayMath: Insert element element of type T into array array of the same type at index.
insertEPubEvoLudoLab(Element, String) - Static method in class EvoLudoWeb: Fighting Apple Books constraints: Insert EvoLudo model in DOM by replacing the placeholder element with an iframe.
insertEvoLudoLab(Element, String) - Static method in class EvoLudoWeb: Insert EvoLudo model in DOM by replacing the placeholder element.
inside(double, double) - Method in class ParaGraph: Check if point (in user coordinates but not yet scaled to axes) lies inside of phase plane.
inside(double, double) - Method in class S3Graph: Check if point (in scaled user coordinates) lies inside of simplex.
inside(int, int) - Method in class AbstractGraph: Check if the event coordinates are inside the interactive plot area.
inside(int, int) - Method in class HistoGraph
inside(int, int) - Method in class LineGraph
inside(int, int) - Method in class ParaGraph
inside(int, int) - Method in class PopGraph2D
inside(int, int) - Method in class S3Graph
INSTANCE - Static variable in interface Git: 'Instantiate' the interface.
INSTANCE - Static variable in interface Resources: 'Instantiate' the interface.
INSTEAD_OF - Static variable in class IBSPopulation: String for formatting log messages
INTEGER_CLOSE - Static variable in class Plist: String constant for closing an integer entry during plist generation.
INTEGER_OPEN - Static variable in class Plist: String constant for opening an integer entry during plist generation.
Integration notes - Section in class org.evoludo.simulator.views.Phase2D
interaction - Variable in class IBSPopulation: The geometry of the interaction graph.
Interaction & Events - Section in class org.evoludo.graphics.PopGraph2D
interactions - Variable in class IBSPopulation: The array of individual interaction counts.
Interaction semantics - Section in class org.evoludo.graphics.AbstractGraph
interest - Variable in class EcoPGG: The multiplication factor of the public good.
interest(int) - Method in class CDL: Helper method to return the interest rate/multiplication factor of the public good with nc contributors.
Interfaces and Extension Points - Section in class org.evoludo.graphics.AbstractGraph
interGroup - Variable in class IBSPopulation: Reference to the interaction group.
interpolate(double, double, double) - Method in class LineGraph: Interpolate linearly between current and prev at x.
interpolateColors(T[], Color[]) - Method in class ColorMap.Gradient: Utility method for creating a smooth gradient spanning all colors in the array colors.
interpolateColors(T[], Color, int, Color, int) - Method in class ColorMap.Gradient: Utility method for creating a smooth gradient ranging from color start to color end in last-first steps.
intersection(Line2D) - Method in class Line2D: Return the intersection of two lines or Double.NaN if no intersection.
intersection(Segment2D) - Method in class Line2D: Return the intersection of the line and the segment s or Double.NaN if there is no intersection.
intersects(Line2D) - Method in class Line2D: Check if the line intersects the line l.
intersects(Line2D) - Method in class Rectangle2D: Check if the line (or line segment) l intersects the rectangle.
intersects(Line2D) - Method in class Segment2D
intersects(Rectangle2D) - Method in class Line2D: Check if the line intersects the rectangle r.
intersects(Segment2D) - Method in class Line2D: Check if the line intersects the line segment s.
intersects(Segment2D) - Method in class Segment2D: Check if this segment and the segment s intersect.
INV_TWO_TO_31M1 - Static variable in class MersenneTwister: Constant: 1/(2^-31 - 1).
INV255 - Static variable in class ColorMap: Useful constant for converting int representations of color channels (0-255) to floating point representations (0-1).
invalidate() - Method in class GenericPopGraph: Invalidate the network.
invalidated - Variable in class GenericPopGraph: The flag to indicate whether the graph has been invalidated and needs to be redrawn.
inverseTransform(double[], int, double[], int, int) - Method in class AffineTransform: Inverse transforms an array of double precision coordinates by this transform.
inverseTransform(Point2D, Point2D) - Method in class AffineTransform: Inverse transforms the specified ptSrc and stores the result in ptDst.
invert() - Method in class AffineTransform: Sets this transform to the inverse of itself.
invFitRange - Variable in class ODE: Array containing the inverse of the fitness range: 1.0/(maxFitness - minFitness) for each species.
invmap(double) - Method in class Map2Fitness: Map fitness to payoff/score, based on currently selected type map.
IR - Static variable in class Network2D: The inverse size of the baseline 2D universe.
IR - Static variable in class Network3D: The inverse size of the baseline 3D universe.
IR2 - Static variable in class Network2D: The inverse squared size of the baseline 2D universe, 1/R<sup>2</sup>.
IR2 - Static variable in class Network3D: The inverse squared size of the baseline 3D universe, 1/R<sup>2</sup>.
isActive - Variable in class AbstractView: The flag to indicate whether this view is currently active.
isActive() - Method in class KeyHandler: Check whether this controller currently receives priority for key events.
isActive() - Method in class AbstractView: Checks if the controller is busy running calculations.
isAdjustedDynamics - Variable in class ODE: true if the adjusted replicator dynamics should be applied.
isAltDown - Variable in class KeyHandler: Tracks whether the Alt modifier is currently pressed.
isAltDown() - Method in class KeyHandler: Determine whether the Alt modifier key is currently engaged.
isAnaglyph() - Method in class PopGraph3D: Check if the graph is displayed as an anaglyph.
isAutoClose() - Method in class ContextMenu: Checks if submenus close automatically when pointer stops hovering over corresponding menu item in parent menu.
isAutoHide() - Method in class ContextMenu: Checks if context menu hides automatically (with some delay) after pointer exited.
isAutoOpen() - Method in class ContextMenu: Checks if submenus open automatically when pointer hovers over corresponding menu item in parent menu.
isChecked - Variable in class ContextMenuCheckBoxItem: true if context menu item is checked.
isChecked() - Method in class ContextMenuCheckBoxItem: Check if menu item is active (checked).
isCLOFieldFocused() - Static method in class KeyHandler: Determines whether any controller's CLO field currently has focus.
isCLOPanelVisible() - Method in class EvoLudoWeb: Check if the CLO settings panel is visible in the GUI.
isConnected() - Method in class Model: Checks if the current data point should be connected to the previous one.
isConsistent() - Method in class AbstractGeometry: Check consistency of links.
isConsistent() - Method in class IBSDPopulation
isConsistent() - Method in class IBSPopulation: Convenience method during development to perform a number of consistency checks of the current state.
isContinuous() - Method in class Model: Checks if model deals with continuous traits.
isDE() - Method in enum class ModelType: Check if this model type is an ordinary differential equations model.
isDebugEnabled - Variable in class GenericPopGraph: The flag to indicate whether the debug submenu is activated.
isDensity - Variable in class ODE: Convenience variable to indicate whether the model is based on densities.
isDensity() - Method in class Model: Check if the current model performs density based dynamics.
isDensity() - Method in class ODE
isDerivedFrom(AbstractGeometry) - Method in class AbstractGeometry: Check whether this geometry was derived from source.
isDone() - Method in class Path2D.Iterator: Tests if the iteration is complete.
isDone() - Method in interface PathIterator: Tests if the iteration is complete.
isDragging - Variable in class TrackballControls: true while the pointer is dragging.
isDynamicUpdate - Variable in class TrackballControls: true to disable dynamic damping of changes to the view..
isElementActive(Element) - Static method in class NativeJS: JSNI method: check if element is active.
isEmpty() - Method in class Path2D: Check if the path is empty.
isEmpty() - Method in class RingBuffer: Check if the ring buffer is empty.
isEnabled - Variable in class ContextMenuItem: Flag to indicate whether menu item is enabled.
isEnabled - Variable in class TrackballControls: true if trackball controls enabled.
isEnabled() - Method in class ContextMenuItem
isEnabled() - Method in class TrackballControls: Check if trackball controls are enabled.
isEPub - Variable in class SettingsController.Settings: true if the lab runs in an ePub reader.
isEPub() - Method in class EvoLudoWeb: Check if this lab is running inside an ePub reader.
isEPub() - Method in class SettingsController: Reports whether the environment is an ePub reader.
isEPub() - Static method in class NativeJS: JSNI method: Check if graph is displayed in an ePub reading system.
isEPubStandalone() - Method in class EvoLudoWeb: Check if this lab is displayed as standalone page in ePub.
isFixedBoundary() - Method in class AbstractLattice: Report whether the lattice uses fixed boundaries instead of periodic ones.
isFixedBoundaryToken(char) - Static method in enum class GeometryType: Helper method to check if the character ch indicates fixed boundaries.
isFull() - Method in class RingBuffer: Check if the ring buffer is at capacity.
isFullscreen() - Static method in class NativeJS: JSNI method: Check if the document is in fullscreen mode.
isFullscreenSupported() - Static method in class NativeJS: JSNI method: Check if fullscreen mode is supported.
isGraphConnected() - Method in class AbstractGeometry: Check if graph is connected.
isGraphConnected(int, boolean[]) - Method in class AbstractGeometry: Depth-first traversal helper used to determine connectivity.
isGWT - Static variable in class EvoLudo: The flag to indicate whether EvoLudo is running in a web browser (or ePub) using javascript generated by GWT or in the java JRE.
isHierarchy - Variable in class PopGraph2D: Convenience variable.
isHit(Point2D) - Method in class Node2D: Check it point hit lies inside of node.
isHit(Point3D) - Method in class Node3D: Check it point hit lies inside of node.
isHTML() - Static method in class NativeJS: JSNI method: Test whether loaded from an HTML document.
isIBS() - Method in enum class ModelType: Check if this model type is individual based simulations model.
isIdentity() - Method in class AffineTransform: Returns true if this AffineTransform is an identity transform.
isInitialViewSet() - Method in class ViewController: Determines whether the --view option has been provided.
isInterspecies - Variable in class AbstractGeometry: true if this geometry links different species/populations.
isInterspecies() - Method in class AbstractGeometry: Check whether this geometry connects individuals from different populations.
isLattice() - Method in class AbstractGeometry: Utility method to determine whether a given geometry type is a lattice.
isLattice() - Method in enum class GeometryType: Check if the geometry is a lattice.
isLinearPGG - Variable in class CDL: The flag to indicate whether the public good is linear, i.e.
isLoaded - Variable in class AbstractView: The flag to indicate whether this view has been loaded.
isMap(Map2Fitness.Map) - Method in class Map2Fitness: Checks if this map is of type aMap.
isMonomorphic() - Method in class IBSDPopulation
isMonomorphic() - Method in class IBSPopulation: Check if population is monomorphic.
isMonomorphic() - Method in class ODE: Check if population is monomorphic.
isMonomorphic() - Method in class PDE
isMonomorphic() - Method in class ATBT.ATBTPop
isMonomorphic(int, int, int, int) - Method in class ODE: Helper method to check if the species with trait indices start through stop is monomorphic.
isMoran() - Method in class PopulationUpdate: Determine whether population update is a variant of Moran updates.
isMouseOver - Variable in class ContextMenu: true if pointer is currently over context (sub)menu.
isMultispecies - Variable in class IBSPopulation: Flag to indicate whether the model entertains multiple species, i.e.
isMultispecies - Variable in class Model: Flag to indicate whether the model entertains multiple species, i.e.
isMultispecies - Variable in class Histogram: Flag to indicate whether the model entertains multiple species, i.e.
isMultispecies() - Method in interface Features: Returns whether the module implements multiple species.
isMultispecies() - Method in interface Features.Multispecies
isNeighborOf(int, int) - Method in class AbstractGeometry: Check whether check is currently a neighbour of focal.
isNeutral - Variable in class IBSPopulation: Flag to indicate whether dynamic is neutral, i.e.
isNeutral() - Method in interface Features.Payoffs: Checks whether dynamic is neutral, i.e.
isNormalized - Variable in class HistoGraph: The flag to indicate whether the data is normalized.
isODE() - Method in enum class ModelType: Check if this model type is an ordinary differential equations model.
isOrthographic() - Method in class PopGraph3D: Check if the camera uses an orthographic projection.
isPairwise() - Method in interface Features.Groups
isPairwise() - Method in interface Features: Returns whether interactions are restricted to pairs (false by default).
isPairwise() - Method in interface Features.Pairs
isPDE() - Method in enum class ModelType: Check if this model type is an [partial differential equations model.
isReady() - Static method in class SettingsController: Reports whether no other ePub lab is currently running, allowing this lab to start execution.
isRegular - Variable in class AbstractGeometry: true if the network structure is regular (all nodes have the same number of neighbours).
isRegular() - Method in class AbstractGeometry: Check whether the geometry is regular (all nodes share the same degree).
isRelaxing - Variable in class Model: The flag to indicate whether the model is currently relaxing the initial configuration.
isRelaxing() - Method in class Model: Check if EvoLudo model is in the process of relaxing.
isRewired - Variable in class AbstractGeometry: true if rewiring should be applied.
isRewired() - Method in class AbstractGeometry: Check if the geometry was modified by rewiring.
isRunning - Variable in class EvoLudo: The flag to indicate whether the active model is running.
isRunning - Variable in class TestEvoLudo: The flag to indicate whether tests are running.
isRunning - Variable in class Network: The flag to indicate whether the layouting process is running.
isRunning() - Method in class EvoLudo: Check if the active model is running.
isRunning() - Method in class AbstractView: Checks if the controller is busy running calculations.
isSameTrait(int) - Method in class IBSCPopulation
isSameTrait(int) - Method in class IBSDPopulation
isSameTrait(int) - Method in class IBSMCPopulation
isSameTrait(int) - Method in class IBSPopulation: Check if individual with index a has switched traits.
isSameTrait(int) - Method in class NetGames.IBSPop
isSampling(IBSGroup.SamplingType) - Method in class IBSGroup: Checks whether the type of sampling of interaction/reference groups is type.
isSDE() - Method in enum class ModelType: Check if this model type is an stochastic differential equations model.
isSeedSet() - Method in class RNGDistribution: Check if seed of random number generator has been set.
isSelfClosing() - Method in class PlistTag: Check if this tag is self-closing.
isSet() - Method in class CLOption: Check if option was set on command line (regardless of whether an argument was provided).
isShiftDown - Variable in class KeyHandler: Tracks whether the Shift modifier is currently pressed.
isShiftDown() - Method in class KeyHandler: Determine whether the Shift modifier key is currently engaged.
isShowing() - Method in class EvoLudoWeb: Check if EvoLudo model is visible on screen.
isShowing() - Static method in class ContextMenu: Check if context menu is visible.
isSingle - Variable in class AbstractGeometry: Convenience flag denoting whether intra- and interspecific competitions are identical.
isSingle() - Method in class AbstractGeometry: Check if a single geometry suffices for interaction and competition structures.
isSquareLattice() - Method in enum class GeometryType: Check if the geometry is a square lattice.
isStandalone() - Method in class SettingsController: Reports whether the ePub lab runs on a standalone page instead of inline within text flow.
isStatic() - Method in interface Features: Modules that are based on static fitness should implement the Features.Static interface and thus return true.
isStatic() - Method in interface Features.Static
isStatistics() - Method in enum class Data: Checks if the data type is a statistics type.
isStatistics() - Method in enum class Mode: Checks if the mode is a statistics mode.
isStatus(Network.Status) - Method in class Network: Checks the status of the layouting process.
isSubmenu() - Method in class ContextMenu: Check if this is a submenu.
isSubtype(GeometryType) - Method in class HierarchicalGeometry: Check if the sub-geometry matches the given type.
issues - Variable in class EvoLudoWeb.GUIState: The number of issues that have occurred during parsing
isSuspended - Variable in class EvoLudo: The flag to indicate whether running of the model is suspended.
isSuspended() - Method in class EvoLudo: Check whether the current model is suspended.
isSymmetric - Variable in class PDE: The flag indicating whether the dynamics is symmetric.
isSymmetric() - Method in class PDE: Gets whether the model preserves symmetry.
isSynchronous - Variable in class IBS: Flag to indicate whether the population updates are synchronous.
isSynchronous() - Method in class PopulationUpdate: Determine whether population update is synchronous.
isTimeReversed() - Method in class Model: Checks if time is reversed.
isTimeReversed() - Method in class ODE
isType(GeometryType) - Method in class AbstractGeometry: Convenience helper to check the geometry type.
isType(ModelType) - Method in enum class ModelType: Check if this model type is the same as the given type.
isUndirected - Variable in class AbstractGeometry: Flag indicating whether the network structure is undirected.
isUndirected() - Method in class AbstractGeometry: Check whether all links are undirected.
isUnique() - Method in class AbstractGeometry: Check if current geometry unique.
isUnique() - Method in enum class GeometryType: Helper method to check uniqueness of the geometry geo.
isUnique() - Method in class HierarchicalGeometry
isVacantAt(int) - Method in class IBSDPopulation
isVacantAt(int) - Method in class IBSPopulation: Check if site with index index is occupied by an individual or vacant.
isValid - Variable in class AbstractGeometry: true if the network structure has been successfully initialized.
isValidDnD(JavaScriptObject) - Static method in class NativeJS: JSNI method: check whether a single plist files was dropped.
isValidInitForType(double[][]) - Method in class PDE: Validate that the parsed init matrix is acceptable for the chosen initialization type.
isValidKey(String) - Method in class CLOption: Check if the key with name aKey is a valid key for this option.
isValidKey(CLOption.Key) - Method in class CLOption: Check if key is a valid key for this option.
isVirgin - Variable in class PlistReader: true if no processing has occurred yet.
isVR() - Method in class PopGraph3D: Check if the graph is displayed with stereo effect.
isWebGLSupported() - Static method in class NativeJS: JSNI method: check whether WebGL and hence 3D graphics are supported.
isXML - Variable in class XMLLogFormatter: false if XML/XHTML compliant encoding of log messages desired.
iterator() - Method in class Network
iterator() - Method in class RingBuffer
Iterator(Path2D) - Constructor for class Path2D.Iterator: Constructs a new path iterator object from an arbitrary Path2D object.

J

Java notes - Section in class org.evoludo.math.MersenneTwister
jrengine - Variable in class simMoran: The EvoLudoJRE engine for running the simulation.
jsPrefix() - Static method in class FullscreenChangeEvent: Determine browser prefix, if any, to use the correct identifier for capturing the fullscreen change event.
justFocussed - Variable in class EvoLudoTrigger.LightboxPanel: Flag to track if window just got focus.

K

KALEIDOSCOPE - Enum constant in enum class IBSD.Init.Type: Symmetric initial distribution, possibly generating evolutionary kaleidoscopes for deterministic synchronous updates.
key - Variable in enum class GeometryType: Key of geometry.
key - Variable in enum class IBS.MigrationType: Key of migration type.
key - Variable in enum class IBS.ScoringType: Key of population update type.
key - Variable in enum class IBS.Statistics.Type: Key of statistics type.
key - Variable in enum class IBSC.Init.Type: Key of initialization type.
key - Variable in enum class IBSD.Init.Type: Key of initialization type.
key - Variable in enum class IBSD.OptimizationType: Key of optimization type.
key - Variable in enum class IBSGroup.SamplingType: Key of interaction type.
key - Variable in enum class ModelType: Identifying key of the model type.
key - Variable in enum class ODEInitialize.InitType: Key of initialization type.
key - Variable in enum class PDEInitialize.Type: Key of initialization type.
key - Variable in enum class PopulationUpdate.Type: Key of population update type.
key - Variable in enum class Continuous.Benefits: The key of the benefit function.
key - Variable in enum class Continuous.ColorModelType: The name of the color model type.
key - Variable in enum class Continuous.Costs: The key of the cost function.
key - Variable in enum class Map2Fitness.Map: Key of map.
key - Variable in enum class Mutation.Continuous.Type: Key of player update.
key - Variable in enum class Mutation.Discrete.Type: Key of player update.
key - Variable in enum class PlayerUpdate.Type: Key of player update.
key - Variable in enum class SpeciesUpdate.Type: Key of species update type.
key - Variable in class CLOption.SimpleKey: The key of the command line option.
KEY_ALT - Static variable in class KeyHandler: String value emitted when the Alt key is pressed.
KEY_BACKSPACE - Static variable in class KeyHandler: String value emitted when the Backspace key is pressed.
KEY_CLOSE - Static variable in class Plist: String constant for closing an key entry during plist generation.
KEY_DELETE - Static variable in class KeyHandler: String value emitted when the Delete key is pressed.
KEY_ENTER - Static variable in class KeyHandler: String value emitted when the Enter key is pressed.
KEY_ESCAPE - Static variable in class KeyHandler: String value emitted when the Escape key is pressed.
KEY_OPEN - Static variable in class Plist: String constant for opening an integer entry during plist generation.
KEY_SHIFT - Static variable in class KeyHandler: String value emitted when the Shift key is pressed.
Key behavioral notes - Section in class org.evoludo.simulator.views.Phase2D
Key Concepts & Fields - Section in class org.evoludo.graphics.PopGraph2D
keyController - Variable in class EvoLudoWeb: Helper that centralizes keyboard handling.
keyController - Variable in class WebListener: The key controller used to manage keyboard events.
KeyHandler - Class in org.evoludo.simulator.ui: Handles global key events and delegates actions to the owning EvoLudoWeb.
KeyHandler(EvoLudoWeb) - Constructor for class KeyHandler: Initializes the key event handler.
keyHandlers - Static variable in class KeyHandler: All handlers that have requested global registration.
Key responsibilities: - Section in class org.evoludo.graphics.GenericPopGraph
Key responsibilities: - Section in class org.evoludo.graphics.ParaGraph
keys - Variable in class CLOption: The list of valid keys (if applicable).
kin - Variable in class AbstractGeometry: The array storing the number of incoming neighbours for each node.
KlemmEguiluzGeometry - Class in org.evoludo.simulator.geometries: Scale-free/small-world network following the Klemm & Eguíluz growth process.
KlemmEguiluzGeometry(EvoLudo) - Constructor for class KlemmEguiluzGeometry: Create a Klemm-Eguíluz small-world geometry managed by the supplied engine.
kout - Variable in class AbstractGeometry: The array storing the number of outgoing neighbours for each node.
kurtosis(double[]) - Static method in class Distributions: Sample kurtosis of data points x[i] stored in double vector x.
kurtosis(double[], double) - Static method in class Distributions: Sample kurtosis of data points x[i] stored in double vector x with known mean m1.

L

label - Variable in class GenericPopGraph: The label of the graph.
label - Variable in class GraphStyle: The label of the graph (if any).
label - Variable in class S3Map: The name of the map.
labelColor - Variable in class GraphStyle: The color of the label of the graph.
labelFont - Variable in class GraphStyle: The font for the graph label as a CSS string.
last() - Method in class RingBuffer: Return last/most recent buffer entry.
last(double[], int) - Static method in class ArrayMath: Find the last occurence of the element b in the array double[] a.
last(int[], int) - Static method in class ArrayMath: Find the last occurence of the element b in the array int[] a.
lastIndexOf(Object) - Method in class Network
lastModule - Variable in class ViewController: Track the module last used for view reuse decisions.
layout - Variable in class Network2DGWT: Helper variable to keep track of the time spent layouting the network.
layout - Variable in class Network3DGWT: Helper variable to keep track of the time spent layouting the network.
LAYOUT_IN_PROGRESS - Enum constant in enum class Network.Status: layout in progress
layoutComplete() - Method in class GenericPopGraph
layoutComplete() - Method in class EvoLudo: Notification from GUI that layout process has finished.
layoutComplete() - Method in class EvoLudoGWT
layoutComplete() - Method in interface Network.LayoutListener: Notification that the layouting process has completed.
layoutComplete() - Method in class AbstractView: Notification of the completion of the layouting process.
layoutComplete() - Method in class GenericPop
layoutFallbackPercent(int) - Method in class Histogram: Assign equal percent heights when pixel measurements are unavailable.
layoutGraphs() - Method in class Histogram: Size histogram panels so their drawable frames have equal height while distributing x-axis decoration space across the stack.
layoutNetwork() - Method in class GenericPopGraph: Draws structures with resulting from dynamic layouting of network.
layoutTimeout - Variable in class Network: The timeout for layout calculations.
layoutUpdate(double) - Method in class GenericPopGraph
layoutUpdate(double) - Method in interface Network.LayoutListener: Requests an incremental update of the current layout.
left - Variable in class Rectangle2D: The left segment of the rectangle.
leftMouseButton - Variable in class AbstractGraph: The flag to indicate whether the left mouse button is pressed.
length() - Method in class Vector2D: Calculate the length of the 2D vector.
length() - Method in class Vector3D: Calculate the length of the 3D vector.
length2() - Method in class Vector2D: Calculate the length squared of the 2D vector, |v|².
length2() - Method in class Vector3D: Calculate the length squared of the 3D vector, |v|².
lengthSquared() - Method in class Vector2D: Same as Vector2D.length2().
lengthSquared() - Method in class Vector3D: Same as Vector3D.length2().
leniencyCoop - Variable in class CDLP: The leniency of peer punishers towards cooperators (0: full leninecy, 1: no leninecy).
leniencyLoner - Variable in class CDLP: The leniency of peer punishers towards loners (0: full leninecy, 1: no leninecy).
level - Variable in class IBSGroup.HierarchyUnit: Current hierarchy level being inspected.
levelColor - Variable in class GraphStyle: The color of the levels.
levelSize - Variable in class IBSGroup.HierarchyUnit: Number of individuals contained at the current level.
levelWidth - Variable in class GraphStyle: The stroke width of the levels.
License - Section in class org.evoludo.math.MersenneTwister
Lifecycle - Section in class org.evoludo.EvoLudoWeb
Lifecycle - Section in class org.evoludo.graphics.AbstractGraph
Lifecycle - Section in class org.evoludo.simulator.views.Histogram
lifecycleController - Variable in class EvoLudo: Controller for lifecycle listeners.
LifecycleController - Class in org.evoludo.simulator: Helper to manage lifecycle listeners and dispatch lifecycle notifications as well as loading and unloading modules and models.
LifecycleController(EvoLudo) - Constructor for class LifecycleController: Create a controller bound to the supplied engine.
LifecycleListener - Interface in org.evoludo.simulator.models: LifecycleListeners are notified about loading and unloading events for modules and models.
lifecycleListeners - Variable in class LifecycleController: List of listeners for module/model load/unload lifecycle events.
light - Variable in class PopGraph3D: The directed light source illuminating the scene.
LightboxPanel() - Constructor for class EvoLudoTrigger.LightboxPanel: Create a new lightbox panel.
Limitations and assumptions - Section in class org.evoludo.simulator.views.Pop2D
Limitations and assumptions - Section in class org.evoludo.simulator.views.Pop3D
lin2log(double) - Method in class Slider: Helper function to convert from linear to logarithmic scales.
line - Variable in class PlistReader: Remainder of plist-string.
Line2D - Class in org.evoludo.geom: Utility class for dealing with straight (infinite) lines in 2D.
Line2D() - Constructor for class Line2D: Create a new 2D line with the slope and y-intercept of zero (corresponding to the x-axis).
Line2D(double, double) - Constructor for class Line2D: Create a new 2D line with slope m and y-intercept b.
Line2D(Line2D) - Constructor for class Line2D: Create a copy of the 2D line l.
Line2D(Point2D, Point2D) - Constructor for class Line2D: Create a new 2D line through points p1 and p2.
LINEAR - Enum constant in enum class GeometryType: Linear lattice, 1D.
linearAsymmetry - Variable in class LinearGeometry: Difference between the number of neighbours on the left vs right.
LinearGeometry - Class in org.evoludo.simulator.geometries: Linear (1D lattice) geometry that supports asymmetric neighbourhoods and optional fixed boundaries.
LinearGeometry(EvoLudo) - Constructor for class LinearGeometry: Create a linear (1D lattice) geometry attached to the given engine.
LineGraph - Class in org.evoludo.graphics: LineGraph visualizes time series data as one or more line plots inside a resizable, pannable and zoomable canvas.
LineGraph(Mean, Module) - Constructor for class LineGraph: Create new line graph for view.
linestyle - Variable in class HistoGraph.Marker: The linestyle of the marker.
lineTo(double, double) - Method in class Path2D: Adds a point to the path by drawing a straight line from the current coordinates to the new specified coordinates specified in double precision.
lineTo(Point2D) - Method in class Path2D: Adds point pt to the path by drawing a stright line to the specified location.
lineWidth - Variable in class GraphStyle: The stroke width of lines on the graph.
linext - Variable in class PDE: The linear extension of the lattice.
Link() - Constructor for class IBSDPopulation.Link: Empty default constructor for a Link.
linkColor - Variable in class GraphStyle: The color of links on the graph.
linkNeighboursAt(int, int, int, int, int, boolean) - Method in class CubicGeometry: Links all neighbors in the specified range [min, max] around bOffset to aPlayer.
linkNodes() - Method in class Network3DGWT
linkNodes() - Method in class Network: Generate the links for the current configuration of the network.
linkNodes() - Method in class Network2D
links - Variable in class Network3DGWT: The links in the network.
links - Variable in class Network2D: The links in this network.
linkstyle - Variable in class PopGraph3D: The line style for the links.
linkWidth - Variable in class GraphStyle: The stroke width of links on the graph.
list2double(List) - Static method in class Plist: Utility method to convert a list of Double's to an array of double's.
list2int(List) - Static method in class Plist: Utility method to convert a list of Integer's to an array of int's.
listener - Variable in class Network: The link to the GUI elements interested in updates about the layouting progress.
listener - Variable in class ContextMenu.Registration: Listener widget for context menu requests.
listener - Variable in class ContextMenu.TouchTimer: Listening widget that triggered the scheduling for the context menu.
listener - Variable in class Tooltip.Registration: Listener widget for tooltips.
listenersInstalled - Static variable in class KeyHandler: Tracks whether the global JS listeners have been installed.
listIterator() - Method in class RingBuffer: Returns a list iterator over all elements in this buffer in chronological order.
listIterator(int) - Method in class RingBuffer: Returns a list iterator over all elements in this buffer in chronological order starting with entry at index.
load() - Method in class IBS: Milestone: Load this model and allocate resources (if applicable).
load() - Method in class Model: Milestone: Load this model and allocate resources (if applicable).
load() - Method in class ODE
load() - Method in class PDE
load() - Method in class SDE
load() - Method in class ATBT
load() - Method in class CDL
load() - Method in class CDLP
load() - Method in class CDLPQ
load() - Method in class Centipede
load() - Method in class CLabour
load() - Method in class Continuous
load() - Method in class CSD
load() - Method in class Discrete
load() - Method in class EcoPGG
load() - Method in class LV
load() - Method in class Module: Load new module and perform basic initializations.
load() - Method in class Moran
load() - Method in class NetGames
load() - Method in class Predator
load() - Method in class RSP
load() - Method in class SIR
load() - Method in class TBT
load() - Method in class AbstractView: Load the view.
load() - Method in class Histogram
load() - Method in class TrackballControls: Initialize and register mouse and touch handlers.
loadModel(ModelType) - Method in class EvoLudo: Set model type and loads the corresponding frameworks for individual based simulations or numerical integration of ODE/SDE/PDE models.
loadModel(ModelType) - Method in class LifecycleController: Set model type and loads the corresponding frameworks for individual based simulations or numerical integration of ODE/SDE/PDE models.
loadModule(String) - Method in class EvoLudo: Load new module with key newModuleKey.
loadModule(String) - Method in class LifecycleController: Load new module with key newModuleKey.
loadModules() - Method in class EvoLudo: Load all available modules.
loadViews(boolean) - Method in class EvoLudoWeb: Helper method to update the views after the command line options have been applied.
loadZipJs() - Static method in class EvoLudoWeb: Ensures ZIP JavaScript is loaded exactly once across all instances.
log - Variable in class Console: The console log.
log(String) - Static method in class NativeJS: JSNI method: log message into JS console.
log(Level, String) - Method in class Console: Log message in console.
Log() - Constructor for class Console.Log: Create an empty log widget.
log10(double[]) - Static method in class ArrayMath: Element-wise logarithm of double array a (base 10).
log10(float[]) - Static method in class ArrayMath: Element-wise logarithm of float array a (base 10).
log2lin(double) - Method in class Slider: Helper function to convert from logarithmic to linear scales.
logAccountingIssue(double, double) - Method in class IBSPopulation: Log an accounting issue.
logAccountingIssue(String, double, double, String) - Method in class IBSPopulation: Log an accounting issue.
logBase - Variable in class Slider: For logarithmic sliders this is the base of the logarithm.
logCheckResult(String, boolean) - Method in class AbstractGeometry: Log a standardized pass/fail outcome for consistency checks.
logClosingTagWarning(int, String) - Static method in class PlistParser: Logs a warning that the closing tag is missing.
logError(String) - Method in class EvoLudo: Convenience method to log errors of simulations.
logError(String) - Method in class TestEvoLudo: Log error message in red color to console or logger.
logError(String) - Method in class CLOParser: Helper method for logging errors.
logEvoHandler - Variable in class EvoLudoWeb: Handler for the log framework to report notifications etc.
logFeatures() - Method in class EvoLudoWeb: Log GWT features and GUI specifics.
logFitnessIssue(int, double, double) - Method in class IBSPopulation: Log a fitness issue.
logger - Variable in class EvoLudoWeb: Logger for keeping track of and reporting events and issues.
logger - Variable in class AbstractGraph: Logger for keeping track of and reporting events and issues.
logger - Variable in class EvoLudo: The logger for keeping track of and reporting events and issues.
logger - Variable in class TestEvoLudo: Logger for keeping track of and reporting events and issues.
logger - Variable in class AbstractGeometry: Logger for keeping track of and reporting events and issues.
logger - Variable in class IBSPopulation: Logger for keeping track of and reporting events and issues.
logger - Variable in class Model: Logger for keeping track of and reporting events and issues.
logger - Variable in class Module: Logger for keeping track of and reporting events and issues.
logger - Variable in class AbstractView: Logger for keeping track of and reporting events and issues.
logger - Variable in class CLOParser: Logger for reporting errors, warnings or other information (optional).
LOGGER - Static variable in class PlistParser: The logger for logging warnings and errors.
Logging - Section in class org.evoludo.EvoLudoWeb
logInvalidTagWarning(int, String, String) - Static method in class PlistParser: Logs a warning that the tag is invalid in the given context.
logMapIssue(int, double, double) - Method in class IBSPopulation: Log a mapping issue.
logMessage(String) - Method in class EvoLudo: Convenience method to log messages of simulations.
logMessage(String) - Method in class TestEvoLudo: Log message to console or logger.
logNodeIssue(int, String) - Method in class AbstractGeometry: Log a standardized node-centric message for consistency checks.
logOk(String) - Method in class TestEvoLudo: Log message in green color to console or logger.
logoSmall() - Method in interface Resources: Get the EvoLudo logo.
logParseFailure(CLOption) - Method in class CLOParser: Logs a parse failure for an option.
logProgress() - Static method in class MersenneTwister: Append newline to buffer.
logProgress(String) - Static method in class MersenneTwister: Append message to buffer (adding newline).
logProgress(String) - Method in class EvoLudo: Utility method to log progress of simulations.
logProgress(String) - Method in class EvoLudoGWT: GWT uses the config channel of the logger to report progress
logRange - Variable in class Slider: Helper variable to the logarithm of the slider range.
logRestoreWarning(String, String) - Method in class IBS: Log warning message for failed restoration of what in population name.
logScaleY - Variable in class GraphStyle: The flag to indicate whether to use logarithmic scaling on the y-axis.
logScoringIssue(int, double, double) - Method in class IBSPopulation: Log a scoring issue.
logScoringIssue(int, double, String) - Method in class IBSPopulation: Log a scoring issue.
logTitle(String) - Method in class TestEvoLudo: Log bold message to console or logger.
logWarning(String) - Method in class EvoLudo: Convenience method to log warnings of simulations.
logWarning(String) - Method in class TestEvoLudo: Log warning message in yellow color to console or logger.
logWarning(String) - Method in class CLOParser: Helper method for logging warnings.
logYAxesMenu - Variable in class LineGraph: The context menu item to toggle logarithmic y-axis scaling.
logYMenu - Variable in class AbstractGraph: The menu item to toggle logarithmic scaling on the y-axis.
loner - Static variable in class IBSGroup: The empty neighbourhood of a lone individual.
LONER - Static variable in class CDL: The trait (and index) value of loners.
LONG_TOUCH_TIME - Static variable in class ContextMenu: Delay in milliseconds before the touch event is considered a 'long touch' instead of a 'tap'.
longTouch - Variable in class ContextMenu: Delay before two finger touch triggers context menu, provided that no other touch event fired during delayTap milliseconds.
LOWER_MASK - Static variable in class MersenneTwister: Mask isolating the least significant r bits.
LstItr() - Constructor for class RingBuffer.LstItr: Creates a new ListIterator over all elements in this buffer starting with the oldest entry.
LstItr(int) - Constructor for class RingBuffer.LstItr: Creates a new ListIterator over all elements in this buffer starting with the entry at index.
LV - Class in org.evoludo.simulator.modules: Lotka-Volterra module for EvoLudo.
LV(EvoLudo) - Constructor for class LV: Create a new instance of the Lotka-Volterra module.
LV.ODE - Class in org.evoludo.simulator.modules: ODE model for the Lotka-Volterra module.
LV.SDE - Class in org.evoludo.simulator.modules: SDE model for the LV module.

M

m - Variable in class Line2D: The slope of the straight line.
M - Static variable in class MersenneTwister: Period parameter m (middle word).
m00 - Variable in class AffineTransform: The X coordinate scaling element of the 3x3 affine transformation matrix.
m01 - Variable in class AffineTransform: The X coordinate shearing element of the 3x3 affine transformation matrix.
m02 - Variable in class AffineTransform: The X coordinate of the translation element of the 3x3 affine transformation matrix.
m10 - Variable in class AffineTransform: The Y coordinate shearing element of the 3x3 affine transformation matrix.
m11 - Variable in class AffineTransform: The Y coordinate scaling element of the 3x3 affine transformation matrix.
m12 - Variable in class AffineTransform: The Y coordinate of the translation element of the 3x3 affine transformation matrix.
MAGENTA - Enum constant in enum class TestEvoLudo.ConsoleColors: Magenta color.
MAGENTA_BACKGROUND - Enum constant in enum class TestEvoLudo.ConsoleColors: Magenta background color.
MAGENTA_BACKGROUND_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Magenta high intensity background.
MAGENTA_BOLD - Enum constant in enum class TestEvoLudo.ConsoleColors: Magenta color.
MAGENTA_BOLD_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Magenta high intensity color.
MAGENTA_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Magenta high intensity color.
MAGENTA_UNDERLINED - Enum constant in enum class TestEvoLudo.ConsoleColors: Magenta color.
magnitude(double) - Static method in class Functions: Returns the order of magnitude of value.
main(String[]) - Static method in class MersenneTwister: Tests the code.
main(String[]) - Static method in class scanCSD: Main method to run the simulation.
main(String[]) - Static method in class simCDL: Main method to run the simulation.
main(String[]) - Static method in class simCDLP: Main method to run the simulation.
main(String[]) - Static method in class simCDLPQ: Main method to run the simulation.
main(String[]) - Static method in class simMoran: Main method to run the simulation.
main(String[]) - Static method in class simTBT: Main method to run the simulation.
main(String[]) - Static method in class simTraits: Main method to run the simulation.
main(String[]) - Static method in class TestEvoLudo: Entry point for test routines of EvoLudo.
Main behaviors and responsibilities: - Section in class org.evoludo.graphics.LineGraph
map - Variable in class ParaGraph: The map for converting data to phase plane coordinates.
map - Variable in class S3Graph: The map for converting data to simplex coordinates (cartesian).
map - Variable in class ColorMap.Gradient1D: Helper variable to make the mapping from a range of data values to indices of the gradient array more efficient: map=nBins/(max-min), where max maximum data value to be mapped.
map - Variable in class ColorMap.Gradient2D: Helper variable to make the mapping from a range of data values to indices of the gradient array more efficient: map=nBins/(max-min), where max maximum data value to be mapped.
map - Variable in class ATBT: The map for projecting the four dimensional dynamical system onto a 2D phase plane.
map - Variable in class EcoPGG: The map for translating the model data into 2D phase plane representation.
map - Variable in class Map2Fitness: Map type.
map - Variable in class Phase2D: The map that transforms the current state of the model to a point on the 2D phase plane.
map(double) - Method in class Map2Fitness: Map score to fitness, based on currently selected type map.
Map(String, String) - Constructor for enum class Map2Fitness.Map: Instantiate new type of map.
map2fit - Variable in class IBSPopulation: The map converting scores to fitness and vice versa.
map2fitness - Variable in class Module: Map to convert score/payoff to fitness
Map2Fitness - Class in org.evoludo.simulator.modules: Map scores/payoffs to fitness and vice versa.
Map2Fitness(Module, Map2Fitness.Map) - Constructor for class Map2Fitness: Instantiate new map of type map for module.
Map2Fitness.Map - Enum Class in org.evoludo.simulator.modules: Enum representing the different types of payoff/score to fitness maps
markDerivedFrom(AbstractGeometry) - Method in class AbstractGeometry: Mark this geometry as derived from source.
Marker(double, String, String) - Constructor for class HistoGraph.Marker: Create a new marker for the histogram at x with color color and description descr.
Marker(double, String, String, int[]) - Constructor for class HistoGraph.Marker: Create a new marker for the histogram at x with color color, description descr, and linestyle linestyle.
markerColors - Variable in class AbstractGraph: The array of colors used for markers.
markerList - Variable in class Markers: The list of markers on graphs.
markers - Variable in class AbstractGraph: Markers for decorating the graph.
markers - Variable in class Model: Markers for annotating graphical representations of the state of the model.
Markers - Class in org.evoludo.simulator.models: The class to manage customised markers for graphs.
Markers(Model) - Constructor for class Markers: Instantiate new population update for use in IBS models.
Markers and interactivity - Section in class org.evoludo.graphics.HistoGraph
markerSize - Variable in class GraphStyle: The radius of marker points.
match(String) - Method in class CLOption: Returns the key that best matches name.
match(String, int) - Method in class CLOption: Returns the key that best matches name with at least min characters matching.
MATRIX_A - Static variable in class MersenneTwister: Constant vector a used in the twist transformation.
MATRIX_DELIMITER - Static variable in class CLOParser: The delimiter for separating rows when passing a matrix as an option.
MATRIX_DELIMITER - Static variable in class Formatter: Delimiter between matrix rows.
max - Variable in class Slider: Maximum value of slider.
max(boolean[]) - Static method in class ArrayMath: Find maximum element in boolean array/vector a.
max(double[]) - Static method in class ArrayMath: Find maximum element in double array/vector a.
max(double[][]) - Static method in class ArrayMath: Find maximum element in double array/matrix a.
max(double[], boolean[]) - Static method in class ArrayMath: Find maximum element in double array a among active elements.
max(double[], double[]) - Static method in class ArrayMath: Find maximum element in two double arrays a and b.
max(double[], int, int) - Static method in class SDE: Find the maximum value in a range of an array.
max(float[]) - Static method in class ArrayMath: Find maximum element in float array/vector a.
max(float[][]) - Static method in class ArrayMath: Find maximum element in float array/matrix a.
max(float[], float[]) - Static method in class ArrayMath: Find maximum element in two float arrays a and b.
max(int[]) - Static method in class ArrayMath: Find maximum element in int array/vector a.
max(int[][]) - Static method in class ArrayMath: Find maximum element in int array/matrix a.
max(long[]) - Static method in class ArrayMath: Find maximum element in long array/vector a.
max(long[][]) - Static method in class ArrayMath: Find maximum element in long array/matrix a.
max(Comparator) - Method in class RingBuffer: Return the maximum entry in this buffer according to the comparator cmp.
MAX_ANIMATE_LAYOUT_LINKS_DEFAULT - Static variable in class GenericPopGraph: Maximum number of edges in network for animated layout.
MAX_ANIMATE_LAYOUT_VERTICES_DEFAULT - Static variable in class GenericPopGraph: Maximum number of nodes in network for animated layout.
MAX_BINS - Static variable in class HistoGraph: The maximum number of bins for the histogram.
MAX_BINS - Static variable in class Distribution: The maximum number of bins for the trait histograms.
MAX_DIGITS - Static variable in class Formatter: The maximum number of decimal digits to format.
MAX_EYE_DIST - Static variable in class TrackballControls: Maximum eye distance.
MAX_EYE_DIST_SQ - Static variable in class TrackballControls: Square of maximum eye distance.
MAX_LINEAR_SIZE - Static variable in class PopGraph2D: The maximum size of a linear graph.
MAX_LINK_COUNT - Static variable in class Network: The maximum number of links drawn in a graphical representation of the network.
MAX_LINKS_PER_STEP - Static variable in class Network2DGWT: The minimum number of links to process in one step.
MAX_LINKS_PER_STEP - Static variable in class Network3DGWT: The minimum number of links to process in one step.
MAX_SEGEMENTS - Static variable in class AbstractGraph: The maximum number of line segments to draw before returning control to the event loop.
MAX_TRIALS - Static variable in class AbstractNetwork: Number of attempts before giving up on constructing the desired graph.
maxDegree(int) - Static method in class Histogram: Calculate the maximum degree for displaying the degree distribution.
maxDensity - Variable in class PDE: The array containing the maximum densities of each trait.
maxEffScoreIdx - Variable in class IBSPopulation: Optimization: The index of the individual that currently holds the maximum score.
maxFitness - Variable in class IBSPopulation: The absolute maximum fitness in the population.
maxFitness - Variable in class PDE: The array containing the maximum fitness of each trait.
maxIn - Variable in class GeometryFeatures: The maximum number of incoming links.
maxIndex(double[]) - Static method in class ArrayMath: Find index of maximum element in double array.
maxIndex(float[]) - Static method in class ArrayMath: Find index of maximum element in float array.
maxIndex(int[]) - Static method in class ArrayMath: Find index of maximum element in integer array.
maxIndex(long[]) - Static method in class ArrayMath: Find index of maximum element in long array.
maxLevel - Variable in class IBSGroup.HierarchyUnit: Highest hierarchy level supported by the geometry.
maxOut - Variable in class GeometryFeatures: The maximum number of outgoing links.
maxRate - Variable in class IBSDPopulation: The maximum rate at which ecological events can occur.
maxScore - Variable in class IBSPopulation: The absolute maximum score in the population.
maxTot - Variable in class GeometryFeatures: The maximum sum of incoming and outgoing links.
maxX - Variable in class TraitMap: The maximum value of the x-axis.
maxY - Variable in class TraitMap: The maximum value of the y-axis.
maybeMutateAt(int, boolean) - Method in class IBSDPopulation
maybeMutateAt(int, boolean) - Method in class IBSMCPopulation
maybeMutateAt(int, boolean) - Method in class IBSPopulation: Consider mutating the trait of the focal individual with index focal.
maybeMutateMoran(int, int) - Method in class IBSDPopulation
maybeMutateMoran(int, int) - Method in class IBSMCPopulation
maybeMutateMoran(int, int) - Method in class IBSPopulation: Consider mutating the trait of the parent individual with index source.
ME_EXP - Enum constant in enum class Continuous.Costs: Exponential cost function (independent of opponent): \(C(x,y)=c_0 (1-\exp(-c_1\,x))\).
ME_LINEAR - Enum constant in enum class Continuous.Benefits: Linear benefit function (independent of opponent): \(B(x,y)=b_0\,x\).
ME_LINEAR - Enum constant in enum class Continuous.Costs: Linear cost function (independent of opponent): \(C(x,y)=c_0\,x\).
ME_LOG - Enum constant in enum class Continuous.Costs: Logarithmic cost function (independent of opponent): \(C(x,y)=c_0 \ln(c_1\,x+1)\).
ME_QUAD - Enum constant in enum class Continuous.Benefits: Quadratic benefit function (independent of opponent): \(B(x,y)=b_0\,x+b_1\,x^2\).
ME_QUAD - Enum constant in enum class Continuous.Costs: Quadratic cost function (independent of opponent): \(C(x,y)=c_0\,x+c_1\,x^2\).
ME_QUBIC - Enum constant in enum class Continuous.Benefits: Cubic benefit function (independent of opponent): \(B(x,y)=b_0\,x+b_1\,x^2+b_2\,x^3\).
ME_SQRT - Enum constant in enum class Continuous.Costs: Square root cost function (independent of opponent): \(C(x,y)=c_0 \sqrt{x}\).
mean - Variable in class RNGDistribution.Binomial: Mean number of successes n p.
mean - Variable in class RNGDistribution.Exponential: The mean of exponential distribution.
mean - Variable in class RNGDistribution.Geometric: Mean of geometric distribution.
mean - Variable in class RNGDistribution.Normal: The mean of the Normal distribution.
mean - Variable in class simCDL: Temporary running mean for fixation probabilities.
mean - Variable in class simCDLP: Temporary running mean for fixation probabilities.
mean - Variable in class simCDLPQ: Temporary running mean for fixation probabilities.
mean - Variable in class simTBT: Temporary variables for fixation probabilities and absorption times.
mean(double[]) - Static method in class Distributions: Mean of data points x[i] stored in double vector x.
mean(float[]) - Static method in class Distributions: Mean of data points x[i] stored in float vector x.
mean(int[]) - Static method in class Distributions: Mean of data points x[i] stored in integer vector x.
Mean - Class in org.evoludo.simulator.views: A view that displays time-series plots of mean trait values or mean fitness for the current EvoLudo model using one or more LineGraph panels.
Mean(EvoLudoGWT, Data) - Constructor for class Mean: Construct a new view to display the time series data of the current EvoLudo model.
meanDensity - Variable in class PDE: The array containing the mean densities of each trait.
meanFitness - Variable in class PDE: The array containing the mean fitness of each trait.
meanmean - Variable in class simCDL: Mean of recorded means (used for statistics).
meanmean - Variable in class simTBT: Temporary variables for fixation probabilities and absorption times.
meanPerformance - Variable in class NetGames.IBSPop: The mean fitness of individuals.
meantrait - Variable in class IBSMCPopulation: The array for calculating and storing the mean traits and their standard deviation.
meanvar - Variable in class simCDL: Variance of recorded means.
meanvar - Variable in class simTBT: Temporary variables for fixation probabilities and absorption times.
measureYTickLabelWidth(String[], boolean) - Method in class AbstractGraph: Measure the width of a y-axis tick label including exponent and percent.
mem - Variable in class IBSGroup: Storage for selected interaction or reference groups.
merge(double[], double[]) - Static method in class ArrayMath: Append double array tail to double array head.
merge(T[], T[]) - Static method in class ArrayMath: Append array tail of type T[] to array head.
MersenneTwister - Class in org.evoludo.math: MersenneTwister and MersenneTwisterFast
MersenneTwister() - Constructor for class MersenneTwister: Constructor using the default seed.
MersenneTwister(int[]) - Constructor for class MersenneTwister: Constructor using an array of integers as seed.
MersenneTwister(long) - Constructor for class MersenneTwister: Constructor using a given seed.
MersenneTwister.Chronometer - Interface in org.evoludo.math: The minimal Chronometer interface is only used to hide differences for measuring execution time in JRE and GWT.
MersenneTwister.StopWatch - Class in org.evoludo.math: Minimal implementation of Chronometer.
MersenneTwister and MersenneTwisterFast - Section in class org.evoludo.math.MersenneTwister
message - Variable in class HistoGraph: The message to display if no histogram is available.
Messages - Section in class org.evoludo.graphics.AbstractGraph
MEYOU_LINEAR - Enum constant in enum class Continuous.Benefits: Linear benefit function (with interaction term): \(B(x,y)=b_0\,x=b_1\,y+\b_2\,x\,y\).
MEYOU_LINEAR - Enum constant in enum class Continuous.Costs: Linear cost function (cross terms of focal, \(x\), and opponent, \(y\), traits): \(C(x,y)=c_0\,x+c_1\,y+c_2\,x\,y\).
migrateMoran(int, int) - Method in class IBSPopulation: Perform a single Moran update for the reproducing node with index source and the node that gets replaced with index dest.
migrationType - Variable in class IBSPopulation: The type of migration.
MigrationType(String, String) - Constructor for enum class IBS.MigrationType: Instantiate new type of migration.
min - Variable in class RNGDistribution.Uniform: Lower bound of uniform interval (inclusive).
min - Variable in class ColorMap.Gradient1D: Minimum data value.
min - Variable in class ColorMap.Gradient2D: Minimum data value.
min - Variable in class Slider: Minimum value of slider.
min(boolean[]) - Static method in class ArrayMath: Find minimum element in boolean array/vector a.
min(double[]) - Static method in class ArrayMath: Find minimum element in double array/vector a.
min(double[][]) - Static method in class ArrayMath: Find minimum element in double array/matrix a.
min(double[], boolean[]) - Static method in class ArrayMath: Find minimum element in double array a among active elements.
min(double[], double[]) - Static method in class ArrayMath: Find minimum element in two double arrays a and b.
min(double[], int, int) - Static method in class SDE: Find the minimum value in a range of an array.
min(float[]) - Static method in class ArrayMath: Find minimum element in float array/vector a.
min(float[][]) - Static method in class ArrayMath: Find minimum element in float array/matrix a.
min(float[], float[]) - Static method in class ArrayMath: Find minimum element in two float arrays a and b.
min(int[]) - Static method in class ArrayMath: Find minimum element in integer array/vector a.
min(int[][]) - Static method in class ArrayMath: Find minimum element in integer array/matrix a.
min(long[]) - Static method in class ArrayMath: Find minimum element in long array/vector a.
min(long[][]) - Static method in class ArrayMath: Find minimum element in long array/matrix a.
min(Comparator) - Method in class RingBuffer: Return the minimum entry in this buffer according to the comparator cmp.
MIN_BIN_WIDTH - Static variable in class HistoGraph: The minimum width of a bin.
MIN_BUFFER_SIZE - Static variable in class AbstractGraph: The minimum buffer size.
MIN_DELAY_ANIMATE_MSEC - Static variable in class Network2DGWT: Minimum delay in milliseconds between subsequent updates of the layout in the GUI.
MIN_DELAY_ANIMATE_MSEC - Static variable in class Network3DGWT: Minimum delay in milliseconds between subsequent updates of the layout in the GUI.
MIN_DH - Static variable in class PopGraph2D: The minimum height of a node in pixels.
MIN_DR - Static variable in class PopGraph2D: The minimum diameter of a node in pixels.
MIN_DW - Static variable in class PopGraph2D: The minimum width of a node in pixels.
MIN_EYE_DIST - Static variable in class TrackballControls: Minimum eye distance.
MIN_EYE_DIST_SQ - Static variable in class TrackballControls: Square of minimum eye distance.
MIN_MSEC_BETWEEN_UPDATES - Static variable in class AbstractView: In order to conserve computational resources the minimum time between subsequent GUI updates has to be at least MIN_MSEC_BETWEEN_UPDATES milliseconds.
MIN_PIXELS - Static variable in class ParaGraph: The minimum distance between two subsequent points in pixels.
MIN_PIXELS - Static variable in class S3Graph: The minimum distance between two subsequent points in pixels.
MIN_STEPS - Static variable in class LineGraph: The minimum number of steps along the x-axis.
MIN_ZOOM_FACTOR - Static variable in class ParaGraph: Minimum zoom level to avoid unbounded ranges.
minDensity - Variable in class PDE: The array containing the minimum densities of each trait.
minFitness - Variable in class IBSPopulation: The absolute minimum fitness in the population.
minFitness - Variable in class PDE: The array containing the minimum fitness of each trait.
minIn - Variable in class GeometryFeatures: The minimum number of incoming links.
minIndex(double[]) - Static method in class ArrayMath: Find index of minimum element in double array.
minIndex(float[]) - Static method in class ArrayMath: Find index of minimum element in float array.
minIndex(int[]) - Static method in class ArrayMath: Find index of minimum element in integer array.
minIndex(long[]) - Static method in class ArrayMath: Find index of minimum element in long array.
MINMAX_ITER - Static variable in class Continuous: The number of iterations for the hill climbing process.
MINMAX_STEPS - Static variable in class Continuous: The linear grid size to sample payoffs in the (possibly multi-dimensional) trait space.
minmaxmean(double[], double[], double[], double[]) - Static method in class PDE: Utility method to update the trait minimum, maximum and mean based on the provided data array.
minOut - Variable in class GeometryFeatures: The minimum number of outgoing links.
minPadding - Variable in class GraphStyle: The minimum padding (in pixels) between boundaries of the HTML element and the graph.
minScore - Variable in class IBSPopulation: The absolute minimum score in the population.
mintime - Variable in class simTraits: The minimal measurement time in nanoseconds.
minTot - Variable in class GeometryFeatures: The minimum sum of incoming and outgoing links.
minX - Variable in class TraitMap: The minimum value of the x-axis.
minY - Variable in class TraitMap: The minimum value of the y-axis.
mixedScores(int[], double[]) - Method in interface Model.HasIBS.DGroups
mixedScores(int[], double[]) - Method in interface Model.HasIBS.DPairs: Calculate the average payoff/score in a finite population with the number of each trait provided in count for pairwise interactions.
mixedScores(int[], double[]) - Method in class ATBT
mixedScores(int[], double[]) - Method in class Centipede
mixedScores(int[], double[]) - Method in class DemesTBT
mixedScores(int[], double[]) - Method in class RSP
mixedScores(int[], double[]) - Method in class TBT
mixedScores(int[], int, double[]) - Method in interface Model.HasIBS.DGroups: Calculate the average payoff/score in a finite population with the number of each trait provided in count for interaction groups of size n.
mixedScores(int[], int, double[]) - Method in class CDL: Calculate the average payoff/score in a finite population with the number of each trait provided in count for interaction groups of size n.
mixedScores(int[], int, double[]) - Method in class CDLP: Calculate the average payoff/score in a finite population with the number of each trait provided in count for interaction groups of size n.
mixedScores(int[], int, double[]) - Method in class CDLPQ
mixedScores(int[], int, double[]) - Method in class EcoPGG: Calculate the average payoff/score in a finite population with the number of each trait provided in count for interaction groups of size n.
mode - Variable in enum class ChangeListener.PendingAction: The pending execution mode of the model.
mode - Variable in class Model: Indicates current mode of IBS model.
Mode - Enum Class in org.evoludo.simulator.models: Modes of the model.
Mode(String) - Constructor for enum class Mode: Construct an enum for the type of mode.
model - Variable in class EvoLudoWeb.GUIState: The active model.
model - Variable in class Markers: The model that is using these markers.
model - Variable in class Module: Reference to current model.
model - Variable in class AbstractView: The reference to the model that supplies the data for this graph.
Model - Class in org.evoludo.simulator.models: Interface for EvoLudo models to interact with Modules, which define interactions (or games), and the engine EvoLudo, which manages the (un)loading and execution of different models based on what model types the module supports.
Model - Static variable in class CLOCategory: The category for model specific options.
Model(EvoLudo) - Constructor for class Model: Creates a model.
Model.HasDE - Interface in org.evoludo.simulator.models: Methods that every Module must implement, which advertises numerical solutions based on differential equations.
Model.HasDE.DGroups - Interface in org.evoludo.simulator.models: Interface for differential equation models with interactions in groups of arbitrary size.
Model.HasDE.DPairs - Interface in org.evoludo.simulator.models: Interface for differential equation models with pairwise interactions.
Model.HasDE.DualDynamics - Interface in org.evoludo.simulator.models: Interface for modules that support differential equation models with both frequency and density based dynamics.
Model.HasDE.EM - Interface in org.evoludo.simulator.models: Interface for ordinary differential equation models using the Euler-Maruyama method.
Model.HasDE.ODE - Interface in org.evoludo.simulator.models: Interface for ordinary differential equation models; defaults to RK5.
Model.HasDE.PDE - Interface in org.evoludo.simulator.models: Interface for partial differential equation models; defaults to PDERD.
Model.HasDE.PDEADV - Interface in org.evoludo.simulator.models: Interface for reaction-diffusion-advection partial differential equation models.
Model.HasDE.PDERD - Interface in org.evoludo.simulator.models: Interface for reaction-diffusion partial differential equation models.
Model.HasDE.RK5 - Interface in org.evoludo.simulator.models: Interface for ordinary differential equation models using the fifth order Runge-Kutta method.
Model.HasDE.SDE - Interface in org.evoludo.simulator.models: Interface for stochastic differential equation models.
Model.HasIBS - Interface in org.evoludo.simulator.models: Modules that offer individual based simulation models must implement this interface.
Model.HasIBS.CGroups - Interface in org.evoludo.simulator.models: Modules that offer individual based simulation models with continuous traits and interactions in groups must implement this interface.
Model.HasIBS.CPairs - Interface in org.evoludo.simulator.models: Modules that offer individual based simulation models with continuous traits and pairwise interactions must implement this interface.
Model.HasIBS.DGroups - Interface in org.evoludo.simulator.models: Modules that offer individual based simulation models with discrete traits and interactions in groups must implement this interface.
Model.HasIBS.DPairs - Interface in org.evoludo.simulator.models: Modules that offer individual based simulation models with discrete traits and pairwise interactions must implement this interface.
Model.HasIBS.MCGroups - Interface in org.evoludo.simulator.models: Modules that offer individual based simulation models with continuous traits and interactions in groups must implement this interface.
Model.HasIBS.MCPairs - Interface in org.evoludo.simulator.models: Modules that offer individual based simulation models with multiple continuous traits and pairwise interactions must implement this interface.
modelChanged(ChangeListener.PendingAction) - Method in class simCDL
modelChanged(ChangeListener.PendingAction) - Method in class simCDLP
modelChanged(ChangeListener.PendingAction) - Method in class simCDLPQ
modelChanged(ChangeListener.PendingAction) - Method in class simTBT
modelChanged(ChangeListener.PendingAction) - Method in interface ChangeListener: Called whenever the state of the EvoLudo model changed.
modelChanged(ChangeListener.PendingAction) - Method in class DemesTBT.IBSPop
modelChanged(ChangeListener.PendingAction) - Method in class WebListener
modelChanged(ChangeListener.PendingAction) - Method in class AbstractView
modelChanged(ChangeListener.PendingAction) - Method in class GenericPop
modelCheck() - Method in class EvoLudo: Check consistency of parameters in all populations.
modelDidInit() - Method in interface RunListener: Called after the EvoLudo model got re-initialized.
modelDidInit() - Method in class WebListener
modelDidInit() - Method in class AbstractView
modelDidInit() - Method in class Distribution
modelDidInit() - Method in class GenericPop
modelDidInit() - Method in class Histogram
modelDidInit() - Method in class Mean
modelDidInit() - Method in class Phase2D
modelDidInit() - Method in class Pop3D
modelDidInit() - Method in class S3
modelDidReset() - Method in interface RunListener: Called after the EvoLudo model was reset.
modelDidReset() - Method in class WebListener
modelDidReset() - Method in class AbstractView
modelInit() - Method in class EvoLudo: Initialize all populations and notify all listeners.
modelInit() - Method in class RunController: Initialize all populations and notify listeners.
modelInit(boolean) - Method in class EvoLudo: Initialize all populations and notify all listeners if requested.
modelInit(boolean) - Method in class RunController: Initialize all populations and optionally notify listeners.
modelLoaded() - Method in interface LifecycleListener: Called when EvoLudo model finished loading.
modelLoaded() - Method in class AbstractView
modelNext() - Method in class EvoLudo: Advance model by one step (reportFreq updates) and notify all listeners.
modelNext() - Method in class RunController: Advance model by one step and notify listeners when done.
modelNextDone(boolean) - Method in class EvoLudo: Called after the calculations of the next state of the model have finished.
modelNextDone(boolean) - Method in class RunController: Called after model next step finished to handle continuation or stop.
modelRelax() - Method in class EvoLudo: Relax model by timeRelax steps and notify all listeners when done.
modelRelax() - Method in class RunController: Relax the model and notify listeners.
modelRelax(boolean) - Method in class EvoLudo: Relax model by timeRelax steps and notify all listeners if requested.
modelRelax(boolean) - Method in class RunController: Relax the model and optionally notify listeners.
modelRelaxed() - Method in interface RunListener: Called after the EvoLudo model has relaxed.
modelReset() - Method in class EvoLudo: Reset all populations and notify all listeners.
modelReset() - Method in class RunController: Reset all populations and notify listeners.
modelReset(boolean) - Method in class EvoLudo: Reset all populations and notify all listeners if requested.
modelReset(boolean) - Method in class RunController: Reset all populations and optionally notify listeners.
modelRunning() - Method in interface RunListener: Called when the EvoLudo model starts running.
modelRunning() - Method in class WebListener
modelSample(boolean) - Method in interface SampleListener: Called whenever the EvoLudo model finished generating a statistics sample.
modelSample(boolean) - Method in class WebListener
modelSample(boolean) - Method in class Histogram
modelSettings() - Method in interface RunListener: Called when the settings of the EvoLudo model changed but no reset was necessary.
modelSettings() - Method in class Moran
modelSettings() - Method in class WebListener
modelSettings() - Method in class Histogram
modelSettings() - Method in class Mean
modelSettings() - Method in class Pop2D
modelSettings() - Method in class Pop3D
modelStopped() - Method in class simCDL
modelStopped() - Method in class simCDLP
modelStopped() - Method in class simCDLPQ
modelStopped() - Method in class simTBT
modelStopped() - Method in class TestEvoLudo
modelStopped() - Method in interface RunListener: Called after a running EvoLudo model stopped because the model converged (or reached an absorbing state).
modelStopped() - Method in class DemesTBT.IBSPop
modelStopped() - Method in class WebListener
modelStopped() - Method in class AbstractView
ModelType - Enum Class in org.evoludo.simulator.models: Model types that modules may support.
ModelType(String, String) - Constructor for enum class ModelType: Construct an enum for model type.
modelUnloaded() - Method in interface LifecycleListener: Called when EvoLudo model is unloading.
modelUnloaded() - Method in class WebListener
modelUnloaded() - Method in class AbstractView
module - Variable in class EvoLudoWeb.GUIState: The active module.
module - Variable in class AbstractGraph: The module backing the graph.
module - Variable in class IBSPopulation: The module associated with this population.
module - Variable in class PDE: Convenience variable: module associated with this model (useful as long as PDE models are restricted to single species).
module - Variable in class SDE: Convenience variable: module associated with this model (useful as long as SDE models are restricted to single species).
module - Variable in class ATBT.ODE: Convenience variable: module associated with this model (useful for single species).
module - Variable in class Map2Fitness: The module that is using this fitness mapping.
module - Variable in class Mutation: The module using this mutation.
module - Variable in class PlayerUpdate: The module that is using this player update.
module - Variable in class SpeciesUpdate: The module that is using this species update.
Module<T> - Class in org.evoludo.simulator.modules: Parent class of all EvoLudo modules.
Module - Static variable in class CLOCategory: The category for module specific options.
Module(EvoLudo, T) - Constructor for class Module: Instantiate a new Module with engine and partner.
moduleLoaded() - Method in interface LifecycleListener: Called when EvoLudo module finished loading.
moduleLoaded() - Method in class WebListener
moduleRestored() - Method in interface LifecycleListener: Called when the state of the EvoLudo module has been restored.
moduleRestored() - Method in class WebListener
moduleRestored() - Method in class AbstractView
modules - Variable in class EvoLudo: The lookup table for all available modules.
moduleUnloaded() - Method in interface LifecycleListener: Called when EvoLudo module is unloading.
moduleUnloaded() - Method in class WebListener
moduleUnloaded() - Method in class AbstractView
moment(double[], int) - Static method in class Distributions: m-th moment of data points x[i] stored in double vector x.
MONO - Enum constant in enum class IBSC.Init.Type: Monomorphic population with trait(s) xi.
MONO - Enum constant in enum class IBSD.Init.Type: Monomorphic initialization of the population with the specified trait.
monoStop - Variable in class ODE: Set to true to requests that the numerical integration stops once the population reaches a monomorphic state.
monoStop - Variable in class Discrete: The flag to indicate whether models should stop once a monomorphic state has been reached.
MooreGeometry - Class in org.evoludo.simulator.geometries: Square lattice with Moore neighbourhood (first and second nearest neighbours).
MooreGeometry(EvoLudo) - Constructor for class MooreGeometry: Create a Moore square lattice geometry tied to the given engine.
Moran - Class in org.evoludo.simulator.modules: The module for investigating the evolutionary dynamics in the classical Moran process with two types of individuals that have constant fitness values.
Moran(EvoLudo) - Constructor for class Moran: Create a new instance of the module for the Moran process.
MORAN - Enum constant in enum class IBSD.OptimizationType: Optimize Moran processes by restring events exclusively to links along which a change in the composition of the population may occur.
MORAN_BIRTHDEATH - Enum constant in enum class PopulationUpdate.Type: Moran process (birth-death, asynchronous).
MORAN_DEATHBIRTH - Enum constant in enum class PopulationUpdate.Type: Moran process (death-birth, asynchronous).
MORAN_IMITATE - Enum constant in enum class PopulationUpdate.Type: Moran process (imitate, asynchronous).
mouseDownHandler - Variable in class AbstractGraph: The handler for MouseDownEvents.
mouseDownHandler - Variable in class TrackballControls: Reference to mouse down event handler for interacting with 3D view.
mouseHitNode(int) - Method in class IBSPopulation: Called from GUI if node/individual with index idx received a mouse click or tap.
mouseHitNode(int, boolean) - Method in class IBSDPopulation
mouseHitNode(int, boolean) - Method in class IBSMCPopulation
mouseHitNode(int, boolean) - Method in class IBSPopulation: Called from GUI if node/individual with index idx received a mouse click or tap and indicates whether the alt-key had been pressed.
mouseHitNode(int, int) - Method in class AbstractView: Notifies the controller that the mouse/tap has hit node with index node on the graph with the tag id.
mouseHitNode(int, int, boolean) - Method in class IBS: Used by GUI to interact with Model.
mouseHitNode(int, int, boolean) - Method in class AbstractView: Notifies the controller that the mouse/tap has hit node with index node on the graph with the tag id.
mouseHitNode(int, int, boolean) - Method in class GenericPop
mouseMoveHandler - Variable in class AbstractGraph: The handler for MouseMoveEvents.
mouseMoveHandler - Variable in class Tooltip.Registration: Reference to mouse move event handler for handling tooltips registered with the listener widget.
mouseMoveHandler - Variable in class TrackballControls: Reference to mouse move event handler for interacting with 3D view.
mouseOnBall - Variable in class TrackballControls: The mouse coordinates on the virtual trackball.
mouseOutHandler - Variable in class AbstractGraph: The handler for MouseOutEvents.
mouseOutHandler - Variable in class ContextMenu: The handler of mouse out events.
mouseOutHandler - Variable in class ContextMenuItem: The handler of mouse out events to close submenu.
mouseOutHandler - Variable in class Tooltip.Registration: Reference to mouse over event handler for handling tooltips registered with the listener widget.
mouseOverHandler - Variable in class ContextMenu: The handler of mouse over events.
mouseOverHandler - Variable in class ContextMenuItem: The handler of mouse over events to open submenu.
mouseOverHandler - Variable in class Tooltip.Registration: Reference to mouse over event handler for handling tooltips registered with the listener widget.
mouseOverLab - Variable in class EvoLudoTrigger: Flag to keep track of mouse position.
mouseSetHit(int, int) - Method in class IBSDPopulation: Process event from GUI: individual with index hit was hit by mouse (or tap) in order to set its trait to trait.
mouseUpHandler - Variable in class AbstractGraph: The handler for MouseUpEvents.
mouseUpHandler - Variable in class TrackballControls: Reference to mouse up event handler for interacting with 3D view.
mouseWheelHandler - Variable in class AbstractGraph: The handler for MouseWheelEvents.
mouseWheelHandler - Variable in class Tooltip.Registration: Reference to mouse wheel event handler for handling tooltips registered with the listener widget.
mouseWheelHandler - Variable in class TrackballControls: Reference to mouse wheel event handler for interacting with 3D view.
mouseX - Variable in class AbstractGraph: The x-coordinate of the previous mouse or tap event.
mouseY - Variable in class AbstractGraph: The y-coordinate of the previous mouse or tap event.
moveTo(double, double) - Method in class Path2D: Adds a point to the path by moving to the specified coordinates specified in double precision.
moveTo(Point2D) - Method in class Path2D: Adds point pt to the path by moving to the specified location.
msecToString(long) - Method in class simMoran: Helper method to convert milliseconds to a more readable string representation in the format 'HH:mm:ss.ss'.
MSG_IGNORE - Static variable in class PlistParser: Helper string for formatting log messages that invalid or missing closing tags are ignored.
MSG_LINE - Static variable in class PlistParser: Helper string for formatting log messages a particular line of the plist file.
msgLabel - Variable in class PopGraph3D: The label for displaying messages.
mt - Variable in class MersenneTwister: The array for the state vector
mti - Variable in class MersenneTwister: The current index for the state vector.
multiply(double[][], double[], double[]) - Static method in class ArrayMath: Non-destructive double matrix multiplication.
multiply(double[], double) - Static method in class ArrayMath: Scalar multiplication of double array dst by scalar.
multiply(double[], double[]) - Static method in class ArrayMath: Element-wise multiplication of double array a and dst.
multiply(double[], double[], double[]) - Static method in class ArrayMath: Non-destructive, element-wise multiplication of double arrays a and b.
multiply(double[], double, double[]) - Static method in class ArrayMath: Scalar multiplication of double array a by scalar with result in dst.
multiply(float[][], float[], float[]) - Static method in class ArrayMath: Non-destructive float matrix multiplication.
multiply(float[], float) - Static method in class ArrayMath: Scalar multiplication of float array dst by scalar.
multiply(float[], float[]) - Static method in class ArrayMath: Element-wise multiplication of float arrays a and dst.
multiply(float[], float[], float[]) - Static method in class ArrayMath: Non-destructive, element-wise multiplication of float arrays a and b.
multiply(float[], float, float[]) - Static method in class ArrayMath: Scalar multiplication of float array a by scalar with result in dst.
multiply(int[][], int[], int[]) - Static method in class ArrayMath: Non-destructive integer matrix multiplication.
multiply(int[], int) - Static method in class ArrayMath: Scalar multiplication of integer array dst by scalar.
multiply(int[], int[]) - Static method in class ArrayMath: Element-wise multiplication of integer arrays a and dst.
multiply(int[], int[], int[]) - Static method in class ArrayMath: Non-destructive, element-wise multiplication of integer array a and b.
multiply(int[], int, int[]) - Static method in class ArrayMath: Scalar multiplication of integer array a by scalar with result in dst.
multiply(long[][], long[], long[]) - Static method in class ArrayMath: Non-destructive long matrix multiplication.
multiply(long[], long) - Static method in class ArrayMath: Scalar multiplication of long array dst by scalar.
multiply(long[], long[]) - Static method in class ArrayMath: Element-wise multiplication of long arrays a and dst.
multiply(long[], long[], long[]) - Static method in class ArrayMath: Non-destructive, element-wise multiplication of long arrays a and b.
multiply(long[], long, long[]) - Static method in class ArrayMath: Scalar multiplication of long array a by scalar with result in dst.
MUTANT - Enum constant in enum class IBSC.Init.Type: Monomorphic resident population with trait ri and single mutant with trait mi.
MUTANT - Enum constant in enum class IBSD.Init.Type: Single mutant with trait m in otherwise homogeneous population with trait r.
MUTANT - Enum constant in enum class ODEInitialize.InitType: Single mutant in homogeneous resident.
MUTANT - Static variable in class Moran: The trait (and index) value of mutants.
mutantNode - Variable in class FixationData: The index of the node (location) where the initial mutant arose.
mutantTrait - Variable in class FixationData: The mutant trait.
mutate() - Method in class IBSPopulation: Perform a mutation event.
mutate(double) - Method in class Mutation.Continuous
mutate(double) - Method in class Mutation: Mutate trait trait in IBS models according to the type of mutation.
mutate(double[], double[], int, int) - Method in class Mutation.Discrete: Mutate traits in DE models according to the type of mutation.
mutate(int) - Method in class Centipede.CentiMutations
mutate(int) - Method in class Mutation.Discrete
mutate(int) - Method in class Mutation: Mutate trait trait in IBS models according to the type of mutation.
mutateAt(int) - Method in class IBSDPopulation
mutateAt(int) - Method in class IBSMCPopulation
mutateAt(int) - Method in class IBSPopulation: Mutate the trait of the focal individual with index focal.
mutateAt(int, boolean) - Method in class IBSMCPopulation: Mutate all traits of the focal individual with index focal if mutate == true.
mutation - Variable in class IBSPopulation: The mutation parameters.
mutation - Variable in class ODE: Array containing the mutation rates/probabilities for each species.
mutation - Variable in class Continuous: The mutation operator for continuous traits.
mutation - Variable in class Discrete: The mutation operator for discrete traits.
Mutation - Class in org.evoludo.simulator.modules: The abstract superclass to implement mutations in IBS models with discrete or continuous traits.
Mutation(Module) - Constructor for class Mutation: Instantiate new mutation.
MUTATION - Enum constant in enum class IBS.Event: Mutation event.
Mutation.Continuous - Class in org.evoludo.simulator.modules: The class to implement mutations in continuous IBS models.
Mutation.Continuous.Type - Enum Class in org.evoludo.simulator.modules: Mutation types.
Mutation.Discrete - Class in org.evoludo.simulator.modules: The class to implement mutations in discrete IBS models.
Mutation.Discrete.Type - Enum Class in org.evoludo.simulator.modules: Mutation types.
MyContext2d() - Constructor for class AbstractGraph.MyContext2d: Create a new custom context.
myFixFormatters - Static variable in class Formatter: Array of formatters with fixed number of digits ranging from 0 to 12.
myFormatters - Static variable in class Formatter: Array of formatters with 0 to up to 12 non-zero decimal digits.
myPercentFormatters - Static variable in class Formatter: Array of percentage formatters with fixed number of digits ranging from 0 to 12.
mySciFormatters - Static variable in class Formatter: Array of scientific formatters with fixed number of digits ranging from 0 to up to 12 non-zero decimal digits.
myTraits - Variable in class IBSMCPopulation: Temporary storage for the traits of the focal individual.

N

N - Static variable in class MersenneTwister: Period parameter n (degree of recurrence).
N_REPEAT - Static variable in class Plist: The number of repeated messages to report before skipping further messages.
nActive - Variable in class Module: The number of active traits.
name - Variable in class AbstractGeometry: Optional descriptive name.
name - Variable in class Module: The name of the species.
name - Variable in class CLOption: The name of the command line option (required).
names - Variable in class ODE: The names of the traits (dynamical variables) in the ODE.
names - Variable in class S3Map: The names of the traits.
nameTrait(int) - Method in class Module: Get default name for trait with index trait.
NativeJS - Class in org.evoludo.util: Collection of native javascript methods.
NativeJS() - Constructor for class NativeJS: Private default constructor to ensure non-instantiability.
nBins - Variable in class HistoGraph: The number of bins.
nBins - Variable in class scanCSD: The number of bins for the histogram.
nColors - Variable in class ColorMap.Index: Number of colors
nDemes - Variable in class DemesTBT: The number of demes.
nDim - Variable in class ODE: Total number of traits (dynamical variables) in the ODE.
NEAR_ZERO - Static variable in class ParaGraph: Threshold below which linear axis bounds are snapped to zero.
needRoom(boolean, int) - Method in class Path2D
NEEDS_LAYOUT - Enum constant in enum class Network.Status: layout pending, process not started
negate() - Method in class Vector2D: Negates the coordinates of 2D vector v to obtain -v.
negate() - Method in class Vector3D: Negates the coordinates of 3D vector v to obtain -v.
NetGames - Class in org.evoludo.simulator.modules: Cooperation in dynamical networks.
NetGames(EvoLudo) - Constructor for class NetGames: Create a new instance of the module for cooperation in dynamical networks, where the network structure encodes the individuals behaviour.
NetGames.IBSPop - Class in org.evoludo.simulator.modules: The extension for IBS simulations implement cooperative actions on dynamical networks.
network - Variable in class GenericPopGraph: The network representation of the population structure or null if not applicable.
Network<N> - Class in org.evoludo.simulator: Abstract graphical representation for generic population geometries.
Network(EvoLudo, AbstractGeometry) - Constructor for class Network: Create a new network for the given engine and geometry.
Network.LayoutListener - Interface in org.evoludo.simulator: Interface for GUI elements that are interested in receiving updates regarding the process of laying out the network.
Network.Status - Enum Class in org.evoludo.simulator: Status of the layout process of networks: Network.Status.HAS_LAYOUT network layout complete.
network2D - Variable in class AbstractGeometry: Local storage for the 2D representation of this graph.
Network2D - Class in org.evoludo.simulator: Graphical representation of generic population geometries in 2D.
Network2D(EvoLudo, AbstractGeometry) - Constructor for class Network2D: Create a new network in 2D for the given engine and geometry.
Network2DGWT - Class in org.evoludo.graphics: Graphical representation of generic population geometries in 2D.
Network2DGWT(EvoLudo, AbstractGeometry) - Constructor for class Network2DGWT: Create a new network in 2D for the given engine and geometry with a layouting process optimzed for GWT.
network3D - Variable in class AbstractGeometry: Local storage for the 3D representation of this graph.
Network3D - Class in org.evoludo.simulator: Graphical representation of generic population geometries in 3D.
Network3D(EvoLudo, AbstractGeometry) - Constructor for class Network3D: Create a new network in 3D for the given engine and geometry.
Network3DGWT - Class in org.evoludo.graphics: Graphical representation of generic population geometries in 3D.
Network3DGWT(EvoLudo, AbstractGeometry) - Constructor for class Network3DGWT: Create a new network in 3D for the given engine and geometry with a layouting process optimzed for GWT.
next - Variable in class PDE: The next density/frequency distribution of traits as a 2D array.
next() - Method in class Path2D.Iterator: Moves the iterator to the next segment of the path forwards along the primary direction of traversal as long as there are more points in that direction.
next() - Method in interface PathIterator: Moves the iterator to the next segment of the path forwards along the primary direction of traversal as long as there are more points in that direction.
next() - Method in class RNGDistribution.Binomial: Generate the number of successful trials drawn from the binomial distribution.
next() - Method in class RNGDistribution.Exponential: Generate an exponentially distributed random number with mean.
next() - Method in class RNGDistribution.Geometric: Generate a geometrically distributed random number with success probability p.
next() - Method in class RNGDistribution.Normal: Generate a normally distributed random number with mean and standard deviation stdev.
next() - Method in class RNGDistribution.Uniform: Generate a uniformly distributed random number from interval [min, max).
next() - Method in class EvoLudo: Advances the EvoLudo model by a single step.
next() - Method in class EvoLudoGWT
next() - Method in class IBS
next() - Method in class Model: Advance model by one step.
next() - Method in class ODE: Advance model by one step.
next() - Method in class PDE: Advance model by one step.
next() - Method in class SDE
next() - Method in class Network
next() - Method in class PlistReader
next() - Method in class RingBuffer.BckItr
next() - Method in class RingBuffer.FwdItr
next(double) - Method in class PDESupervisor: Advances the PDE model by a time step of stepDt.
next(double) - Method in class PDESupervisorGWT: Advances the PDE model by a time step of stepDt.
next(double[]) - Method in class RNGDistribution.Gillespie: Return a random integer with support [0, weights.length) from the discrete distribution of weights defined by the double[] array weights.
next(int[]) - Method in class RNGDistribution.Gillespie: Return a random integer with support [0, weights.length) from the discrete distribution of weights defined by the int[] array weights.
next(MersenneTwister, double) - Static method in class RNGDistribution.Exponential: Exponentially distributed random number with mean using random number generator rng.
next(MersenneTwister, double) - Static method in class RNGDistribution.Geometric: Creates geometric distribution with success probability p (mean 1/p) and the random number generator rng.
next(MersenneTwister, double, double) - Static method in class RNGDistribution.Normal: Normally distributed random number with mean and standard deviation stdev using random number generator rng.
next(MersenneTwister, double, double) - Static method in class RNGDistribution.Uniform: Uniformly distributed random number in [min, max) using random number generator rng.
next(MersenneTwister, double, int) - Static method in class RNGDistribution.Binomial: Creates binomial distribution for n trials with success probability p (mean n p) and the random number generator rng.
nextBinomial(double, int) - Method in class IBSPopulation: Draw a binomially distributed random integer.
nextBoolean() - Method in class MersenneTwister: Generates a random boolean.
nextBoolean() - Method in class RNGDistribution: Uniformly distributed random boolean.
nextBoolean(double) - Method in class MersenneTwister: This generates a coin flip with a probability probability of returning true, else returning false.
nextBoolean(float) - Method in class MersenneTwister: This generates a coin flip with a probability probability of returning true, else returning false.
nextByte() - Method in class MersenneTwister: Generates a random byte on [0, 0xff]-interval.
nextByte() - Method in class RNGDistribution: Uniformly distributed random byte in [0, Byte.MAX_VALUE).
nextBytes(byte[]) - Method in class MersenneTwister: Fill array bytes with random bytes.
nextBytes(byte[]) - Method in class RNGDistribution: Fill byte array bytes with uniformly distributed random bytes in [0, Byte.MAX_VALUE).
nextChar() - Method in class MersenneTwister: generates a random char on [0, 0xffff]-interval.
nextDouble() - Method in class MersenneTwister: Generate random double on half-open [0, 1)-interval.
nextDouble() - Method in class RNGDistribution: Uniformly distributed random number from interval [0, 1) with regular precision (based on 31bit random integer).
nextDoubleClosed() - Method in class MersenneTwister: Generate random double on closed [0, 1]-interval
nextDoubleHigh() - Method in class MersenneTwister: Generates a random high-precision double on half-open [0, 1)-interval.
nextDoubleOpen() - Method in class MersenneTwister: Generate random double on open (0, 1)-interval
nextFloat() - Method in class MersenneTwister: Generates a random float on half-open [0, 1)-interval.
nextGaussian - Variable in class MersenneTwister: Gaussian random numbers are generated in pairs.
nextGaussian() - Method in class MersenneTwister: Generate random number from standard normal distribution (Gaussian distribution).
nextGaussian() - Method in class RNGDistribution: Gaussian distributed random number with mean 0 and variance 1 (standard Normal distribution) with regular precision (based on 31bit random integer).
nextGeometryId - Static variable in class AbstractGeometry: Unique identifier for this geometry instance.
nextHit(double[], double) - Static method in class RNGDistribution.Gillespie: Helper method for RNGDistribution.Gillespie.nextSum(double[], double) and RNGDistribution.Gillespie.nextSum(MersenneTwister, double[], double).
nextIndex() - Method in class RingBuffer.LstItr
nextInt() - Method in class MersenneTwister: Generate a 31bit (signed) random int in [0, Integer.MAX_VALUE).
nextInt() - Method in class RNGDistribution: Uniformly distributed random integer in [0, Integer.MAX_VALUE).
nextInt(int) - Method in class MersenneTwister: Generate a random int in [0, n-1]-interval.
nextInt(int) - Method in class RNGDistribution: Uniformly distributed random integer in [0, n).
nextLayoutNode - Variable in class Network2DGWT: Helper variable to store the index of the node that needs to be processed next.
nextLayoutNode - Variable in class Network3DGWT: Helper variable to store the index of the node that needs to be processed next.
nextLong() - Method in class MersenneTwister: Generate a 63bit (signed) random long integer in [0, Long.MAX_VALUE).
nextLong(long) - Method in class MersenneTwister: Generate a random long integer in [0, n) with n > 0.
nextMax(double[], double) - Method in class RNGDistribution.Gillespie: Return a random integer with support [0, weights.length) from the discrete distribution of weights defined by the double[] array weights.
nextMax(int[], int) - Method in class RNGDistribution.Gillespie: Return a random integer with support [0, weights.length) from the discrete distribution of weights defined by the int[] array weights.
nextMax(MersenneTwister, double[], double) - Static method in class RNGDistribution.Gillespie: Static implementation of RNGDistribution.Gillespie.nextMax(double[], double).
nextShort() - Method in class MersenneTwister: Generates a random short integer on [0, 0xffff]-interval.
nextSpeciesIdx - Variable in class IBS: Index for turn-based-selection to determine which species to pick next.
nextSum(double[], double) - Method in class RNGDistribution.Gillespie: Return a random integer with support [0, weights.length) from the discrete distribution of weights defined by the double[] array weights.
nextSum(int[], int) - Method in class RNGDistribution.Gillespie: Return a random integer with support [0, weights.length) from the discrete distribution of weights defined by the int[] array weights.
nextSum(MersenneTwister, double[], double) - Static method in class RNGDistribution.Gillespie: Static implementation of RNGDistribution.Gillespie.nextSum(double[], double).
nextUInt() - Method in class MersenneTwister: Generates a 32bit 'unsigned' random int in [0, 2^³³-1].
nextULong() - Method in class MersenneTwister: Generate a 64bit unsigned random long in [0, 2^⁶⁵-1].
nFirst - Variable in class Centipede: The number of first mover rounds.
nGradient - Variable in class ColorMap.Gradient1D: Number of colors in the gradient: nGradient+1.
nGradient - Variable in class ColorMap.Gradient2D: Number of colors in the gradient: nGradient+1.
nGroup - Variable in class Module: The interaction group size.
ninterest - Variable in class CDL: Helper variable containing the interpolated interest rates for 0, 1, ..., N cooperators among the up to N interacting individuals.
nIssues - Variable in class IBSPopulation: The number of concistency issues encountered in the state of the IBS model.
nIssues - Variable in class Plist: The number of issues found.
nLines - Variable in class LineGraph: The number of lines to plot.
nLinks - Variable in class Network: The number of links in the network.
nMixedInter - Variable in class IBSPopulation: Optimization: Number of interactions in well-mixed populations for update rules that take advantage of IBSDPopulation.updateMixedScores().
nNodes - Variable in class Centipede: The number of decision nodes in the centipede game.
nNodes - Variable in class Network: The number of nodes in the network.
nNumerical - Variable in class Plist: The number of numerical issues found.
NO_LAYOUT - Enum constant in enum class Network.Status: no layout needed (e.g.
Node - Interface in org.evoludo.geom: Interface representing a (network) node in 2D or 3D space with a position and a radius.
Node2D - Class in org.evoludo.geom: Class representing a (network) node in 2D space with position and radius.
Node2D() - Constructor for class Node2D: Create a new 2D node at (0,0) with radius r=0.
Node2D(double, double, double) - Constructor for class Node2D: Create a new 2D node at (x,y) with radius r.
Node2D(Node2D) - Constructor for class Node2D: Create a copy of the 2D node n.
Node3D - Class in org.evoludo.geom: Class representing a (network) node in 3D space with position and radius.
Node3D() - Constructor for class Node3D: Create a new 3D node at (0,0,0) with radius r=0.
Node3D(double, double, double, double) - Constructor for class Node3D: Create a new 3D node at (x,y,z) with radius r.
Node3D(Node3D) - Constructor for class Node3D: Create a copy of 3D node n.
nodes - Variable in class Network: The array with all nodes of this network.
noGraph - Variable in class GenericPopGraph: The flag to indicate whether the graph needs to be drawn.
noise - Variable in class PlayerUpdate: The noise of the updating process of players.
noLogY() - Method in class LineGraph: Helper method to disable log scale on y-axis and issue warning.
NONE - Enum constant in enum class ChangeListener.PendingAction: No action requested, continue.
NONE - Enum constant in enum class IBS.MigrationType: No migration.
NONE - Enum constant in enum class IBS.ScoringType: Individuals do not have payoffs/fitness.
NONE - Enum constant in enum class IBSD.OptimizationType: No optimization (default).
NONE - Enum constant in enum class IBSGroup.SamplingType: No sampling.
NONE - Enum constant in enum class ModelType: Place holder if no model available.
NONE - Enum constant in enum class Map2Fitness.Map: no mapping, scores/payoffs equal fitness, \(fit = score\)
NONE - Enum constant in enum class Mutation.Continuous.Type: No mutations.
NONE - Enum constant in enum class Mutation.Discrete.Type: No mutations.
NONE - Enum constant in enum class CLOption.Argument: NONE: no argument.
NoninvertibleTransformException - Exception Class in org.evoludo.geom: The NoninvertibleTransformException class represents an exception that is thrown if an operation is performed requiring the inverse of an AffineTransform object but the AffineTransform is in a non-invertible state.
NoninvertibleTransformException(String) - Constructor for exception class NoninvertibleTransformException: Constructs an instance of NoninvertibleTransformException with the specified detail message.
norm - Variable in class Network: The normalization factor for the network potential.
norm(double[]) - Static method in class ArrayMath: Norm of double array a.
norm(float[]) - Static method in class ArrayMath: Norm of float array a.
norm(int[]) - Static method in class ArrayMath: Norm of integer array a.
norm(long[]) - Static method in class ArrayMath: Norm of long array a.
Normal() - Constructor for class RNGDistribution.Normal: Creates a standard Normal distribution with mean==0 and standard deviation stdev==1 using and a new instance of MersenneTwister.
Normal(double, double) - Constructor for class RNGDistribution.Normal: Creates Normal distribution with mean and standard deviation stdev using and a new instance of MersenneTwister.
Normal(MersenneTwister, double, double) - Constructor for class RNGDistribution.Normal: Creates Normal distribution with mean and standard deviation stdev using the random number generator rng.
normalize() - Method in class Vector2D: Normalizes the 2D vector v such that its length is |v|=1 while preserving the direction.
normalize() - Method in class Vector3D: Normalizes the 3D vector v such that its length is |v|=1 while preserving the direction.
normalize(double) - Method in class Vector2D: Normalizes the 2D vector v such that its length is l, i.e.
normalize(double) - Method in class Vector3D: Normalizes the 3D vector v such that its length is l, i.e.
normalize(double[]) - Static method in class ArrayMath: Normalize double array a.
normalize(double[], int, int) - Static method in class ArrayMath: Normalize elements ranging from index from to index to in double array a.
normalize(float[]) - Static method in class ArrayMath: Normalize float array a.
normalize(float[], int, int) - Static method in class ArrayMath: Normalize elements ranging from index from to index to in float array a.
normalizeMeanDensity() - Method in class PDE: Normalizes the mean density after the diffusion step is complete.
normalizeMeanFitness() - Method in class PDE: Normalizes the mean fitnesses after the reaction step is complete.
normalizeState(double[]) - Method in class ODE: Convenience method to normalize state in frequency based models.
normIdx - Variable in class HistoGraph: The index of the data row used for normalization.
Note: - Section in org.evoludo.simulator.Network.repulsion(int)
Note: - Section in org.evoludo.simulator.Network.repulsion(int)
Note: - Section in org.evoludo.simulator.Network.repulsion(int)
Note: - Section in org.evoludo.simulator.models.IBSDPopulation.optimizeMoran
Note: - Section in org.evoludo.simulator.models.Model.HasIBS.CGroups.groupScores(double, double[], int, double[])
Note: - Section in org.evoludo.simulator.models.Model.HasIBS.CPairs.pairScores(double, double[], int, double[])
Note: - Section in org.evoludo.simulator.models.Model.HasIBS.CPairs.pairScores(double, double[], int, double[])
Note: - Section in org.evoludo.simulator.models.Model.HasIBS.MCGroups.groupScores(double[], double[], int, double[])
Note: - Section in org.evoludo.simulator.models.Model.HasIBS.MCPairs.pairScores(double[], double[], int, double[])
Note: - Section in org.evoludo.simulator.models.Model.HasIBS.MCPairs.pairScores(double[], double[], int, double[])
Note: - Section in org.evoludo.simulator.models.Model.HasIBS.MCPairs.pairScores(double[], double[], int, double[])
Note: - Section in org.evoludo.simulator.modules.Module.setNTraits(int)
Notes - Section in class org.evoludo.simulator.views.Distribution
Notes - Section in org.evoludo.simulator.models.IBSGroup.self
Notes: - Section in org.evoludo.simulator.models.IBSPopulation.adjustScores
Notes: - Section in org.evoludo.simulator.models.IBSPopulation.debugUpdatePopulationAt(int)
Notes: - Section in org.evoludo.simulator.models.IBSPopulation.getFitnessHistogramData(double[][])
Notes: - Section in org.evoludo.simulator.models.IBSPopulation.getFitnessHistogramData(double[][])
Notes: - Section in org.evoludo.simulator.models.IBSPopulation.getFitnessHistogramData(double[][])
Notes: - Section in org.evoludo.simulator.models.IBSPopulation.pickNeighborSiteAt(int)
Notes: - Section in org.evoludo.simulator.models.IBSPopulation.updatePlayerBest(int, int[], int)
Notes: - Section in org.evoludo.simulator.models.IBSPopulation.updatePlayerBestHalf(int, int[], int)
Notes: - Section in org.evoludo.simulator.models.Model.HasIBS.DGroups.mixedScores(int[], int, double[])
Notes: - Section in org.evoludo.simulator.models.Model.HasIBS.DGroups.mixedScores(int[], int, double[])
Notes: - Section in org.evoludo.simulator.models.Model.HasIBS.DGroups.mixedScores(int[], int, double[])
Notes: - Section in org.evoludo.simulator.models.Model.HasIBS.DGroups.mixedScores(int[], int, double[])
Notes: - Section in org.evoludo.simulator.models.Model.HasIBS.DGroups.mixedScores(int[], int, double[])
Notes and assumptions - Section in class org.evoludo.graphics.S3Graph
Notes and implementation details - Section in class org.evoludo.graphics.AbstractGraph
notifyGUI - Variable in class EvoLudoGWT: The field to store the command to execute after parsing the command line options.
nParams - Variable in enum class IBSC.Init.Type: The number of parameters of the cost function.
nParams - Variable in enum class Continuous.Benefits: The number of parameters of the benefit function.
nParams - Variable in enum class Continuous.Costs: The number of parameters of the cost function.
nPopulation - Variable in class IBSPopulation: The size of the population.
nPopulation - Variable in class Module: The population size.
nRepeat - Variable in class Plist: The number of times a particular type of issue is reported before skipping any further ones.
nRuns - Variable in class simTBT: The number of runs.
nSampled - Variable in class IBSGroup: The effective sample size.
nSamples - Variable in class HistoGraph: The number of samples in the histogram.
nSamples - Variable in class IBSGroup: The sample size requested.
nSamples - Variable in class Model: The number of statistical samples to collect before returning the results.
nSecond - Variable in class Centipede: The number of second mover rounds.
nSpecies - Variable in class Model: The number of species in multi-species models.
nStatisticsFailed - Variable in class Model: Number of failed statistics samples.
nStatisticsSamples - Variable in class Model: Number of statistics samples collected.
nSteps - Variable in class simCDL: The number of steps for initial frequencies.
nTestFailures - Variable in class TestEvoLudo: The number of failed tests.
nTestMinor - Variable in class TestEvoLudo: The number of tests failing with minor errors.
nTests - Variable in class TestEvoLudo: The total number of tests.
nTestWarnings - Variable in class TestEvoLudo: The number of tests with warnings.
nTotal - Variable in class IBS: Total population size across all species.
nTraits - Variable in class ColorMap.Gradient2D: Number of traits in the gradient: nTraits=2.
nTraits - Variable in class IBSPopulation: The number of traits in module.
nTraits - Variable in class Module: The number of traits in this module
numCoords - Variable in class Path2D
numTypes - Variable in class Path2D
nUnits - Variable in class PDESupervisor: The number of units in the discretization of the PDE.

O

ode - Variable in class ODEInitialize: Hosting ODE model used to access species and state arrays.
ODE - Class in org.evoludo.simulator.models: Common base class for all differential equations models.
ODE - Enum constant in enum class ModelType: Ordinary differential equation model, defaults to RK5.
ODE() - Constructor for class ATBT.ODE: Constructs a new ODE solver taylored for the integration of asymmetric 2×2 games with environmental feedback.
ODE() - Constructor for class LV.ODE: Constructor for the classic Lotka-Volterra model based on ordinary differential equations.
ODE() - Constructor for class SIR.ODE: Constructor for the classic SIR model based on ordinary differential equations.
ODE(EvoLudo) - Constructor for class ODE: Constructs a new model for the numerical integration of the system of ordinary differential equations representing the dynamics specified by the Module module using the EvoLudo pacemaker engine to control the numerical evaluations.
ODEInitialize - Class in org.evoludo.simulator.models: Helper responsible for configuring initial conditions of ODE/SDE models.
ODEInitialize(ODE) - Constructor for class ODEInitialize: Create an initializer bound to the supplied ODE model.
ODEInitialize.InitType - Enum Class in org.evoludo.simulator.models: Types of initial configurations.
offsetX - Variable in class ContextMenu: Horizontal offset of context menu relative to coordinates of context menu triggering event.
offsetX - Variable in class Tooltip: Horizontal offset of tooltip relative to coordinates of pointer or the location of the tap triggering the tooltip, respectively.
offsetXTickLabels - Variable in class GraphStyle: The flag to indicate whether x-axis tick labels are offset (e.g.
offsetY - Variable in class ContextMenu: Vertical offset of context menu relative to coordinates of context menu triggering event.
offsetY - Variable in class Tooltip: Vertical offset of tooltip relative to coordinates of pointer or the location of the tap triggering the tooltip, respectively.
oldScores - Variable in class IBSMCPopulation: Temporary storage for the scores of each participant prior to group interactions.
oldTraits - Variable in class IBSMCPopulation: Temporary storage for the traits of the focal individual before the update.
onApplyClick(ClickEvent) - Method in class EvoLudoWeb: Apply command line parameters to EvoLudo model.
onBrowserEvent(Event) - Method in class EvoLudoTrigger.LightboxPanel
ONCE - Enum constant in enum class PopulationUpdate.Type: Every individual updates exactly once per generation.
onChange(ChangeEvent) - Method in class Slider
onClick(ClickEvent) - Method in class ContextMenuItem
onClick(ClickEvent) - Method in class Slider
onCLOFocusGained() - Method in class KeyHandler: Marks this handler as active because its CLO field just gained focus.
onCLOFocusLost() - Method in class KeyHandler: Releases priority when this handler's CLO field loses focus.
onContextError(Context3dErrorEvent) - Method in class PopGraph3D
onContextMenu(ContextMenuEvent) - Method in class ContextMenu
onContextMenu(ContextMenuEvent) - Method in class ContextMenuItem
onDefaultClick(ClickEvent) - Method in class EvoLudoWeb: Discard current parameter settings and revert to default settings on initial launch of current model.
onDoubleClick(DoubleClickEvent) - Method in class GenericPopGraph
onDoubleClick(DoubleClickEvent) - Method in class ParaGraph
onDoubleClick(DoubleClickEvent) - Method in class S3Graph
onDragLeave(DragLeaveEvent) - Method in class EvoLudoWeb: Handler for drag'n'drop operation exiting lab.
onDragOver(DragOverEvent) - Method in class EvoLudoWeb: Handler for drag'n'drop operation entering lab.
onDrop(DropEvent) - Method in class EvoLudoWeb: Handler for dropping and restoring saved state.
onFullscreenChange(FullscreenChangeEvent) - Method in class FSController: React to browser fullscreen toggles by adding/removing the helper CSS class.
onFullscreenChange(FullscreenChangeEvent) - Method in class ContextMenu: Called when a FullscreenChangeEvent is fired.
onFullscreenChange(FullscreenChangeEvent) - Method in interface FullscreenChangeHandler: Called when a FullscreenChangeEvent is fired.
onFullscreenChange(FullscreenChangeEvent) - Method in class Tooltip: Called when a FullscreenChangeEvent is fired.
onHelpClick(ClickEvent) - Method in class EvoLudoWeb: Displays a list and brief description of all parameters in the console, EvoLudoWeb.viewConsole, including the default and current settings.
onInitResetClick(ClickEvent) - Method in class EvoLudoWeb: Initialize or reset EvoLudo model (action depends on title of button).
onInitResetTouchEnd(TouchEndEvent) - Method in class EvoLudoWeb: Touch of Init (or Reset) button ended.
onInitResetTouchStart(TouchStartEvent) - Method in class EvoLudoWeb: Touch of Init button started.
onInput(InputEvent) - Method in interface InputHandler: Called when a InputEvent is fired.
onInput(InputEvent) - Method in class Slider
onKeyDown(String) - Method in class KeyHandler: Process keydown events to allow for repeating keyboard shortcuts.
onKeyDown(String) - Method in class AbstractView: Opportunity for view to implement keyboard shortcut for actions (repeating).
onKeyDown(String) - Method in class GenericPop: Opportunity for view to implement keyboard shortcut for actions (repeating).
onKeyUp(String) - Method in class KeyHandler: Process keyup events to allow for non-repeating keyboard shortcuts.
onKeyUp(String) - Method in class AbstractView: Opportunity for view to implement keyboard shortcut for actions (non repeating).
onKeyUp(String) - Method in class Console: Opportunity for view to implement keyboard shortcut for actions (non repeating).
onLoad() - Method in class EvoLudoWeb
onLoad() - Method in class AbstractGraph
onLoad() - Method in class GenericPopGraph
onLoad() - Method in class HistoGraph
onLoad() - Method in class LineGraph
onLoad() - Method in class ParaGraph
onLoad() - Method in class PopGraph2D
onLoad() - Method in class PopGraph3D
onLoad() - Method in class S3Graph
onLoad() - Method in class Console
onLoad() - Method in class ContextMenu
onLoad() - Method in class ContextMenuCheckBoxItem
onLoad() - Method in class ContextMenuHeader
onLoad() - Method in class ContextMenuItem
onLoad() - Method in class ContextMenuSeparator
onLoad() - Method in class Slider
onLoad() - Method in class Tooltip
onModelRunning(EvoLudoWeb) - Static method in class SettingsController: Marks the supplied lab as the currently running ePub instance.
onModelStopped(EvoLudoWeb) - Static method in class SettingsController: Clears the running lab marker once execution stops.
onModuleLoad() - Method in class EvoLudoWeb: Entry point method.
onMouseDown(MouseDownEvent) - Method in class AbstractGraph
onMouseDown(MouseDownEvent) - Method in class PopGraph2D
onMouseDown(MouseDownEvent) - Method in class PopGraph3D
onMouseDown(MouseDownEvent) - Method in class TrackballControls
onMouseMove(MouseMoveEvent) - Method in class AbstractGraph
onMouseMove(MouseMoveEvent) - Method in class PopGraph2D
onMouseMove(MouseMoveEvent) - Method in class Tooltip
onMouseMove(MouseMoveEvent) - Method in class TrackballControls
onMouseOut(MouseOutEvent) - Method in class AbstractGraph
onMouseOut(MouseOutEvent) - Method in class ContextMenu
onMouseOut(MouseOutEvent) - Method in class ContextMenuItem
onMouseOut(MouseOutEvent) - Method in class Tooltip
onMouseOver(MouseOverEvent) - Method in class ContextMenu
onMouseOver(MouseOverEvent) - Method in class ContextMenuItem
onMouseOver(MouseOverEvent) - Method in class Tooltip
onMouseUp(MouseUpEvent) - Method in class AbstractGraph
onMouseUp(MouseUpEvent) - Method in class PopGraph2D: .evoludo-cursorGrabNode removed from graph element. .evoludo-cursorMoveNode removed from graph element.
onMouseUp(MouseUpEvent) - Method in class PopGraph3D
onMouseUp(MouseUpEvent) - Method in class TrackballControls
onMouseWheel(MouseWheelEvent) - Method in class AbstractGraph
onMouseWheel(MouseWheelEvent) - Method in class Tooltip
onMouseWheel(MouseWheelEvent) - Method in class TrackballControls
onResize() - Method in class AbstractGraph
onResize() - Method in class GenericPopGraph
onResize() - Method in class PopGraph3D
onResize() - Method in class PopGraph3D.Pop3DScene
onResize() - Method in class AbstractView
onResize() - Method in class Histogram
onResize() - Method in class TrackballControls
onSettingsClick(ClickEvent) - Method in class EvoLudoWeb: Toggle visibility of the text field EvoLudoWeb.evoludoCLOPanel to view or modify the parameter settings.
onSettingsTouchEnd(TouchEndEvent) - Method in class EvoLudoWeb: Toggle visibility of EvoLudoWeb.evoludoCLOPanel to view or modify the parameter settings.
onSettingsTouchStart(TouchStartEvent) - Method in class EvoLudoWeb: Touch of parameter button started.
onSliderClick(ClickEvent) - Method in class EvoLudoWeb: Slider changed, adjust delay between updates.
onSliderInput(InputEvent) - Method in class EvoLudoWeb: Slider changed, adjust delay between updates.
onStart() - Method in class PopGraph3D.Pop3DScene
onStartStopClick(ClickEvent) - Method in class EvoLudoWeb: Start, Stop button clicked.
onStartStopTouchEnd(TouchEndEvent) - Method in class EvoLudoWeb: Touch of Start, Stop button ended.
onStartStopTouchStart(TouchStartEvent) - Method in class EvoLudoWeb: Touch of Start, Stop button started.
onStepClick(ClickEvent) - Method in class EvoLudoWeb: Next button clicked.
onStepTouchEnd(TouchEndEvent) - Method in class EvoLudoWeb: Touch of Next button ended.
onStepTouchStart(TouchStartEvent) - Method in class EvoLudoWeb: Touch of Next button started.
onTouchCancel(TouchCancelEvent) - Method in class ContextMenu
onTouchEnd(TouchEndEvent) - Method in class AbstractGraph
onTouchEnd(TouchEndEvent) - Method in class PopGraph2D
onTouchEnd(TouchEndEvent) - Method in class PopGraph3D
onTouchEnd(TouchEndEvent) - Method in class ContextMenu
onTouchEnd(TouchEndEvent) - Method in class Slider
onTouchEnd(TouchEndEvent) - Method in class Tooltip
onTouchEnd(TouchEndEvent) - Method in class TrackballControls
onTouchMove(TouchMoveEvent) - Method in class AbstractGraph
onTouchMove(TouchMoveEvent) - Method in class PopGraph2D: move one finger on node shift node.
onTouchMove(TouchMoveEvent) - Method in class ContextMenu
onTouchMove(TouchMoveEvent) - Method in class Slider
onTouchMove(TouchMoveEvent) - Method in class Tooltip
onTouchMove(TouchMoveEvent) - Method in class TrackballControls
onTouchStart(TouchStartEvent) - Method in class AbstractGraph
onTouchStart(TouchStartEvent) - Method in class GenericPopGraph
onTouchStart(TouchStartEvent) - Method in class ParaGraph
onTouchStart(TouchStartEvent) - Method in class S3Graph
onTouchStart(TouchStartEvent) - Method in class ContextMenu
onTouchStart(TouchStartEvent) - Method in class Slider
onTouchStart(TouchStartEvent) - Method in class Tooltip
onTouchStart(TouchStartEvent) - Method in class TrackballControls
onUnload() - Method in class EvoLudoWeb
onUnload() - Method in class AbstractGraph
onUnload() - Method in class GenericPopGraph
onUnload() - Method in class PopGraph3D
onUnload() - Method in class AbstractView
onUnload() - Method in class Console
onUnload() - Method in class ContextMenu
onUnload() - Method in class ContextMenuItem
onUnload() - Method in class Slider
onUnload() - Method in class Tooltip
onUpdate(double) - Method in class PopGraph3D.Pop3DScene
onViewChange(ChangeEvent) - Method in class EvoLudoWeb: Handler for changes of the view selector (EvoLudoWeb.evoludoViews).
onViewChanged - Variable in class ViewController: Callback invoked whenever the view changes.
open() - Method in class ContextMenu: Open submenu.
open() - Method in class ContextMenuItem: Open submenu if context menu item is enabled and controls a submenu with autoOpen set to true.
openChildMenu(ContextMenu) - Method in class ContextMenu: Open submenu child.
openSnapshot(String) - Method in class scanCSD: Open file for exporting the snapshot.
openSnapshot(String) - Method in class simCDLPQ: Open file for exporting the snapshot.
openSnapshot(String) - Method in class simTBT: Open file for exporting the snapshot.
openSubmenu() - Method in class ContextMenuItem: Open submenu.
opponent - Variable in class IBSPopulation: The interaction partner/opponent of this population opponent.getModule()==getModule().getOpponent().
opponent - Variable in class Module: Reference to Module of opponent.
OptimizationType(String, String) - Constructor for enum class IBSD.OptimizationType: Instantiate new optimization type.
optimizeHomo - Variable in class IBSPopulation: true if optimizations for homogeneous populations requested.
optimizeHomo() - Method in class IBSPopulation: Optimize homogeneous population states by skipping to the next mutation event.
optimizeMigration - Variable in class DemesTBT.IBSPop: The flag to indicate whether to optimize migration.
optimizeMoran - Variable in class IBSDPopulation: The flag to indicate whether optimizations of Moran processes are requested.
optimizeMoran2Traits() - Method in class IBSDPopulation: Optimized Moran process for two traits: a significant speed boost is achieved when restricting events along links that potentially result in an actual change of the population composition, i.e.
optimizeMoranNTraits() - Method in class IBSDPopulation: Optimized Moran process for more than two traits: a significant speed boost is achieved when restricting events along links that potentially result in an actual change of the population composition, i.e.
OPTION_PREFIX - Static variable in class CLOParser: The prefix for reporting issues with command line options
OPTIONAL - Enum constant in enum class CLOption.Argument: OPTIONAL: optional argument.
optionArg - Variable in class CLOption: The argument provided on the command line (if any).
options - Variable in class AbstractView: The string with view specific options.
options - Variable in class CLOParser: List of command line options available (after parsing).
order - Variable in class S3Map: The indices of the traits on the simplex.
ordered() - Method in class RingBuffer: Returns an iterator over all elements in this buffer in chronological order.
org.evoludo - package org.evoludo: EvoLudo - A platform for the exploration of evolutionary models.
org.evoludo.geom - package org.evoludo.geom: The geometric utilities for working with shapes and spatial relationships.
org.evoludo.graphics - package org.evoludo.graphics: The GWT graphics for rendering and visualizing evolutionary models.
org.evoludo.math - package org.evoludo.math: A collection of mathematical utilities and functions.
org.evoludo.simulator - package org.evoludo.simulator: The toolkit to explore interactive evolutionary models.
org.evoludo.simulator.exec - package org.evoludo.simulator.exec: Custom modules for running simulations on the command line.
org.evoludo.simulator.geometries - package org.evoludo.simulator.geometries: Geometries for population interaction and competition graphs used by the simulator.
org.evoludo.simulator.models - package org.evoludo.simulator.models: The models that generate evolutionary trajectories based on the specifications of each module.
org.evoludo.simulator.modules - package org.evoludo.simulator.modules: The modules to implement various evolutionary models.
org.evoludo.simulator.resources - package org.evoludo.simulator.resources: The GWT specific resources.
org.evoludo.simulator.ui - package org.evoludo.simulator.ui
org.evoludo.simulator.views - package org.evoludo.simulator.views: The views to visualize results and interact with evolutionary models.
org.evoludo.ui - package org.evoludo.ui: Extensions to the GWT user interface elements.
org.evoludo.util - package org.evoludo.util: Utility classes and functions.
orientation(Point2D, Point2D, Point2D) - Static method in class Segment2D: Find the orientation of the ordered triplet (p, q, r).
origin - Variable in class Rectangle2D: The origin of the rectangle (lower left corner).
osMBean - Variable in class simTraits: The operating system management bean to measure the CPU time.
OTHER - Enum constant in enum class Mutation.Discrete.Type: Mutate to any other trait.
othersOnly - Variable in class CDL: The flag to indicate whether cooperators benefit from their own contributions to the common pool.
out - Variable in class scanCSD: The output stream.
out - Variable in class simCDL: The output stream.
out - Variable in class simCDLP: The output stream.
out - Variable in class simCDLPQ: The output stream.
out - Variable in class simMoran: The output stream.
out - Variable in class simTBT: The output stream.
out - Variable in class simTraits: The output stream.
out - Variable in class AbstractGeometry: The array storing the neighbourhood of each node by listing the indices of nodes that this one connects to.
outline - Variable in class S3Graph: The path that outlines the simplex.
output - Variable in class TestEvoLudo: The output stream for logging messages.

P

p - Variable in class RNGDistribution.Binomial: Success probability of single trial.
p - Variable in class RNGDistribution.Geometric: Success probability of single trial.
p1 - Variable in class Segment2D: The first point of the line segment.
p2 - Variable in class Segment2D: The second point of the line segment.
pad(String) - Static method in class ColorMapCSS: Utility function to add padding (if needed) of leading zero'es to ensure that each color component is encoded by a two digit hexadecimal.
pAddwire - Variable in class AbstractGeometry: Probability for adding new links.
pAddwire - Variable in class IBSPopulation: The array containing the probabilities for adding links to the interaction and competition graphs.
paint() - Method in class AbstractGraph: Draw the graph.
paint(boolean) - Method in class AbstractGraph: Draw the graph.
paint(boolean) - Method in class HistoGraph
paint(boolean) - Method in class LineGraph
paint(boolean) - Method in class ParaGraph
paint(boolean) - Method in class PopGraph2D: Draw the graph.
paint(boolean) - Method in class PopGraph3D
paint(boolean) - Method in class S3Graph
Painting and Helpers - Section in class org.evoludo.graphics.AbstractGraph
paintPara(boolean) - Method in class ParaGraph: Paint the trajectory in the phase plane.
paintS3(boolean) - Method in class S3Graph: Paint the trajectory in the simplex.
paintScheduled - Variable in class LineGraph: The flag to indicate whether painting is already scheduled.
paintScheduled - Variable in class ParaGraph: The flag to indicate whether painting is already scheduled.
pairmodule - Variable in class IBSDPopulation: For pairwise interaction modules module==pairmodule holds and null otherwise.
pairmodule - Variable in class IBSMCPopulation: For pairwise interaction modules module==pairmodule holds and null otherwise.
pairScores(double[], double[], int, double[]) - Method in interface Model.HasIBS.CPairs
pairScores(double[], double[], int, double[]) - Method in interface Model.HasIBS.MCPairs: Calculate the payoff/score for modules with interactions in pairs and multiple continuous traits.
pairScores(double[], double[], int, double[]) - Method in class CLabour
pairScores(double, double[], int, double[]) - Method in interface Model.HasIBS.CPairs: Calculate the payoff/score for modules with interactions in pairs and a single continuous trait.
pairScores(double, double[], int, double[]) - Method in class CSD
pairScores(int, int[], double[]) - Method in interface Model.HasIBS.DPairs: Calculate and return total (accumulated) payoff/score for pairwise interactions of the focal individual with trait me against opponents with different traits.
pairScores(int, int[], double[]) - Method in class ATBT
pairScores(int, int[], double[]) - Method in class CDL
pairScores(int, int[], double[]) - Method in class CDLP: Calculate and return total (accumulated) payoff/score for pairwise interactions of the focal individual with trait me against opponents with different traits.
pairScores(int, int[], double[]) - Method in class CDLPQ
pairScores(int, int[], double[]) - Method in class Centipede
pairScores(int, int[], double[]) - Method in class EcoPGG
pairScores(int, int[], double[]) - Method in class RSP
pairScores(int, int[], double[]) - Method in class TBT
panCamera() - Method in class TrackballControls: Update eye and target for (dynamical) panning.
panEnd - Variable in class TrackballControls: End coordinates on trackball for panning.
panSpeed - Variable in class TrackballControls: Speed for panning (shifting).
panStart - Variable in class TrackballControls: Starting coordinates on trackball for panning.
PAPER - Static variable in class RSP: The trait (and index) value of the trait 'paper'.
paraGraph - Variable in class TraitMap: The ParaGraph instance.
ParaGraph - Class in org.evoludo.graphics: ParaGraph is a specialized 2D parametric/phase-plane graph component for visualizing trajectories produced by a simulation module.
ParaGraph(Phase2D, Module) - Constructor for class ParaGraph: Create new parametric graph for module running in view.
ParaGraph.ViewState - Class in org.evoludo.graphics: Helper that caches derived view quantities for the current bounds, ranges, and zoom factor.
parallel(Line2D) - Method in class Line2D: Check if two lines are parallel.
parameters - Variable in class CLOParser: List of command line options as provided.
paramsDidChange() - Method in class EvoLudo: Called after parameters have changed.
parentMenu - Variable in class ContextMenu: Reference to the parent menu.
parse() - Method in class AbstractGeometry: Re-parse the stored specification string.
parse() - Method in class AbstractView: Parse the arguments provided to this view.
parse() - Method in class CLOption: Parses the option and its argument, if applicable, through the delegate.
parse(boolean) - Method in interface CLODelegate: Parse string arg and set configurable parameters that correspond to this command line option.
parse(boolean) - Method in class CLOption: Delegate parsing helper that handles optional vs required arguments.
parse(String) - Method in class AbstractGraph: Parse the arguments for the graph.
parse(String) - Method in class LineGraph
parse(String) - Method in class AbstractGeometry: Parse geometry-specific CLI options.
parse(String) - Method in class BarabasiAlbertGeometry
parse(String) - Method in class CubicGeometry
parse(String) - Method in class HexagonalGeometry
parse(String) - Method in class HierarchicalGeometry
parse(String) - Method in class KlemmEguiluzGeometry
parse(String) - Method in class LinearGeometry
parse(String) - Method in class MooreGeometry
parse(String) - Method in class RandomDirectedGeometry
parse(String) - Method in class RandomGeometry
parse(String) - Method in class RandomRegularGeometry
parse(String) - Method in class ScalefreeGeometry
parse(String) - Method in class SecondNeighbourGeometry
parse(String) - Method in class SquareGeometry
parse(String) - Method in class SuperstarGeometry
parse(String) - Method in class TriangularGeometry: Configure the triangular geometry.
parse(String) - Method in class VonNeumannGeometry
parse(String) - Static method in enum class ModelType: Parse the string arg and return the best matching model type.
parse(String) - Method in class ODE: Parse initializer string arg.
parse(String) - Method in class ODEInitialize: Parse the CLI string describing initial conditions.
parse(String) - Method in class PDE: Parse initializer string arg.
parse(String) - Method in interface CLODelegate: Parse string arg and set configurable parameters that correspond to this command line option.
parse(String) - Static method in class PlistParser: Parses the contents of a plist file supplied as a String and returns a Plist with key and object associations.
parse(String[]) - Method in class TestEvoLudo: Parse the command line options.
parse(String, boolean) - Method in interface CLODelegate: Parse string arg and set configurable parameters that correspond to this command line option.
parseArgs(String) - Method in class LineGraph: Parse command line options for the graph.
parseArray(PlistReader, List) - Static method in class PlistParser: Parses an array entry, <array>, in the plist-string provided by reader and writes all elements to the list array.
parseBoolVector(String) - Static method in class CLOParser: Parse string aVector as a boolean[] array.
parseCLO() - Method in class CLOController: Parse the cached command-line string.
parseCLO() - Method in class EvoLudo: Parse command line options.
parseCLO(String[]) - Method in class CLOController: Parse the provided command-line arguments.
parseCLO(String[]) - Method in class EvoLudo: Pre-process and parse array of command line arguments.
parseCLO(String[]) - Method in class CLOParser: Parses String array of command line arguments in two stages.
parseCLO(EvoLudo.Directive) - Method in class EvoLudoGWT: Parse command line options and set the command to execute after parsing completed.
parseColor(String) - Static method in class CLOParser: Parse string aColor as a Color.
parseDict(PlistReader, Plist) - Static method in class PlistParser: Parses a dictionary entry, <dict>, in the plist-string provided by reader and writes <key> and plist element pairs to the lookup table dict.
parseDim(String) - Static method in class CLOParser: Parse string arg as an integer.
parseDouble(String) - Static method in class CLOParser: Parse string aDouble as a double.
parseFloat(String) - Static method in class CLOParser: Parse string aFloat as a float.
parseHeader() - Method in class PlistReader: Parse (and discard) header of plist-string.
parseHierarchy() - Method in class HierarchicalGeometry: Parse the hierarchy-related CLI spec, updating subtype, boundary flag and weight, and storing the raw hierarchy levels (without the computed leaf size).
parseInteger(String) - Static method in class CLOParser: Parse string anInteger as an int.
parseIntMatrix(String) - Static method in class CLOParser: Parse string aMatrix as a int[][] matrix (two dimensional array).
parseIntVector(String) - Static method in class CLOParser: Parse string aVector as an int[] array.
parseIntVector(String, String) - Static method in class CLOParser: Parse string aVector as a int[] array.
parseLong(String) - Static method in class CLOParser: Parse string aLong as a long.
parseMatrix(String) - Static method in class CLOParser: Parse string aMatrix as a double[][] matrix (two dimensional array).
parser - Variable in class CLOController: Parser used to manage all registered command-line options.
parseReal(String) - Static method in class PlistParser: Parses a real number from a string.
parseSize() - Method in class FSController: Apply the --size option (or its default) using the currently registered widget.
parseVector(String) - Static method in class CLOParser: Parse string aVector as a double[] array.
parseVector(String, String) - Static method in class CLOParser: Parse string aVector as a double[] array.
participants - Variable in class ContextMenu: Lookup table of listener widgets sporting context menus and their corresponding providers of the context menu contents.
participants - Variable in class Tooltip: Lookup table of listener widgets sporting tooltips and their corresponding providers of the tooltip contents.
path - Variable in class Path2D.Iterator
Path2D - Class in org.evoludo.geom: The Path2D class provides a simple, yet flexible shape which represents an arbitrary geometric path.
Path2D() - Constructor for class Path2D: Constructs a new empty double precision Path2D object with a default winding rule of Path2D.WIND_NON_ZERO.
Path2D(int) - Constructor for class Path2D: Constructs a new empty double precision Path2D object with the specified winding rule to control operations that require the interior of the path to be defined.
Path2D(int, int) - Constructor for class Path2D: Constructs a new empty double precision Path2D object with the specified winding rule and the specified initial capacity to store path segments.
Path2D(Path2D, AffineTransform) - Constructor for class Path2D: Constructs a new double precision Path2D object from an arbitrary Path2D object, transformed by an AffineTransform object.
Path2D.Iterator - Class in org.evoludo.geom: Adapted from java.awt.geom.PathIterator, merged with Path2D Iterator and CopyIterator.
PathIterator - Interface in org.evoludo.geom: The PathIterator interface provides the mechanism for objects that implement the Shape interface to return the geometry of their boundary by allowing a caller to retrieve the path of that boundary a segment at a time.
payFirst - Variable in class Centipede: The payoff matrix for the first mover.
payLoneCoop - Variable in class CDL: The payoff to lone cooperators.
payLoneCoop - Variable in class EcoPGG: The payoff to lone cooperators.
payLoneDefect - Variable in class CDL: The payoff to lone defectors.
payLoneDefect - Variable in class EcoPGG: The payoff to lone defectors.
payLoner - Variable in class CDL: The payoff to loners.
payoff - Variable in class RSP: The 3×3 payoff matrix for interactions between the three types.
payoff(double[], double[]) - Method in class Continuous.Traits2Payoff: Calculate the payoff to the focal individual with traits me when interacting with an opponent with traits you.
payoff(double, double) - Method in class Continuous.Traits2Payoff: Calculate the payoff to the focal individual with trait me when interacting with an opponent with trait you.
payoffs - Variable in class TBT: The 2×2 payoff matrix for interactions between cooperators and defectors.
paySecond - Variable in class Centipede: The payoff matrix for the second mover.
pde - Variable in class PDEInitialize: Owning PDE model providing geometry and background data.
PDE - Class in org.evoludo.simulator.models: Numerical integration of partial differential equations for reaction-diffusion systems based on Euler's method (fixed step size)
PDE - Enum constant in enum class ModelType: Partial differential equation model, defaults to PDERD (no advection).
PDE() - Constructor for class SIR.PDE: Constructor for the spatial SIR model based on partial differential equations.
PDE(EvoLudo) - Constructor for class PDE: Constructs a new model for the numerical integration of the system of partial differential equations representing the dynamics specified by the Module module using the EvoLudo pacemaker engine to control the numerical evaluations.
PDEADV - Enum constant in enum class ModelType: Reaction-diffusion-advection model.
PDEInitialize - Class in org.evoludo.simulator.models: Helper class responsible for initializing spatial density fields for PDE based simulations in the EvoLudo framework.
PDEInitialize(PDE) - Constructor for class PDEInitialize: Create an initializer tied to the supplied PDE model.
PDEInitialize.Type - Enum Class in org.evoludo.simulator.models: Types of initial configurations.
PDERD - Enum constant in enum class ModelType: Reaction-diffusion model.
PDESupervisor - Class in org.evoludo.simulator.models: Supervisor of reaction-diffusion processes.
PDESupervisor(EvoLudo, PDE) - Constructor for class PDESupervisor: Creates a new supervisor to manage the PDE calculations of model charge.
PDESupervisorGWT - Class in org.evoludo.simulator.models: Supervisor of reaction-diffusion processes.
PDESupervisorGWT(EvoLudo, PDE) - Constructor for class PDESupervisorGWT: Creates a new supervisor to manage the PDE calculations of model charge with scheduling in GWT.
PDF - Enum constant in enum class AbstractView.ExportType: Portable document format, pdf (not yet implemented).
pendingAction - Variable in class EvoLudo: The action that is pending (if any).
PendingAction() - Constructor for enum class ChangeListener.PendingAction
percentX - Variable in class GraphStyle: The flag to indicate whether tick marks along the horizontal axis are in percent.
percentY - Variable in class GraphStyle: The flag to indicate whether tick marks along the vertical axis are in percent.
performance - Variable in class NetGames.IBSPop: The array with the mean, minimum, and maximum fitness of individuals.
Performance - Section in class org.evoludo.graphics.PopGraph2D
performTest - Variable in class TestEvoLudo: The flag to indicate whether to perform tests or generate test cases.
permitsDebugStep() - Method in class IBS
permitsDebugStep() - Method in class Model: Checks if debugging single steps is supported.
permitsMode(Mode) - Method in class Model: Check if current model implements mode test; by default only Mode.DYNAMICS is permitted.
permitsSampleStatistics() - Method in class IBS
permitsSampleStatistics() - Method in class IBSD
permitsSampleStatistics() - Method in class Model: Check if the current model settings permit sample statistics.
permitsSampleStatistics() - Method in class SDE: Check if the current model settings permit sample statistics.
permitsTimeReversal() - Method in class Model: Checks if time reversal is permitted.
permitsTimeReversal() - Method in class ODE: Checks if time reversal is permitted.
permitsTimeReversal() - Method in class PDE: Checks if time reversal is permitted.
permitsTimeReversal() - Method in class ATBT.ODE: Checks if time reversal is permitted.
permitsUpdateStatistics() - Method in class IBS
permitsUpdateStatistics() - Method in class Model: Check if the current model settings permit update statistics.
permitsUpdateStatistics() - Method in class SDE
PERTURBATION - Enum constant in enum class PDEInitialize.Type: Perturbation of a spatially homogeneous distribution with densities <d1,...dn>.
petals - Variable in class SuperstarGeometry: Number of petals in the superstar structure.
PGROW - Static variable in class RungeKutta: The exponent for increasing the time step if error outside margin.
Phase2D - Class in org.evoludo.simulator.views: Phase2D is a view that renders the model's mean trait trajectory in a two‑dimensional phase plane.
Phase2D(EvoLudoGWT) - Constructor for class Phase2D: Construct a new view to display the time series data of the current EvoLudo model as a trajectory in a 2D phase plane.
Phase2D.TraitCommand - Class in org.evoludo.simulator.views: Command to toggle the inclusion of a trait on the phase plane axes.
phase2Data(Point2D, double[]) - Method in class TraitMap
phase2Data(Point2D, double[]) - Method in class ATBT.ATBTMap
phase2Data(Point2D, double[]) - Method in class EcoPGG.EcoPGGMap
phase2Data(Point2D, double[]) - Method in interface HasPhase2D.Data2Phase: Convert point on phase plane to data array.
pickAt(int, boolean) - Method in class IBSGroup: Picks an interaction/reference group for the focal individual focal and the population structure geom.
pickEvent(IBSPopulation) - Method in class IBS: Pick type of next event in focal population.
pickFailed() - Method in class IBSPopulation: Handle failed pick.
pickFailed(double) - Method in class IBSPopulation: Handle failed pick and report details about failure.
pickFitFocalIndividual() - Method in class IBSPopulation: Draws the index of a member of the population with a probability proportional to fitness.
pickFitFocalIndividual(int) - Method in class IBSPopulation: Draws the index of a member of the population with a probability proportional to fitness but excluding the individual with the index excl.
pickFitFocalNoVacant() - Method in class IBSPopulation: Draws the index of a member of the population with a probability proportional to fitness but assuming no vacant sites.
pickFitFocalNoVacant(int) - Method in class IBSPopulation: Draws the index of a member of the population with a probability proportional to fitness but assuming no vacant sites.
pickFitFocalNoVacantGillespieOptimized(int) - Method in class IBSPopulation: Draws the index of a member of the population with a probability proportional to fitness but assuming no vacant sites.
pickFitFocalSkipVacant() - Method in class IBSPopulation: Draws the index of a member of the population with a probability proportional to fitness but assuming vacant sites.
pickFitFocalSkipVacant(int) - Method in class IBSPopulation: Draws the index of a member of the population with a probability proportional to fitness but assuming vacant sites.
pickFitFocalSkipVacantGillespieOptimized(int) - Method in class IBSPopulation: Draws the index of a member of the population with a probability proportional to fitness but assuming vacant sites.
pickFitNeighborAt(int) - Method in class IBSPopulation: Pick a neighbour of the focal individual me with probability proportional to their fitness.
pickFitNeighborAt(int, boolean) - Method in class IBSPopulation: Pick a neighbour of the focal individual me with probability proportional to their fitness.
pickFitNeighborNoVacantAt(int, boolean) - Method in class IBSPopulation: Pick a neighbour of the focal individual me with probability proportional to their fitness assuming no vacant sites.
pickFitNeighborSkipVacantAt(int, boolean) - Method in class IBSPopulation: Pick a neighbour of the focal individual me with probability proportional to their fitness assuming vacant sites.
pickFocalHead(int) - Method in class IBSPopulation: Pick a focal individual uniformly at random starting from head.
pickFocalHead(int, int) - Method in class IBSPopulation: Pick a focal individual uniformly at random starting from head, excluding individual excl.
pickFocalIndividual() - Method in class IBSPopulation: Draws the index of a individual of the population uniformly at random.
pickFocalIndividual(int) - Method in class IBSPopulation: Draws the index of a individual of the population uniformly at random but excluding the individual with index excl.
pickFocalSite() - Method in class IBSPopulation: Draws the index of a site in the population uniformly at random, irrespective of whether it is occupied or not.
pickFocalSite(int) - Method in class IBSPopulation: Draws the index of a site in the population uniformly at random, irrespective of whether it is occupied or not.
pickFocalSkipVacant() - Method in class IBSPopulation: Pick a focal individual uniformly at random but skipping vacant sites.
pickFocalSkipVacant(int) - Method in class IBSPopulation: Pick a focal individual uniformly at random but excluding the individual with index excl.
pickFocalSpecies() - Method in class IBS: Pick focal population according to the selected scheme.
pickFocalSpecies(double[], double) - Method in class IBS: Pick focal species with a probability proportional to the entries in rates.
pickFocalSpecies(int) - Method in class IBS: Pick next focal species.
pickFocalTail(int) - Method in class IBSPopulation: Pick a focal individual uniformly at random starting from tail.
pickFocalTail(int, int) - Method in class IBSPopulation: Pick a focal individual uniformly at random starting from tail, excluding individual excl.
pickGroup(int) - Method in class IBSGroup: Pick group of nSampled random individuals with indices 0 - (size-1).
pickGroup(int, int) - Method in class IBSGroup: Pick group of nSampled random individuals with indices 0 - (size-1).
pickHierarchyMean(IBSGroup.HierarchyUnit, boolean) - Method in class IBSGroup: Pick a single random individual in hierarchical mean-field structure either from the outgoing (downstream) or incoming (upstream) neighbours.
pickHierarchySquare(IBSGroup.HierarchyUnit, boolean) - Method in class IBSGroup: Pick a single random individual in hierarchical square lattice structure either from the outgoing (downstream) or incoming (upstream) neighbours.
pickLinkMoran(double, int) - Method in class IBSDPopulation: Select a reproduction event along one of the active links according to the accumulated scores.
pickNeighborSiteAt(int) - Method in class IBSPopulation: Picks a neighbouring site of the focal individual me uniformly at random.
pickNeutralNeighbourAt(int, boolean) - Method in class IBSPopulation: Helper method to do picking under neutral conditions (no or negligible fitness differences).
pickPreferentialNode(int, int) - Method in class BarabasiAlbertGeometry: Picks a node according to preferential attachment.
pickRandom(int) - Method in class IBSGroup: Pick group of nSamples random individual with indices 0 - (size-1).
pickRandomHierarchy(boolean) - Method in class IBSGroup: Pick group of nSamples random individual in hierarchical structures either from the outgoing (downstream) or incoming (upstream) neighbours.
pickRandomStructured(boolean) - Method in class IBSGroup: Pick group of nSamples random individual in structured populations either from the outgoing (downstream) or incoming (upstream) neighbours.
pickSingle(int) - Method in class IBSGroup: Pick a single random individual with indices 0 - (size-1).
PIHALF - Static variable in class AbstractGraph: Constant representing the numerical value of \(\pi/2\)
pinch - Variable in class LineGraph: The center of the pinch gesture.
pinchDist - Variable in class AbstractGraph: The distance between the pinching gesture.
pinchScale - Variable in class LineGraph: The field to track the progress of the pinch gesture.
pinchX - Variable in class AbstractGraph: The x-coordinate of the center of the pinching gesture.
pinchY - Variable in class AbstractGraph: The y-coordinate of the center of the pinching gesture.
pinchZoom - Variable in class TrackballControls: Helper variable to keep track of the distance of two touches between subsequent touch events.
pIR - Variable in class SIR: The transition probability/rate for infected to recovered, I → R.
pIS - Variable in class SIR: The transition probability/rate for infected to susceptible, I → S.
playerScoreAveraged - Variable in class IBSPopulation: Flag to indicate whether player scores are averaged (default) or accumulated.
playerScoring - Variable in class IBSPopulation: Flag to indicate whether scores are reset whenever a player adopts the trait of another (default) or only if an actual change of trait occurred.
playerUpdate - Variable in class IBSPopulation: The update type of players.
playerUpdate - Variable in class Module: Map to convert score/payoff to fitness
PlayerUpdate - Class in org.evoludo.simulator.modules: The implementation of player updates.
PlayerUpdate(Module) - Constructor for class PlayerUpdate: Instantiate new player update for use in module.
PlayerUpdate.Type - Enum Class in org.evoludo.simulator.modules: Player update types.
playGameAt(int) - Method in class IBSPopulation: Update the score of individual me.
playGameSyncAt(int) - Method in class IBSPopulation: Update the score of individual me.
playGameSyncAt(int) - Method in class NetGames.IBSPop
playGroupGameAt(IBSGroup) - Method in class IBSCPopulation: Play a group interaction with the individuals in group.
playGroupGameAt(IBSGroup) - Method in class IBSDPopulation
playGroupGameAt(IBSGroup) - Method in class IBSMCPopulation: Play a group interaction with the individuals in group.
playGroupGameAt(IBSGroup) - Method in class IBSPopulation: Play a group interaction with the individuals in group.
playGroupGameAt(IBSGroup) - Method in class NetGames.IBSPop
playGroupOnceAt(int, int, IBSGroup) - Method in class IBSDPopulation: Focal individual plays game once with the entire group.
playGroupOnceAt(int, IBSGroup) - Method in class IBSCPopulation
playGroupOnceAt(int, IBSGroup) - Method in class IBSMCPopulation: Evaluate a single group interaction with the sampled opponents.
playGroupSequentiallyAt(int, int, IBSGroup, int) - Method in class IBSDPopulation: Focal individual plays game sequentially with parts of the group.
playGroupSequentiallyAt(int, IBSGroup, int) - Method in class IBSCPopulation
playGroupSequentiallyAt(int, IBSGroup, int) - Method in class IBSMCPopulation: Evaluate sequential group interactions when not enough opponents are available simultaneously.
playNoGameAt(int) - Method in class IBSMCPopulation: Handle the case where a focal player has no opponents and should not play a game.
playNoGameAt(int, int) - Method in class IBSDPopulation: No game is played because the focal individual is isolated or all neighbors are vacant.
playPairGameAt(IBSGroup) - Method in class IBSCPopulation: Play a pairwise interaction with the individuals in group.
playPairGameAt(IBSGroup) - Method in class IBSDPopulation
playPairGameAt(IBSGroup) - Method in class IBSMCPopulation: Play a pairwise interaction with the individuals in group.
playPairGameAt(IBSGroup) - Method in class IBSPopulation: Play a pairwise interaction with the individuals in group.
playPairGameAt(IBSGroup) - Method in class NetGames.IBSPop
plist - Variable in class EvoLudoWeb.GUIState: The the configuration to restore, if any.
Plist - Class in org.evoludo.util: Utility class to read and write plist-files with some customizations to store the bit-patterns for doubles to allow for perfect reproducibility.
Plist() - Constructor for class Plist: Construct a new plist.
PlistParser - Class in org.evoludo.util: Basic parser for plist-files.
PlistParser() - Constructor for class PlistParser: Suppresses default constructor, ensuring non-instantiability.
PlistReader - Class in org.evoludo.util: Iterator over tags in plist-string.
PlistReader(String) - Constructor for class PlistReader: Create reader for plist-string.
PlistTag - Class in org.evoludo.util: Entry in plist-string.
PlistTag(String, String) - Constructor for class PlistTag: Create a plist entry with <key> name tag without attributes associated with value.
PlistTag(String, String, String) - Constructor for class PlistTag: Create a plist entry with name <key> tag and attributes associated with value.
PlistTag(String, String, String, boolean) - Constructor for class PlistTag: Create a plist entry with name <key> tag and attributes associated with value.
pMigration - Variable in class IBSPopulation: The probability of migration.
PNG - Enum constant in enum class AbstractView.ExportType: Portable network graphics format, png
Point - Interface in org.evoludo.geom: Interface representing a point in 2D or 3D space determined by Cartesian coordinates.
Point2D - Class in org.evoludo.geom: Class representing a point in 2D Cartesian space.
Point2D() - Constructor for class Point2D: Create a new 2D point with coordinates (0,0).
Point2D(double, double) - Constructor for class Point2D: Create a new 2D point with coordinates (x,y).
Point2D(Point2D) - Constructor for class Point2D: Create a copy of the 2D point p.
Point3D - Class in org.evoludo.geom: Class representing a point in 3D Cartesian space.
Point3D() - Constructor for class Point3D: Create a new 3D point with coordinates (0,0,0).
Point3D(double, double, double) - Constructor for class Point3D: Create a new 3D point with coordinates (x,y,z).
Point3D(Point3D) - Constructor for class Point3D: Create a copy of the 3D point p.
pointIdx - Variable in class Path2D.Iterator
pointTypes - Variable in class Path2D
POOR - Static variable in class ATBT: The identifier of poor sites: (int) (trait / 2).
pop - Variable in class simTraits: The population.
Pop2D - Class in org.evoludo.simulator.views: 2D population view for the EvoLudo model.
Pop2D(EvoLudoGWT, Data) - Constructor for class Pop2D: Construct a new view to display the configuration of the current state of the EvoLudo model in 2D.
Pop3D - Class in org.evoludo.simulator.views: 3D population view for the EvoLudo model.
Pop3D(EvoLudoGWT, Data) - Constructor for class Pop3D: Construct a new view to display the configuration of the current state of the EvoLudo model in 3D.
Pop3DScene() - Constructor for class PopGraph3D.Pop3DScene: Create a scene wrapper for the outer graph; scene elements are configured in PopGraph3D.drawUniverse().
PopGraph2D - Class in org.evoludo.graphics: The graphical representation of lattices and network structures in 2D.
PopGraph2D(AbstractView, Module) - Constructor for class PopGraph2D: Create a graph for graphically visualizing the structure of a network (or population).
PopGraph3D - Class in org.evoludo.graphics: The graphical representation of network structures in 3D.
PopGraph3D(Pop3D, Module) - Constructor for class PopGraph3D: Create a graph for graphically visualizing the structure of a network (or population).
PopGraph3D.Pop3DScene - Class in org.evoludo.graphics: The class for animating the 3D network structure.
popMeanVar(double[], double) - Static method in class Distributions: Remove sample x from running (or online) mean and variance.
popsizes - Variable in class simTraits: The population sizes to be tested.
populateContextMenu(ContextMenu) - Method in class EvoLudoGWT: Opportunity to contribute entries to the context menu for models.
populateContextMenu(ContextMenu) - Method in class AbstractView: Opportunity for the controller to add functionality to the context menu (optional implementation).
populateContextMenu(ContextMenu) - Method in class Histogram
populateContextMenu(ContextMenu) - Method in class Phase2D
populateContextMenu(ContextMenu) - Method in class Pop3D
populateContextMenuAt(ContextMenu, int) - Method in class AbstractView: Opportunity for the controller to add functionality to the context menu (optional implementation).
populateContextMenuAt(ContextMenu, int) - Method in class Distribution
populateContextMenuAt(ContextMenu, int, int) - Method in class AbstractGraph: Populate context menu menu in listening widget at (relative) position (x,y).
populateContextMenuAt(ContextMenu, int, int) - Method in class GenericPopGraph
populateContextMenuAt(ContextMenu, int, int) - Method in class HistoGraph
populateContextMenuAt(ContextMenu, int, int) - Method in class LineGraph
populateContextMenuAt(ContextMenu, int, int) - Method in class ParaGraph
populateContextMenuAt(ContextMenu, int, int) - Method in class S3Graph
populateContextMenuAt(ContextMenu, int, int) - Method in class Console
populateContextMenuAt(ContextMenu, int, int) - Method in interface ContextMenu.Provider: Populate context menu menu in listening widget at (relative) position (x,y).
populateTraitItems(List, boolean) - Method in class Phase2D: Populate the trait menu items and optional species headers.
populateZoomMenu(ContextMenu) - Method in class AbstractGraph: Populate the zoom submenu with standard zoom actions.
populateZoomMenu(ContextMenu) - Method in class LineGraph
populateZoomMenu(ContextMenu) - Method in class ParaGraph
population - Variable in class IBS: Short-cut to species.get(0).getIBSPopulation() for single species models; null in multi-species models.
population - Variable in class Continuous: Shortcut for species.get(0) as long as continuous modules are restricted to a single species.
populationUpdate - Variable in class IBSPopulation: The population update.
PopulationUpdate - Class in org.evoludo.simulator.models: The implementation of population updates.
PopulationUpdate(IBS) - Constructor for class PopulationUpdate: Instantiate new population update for use in IBS models.
PopulationUpdate.Type - Enum Class in org.evoludo.simulator.models: Types of species updates (only relevant for multi-species models): synchronous Synchronized population updates.
popup - Variable in class EvoLudoWeb: The transparent backdrop of popup EvoLudo labs is stored here to reuse.
popup - Variable in class EvoLudoTrigger: Lightbox panel to overlay the page.
positionCamera() - Method in class PopGraph3D.Pop3DScene: Positions the camera.
positiveMinFitness() - Method in class IBS: Checks whether all species have positive minimum fitness.
postProcessChanges(double[], double[], double[]) - Method in class ODE: Apply adjusted dynamics scaling and mutation for all species.
potential - Variable in class Network: The potential energy of the current network layout/configuration.
pow(double, int) - Static method in class Combinatorics: Calculate x^n for double x and integer n.
pow(int, int) - Static method in class Combinatorics: Calculate x^n for integer x and integer n.
powabs(double, int) - Static method in class Combinatorics: Helper method to calculate \(x^n\) with \(n>0\).
powabs(int, int) - Static method in class Combinatorics: Helper method to calculate \(x^n\) with \(n>0\).
pRandomSample - Variable in class NetGames: The probability to pick a random model for comparison.
PRECISION_DIGITS - Static variable in class Plist: The number of significant digits.
preConcatenate(AffineTransform) - Method in class AffineTransform: Concatenates an AffineTransform Tx to this AffineTransform Cx in a less commonly used way such that Tx modifies the coordinate transformation relative to the absolute pixel space rather than relative to the existing user space.
predator - Variable in class LV: The reference to the predator species.
Predator - Class in org.evoludo.simulator.modules: Predator class representing the predator species in the Lotka-Volterra model.
Predator(LV) - Constructor for class Predator: Create a new instance of the phage population.
PREDATOR - Static variable in class Predator: The index of the predator.
preferredPlayerBest(int, int, int) - Method in class IBSDPopulation: For deterministic updating with multiple traits (more than two), it must be specified which trait is the preferred one.
preferredPlayerBest(int, int, int) - Method in class IBSMCPopulation: For deterministic updating with multiple traits (more than two), it must be specified which trait is the preferred one.
preferredPlayerBest(int, int, int) - Method in class IBSPopulation: For deterministic updating with multiple traits (more than two), it must be specified which trait is the preferred one.
preferredPlayerBest(int, int, int) - Method in class NetGames.IBSPop
prepareForCLO() - Method in class ViewController: Ensure the console is present while applying CLO changes and temporarily show it while parsing options.
prepareSquareLattice() - Method in class SquareGeometry: Common setup for square geometries.
prepareTraits() - Method in class IBSCPopulation
prepareTraits() - Method in class IBSDPopulation
prepareTraits() - Method in class IBSMCPopulation
prepareTraits() - Method in class IBSPopulation: Prior to a synchronous update step the current state must be duplicated in preparation for processing the next step.
prepareTraits() - Method in class NetGames.IBSPop
prepCanvas() - Method in class PopGraph2D: Helper method to get the canvas ready for drawing the graph.
prependTime2Data(double, double[]) - Method in class AbstractGraph: Utility method to prepend time to data point.
preprocessCLO(String[]) - Method in class CLOController: Apply preprocessing to the command-line arguments (module/model resolution, helper options).
preprocessCLO(String[]) - Method in class EvoLudo: Pre-process array of command line arguments.
preprocessCLO(String[]) - Method in class EvoLudoGWT: Pre-process array of command line arguments.
preprocessModelOption(String[], boolean, String[]) - Method in class Module: Preprocess the --model option based on the selected module.
pretty(double[][], int) - Static method in class Formatter: Same as Formatter.formatSci(double[], int) but formatting of exponents 'prettyfied' using HTML.
pretty(double[], int) - Static method in class Formatter: Same as Formatter.formatSci(double[], int) but formatting of exponents 'prettyfied' using HTML.
pretty(double, int) - Static method in class Formatter: Same as Formatter.formatSci(double, int) but formatting of exponent 'prettyfied' using HTML.
prettyFormat(double, int, String, String) - Static method in class Formatter: Helper method to format a double aDouble as HTML string with digits decimal places (trailing zeroes are included).
prettyThresholds - Static variable in class Formatter: The thresholds for 'pretty' formatting of exponents for each number of digits.
prev() - Method in class EvoLudo: Attempts to backtrack a single step of the EvoLudo model.
prev() - Method in class RunController: Attempts to backtrack a single step of the EvoLudo model.
prevAdjust - Variable in class Network: The best (smallest) adjustment (lowering of the energy state) of previous layouting steps.
prevgen - Variable in class NetGames.IBSPop: The previous generation time.
previous() - Method in class RingBuffer.LstItr
previousIndex() - Method in class RingBuffer.LstItr
prevLayout - Variable in class Network2DGWT: Time when last layout update was processed.
prevLayout - Variable in class Network3DGWT: Time when last layout update was processed.
prevmsg - Variable in class Plist: The previous message.
prevNextDebug() - Method in class EvoLudoWeb: Helper method to advance the EvoLudo model by a single step.
prevPotential - Variable in class Network: The potential energy of the previous network layout/configuration.
prevsample - Variable in class simCDL: Time of previous sample.
prevsample - Variable in class simCDLP: Time of previous sample.
prevsample - Variable in class simCDLPQ: Time of previous sample.
prevsample - Variable in class simTBT: Time of previous sample.
prevsample - Variable in class DemesTBT.IBSPop: Time of previous sample.
pRewire - Variable in class AbstractGeometry: Probability for rewiring.
pRewire - Variable in class IBSPopulation: The array containing the probabilities for rewiring links of the interaction and competition graphs.
prey - Variable in class Predator: The reference to the prey species.
PREY - Static variable in class LV: The index of the prey.
Primary responsibilities - Section in class org.evoludo.graphics.AbstractGraph
printDistr - Variable in class scanCSD: The flag to indicate whether to print the distribution.
printState(double[], double[]) - Method in class scanCSD: Print the distributions of the strategies.
priority - Variable in class CLOCategory: The priority of this category.
prob - Variable in class IBSGroup.HierarchyUnit: Probability threshold used to progress through the hierarchy.
probability - Variable in class Mutation: The probability of mutations.
probRead - Variable in class FixationData: The flag indicating whether the fixation data (probabilities) has been read.
process2Traits(int, double, double, double, double) - Method in class SDE: Process noise with two dependent traits.
process3Traits(double, double) - Method in class SDE: Process the three-trait stochastic update (including vacant).
processAnyTraits(double, double) - Method in class SDE: Process the default case (any number of traits).
processBR(double, boolean[], double[], int, int, double[]) - Method in class ODE: Process best responses for active traits with given fitness values (within tolerance).
processChangeMode(ChangeListener.PendingAction) - Method in class RunController: Process change of mode request.
processCLOSnap() - Method in class EvoLudoWeb: Process the command line options for snap execution, EvoLudoGWT.cloSnap, and start the model accordingly.
processColorMap(ColorMap) - Method in class Module: Opportunity for modules to make adjustments to the color map in graphs such as Pop2D or Pop3D.
processColorMap(ColorMap) - Method in class NetGames: Opportunity for modules to make adjustments to the color map in graphs such as Pop2D or Pop3D.
processCommandLineOption(String) - Method in class CLOParser: Parses a single command line option.
processDensity(Module, String, int) - Method in class ODEInitialize: Parse a density specification and append it to ODE.y0.
processDiff(String) - Method in class Plist: Process a difference.
processEcologyDensity(Module, int, int, double) - Method in class SDE: Process density-based ecological dynamics with demographic noise from birth and death events.
processEcologyFrequency(Module, int, int, double) - Method in class SDE: Process ecological dynamics with demographic noise from birth and death events.
processEnvironmentalAsymmetryAt(int, boolean) - Method in class ATBT.ATBTPop: Helper method to process environmental asymmetries.
processEPubSettings() - Method in class EvoLudoWeb: Helper method to deal with ePub specifics.
processEvent() - Method in class IBS: Processes a single event.
processEvents(int, double, double) - Method in class IBS: Processes up to nUpdates events, updating time and updates appropriately.
processEvoLudoLabs() - Method in class EvoLudoWeb: Process DOM and add/allocate an EvoLudo lab whenever a <div> element with class="evoludo-simulation" is found.
processEvoLudoTriggers() - Method in class EvoLudoWeb: Process DOM and replace all <div> elements with class="evoludo-trigger-html" by a button that triggers a popup EvoLudo lab.
processFrequency(Module, String, int) - Method in class ODEInitialize: Parse a frequency specification and append it to ODE.y0.
processInit(Module, ODEInitialize.InitType, String, int) - Method in class ODEInitialize: Process initialization for a single population and append it to ODE.y0.
processInitXY(double, double) - Method in class ParaGraph: Helper method to convert screen coordinates into an initial configuration and set the controller's initial state.
processInitXY(int, int) - Method in class S3Graph: Helper method to convert screen coordinates into an initial configuration and set the controller's initial state.
processMatchedOption(CLOption, String[], String) - Method in class CLOParser: Processes a matched option with its arguments.
processMouseEvent(MouseEvent) - Method in class Tooltip: Update tooltip and save pointer locations.
processMutant(Module, String, int) - Method in class ODEInitialize: Parse a mutant initialization specification and append it to ODE.y0.
processPendingAction() - Method in class EvoLudo: Helper to process pending actions.
processPendingAction() - Method in class RunController: Helper method for handling model changed events and processing pending actions.
processScore(double, int) - Method in class IBSPopulation: Process the accumulated score in this population, taking the updating into account.
progress - Variable in class scanCSD: The flag to indicate whether to show progress.
progress - Variable in class simCDL: The flag to indicate whether to show progress.
progress - Variable in class simMoran: The flag to indicate whether to show progress.
progress - Variable in class simTBT: The flag to indicate whether to show progress.
progress - Variable in class simTraits: The flag to indicate whether to show progress.
projectionMenu - Variable in class Pop3D: The context menu item for selecting parallel projection of the graph instead of the default perspective projection.
PROPORTIONAL - Enum constant in enum class PlayerUpdate.Type: proportional to payoff
provider - Variable in class ContextMenu.Registration: Provider of context menu entries for this listener widget.
provider - Variable in class Tooltip.Registration: Provider of tooltips for this listener widget.
providers - Variable in class CLOParser: List of providers of command line options.
providesCLO(String) - Method in class CLOController: Check whether this controller (or its providers) supplies the given option.
providesCLO(String) - Method in class CLOParser: Check if current list of command line options includes option with name.
pRS - Variable in class SIR: The transition probability/rate for recovered to susceptible, R → S.
PSHRNK - Static variable in class RungeKutta: The exponent for decreasing the time step if error outside margin.
pSI - Variable in class SIR: The transition probability/rate for susceptibles to infected, S → I, including seasonal variation pSI = pSI[0] + pSI[1] cos(pSI[2] t).
pSmallWorld - Variable in class KlemmEguiluzGeometry: Probability to rewire links to create small-world shortcuts.
Public API highlights - Section in class org.evoludo.graphics.S3Graph
publish(LogRecord) - Method in class EvoLudoWeb.EvoLogHandler
PUNISH - Static variable in class CDLP: The trait (and index) value of peer punishers.
pure - Variable in class DemesTBT.IBSPop: The time spent in homogenous states.
pushMeanVar(double[], double) - Static method in class Distributions: Add sample x to running (or online) mean and variance.
pushTag(PlistTag) - Method in class PlistReader: Push a tag to the stream and return it on the next PlistReader.next() call.

Q

quadrantRotate(int) - Method in class AffineTransform: Concatenates this transform with a transform that rotates coordinates by the specified number of quadrants.
quadrantRotate(int, double, double) - Method in class AffineTransform: Concatenates this transform with a transform that rotates coordinates by the specified number of quadrants around the specified anchor point.
quadTo(double, double, double, double) - Method in class Path2D: Adds a curved segment, defined by two new points, to the path by drawing a Quadratic curve that intersects both the current coordinates and the specified coordinates (x2,y2), using the specified point (x1,y1) as a quadratic parametric control point.
querySelectorAll(String) - Static method in class NativeJS: JSNI method: expose convenient javascript method to obtain a list of elements in the DOM that match the selection criterion selector.
quiet() - Method in class Plist: Set quiet mode to suppress all differences.

R

r - Variable in class Node2D: The radius r of the 2D node.
r - Variable in class Node3D: The radius r of 3D node.
R - Static variable in class SIR: The index of the recovered trait/cohort.
R - Static variable in class Network2D: The baseline size of the 2D universe.
r1 - Variable in class CDL: The multiplication factor of the (non-linear) public good with a single cooperator.
radius - Variable in class Network: The radius of the network.
radius - Variable in class TrackballControls: Radius of trackball.
RANDOM - Enum constant in enum class IBSGroup.SamplingType: Sample some random neighbours.
RANDOM - Enum constant in enum class ODEInitialize.InitType: Random initial trait frequencies.
RANDOM - Enum constant in enum class PDEInitialize.Type: Random trait frequencies.
RANDOM_GRAPH - Enum constant in enum class GeometryType: Random graph.
RANDOM_GRAPH_DIRECTED - Enum constant in enum class GeometryType: Directed random graph.
RANDOM_REGULAR_GRAPH - Enum constant in enum class GeometryType: Random regular graph.
random01() - Method in class RNGDistribution: Uniformly distributed random number from interval [0, 1) with regular precision (based on 31bit random integer).
random01() - Method in class IBS: Random number from interval [0, 1) with 32bit resolution.
random01() - Method in class IBSPopulation: Draw a uniformly distributed random double from the semi-closed interval [0, 1) with 32bit resolution.
random01d() - Method in class RNGDistribution: Uniformly distributed random number from interval [0, 1) with high precision (based on 53bit random integer).
random0n(int) - Method in class RNGDistribution: Uniformly distributed integer random number from interval [0, n).
random0n(int) - Method in class IBS: random integer number from interval [0, n).
random0n(int) - Method in class IBSPopulation: Draw a uniformly distributed random integer number from the semi-closed interval [0, n).
random0N(int) - Method in class RNGDistribution: Uniformly distributed integer random number from interval [0, n].
RandomDirectedGeometry - Class in org.evoludo.simulator.geometries: Random directed graph geometry that wires a spanning tree first to ensure connectivity before adding remaining edges uniformly at random.
RandomDirectedGeometry(EvoLudo) - Constructor for class RandomDirectedGeometry: Create a directed random-graph geometry controlled by the provided engine.
randomGaussian(double, double) - Method in class IBSPopulation: Draw a Gaussian (normal) distributed random double.
RandomGeometry - Class in org.evoludo.simulator.geometries: Random (undirected) graph geometry that ensures the generated network is connected before sprinkling additional random edges.
RandomGeometry(EvoLudo) - Constructor for class RandomGeometry: Create an undirected random-graph geometry coordinated by the provided engine.
RandomRegularGeometry - Class in org.evoludo.simulator.geometries: Random regular graph geometry that repeatedly samples degree distributions until a connected realization is found.
RandomRegularGeometry(EvoLudo) - Constructor for class RandomRegularGeometry: Create a random regular geometry tied to the given engine.
range - Variable in class RNGDistribution.Uniform: Width of interval of uniform random numbers, max-min.
range - Variable in class Mutation: The range of mutations.
RANGE - Enum constant in enum class Mutation.Continuous.Type: Mutate parental trait t to t &pm; <r>.
RANGE - Enum constant in enum class Mutation.Discrete.Type: Mutate trait t to t &pm; <r>.
RATE - Enum constant in enum class SpeciesUpdate.Type: Pick focal species based on update rate.
rates - Variable in class LV: The reaction rates for prey reproduction, predation, and competition.
rates - Variable in class Predator: The reaction rates for predator reproduction, predation, and competition.
ratio - Variable in class NetGames: The cost-to-benefit ratio of cooperation.
raycaster - Variable in class PopGraph3D: Helper field for determining which node has been hit by mouse or tap.
react() - Method in class PDESupervisor: Perform the reaction step.
react(int, int) - Method in class PDE: Reaction step.
read - Variable in class PlistReader: Number of lines read in plist-string.
readStatisticsSample() - Method in class IBSD
readStatisticsSample() - Method in class Model: Signal that statistics sample is ready to process.
readStatisticsSample() - Method in class SDE
REAL_CLOSE - Static variable in class Plist: String constant for closing an real entry during plist generation.
REAL_OPEN - Static variable in class Plist: String constant for opening an real entry during plist generation.
Rectangle2D - Class in org.evoludo.geom: Utility class for dealing with rectangles in 2D.
Rectangle2D() - Constructor for class Rectangle2D: Create a new empty 2D rectangle with lower left corner at (0,0) and zero width and zero height.
Rectangle2D(double, double, double, double) - Constructor for class Rectangle2D: Create a new 2D rectangle with lower left corner at (x,y), width width and height height.
Rectangle2D(Rectangle2D) - Constructor for class Rectangle2D: Create a copy of 2D the rectangle r.
RED - Enum constant in enum class TestEvoLudo.ConsoleColors: Red color.
RED_BACKGROUND - Enum constant in enum class TestEvoLudo.ConsoleColors: Red background color.
RED_BACKGROUND_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Red high intensity background.
RED_BOLD - Enum constant in enum class TestEvoLudo.ConsoleColors: Red color.
RED_BOLD_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Red high intensity color.
RED_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Red high intensity color.
RED_UNDERLINED - Enum constant in enum class TestEvoLudo.ConsoleColors: Red color.
referencesDir - Variable in class TestEvoLudo: Directory with reference results.
refreshViews() - Method in class ViewController: Updates the list of available views based on the current module and model.
register() - Method in class KeyHandler: Registers the handler and installs global listeners if needed.
registered - Variable in class KeyHandler: Indicates whether this controller has been registered globally.
registerGlobal(KeyHandler) - Static method in class KeyHandler: Registers a handler for global key event handling.
Registration(FocusPanel, Tooltip.Provider) - Constructor for class Tooltip.Registration: Register all event handlers relevant for handling tooltips with listener widget and associate with the tooltip provider.
Registration(ContextMenu.Listener, ContextMenu.Provider) - Constructor for class ContextMenu.Registration: Register all event handlers relevant for handling context menus with listener widget and associate with the context menu provider.
registrationCount - Static variable in class KeyHandler: Number of handlers that have requested registration.
relax() - Method in class Model: Relax the initial configuration of the model over timeRelax generations.
relax(int) - Method in class Network: Relax the potential energy a single node with index nodeidx by adjusting its position.
relax(int) - Method in class Network2D
relax(int) - Method in class Network3D
relax(int, double) - Method in class Network: Relaxes the network node with index nodeidx.
relax(int, double) - Method in class Network2D
relax(int, double) - Method in class Network3D
remove() - Method in class RingBuffer.LstItr
removeCandidate(int, int) - Method in class NetGames.IBSPop: The focal individual with index focal considers to stop acts of cooperation towards the candidate member with index mdl through a probabilistic comparison of their differences in fitness as well as in levels of cooperativity.
removeChangeListener(ChangeListener) - Method in class EvoLudo: Remove the change listener from the list of listeners that get notified when the model changes.
removeCLO(String) - Method in class CLOParser: Remove option with name from current list of command line options.
removeCLO(String[]) - Method in class CLOParser: Remove all options with names listed in names.
removeCLO(CLOption) - Method in class CLOParser: Remove option from current list of command line options.
removeCLOProvider(CLOProvider) - Method in class CLOController: Remove a previously registered provider.
removeCLOProvider(CLOProvider) - Method in class EvoLudo: Unregister clo as a provider of command line options.
removeCLOProvider(CLOProvider) - Method in class CLOParser: Remove provider from the list of providers.
removeEdgeAt(int, int) - Method in class AbstractGeometry: Remove edge (undirected link) from nodea to nodeb.
removeFullscreenChangeHandler(String, FullscreenChangeHandler) - Static method in class NativeJS: JSNI method: Remove the fullscreen change handler.
removeGlobalKeyListeners() - Static method in class KeyHandler: Removes the JS listeners that were installed by KeyHandler.addGlobalKeyListeners().
removeHandler() - Method in class ContextMenu.Registration
removeHandler() - Method in class Tooltip.Registration
removeInLink(int, int) - Method in class AbstractGeometry: Remove an incoming link (directed) to node to from node from.
removeKey(String) - Method in class CLOption: Remove key with name aKey from the option's key collection.
removeKey(CLOption.Key) - Method in class CLOption: Remove key from the option's key collection.
removeLifecycleListener(LifecycleListener) - Method in class EvoLudo: Remove the lifecycle listener from the list of listeners that get notified when the model reaches lifecycle milestones.
removeLinkAt(int, int) - Method in class AbstractGeometry: Remove a directed link from node from to node to.
removeListener(LifecycleListener) - Method in class LifecycleController: Remove the lifecycle listener from the list of listeners that get notified when the model reaches lifecycle milestones.
removeListener(RunListener) - Method in class RunController: Remove the run listener from the list of listeners that get notified when the model run state changes.
removeListener(ContextMenu.Listener) - Method in class ContextMenu: Remove a previously registered listener widget from context menu requests.
removeOutLink(int, int) - Method in class AbstractGeometry: Remove an outgoing link (directed) from node from to node to.
removeRunListener(RunListener) - Method in class EvoLudo: Remove the run listener from the list of listeners that get notified when the model run state changes.
removeSampleListener(SampleListener) - Method in class EvoLudo: Remove the change listener from the list of listeners that get notified when the model changes.
removeScoreAt(int, double) - Method in class IBSPopulation: Removes the score nilscore based on a single interaction from the individual with index index.
removeScoreAt(int, double, int) - Method in class IBSPopulation: Removes the score nilscore based on incr interactions from the individual with index index.
Rendering - Section in class org.evoludo.graphics.PopGraph2D
Rendering and autoscaling - Section in class org.evoludo.graphics.HistoGraph
Rendering details - Section in class org.evoludo.graphics.S3Graph
Rendering details: - Section in class org.evoludo.graphics.ParaGraph
renderingPanel - Variable in class PopGraph3D.Pop3DScene: Helper variable to fix unnecessary exceptions in parallax (renderingPanel is private in RenderingPanel class).
reparseCLO - Variable in class CLOController: Flag indicating whether the CLI string needs to be reparsed.
repeat - Variable in class Plist: The number of times the previous message was repeated.
replace(int, T) - Method in class RingBuffer: Replace buffer entry at position index with entry.
replace(String) - Method in class Console.Log: Replace the most recent entry in the log with msg.
replace(T) - Method in class RingBuffer: Replace most recent entry in ring buffer with entry.
REPLICATION - Enum constant in enum class IBS.Event: Replication event.
reportDiff(String) - Method in class Plist: Report a difference.
reportsDir - Variable in class TestEvoLudo: Directory for storing reports of failed tests.
repulsion - Variable in class Network2D: Helper variable to store intermediate results when considering the potential energy resulting from the repulsion between nodes.
repulsion - Variable in class Network3D: Helper variable to store intermediate results when considering the potential energy resulting from the repulsion between nodes.
repulsion(int) - Method in class Network: Calculate the potential energy based on repulsion for the node with index nodeidx.
repulsion(int) - Method in class Network2D
repulsion(int) - Method in class Network3D
requestAction(ChangeListener.PendingAction) - Method in class EvoLudo: Requests a ChangeListener.PendingAction to be processed on the next opportunity.
requestAction(ChangeListener.PendingAction) - Method in class RunController: Requests a ChangeListener.PendingAction to be processed on the next opportunity.
requestAction(ChangeListener.PendingAction, boolean) - Method in class EvoLudo: Requests a ChangeListener.PendingAction to be processed on the next opportunity.
requestAction(ChangeListener.PendingAction, boolean) - Method in class RunController: Requests a ChangeListener.PendingAction to be processed on the next opportunity.
requestFullscreen(Element) - Static method in class NativeJS: JSNI method: Request fullscreen mode for the element ele.
requestMode(Mode) - Method in class Model: Request a change of the Mode of the model.
requestParseCLO() - Method in class CLOController: Request that the command-line string be reparsed before the next run.
requestParseCLO() - Method in class EvoLudo: Request full reparsing of the command line options.
requestSymmetric - Variable in class PDE: The flag indicating whether preservation of symmetry in the dynamics is requested.
REQUIRED - Enum constant in enum class CLOption.Argument: REQUIRED: required argument.
Requirements: - Section in org.evoludo.simulator.models.IBSPopulation.doAdjustScores()
Requirements: - Section in org.evoludo.simulator.models.IBSPopulation.doAdjustScores()
Requirements: - Section in org.evoludo.simulator.models.IBSPopulation.doAdjustScores()
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.addDirected()
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.addLinkAt(int, int)
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.addUndirected()
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.clone()
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.clone()
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.clone()
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.clone()
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.clone()
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.clone()
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.clone()
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.decodeGeometry(Plist)
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.displaySingle(AbstractGeometry, AbstractGeometry)
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.isConsistent()
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.isUnique()
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.isUnique()
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.rewire()
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.rewireDirected()
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.rewireUndirected(double)
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractGeometry.swapEdges(int, int, int, int)
Requirements/notes: - Section in org.evoludo.simulator.geometries.AbstractNetwork.initGeometryDegreeDistr(int[])
Requirements/notes: - Section in org.evoludo.simulator.geometries.GeometryType.isUnique()
Requirements/notes: - Section in org.evoludo.simulator.geometries.HierarchicalGeometry.init()
Requirements/notes: - Section in org.evoludo.simulator.geometries.LinearGeometry.init()
Requirements/notes: - Section in org.evoludo.simulator.geometries.SquareGeometry.init()
Requirements/notes: - Section in org.evoludo.simulator.geometries.SquareGeometry.init()
Requirements/notes: - Section in org.evoludo.simulator.geometries.SquareGeometry.init()
Requirements/notes: - Section in org.evoludo.simulator.geometries.SquareGeometry.init()
Requirements/notes: - Section in org.evoludo.simulator.geometries.SuperstarGeometry.init()
Requirements/notes: - Section in org.evoludo.simulator.models.IBSPopulation.adjustGameScoresAt(int)
Requirements/notes: - Section in org.evoludo.simulator.models.IBSPopulation.adjustGameScoresAt(int)
Requirements/notes: - Section in org.evoludo.simulator.models.IBSPopulation.adjustGameScoresAt(int)
requiresLayout() - Method in enum class Network.Status: Checks if network requires layout.
requiresReset(boolean) - Method in class EvoLudo: Request reset the active model, e.g.
reset() - Method in class Path2D: Resets the path to empty.
reset() - Method in class AbstractGraph: Reset the graph.
reset() - Method in class GenericPopGraph
reset() - Method in class HistoGraph
reset() - Method in class LineGraph
reset() - Method in class Network2DGWT
reset() - Method in class Network3DGWT
reset() - Method in class S3Graph
reset() - Method in class TraitMap
reset() - Method in class MersenneTwister: Resets the random number generator to its initial state.
reset() - Method in class RNGDistribution: Pass seed to random number generator.
reset() - Method in class FixationData: Reset the fixation data to get ready for the next sample.
reset() - Method in class IBS
reset() - Method in class IBSDPopulation: Reset the model.
reset() - Method in class IBSMCPopulation
reset() - Method in class IBSPopulation: Reset the model.
reset() - Method in class Model: Milestone: Reset this model
reset() - Method in class ODE
reset() - Method in class PDE
reset() - Method in class PDESupervisor: Reset supervisor and update settings.
reset() - Method in class RungeKutta
reset() - Method in class SDE
reset() - Method in class Module: Reset Module based on current parameters.
reset() - Method in class NetGames.IBSPop
reset() - Method in class Network: Reset the network (discard any existing layouts).
reset() - Method in interface HasPhase2D.Data2Phase: Reset the map.
reset() - Method in class CLOption: Reset option.
reset(boolean) - Method in class AbstractView: Called when a module has been reset.
reset(boolean) - Method in class Distribution
reset(boolean) - Method in class Histogram
reset(boolean) - Method in class Mean
reset(boolean) - Method in class Phase2D
reset(boolean) - Method in class Pop2D
reset(boolean) - Method in class Pop3D
reset(boolean) - Method in class S3
RESET - Enum constant in enum class TestEvoLudo.ConsoleColors: Reset all styling.
RESET - Enum constant in enum class ChangeListener.PendingAction: Reset model (re-initialize geometry and traits, stop execution).
RESET_ALWAYS - Enum constant in enum class IBS.ScoringType: Reset when updating from reference individual (not necessarily a change in trait).
RESET_GEOMETRY - Enum constant in enum class IBS.Statistics.Type: Skip homogeneous states by introducing a mutant and advancing the time according to an exponential distribution for an event happening with probability Module#getMutationProb().
RESET_ON_CHANGE - Enum constant in enum class IBS.ScoringType: Reset when changing trait (only after updating from reference model with a different trait).
resetCLO() - Method in class CLOParser: Reset current collection of options to their respective defaults.
resetCPUSample() - Method in class RunController: Reset collected CPU sampling statistics.
resetDegreeGraphs() - Method in class Histogram: Reset degree graphs.
resetDensity() - Method in class PDE: Resets minimum, maximum and mean density prior to diffusion step.
resetEphemeral(int) - Method in class IBSPopulation: Precalculate the number of interactions for ephemeral payoffs and store in the interactions array.
resetFitness() - Method in class PDE: Resets minimum, maximum and mean fitnesses prior to reaction step.
resetFitnessGraphs() - Method in class Histogram: Reset fitness graphs.
resetFixationProbabilityGraphs() - Method in class Histogram: Reset fixation probability graphs.
resetFixationTimeGraphs() - Method in class Histogram: Reset fixation time graphs.
resetInterval - Variable in class IBS.Statistics: The number of samples before resetting the geometry.
resetMoran() - Method in class IBSPopulation: Ensure that Moran type population updates have non-negative fitness values.
resetRequested - Variable in class EvoLudo: The flag to indicate whether a reset of the active model has been requested.
resetScoreAt(int) - Method in class IBSDPopulation
resetScoreAt(int) - Method in class IBSPopulation: Reset score of individual at index index.
resetScores() - Method in class IBS: Resets the scores for all populations that use ephemeral payoffs.
resetScores() - Method in class IBSDPopulation
resetScores() - Method in class IBSPopulation: Reset scores and fitness of all individuals to zero.
resetScores() - Method in class NetGames.IBSPop
resetSelection() - Method in class ViewController: Resets the selection state when modules/models unload.
resetState() - Method in class IBS
resetState() - Method in class Model: Reset the internal state of this model; called by Model.reset() and Model.init().
resetStationaryGraphs() - Method in class Histogram: Reset stationary distribution graphs.
resetStatistics() - Method in class simCDL: Reset statistics.
resetStatistics() - Method in class simCDLP: Reset statistics.
resetStatistics() - Method in class simCDLPQ: Reset statistics.
resetStatistics() - Method in class DemesTBT.IBSPop: Reset statistics.
resetStatisticsSample() - Method in class IBSD
resetStatisticsSample() - Method in class Model: Reset statistics and get ready to start new collection.
resetStatisticsSample() - Method in class SDE
resetStatusThreshold() - Method in class EvoLudoWeb: Restore the default log threshold (display all severities).
resetTimestamps() - Method in class AbstractView: Reset the timestamps used for throttling view and status updates.
resetTrait(PopGraph2D, boolean) - Method in class Distribution: Reset the given graph for displaying trait distributions.
resetTraitGraphs() - Method in class Histogram: Reset trait graphs.
resetTraits() - Method in class IBS: Resets the traits for all populations and returns the total update rate across all species.
resetTraits() - Method in class IBSDPopulation: Reset all traits in preparation of the next update step.
resetTraits() - Method in class IBSPopulation: Reset all traits in preparation of the next update step.
resetTraits() - Method in class NetGames.IBSPop
resetTransforms() - Method in class AbstractGraph: Reset the transformation of the graphics context to the identity transform.
resetViewSelection() - Method in class EvoLudoWeb: Reset the current view selection to the default entry.
RESIDENT - Static variable in class Moran: The trait (and index) value of residents.
residentTrait - Variable in class FixationData: The resident trait.
resizeColors(Color[], int) - Method in class Mean: Resize the color array to the specified length by repeating colors as needed.
resolveInitialView(Logger) - Method in class ViewController: Parse the initial view specification (if provided) and resolve the matching view.
Resources - Interface in org.evoludo.simulator: The interface to provide access to GWT specific resource files.
Responsibilities - Section in class org.evoludo.EvoLudoWeb
Responsibilities - Section in class org.evoludo.graphics.PopGraph2D
Responsibilities - Section in class org.evoludo.graphics.S3Graph
Responsibilities - Section in class org.evoludo.simulator.views.Distribution
Responsibilities - Section in class org.evoludo.simulator.views.Histogram
Responsibilities - Section in class org.evoludo.simulator.views.Mean
Responsibilities - Section in class org.evoludo.simulator.views.Phase2D
Responsibilities - Section in class org.evoludo.simulator.views.Pop2D
Responsibilities - Section in class org.evoludo.simulator.views.Pop3D
Responsibilities: - Section in class org.evoludo.simulator.views.GenericPop
restoreFitness(Plist) - Method in class IBSDPopulation: Restore the fitness of all individuals encoded in the plist inspired map of key, value-pairs.
restoreFitness(Plist) - Method in class IBSPopulation: Restore the fitness of all individuals encoded in the plist inspired map of key, value-pairs.
restoreFitness(Plist) - Method in class ODE: Restores the fitness encoded in plist.
restoreFitness(Plist) - Method in class PDE
restoreFromFile() - Method in class EvoLudo: Restore state of EvoLudo model from saved plist, which encodes engine state.
restoreFromFile() - Method in class EvoLudoGWT: Restore state of EvoLudo model from saved plist, which encodes engine state.
restoreFromFile(EvoLudoWeb) - Static method in class NativeJS: JSNI method: opens javascript file chooser and attempts to restore state from selected file
restoreFromString(String, String) - Method in class EvoLudoWeb: Restore state of EvoLudo model from String content.
restoreGeometry(Plist) - Method in class IBSPopulation: Restore the interaction and competition structures encoded in the plist inspired map of key, value-pairs.
restoreGeometry(Plist) - Method in class PDE: Restores the geometry of the spatial structure encoded in plist.
restoreInteractions(Plist) - Method in class IBSPopulation: Restore the interactions of all individuals encoded in the plist inspired map of key, value-pairs.
restoreMenu - Variable in class AbstractView: The field to store the restore context menu.
restorePopulationState(Plist, IBSPopulation, String) - Method in class IBS: Restore the state of population pop from plist plist.
restoreState(Plist) - Method in class MersenneTwister: Restore state of random number generator from plist encoded string.
restoreState(Plist) - Method in class EvoLudo: Restore state of EvoLudo model from pre-processed plist, which encodes engine state (see EvoLudo.encodeState()).
restoreState(Plist) - Method in class IBS
restoreState(Plist) - Method in class Model: Restore the state encoded in the plist inspired map of key, value-pairs.
restoreState(Plist) - Method in class ODE
restoreState(Plist) - Method in class PDE
restoreState(Plist) - Method in class StateEncoder: Restore state of EvoLudo model from pre-processed plist, which encodes engine state (see StateEncoder.encodeState()).
restoreTraits(Plist) - Method in class IBSDPopulation
restoreTraits(Plist) - Method in class IBSMCPopulation
restoreTraits(Plist) - Method in class IBSPopulation: Restore the traits of all individuals encoded in the plist inspired map of key, value-pairs.
restoreTraits(Plist) - Method in class ODE: Restores the state encoded in plist.
restoreTraits(Plist) - Method in class PDE
resume - Variable in class EvoLudoWeb.GUIState: The flag to indicate whether to resume execution of the model.
reversed - Variable in class Slider: true if minimum and maximum of slider are reversed.
revertCLO() - Method in class EvoLudoWeb: CLOParser issues warnings for unknown options but do not throw them away (can be annoying when switching between models).
revertToODE(String) - Method in class SDE: Log a warning and request switching to the ODE model.
rewire() - Method in class AbstractGeometry: Add/rewire directed and undirected random links.
rewireDirected() - Method in class AbstractGeometry: Rewire directed links.
rewireEdgeAt(int, int, int) - Method in class AbstractGeometry: Rewire an undirected edge so that an edge formerly connecting focal and oldneigh now connects focal and newneigh.
rewireLinkAt(int, int, int) - Method in class AbstractGeometry: Rewire a directed link so that an edge formerly connecting from to prev now connects to to.
rewireNeighbourEdge(int, int, int[], int) - Method in class AbstractNetwork: Attempt to rewire existing edges so that nodes nodeA and nodeB can gain additional neighbours without introducing duplicate links.
rewireNeighbourEdge(RNGDistribution, int, int, int[], int) - Method in class StrongAmplifierGeometry: Attempt to rewire edges so that nodeA and nodeB can connect without duplicating links.
rewireUndirected(double) - Method in class AbstractGeometry: Rewire undirected links.
RGB2Css(int, int, int) - Static method in class ColorMapCSS: Convert the three components of a 24bit color, r, g, and b to a CSS color style.
RGBA2Css(int, int, int, int) - Static method in class ColorMapCSS: Convert the four components of a 32bit color, r, g, b, and a to a CSS color style.
rhoA(int, int) - Method in class Moran: The fixation probability of i mutants in a population of constant size N (and N-i residents).
rhoAi - Variable in class Moran: Store fixation probability of i individuals of type A.
RICH - Static variable in class ATBT: The identifier of rich sites: (int) (trait / 2).
right - Variable in class Rectangle2D: The right segment of the rectangle.
rightYAxisMenu - Variable in class HistoGraph: The context menu item to toggle the y-axis side.
rightYAxisMenu - Variable in class LineGraph: The context menu item to toggle the y-axis side.
rightYAxisMenu - Variable in class Phase2D: The context menu item to toggle the y-axis side.
RING - Enum constant in enum class PDEInitialize.Type: Ring distribution in the center with Gaussian distributed densities along the radius.
RingBuffer<T> - Class in org.evoludo.util: Non-blocking ring buffer.
RingBuffer(int) - Constructor for class RingBuffer: Create new ring buffer for storing up to capacity entries.
RingBuffer.BckItr - Class in org.evoludo.util: Iterates backwards over all elements in this buffer starting with the most recent entry.
RingBuffer.FwdItr - Class in org.evoludo.util: Iterates forward over all elements in this buffer starting with the oldest entry.
RingBuffer.LstItr - Class in org.evoludo.util: Iterates forward over all elements in this buffer starting with the oldest entry.
RK5 - Enum constant in enum class ModelType: Fifth order Runge-Kutta method for ordinary differential equation models.
rkck(double) - Method in class RungeKutta: Given values for n variables y[1..n] and their derivatives dydx[1..n] known at x, use the fifth-order Cash-Karp Runge-Kutta method to advance the solution over an interval h and return the incremented variables as yout[1..n].
rN - Variable in class CDL: The multiplication factor of the (non-linear) public good with all cooperators.
rng - Variable in class RNGDistribution: Reference to the MersenneTwister that supplies the random numbers for the different distributions.
rng - Variable in class EvoLudo: The shared random number generator to ensure reproducibility of results.
rng - Variable in class AbstractNetwork: The random number generator distribution used for network construction.
rng - Variable in class IBSGroup: The shared random number generator to ensure reproducibility of results.
rng - Variable in class IBSPopulation: The shared random number generator to ensure reproducibility of results.
rng - Variable in class Model: The shared random number generator to ensure reproducibility of results.
rng - Variable in class Mutation: Convenience field: the shared random number generator to ensure reproducibility of results.
rng - Variable in class Network: The random number generator used for layout of networks.
RNGDistribution - Class in org.evoludo.math: Collection of distributions of random numbers based on the Mersenne Twister.
RNGDistribution(MersenneTwister) - Constructor for class RNGDistribution: Create new random number distribution using rng as the random number generator.
RNGDistribution.Binomial - Class in org.evoludo.math: Binomially distributed random numbers with support {0,1,2,3,..., n}.
RNGDistribution.Exponential - Class in org.evoludo.math: Exponentially distributed random numbers with support [0.0, Double.MAX_VALUE).
RNGDistribution.Geometric - Class in org.evoludo.math: Geometrically distributed random numbers with support {1,2,3,...}.
RNGDistribution.Gillespie - Class in org.evoludo.math: Gillespie algorithm for selecting integers with support {0,1,2,3,..., n} but with different weights.
RNGDistribution.Normal - Class in org.evoludo.math: Normally (or Gaussian) distributed random numbers with support (-Double.MAX_VALUE, Double.MAX_VALUE).
RNGDistribution.Uniform - Class in org.evoludo.math: Uniformly distributed random numbers with support [min, max).
ROCK - Static variable in class RSP: The trait (and index) value of the trait 'rock'.
role - Variable in class S3Graph: The identifier of the role of the data.
role - Variable in class S3Map: The role of this map.
root - Variable in class PlistReader: Name of root tag as specified in DOCTYPE declaration
rot90conversion - Static variable in class AffineTransform
rotate(double) - Method in class AffineTransform: Concatenates this transform with a rotation transformation.
rotate(double, double) - Method in class AffineTransform: Concatenates this transform with a transform that rotates coordinates according to a rotation vector.
rotate(double, double, double) - Method in class AffineTransform: Concatenates this transform with a transform that rotates coordinates around an anchor point.
rotate(double, double, double, double) - Method in class AffineTransform: Concatenates this transform with a transform that rotates coordinates around an anchor point according to a rotation vector.
rotate180() - Method in class AffineTransform
rotate270() - Method in class AffineTransform
rotate90() - Method in class AffineTransform
rotateCamera() - Method in class TrackballControls: Update eye and target for (dynamical) rotating.
rotateEnd - Variable in class TrackballControls: End coordinates on trackball for rotations.
rotateSpeed - Variable in class TrackballControls: Speed of rotation;
rotateStart - Variable in class TrackballControls: Starting coordinates on trackball for rotations.
round(double) - Static method in class Functions: Round value to next order of magnitude.
roundDown(double) - Static method in class Functions: Round value down to the next lower order of magnitude.
roundUp(double) - Static method in class Functions: Round value up to the next lower order of magnitude.
row - Variable in class HistoGraph: The index of the data row.
RSP - Class in org.evoludo.simulator.modules: Cyclical dynamics of the rock-scissors-paper game.
RSP(EvoLudo) - Constructor for class RSP: Create a new instance of the module for rock-scissors-paper games.
RSP.IBSPop - Class in org.evoludo.simulator.modules: The extension for IBS simulations specific to 3×3 games.
run() - Method in class EvoLudo: Start the EvoLudo model and calculate the dynamics one step at a time.
run() - Method in class EvoLudoGWT
run() - Method in class scanCSD
run() - Method in class simCDL
run() - Method in class simCDLP
run() - Method in class simCDLPQ
run() - Method in class simMoran
run() - Method in class simTBT
run() - Method in class simTraits
run() - Method in class TestEvoLudo: Generate or run all tests.
run() - Method in class Module
run() - Method in class ContextMenu.TouchTimer
runController - Variable in class EvoLudo: Controller for run listeners.
RunController - Class in org.evoludo.simulator: Controller for managing the execution and lifecycle of EvoLudo model simulations.
RunController(EvoLudo) - Constructor for class RunController: Constructs a new RunController for the specified EvoLudo engine.
RungeKutta - Class in org.evoludo.simulator.models: Implementation of Runge-Kutta method with adaptive step size for the numerical integration of systems of differential equations.
RungeKutta(EvoLudo) - Constructor for class RungeKutta: Constructs a new model for the numerical integration of the system of ordinary differential equations representing the dynamics specified by the Module module using the EvoLudo pacemaker engine to control the numerical evaluations.
RunListener - Interface in org.evoludo.simulator.models: RunListeners are informed about the state of model execution.
runListeners - Variable in class RunController: List of listeners that are notified about model run state changes.
runModule(String, String) - Method in class TestEvoLudo: Load and run module with parameters clo.
runningLab - Static variable in class SettingsController: Reference to the currently running lab in ePub mode.

S

S - Static variable in class SIR: The index of the susceptible trait/cohort.
S3 - Class in org.evoludo.simulator.views: The view to display time series of data as a trajectory on the \(S_3\) simplex.
S3(EvoLudoGWT) - Constructor for class S3: Construct a new view to display the time series data of the current EvoLudo model as a trajectory in a \(S_3\) simplex.
s32Data(double, double, double[]) - Method in class S3Map: Convert scaled cartesian coordinates of point on simplex to data array.
S3Graph - Class in org.evoludo.graphics: Graph for the simplex \(S_3\).
S3Graph(S3, Module, int) - Constructor for class S3Graph: Create a new simplex \(S_3\) graph for module running in view with the specified role.
S3Map - Class in org.evoludo.simulator.views: Default mapping of data to simplex \(S_3\) projections.
S3Map() - Constructor for class S3Map: Create a new mapping of data to simplex projections.
S3Map(int, String) - Constructor for class S3Map: Create a new mapping of data to simplex projections for different roles.
SAFETY - Static variable in class RungeKutta: The safety margin for adjusting time steps.
sampleDegree(RNGDistribution, double[]) - Method in class ScalefreeGeometry: Sample a degree from the given distribution.
SampleListener - Interface in org.evoludo.simulator.models: All SampleListener's get informed about state changes of the core of EvoLudo models.
sampleListeners - Variable in class EvoLudo: List of change listeners that get notified when the model changes.
samplingType - Variable in class IBSGroup: The current sampling type for the formation of interaction or reference groups.
SamplingType(String, String) - Constructor for enum class IBSGroup.SamplingType: Instantiate new type of interactions.
SANCTIONING - Static variable in class CDLPQ: The trait (and index) value of pool punishers.
save(ContextMenu.Listener, int, int) - Method in class ContextMenu.TouchTimer: Save the listener widget as well as the position (relative to browser window) where the context menu will be displayed when (and if) the timer fires.
saveSnapshot() - Method in class scanCSD: Save snapshot of current configuration.
saveSnapshot(int) - Method in class simCDLPQ: Save snapshot of current configuration.
saveSnapshot(int) - Method in class simTBT: Save snapshot of current configuration.
scale - Variable in class AbstractGraph: The scale of this graph.
scale(double) - Method in class Point2D: Scale the coordinates of this 2D point by a factor s to (s*x,s*y).
scale(double) - Method in class Point3D: Scale the coordinates of this 3D point by a factor s to (s*x,s*y,s*z).
scale(double, double) - Method in class AffineTransform: Concatenates this transform with a scaling transformation.
scale(double, double) - Method in class Point2D: Scale the coordinates of this 2D point by scalar factors sx and sy, respectively, to (sx*x, sy*y).
scale(double, double, double) - Method in class Point3D: Scale the coordinates of this 3D point by scalar factors sx, sy and sz, respectively, to (sx*x, sy*y, sz*z).
scale2bins - Variable in class Histogram: The scaling factor to map the data onto bins.
scaleAdd(double, Vector2D) - Method in class Vector2D: Scales the 2D vector by the scalar factor s and adds the 2D vector a to obtain s*v+a.
scaleAdd(double, Vector3D) - Method in class Vector3D: Scales the 3D vector v by the scalar factor s and adds the 3D vector a, v=s*v+a.
scaleDensity(double[], double, double[]) - Method in class PDEInitialize: Helper method to scale the density vector d by the scalar factor scale.
scaledX(double) - Method in class S3Graph: Convert the x-component of the screen coordinates (x, y) into scaled (Cartesian) coordinates in [0, 1].
scaledY(double) - Method in class S3Graph: Convert the y-component of the screen coordinates (x, y) into scaled (Cartesian) coordinates in [0, 1].
SCALEFREE - Enum constant in enum class GeometryType: Scale-free network.
SCALEFREE_BA - Enum constant in enum class GeometryType: Scale-free network.
SCALEFREE_KLEMM - Enum constant in enum class GeometryType: Scale-free network.
ScalefreeGeometry - Class in org.evoludo.simulator.geometries: Scale-free network that samples a power-law degree distribution and then constructs a matching undirected graph.
ScalefreeGeometry(EvoLudo) - Constructor for class ScalefreeGeometry: Create a scale-free geometry tied to the given engine.
scaleR(double) - Method in interface Node: Scales the radius of this node by scale.
scaleR(double) - Method in class Node2D
scaleR(double) - Method in class Node3D
scaleRadiusTo(double) - Method in class Network: Scale the radius of the network to newradius.
scanCSD - Class in org.evoludo.simulator.exec: Simulations of the evolution of continuous investement levels in social dilemmas.
scanCSD(EvoLudo) - Constructor for class scanCSD: Create a new scanCSD simulation.
scanDG - Variable in class simTBT: The scan parameters for the donation game.
scanNL - Variable in class simCDL: The scan range for non-linearity in public goods games.
scanST - Variable in class simTBT: The scan parameters for the S-T-plane.
scheduleAltButtons(TouchStartEvent) - Method in class EvoLudoWeb: Schedule showing alternate/context buttons after a long touch and prevent default handling.
schedulePaint() - Method in class LineGraph: Schedule painting of the graph.
schedulePaint() - Method in class ParaGraph: Schedule painting of the graph.
scheduleSample() - Method in class EvoLudoGWT: Schedule the next sample.
scheduleStep() - Method in class EvoLudoGWT: Schedule the next step.
scheduleUpdate(boolean) - Method in class AbstractView: Schedule an update of the view.
SCISSORS - Static variable in class RSP: The trait (and index) value of the trait 'scissors'.
scores - Variable in class IBSPopulation: The array of individual scores.
ScoringType(String, String) - Constructor for enum class IBS.ScoringType: Instantiate new type of population update.
SDE - Class in org.evoludo.simulator.models: Integrator for stochastic differential equations (SDE) based on Euler's method.
SDE - Enum constant in enum class ModelType: Euler-Maruyama method for stochastic differential equation models.
SDE() - Constructor for class LV.SDE: Constructor for the classic Lotka-Volterra model based on stochastic differential equations.
SDE() - Constructor for class SIR.SDE: Constructor for the SIR model in finite populations based on stochastic differential equations.
SDE(EvoLudo) - Constructor for class SDE: Constructs a new model for the numerical integration of the system of stochastic differential equations representing the dynamics specified by the Module module using the EvoLudo pacemaker engine to control the numerical evaluations.
search(File, String) - Static method in class TestEvoLudo: Recursively search for a file whose name starts with search in directory file.
second(int) - Method in class IBSPopulation: Find the second highest score.
SecondNeighbourGeometry - Class in org.evoludo.simulator.geometries: Square lattice with second-neighbour von Neumann connectivity (diagonals only).
SecondNeighbourGeometry(EvoLudo) - Constructor for class SecondNeighbourGeometry: Create a second-neighbour square lattice geometry tied to the given engine.
seed - Variable in class MersenneTwister: The seed used for the random number generator.
seedSet - Variable in class RNGDistribution: true if seed was set.
SEG_CLOSE - Static variable in class Path2D
SEG_CLOSE - Static variable in interface PathIterator: The segment type constant that specifies that the preceding subpath should be closed by appending a line segment back to the point corresponding to the most recent SEG_MOVETO.
SEG_CUBICTO - Static variable in class Path2D
SEG_CUBICTO - Static variable in interface PathIterator: The segment type constant for the set of 3 points that specify a cubic parametric curve to be drawn from the most recently specified point.
SEG_LINETO - Static variable in class Path2D
SEG_LINETO - Static variable in interface PathIterator: The segment type constant for a point that specifies the end point of a line to be drawn from the most recently specified point.
SEG_MOVETO - Static variable in class Path2D
SEG_MOVETO - Static variable in interface PathIterator: The segment type constant for a point that specifies the starting location for a new subpath.
SEG_QUADTO - Static variable in class Path2D
SEG_QUADTO - Static variable in interface PathIterator: The segment type constant for the pair of points that specify a quadratic parametric curve to be drawn from the most recently specified point.
Segment2D - Class in org.evoludo.geom: Utility class for deal with (finite) line segments in 2D.
Segment2D() - Constructor for class Segment2D: Create a new empty 2D line with coordinates (0,0) and zero length.
Segment2D(double, double, double, double) - Constructor for class Segment2D: Create a new 2D line from point (x1,y1) to point (x2,y2).
Segment2D(Point2D, Point2D) - Constructor for class Segment2D: Create a new 2D line from point p1 to point p2.
Segment2D(Segment2D) - Constructor for class Segment2D: Create a copy of the 2D line l.
selectAutoscaleIndexForYMax(double) - Method in class HistoGraph: Adjust HistoGraph.autoscaleidx to match the given yMax.
selection - Variable in class Map2Fitness: Selection strength for map.
selection - Variable in class NetGames: The selection strength on differences in payoff or cooperativity.
selector - Variable in class ViewController: List box controlling the active view selection.
self - Variable in class IBSGroup: The flag indicating whether to include the focal individual when sampling.
selfClosing - Variable in class PlistTag: Indicates if this tag is self-closing.
serialVersionUID - Static variable in exception class IllegalPathStateException: Use serialVersionUID from JDK 9 for interoperability.
serialVersionUID - Static variable in exception class NoninvertibleTransformException: Use serialVersionUID for interoperability.
set(double, double) - Method in class Line2D: Set the slope m and y-intercept b of the line.
set(double, double) - Method in class Point2D: Set x- and y-coordinates of the point.
set(double, double, double) - Method in class Node2D: Set the x- and y-coordinates and the radius r of 2D node.
set(double, double, double) - Method in class Point3D: Set x-, y- and z-coordinates of the 3D point.
set(double, double, double, double) - Method in class Line2D: Set the slope m and y-intercept b of the line passing through points (x1,y1) and (x2,y2).
set(double, double, double, double) - Method in class Node3D: Set the x-, y- and z-coordinates and the radius r of the 3D node.
set(double, double, double, double) - Method in class Rectangle2D: Set the coordinates of the lower left corner (x,y) and the dimensions of the rectangle.
set(double, double, double, double) - Method in class Segment2D: Set the line segment from point (x1,y1) to point (x2,y2).
set(int, N) - Method in class Network
set(Node2D) - Method in class Node2D: Set the coordinates and radious to those of node n.
set(Node3D) - Method in class Node3D: Set the coordinates and radius to those of node n.
set(Point2D) - Method in class Point2D: Set x- and y-coordinates of the point to those of the 2D point p.
set(Point2D, Point2D) - Method in class Line2D: Set the line to pass through points p1 and p2.
set(Point2D, Point2D) - Method in class Segment2D: Set the line segment from point p1 to point p2.
set(Point2D, Point2D) - Method in class Vector2D: Set the 2D vector to pointing from from to to.
set(Point2D, Vector2D) - Method in class Line2D: Set the line to pass through point p in the direction of vector v.
set(Point3D) - Method in class Point3D: Set x-, y- and z-coordinates of the point to those of the 3D point p.
set(Point3D, Point3D) - Method in class Vector3D: Set the 3D vector pointing from from to to.
set(T) - Method in class RingBuffer.LstItr
setAccuracy(double) - Method in class ODE: Sets the desired accuracy for determining convergence.
setActive(KeyHandler) - Static method in class KeyHandler: Sets the active handler that receives priority for key events.
setActiveTraits(boolean[]) - Method in class Module: Sets which traits are currently active.
setAddwire(double) - Method in class AbstractGeometry: Sets the probability for adding links to the network.
setAddwire(double[]) - Method in class IBSPopulation: Set the probabilities for adding links to the interaction and competition graphs.
setAdjustedDynamics(boolean) - Method in class ODE: Sets whether adjusted dynamics is requested.
setAltruistColor(Color) - Method in class NetGames: Set the color of pure altruists (only help others, don't receive any help from others).
setAnaglyph(boolean) - Method in class PopGraph3D: Set the anaglyph effect for the 3D view.
setArg(String) - Method in class CLOption: Set the argument for the command line option.
setAutoClose(boolean) - Method in class ContextMenu: Sets whether submenus should close automatically when pointer stops hovering over corresponding menu item in parent menu.
setAutoDt(boolean) - Method in class RungeKutta: Sets whether adaptive step sizes should be used.
setAutoHide(boolean) - Method in class ContextMenu: Sets whether context menu hides automatically (with delay) after pointer exits context menu.
setAutoOpen(boolean) - Method in class ContextMenu: Sets whether submenus should open automatically when pointer hovers over corresponding menu item in parent menu.
setBaseline(double) - Method in class Map2Fitness: Sets the baseline fitness of the map.
setBenefit(double) - Method in class Centipede: Set the benefit of cooperation, i.e.
setBenefitFunction(Continuous.Benefits, double[], int) - Method in class Continuous.Traits2Payoff: Set the benefit function of the trait index to benefitfcn.
setBenefitParameters(double[], int) - Method in class Continuous.Traits2Payoff: Set the array of benefit function parameters for trait with index idx to array params.
setBirthRate(double) - Method in class Module: Set the per capita birth rate for ecological population updates.
setBounds(int, int) - Method in class AbstractView: Set the bounds of the view to the given width and height.
setBufferCapacity(int) - Method in class AbstractGraph: Sets the buffer capacity to capacity, if applicable.
setCapacity(int) - Method in class RingBuffer: Set maximum number of entries in ring buffer to capacity.
setCenteredX(double, boolean, double, double) - Method in class ParaGraph: Center and optionally clamp the x-range.
setCenteredY(double, boolean, double, double) - Method in class ParaGraph: Center and optionally clamp the y-range.
setChecked(boolean) - Method in class ContextMenuCheckBoxItem: Set state of check box in menu item to checked.
setCLO(String) - Method in class CLOController: Update the cached command-line string to be parsed.
setCLO(String) - Method in class EvoLudo: Set the raw command line options, as shown e.g.
setColor(double[], Color) - Method in class ColorMap.Gradient2D: Assign a new color to the gradient for value.
setColor(double[], Color) - Method in class ColorMap3D.Gradient2D
setColor(double[], Color, int) - Method in class ColorMap.Gradient2D: Assign a new color to the gradient for value with transparency alpha.
setColor(double, Color) - Method in class ColorMap.Gradient1D: Assign a new color to the gradient for value.
setColor(double, Color, int) - Method in class ColorMap.Gradient1D: Assign a new color to the gradient for value with transparency alpha.
setColor(int, Color) - Method in class ColorMap.Index: Assign a new color to index.
setColor(int, Color, int) - Method in class ColorMap.Index: Assign a new color to index with transparency alpha.
setColorMap(ColorMap) - Method in class GenericPopGraph: Set the map for translating trait values into colors.
setColorModelType(Continuous.ColorModelType) - Method in class Continuous: Set the type of the color model for translating continuous traits into colors.
setColors(Color[]) - Method in class S3Map: Set the colors of the traits.
setColors(String[]) - Method in class AbstractGraph: Assign a list of colors to the graph.
setColors(String[]) - Method in class LineGraph
setCompetitionRates(double[]) - Method in class Module: Sets the competition rate for ecological population updates.
setConnectivity(double) - Method in class AbstractGeometry: Sets the connectivity (average number of neighbors).
setConsistencyCheck(boolean) - Method in class IBSPopulation: Enable consistency checks of the state of the IBS model.
setConverged() - Method in class PDE: Indicates that the numerical integration has converged to a homogeneous state.
setCost(double) - Method in class Centipede: Set the cost of cooperation, i.e.
setCostCoop(double) - Method in class CDL: Set the cost of cooperation.
setCostCoop(double) - Method in class EcoPGG: Set the cost of cooperation.
setCostFunction(Continuous.Costs, double[], int) - Method in class Continuous.Traits2Payoff: Set the cost function of the trait index to costfcn with parameters in the array cparams.
setCostParameters(double[], int) - Method in class Continuous.Traits2Payoff: Set the array of cost function parameters for trait with index idx to array params.
setData(double[][]) - Method in class HistoGraph: Set the data for the histogram.
setDeathRate(double) - Method in class Module: Sets the death rate for ecological population updates.
setDebugEnabled(boolean) - Method in class GenericPopGraph: Set whether the debugging menu is enabled.
setDefault(String) - Method in class CLOption: Set the default argument.
setDelay(int) - Method in class EvoLudo: Set delay between subsequent updates.
setDelay(int) - Method in class EvoLudoGWT
setDelay(int) - Method in class RunController: Set delay between updates.
setDelayHide(int) - Method in class ContextMenu: Set delay before hiding the context (sub)menu (in milliseconds) after the pointer has exited the context menu, provided that autoHide is set to true.
setDelays(int, int) - Method in class Tooltip: Set delay before showing the tooltip as well as the timeout after which the tooltip is hidden again (both in milliseconds).
setDensity() - Method in class PDE: Initializes minimum, maximum and mean density based on current state.
setDescription(String) - Method in class CLOption: Set short description of option.
setDiscretization(int) - Method in class PDE: Sets the number of units used to discretize the spatial dimensions for numerical integration of the PDE.
setDt(double) - Method in class ODE: Sets the discretization of time increments in continuous time models.
setDynamicDampingFactor(double) - Method in class TrackballControls: Set dynamic damping factor (default: 0.2).
setDynamicUpdate(boolean) - Method in class TrackballControls: Enable/disable dynamic moving of 3D view (default: enabled).
setEgoistColor(Color) - Method in class NetGames: Set the color of pure egoists (only receive help from others, don't provide any help to others).
setEnabled(boolean) - Method in class ContextMenuItem
setEnabled(boolean) - Method in class Slider
setEnabled(boolean) - Method in class TrackballControls: Enable/disable trackball controls (default: enabled).
setEnvironment(double[]) - Method in class ATBT: Set the (array of) environmental values or patch qualities for rich and poor sites.
setEnvironmentalAsymmetry(boolean) - Method in class ATBT: Set the flag whether asymmetries are due to environmental differences, i.e.
setError(double) - Method in class PlayerUpdate: Set the error of the updating process.
setExtremalScores() - Method in class Continuous: Helper method to numerically determine the minimum and maximum scores in the game through a brute force hill climbing algorithm for two competing traits as well as monomorphic populations.
setFairColor(Color) - Method in class NetGames: Set the color of fair individuals (help the same number of individuals as help them, regardless of any potential reciprocity).
setFeedback(double[]) - Method in class ATBT: Set the feedback between traits and patch qualities: cooperators restoring poor sites defectors degrading rich sites cooperators degrading rich sites defectors restoring poor sites The array feedback can have one, two or four elements: all four rates/probabilities are the same rates/probabilities for cooperators restoring poor sites and defectors degrading rich sites.
setFitness(double[]) - Method in class Moran: Set the fitness values for residents and mutants.
setFitness(double, int) - Method in class Moran: Set the fitness value for trait aType to aValue.
setFitRange(LineGraph) - Method in class Mean: Set the y-range for fitness graphs; returns true if the range changed.
setFixedAxes(boolean) - Method in class TraitMap
setFixedAxes(boolean) - Method in interface HasPhase2D.Data2Phase: Set whether axes of the phase plane are customizable.
setFixedBoundary(boolean) - Method in class AbstractLattice: Set whether the lattice uses fixed boundaries.
setFont(String) - Method in class AbstractGraph: Set the font to cssfont in CSS format for drawing on the canvas.
setFullscreen(boolean) - Method in class EvoLudoGWT: Enter or exit fullscreen mode.
setFullscreenElement(Element) - Method in class EvoLudoGWT: Set the fullscreen element.
setGeometry(AbstractGeometry) - Method in class GenericPopGraph: Set the geometry backing the graph.
setGeometry(AbstractGeometry) - Method in class PopGraph2D
setGeometry(AbstractGeometry) - Method in class IBSGroup: Set the geometry associated with this group.
setGeometryNames() - Method in class IBSPopulation: Set the names of the interaction and competition geometries based on the module name and whether the geometries are the same or different.
setGradient(Color[]) - Method in class ColorMap.Gradient1D: Sets the gradient to span the colors in the array colors.
setGradient(Color[], int) - Method in class ColorMap.Gradient1D: Sets the gradient for the trait with index trait to span the colors in the array colors.
setGraphGeometry(GenericPopGraph, boolean) - Method in class GenericPop: Helper method to assign a geometry to a graph.
setGraphLabel(String) - Method in class GenericPopGraph: Set the graph label to the string msg (no HTML formatting).
setGroupAt(int, int[], int) - Method in class IBSGroup: Sets the interaction/reference group to group with a size size and the focal indiviual focal.
setHeader(String) - Method in class CLOCategory: Set the header of category for help display.
setHideTimer() - Method in class ContextMenu: Set timer for delayed hiding of context menu if autoClose is true.
setHueRange(double, double) - Method in class ColorMap.Hue: Set hues ranging from start to end in increasing colors.
setHueRange(double, double, boolean) - Method in class ColorMap.Hue: Set the hues ranging from start to end in increasing or decreasing colors.
setIBSPopulation(IBSPopulation) - Method in class Module: Sets the reference to the IBSPopulation that represents this module in individual based simulations.
setInit(IBSC.Init) - Method in class IBSMCPopulation: Sets the type of the initial configuration and any accompanying arguments.
setInit(IBSD.Init) - Method in class IBSDPopulation: Sets the type of the initial configuration and any accompanying arguments.
setInitialState(double[]) - Method in class AbstractView: Notifies the controller that the user requested setting a new initial configuration init (optional implementation).
setInitialState(double[]) - Method in class Phase2D
setInitialState(double[]) - Method in class S3
setInitialTraits(double[]) - Method in interface DModel: Set initial traits in one or all species.
setInitialTraits(double[]) - Method in class IBSD
setInitialTraits(double[]) - Method in class IBSDPopulation: Set the initial trait frequencies in the population.
setInitialTraits(double[]) - Method in class ODE
setInitialTraits(double[]) - Method in class IBSPop
setInitialTraits(int, double[]) - Method in interface DModel: Set initial trait values for species with ID id.
setInitialTraits(int, double[]) - Method in class IBSD
setInitialTraits(int, double[]) - Method in class ODE
setInterest(double) - Method in class CDL: Set interest (multiplication factor) in linear public goods interaction.
setInterest(double) - Method in class EcoPGG: Set the multiplication factor of the linear public goods game.
setInterest(double, double) - Method in class CDL: Set non-linear interest (multiplication factor) in public goods interaction with interest r1 with a single contributor and rN if all N participants contribute.
setInterspecies(boolean) - Method in class AbstractGeometry: Set whether this geometry links different populations.
setLayoutListener(Network.LayoutListener) - Method in class Network: Set the layout listener for this network.
setLayoutTimout(int) - Method in class Network: Set the timeout for layout calculations.
setLeniencyCoop(double) - Method in class CDLP: Set the leniency towards cooperators, provided the composition of the interaction group reveals them as second-order free riders.
setLeniencyLoner(double) - Method in class CDLP: Set the leniency of punishment towards loners.
setLine(Point2D, Point2D) - Method in class Line2D: Set the line to pass through the points p1 and p2.
setLinear() - Method in class Slider: Sets a linear scale for the slider.
setLinearAsymmetry(int) - Method in class LinearGeometry: Set the left-right neighbour difference.
setLinearExtension(double) - Method in class PDE: Sets the linear extension of the lattice.
setLineDash(int[]) - Method in class AbstractGraph.MyContext2d: Set the line dash pattern for drawing lines.
setLocation(double, double) - Method in class Point2D: Compatibility method to cover Point2D.setLocation(double, double).
setLocation(double, double, double) - Method in class Point3D: Compatibility method (following Point2D.setLocation(double, double)).
setLocation(Point2D) - Method in class Point2D: Compatibility method to cover Point2D.setLocation(java.awt.geom.Point2D).
setLocation(Point3D) - Method in class Point3D: Compatibility method (following Point2D.setLocation(Point2D p)).
setLogBase(double) - Method in class Slider: Set the base for a logarithmic slider.
setLogCapacity(int) - Method in class Console: Set the capacity of the log buffer.
setLogger(Logger) - Method in class CLOParser: Sets the logger for reporting warnings while parsing options.
setLogY(boolean) - Method in class AbstractGraph: Set the y-axis to logarithmic scale if logY is true and if yMin ≥ 0.
setLogY(boolean) - Method in class LineGraph
setLongTouch(int) - Method in class ContextMenu: Set delay (in milliseconds) before showing the context menu after a two finger touch, provided that no other touch events fired during delay.
setMap(Map2Fitness.Map) - Method in class Map2Fitness: Sets type of map to map.
setMap(HasPhase2D.Data2Phase) - Method in class ParaGraph: Set the map for converting data to phase plane coordinates.
setMap(S3Map) - Method in class S3Graph: Set the map for converting data to simplex coordinates.
setMarkers(List) - Method in class AbstractGraph: Assign a list of markers to the graph.
setMarkers(List, String[]) - Method in class AbstractGraph: Assign a list of markers with custom colors to the graph.
setMaxEffScoreIdx() - Method in class IBSPopulation: Find the index of the individual with the highest score.
setMigrationProb(double) - Method in class IBSPopulation: Sets the migration probability to aValue.
setMigrationType(IBS.MigrationType) - Method in class IBSPopulation: Sets the type of migrations to type.
setMode(Mode) - Method in class IBS
setMode(Mode) - Method in class Model: Sets the Mode of model/simulator.
setMode(Mode) - Method in class SDE
setModel(Model) - Method in class Module: Set the current model.
setMonoStop(boolean) - Method in class Discrete: Set whether models should stop once a monomorphic state has been reached.
setName(String) - Method in class AbstractGeometry: Set a descriptive name for this geometry (used in UI/tooltips).
setName(String) - Method in class Module: Sets the name of this species.
setNames(String[]) - Method in class S3Map: Set the names of the traits.
setNetwork2D(Network2D) - Method in class AbstractGeometry: Store the 2D network representation.
setNetwork3D(Network3D) - Method in class AbstractGeometry: Store the 3D network representation.
setNextTraitAt(int, int) - Method in class IBSDPopulation: Sets the next trait of the individual with index idx to trait.
setNGroup(int) - Method in class Module: Sets the interaction group size.
setNodes(int) - Method in class Centipede: Set the number of decision nodes for the centipede game.
setNoise(double) - Method in class PlayerUpdate: Set the noise of the updating process of players.
setNormalized(boolean) - Method in class HistoGraph: Set whether the data is normalized.
setNormalized(int) - Method in class HistoGraph: Set the index of the data row that is used for normalization.
setNPopulation(int) - Method in class Module: Sets the population size.
setNSamples(double) - Method in class Model: Sets the number of statistical samples taken after which the active Model is halted.
setNSamples(int) - Method in class IBSGroup: Set the number of interactions with random neighbours.
setNTraits(int) - Method in class Module: Sets the number of traits in this Module.
setNTraits(int, int) - Method in class Module: Sets the number of traits and the index of the vacant type (empty site).
setOffset(int, int) - Method in class ContextMenu: Sets the horizontal and vertical offset between the location where the context menu was triggered and the position of the top left corner of the context menu.
setOffset(int, int) - Method in class Tooltip: Sets the horizontal and vertical offset between the location where the tooltip was triggered and the position of the top left corner of the tooltip.
setOpponent(T) - Method in class Module: Sets the opponent of this module/population.
setOpponentPop(IBSPopulation) - Method in class IBSCPopulation
setOpponentPop(IBSPopulation) - Method in class IBSDPopulation
setOpponentPop(IBSPopulation) - Method in class IBSMCPopulation
setOpponentPop(IBSPopulation) - Method in class IBSPopulation: Set the interaction partner/opponent of this population.
setOptions(String) - Method in class AbstractView: Set the options string for this view.
setOrder(int[]) - Method in class S3Map: Set the indices of the traits displayed on the simplex.
setOrigin(double, double) - Method in class Rectangle2D: Set the coordinates of the origin, lower left corner (x,y), of the rectangle.
setOrtho(boolean) - Method in class PopGraph3D.Pop3DScene: Helper method to allocate, set, or change the camera for the scene.
setOrthographic(boolean) - Method in class PopGraph3D: Set the projection of the camera.
setOthersOnly(boolean) - Method in class CDL: Set the flag whether the return of the public good is split among all members of the group or only all other's, i.e.
setPan(boolean) - Method in class TrackballControls: Enable/disable pan (default: enabled).
setPanSpeed(double) - Method in class TrackballControls: Set pan speed (default: 0.3).
setPayLoneCoop(double) - Method in class CDL: Set the payoff to lone cooperators.
setPayLoneCoop(double) - Method in class EcoPGG: Set the payoff to lone cooperators.
setPayLoneDefect(double) - Method in class CDL: Set the payoff to lone defectors.
setPayLoneDefect(double) - Method in class EcoPGG: Set the payoff to lone defectors.
setPayLoner(double) - Method in class CDL: Set the payoff of loners.
setPayoff(double, int, int) - Method in class TBT: Set the payoff for type me against type you to payoff.
setPayoffs(double[][]) - Method in class ATBT: Set the payoff matrix to payoffs, which can be a 2×2 or 4×4 matrix.
setPayoffs(double[][]) - Method in class RSP: Set the payoff matrix to payMatrix.
setPayoffs(double[][]) - Method in class TBT: Set the payoffs from the 2×2 matrix payoffs.
setPhase2DMap(HasPhase2D.Data2Phase) - Method in class LV
setPhase2DMap(HasPhase2D.Data2Phase) - Method in interface HasPhase2D: Set the map that transforms the data of the module to a 2D phase plane (projection) to map.
setPlayerScoreAveraged(boolean) - Method in class IBSPopulation: Sets whether scores of individuals are averaged over multiple interactions or accumulated.
setPlayerScoring(IBS.ScoringType) - Method in class IBSPopulation: Sets the type for managing scores of individuals.
setPoolPunishCost(double) - Method in class CDLPQ: Set the cost of pool punishment.
setPoolPunishFine(double) - Method in class CDLPQ: Set the pool punishment fine.
setPopulationUpdate(PopulationUpdate) - Method in class IBSPopulation: Sets the population update.
setPosition(int, int) - Method in class Tooltip: Set position (x, y) of tooltip relative to browser window.
setProbability(double) - Method in class RNGDistribution.Geometric: Set the probability of success p for the geometric distribution.
setProbability(double) - Method in class Mutation: Set the probability of mutations.
setProbabilityTrials(double, int) - Method in class RNGDistribution.Binomial: Set the probability of success p and the number of trials n.
setPunishCost(double) - Method in class CDLP: Set the cost of peer punishment of non-contributors.
setPunishFine(double) - Method in class CDLP: Set the fine peer punishment for non-contributors.
setR(double) - Method in class Node2D: Set the radius r of this 2D node.
setR(double) - Method in class Node3D: Set the radius r of the 3D node.
setRadius(double) - Method in class Network: Set the radius of the network to radius.
setRandomSampleProb(double) - Method in class NetGames: Set the probability of picking a random model for comparison.
setRange(double[], double[]) - Method in class ColorMap.Gradient2D: Sets the range of values spanned by the gradient to [min,max] in both dimensions.
setRange(double[], double[]) - Method in class ColorMap3D.Gradient2D
setRange(double[], double[], int) - Method in class ColorMap.Gradient2D: Set the range of data values for three dimensional data with dependent trait.
setRange(double, double) - Method in class ColorMap.Gradient1D: Sets the range of values spanned by the gradient to [min,max].
setRange(double, double) - Method in class ColorMap.Gradient2D: Sets the range of values spanned by the gradient to [min,max] in both dimensions.
setRange(double, double) - Method in class ColorMap3D.Gradient2D
setRange(double, double) - Method in class Slider: Set left and right values of slider.
setRange(double, double, int) - Method in class ColorMap.Gradient2D: Sets the range of values spanned by the gradient to [min,max] for the trait with index index.
setRatio(double) - Method in class NetGames: Set the cost-to-benefit ratio of cooperation.
setRewire(double) - Method in class AbstractGeometry: Sets the probability for rewiring existing links.
setRewire(double[]) - Method in class IBSPopulation: Set the probabilities for rewiring links of the interaction and competition graphs.
setRNG(MersenneTwister) - Method in class RNGDistribution: Set custom random number generator rng of this distribution.
setRotate(boolean) - Method in class TrackballControls: Enable/disable rotation (default: enabled).
setRotateSpeed(double) - Method in class TrackballControls: Set rotation speed (default: 1.0).
setS3Map(S3Map) - Method in interface HasS3: Set the map that transforms the data of the model to a 2D phase plane (projection) to map.
setSampling(IBSGroup.SamplingType) - Method in class IBSGroup: Sets the type of sampling of interaction/reference groups to type.
setScoreAt(int, double, int) - Method in class IBSDPopulation
setScoreAt(int, double, int) - Method in class IBSPopulation: Sets the score of individual with index index to newscore as the result of inter interactions.
setSeed(int[]) - Method in class MersenneTwister: Sets the seed of the MersenneTwister using an array of integers.
setSeed(long) - Method in class MersenneTwister: Initialize the pseudo random number generator.
setSeed(long) - Method in class RNGDistribution: Set seed of random number generator to seed.
setSelection(double) - Method in class Map2Fitness: Sets the selection strength of the map.
setSelection(double) - Method in class NetGames: Set the selection strength on differences in payoffs and cooperativity.
setSelf(boolean) - Method in class IBSGroup: Sets whether random sampling should include the focal individual or not.
setSingle(boolean) - Method in class AbstractGeometry: Sets whether a single geometry is used for both interaction and competition graphs.
setSize(double, double) - Method in class Rectangle2D: Set the dimensions, the width and height, of the rectangle.
setSize(int) - Method in class AbstractGeometry: Set the size of the network.
setSolo(boolean) - Method in class CDL: Set whether public goods is produced already with a single contributor and no other participants.
setStatus(Network.Status) - Method in class Network: Set the status of the layouting process to status.
setSteps(double) - Method in class LineGraph: Set the number of steps along the x-axis.
setSteps(int) - Method in class Slider: Set the number of steps between the minimum and maximum values of the slider.
setStrokeStyleAt(int) - Method in class AbstractGraph: Set the stroke colour for node with index node.
setSuspended(boolean) - Method in class EvoLudo: Set the flag indicating whether the model is suspended.
setSymmetric(boolean) - Method in class PDE: Sets whether symmetries should be preserved.
setSyncFraction(double) - Method in class IBSPopulation: Set the fraction of the population that gets updated in synchronous updates.
setTagAt(int, double) - Method in class IBSPopulation: Sets the tag of the individual with index idx.
setTarget(Vector3) - Method in class TrackballControls: Set the target point where the eye is looking.
setTimeRelax(double) - Method in class Model: Sets the number of generations to relax the initial configuration of the active Model.
setTimeReversed(boolean) - Method in class Model: Request time reversal if reversed==true.
setTimeReversed(boolean) - Method in class ODE
setTimeStep(double) - Method in class Model: Set the report interval, i.e.
setTimeStop(double) - Method in class Model: Sets the number of generations after which the active Model is halted.
Settings() - Constructor for class SettingsController.Settings: Create a new settings record with default capability flags.
SETTINGS - Static variable in class SettingsController: Global settings describing the capabilities of the surrounding ePub environment.
settingsButton - Variable in class SettingsController: Button used to open the settings dialog.
settingsController - Variable in class EvoLudoWeb: Controller for ePub specific behaviour and emulation.
SettingsController - Class in org.evoludo.simulator.ui: Controller responsible for tracking ePub specific settings and emulation flags.
SettingsController(Label, Button, Button, Button, Button) - Constructor for class SettingsController: Creates a new settings controller.
SettingsController.Settings - Class in org.evoludo.simulator.ui: Shared settings describing the current ePub environment.
setTitle(String) - Method in class Slider
setToIdentity() - Method in class AffineTransform: Resets this transform to the Identity transform.
setTooltipProvider(BasicTooltipProvider) - Method in class AbstractGraph: Set the provider for tooltips.
setToQuadrantRotation(int) - Method in class AffineTransform: Sets this transform to a rotation transformation that rotates coordinates by the specified number of quadrants.
setToQuadrantRotation(int, double, double) - Method in class AffineTransform: Sets this transform to a translated rotation transformation that rotates coordinates by the specified number of quadrants around the specified anchor point.
setToRotation(double) - Method in class AffineTransform: Sets this transform to a rotation transformation.
setToRotation(double, double) - Method in class AffineTransform: Sets this transform to a rotation transformation that rotates coordinates according to a rotation vector.
setToRotation(double, double, double) - Method in class AffineTransform: Sets this transform to a translated rotation transformation.
setToRotation(double, double, double, double) - Method in class AffineTransform: Sets this transform to a rotation transformation that rotates coordinates around an anchor point according to a rotation vector.
setToScale(double, double) - Method in class AffineTransform: Sets this transform to a scaling transformation.
setToShear(double, double) - Method in class AffineTransform: Sets this transform to a shearing transformation.
setToTranslation(double, double) - Method in class AffineTransform: Sets this transform to a translation transformation.
setTraitAt(int, double) - Method in class IBSMCPopulation: Set the trait of individual with index idx to trait.
setTraitAt(int, int) - Method in class IBSDPopulation: Sets the trait of the individual with index idx to trait.
setTraitAt(int, int, double) - Method in class IBSMCPopulation: Set trait d of the individual with index idx.
setTraitColors(Color[]) - Method in class Module: Sets trait colors specified in colors.
setTraitMenu - Variable in class S3Graph: The context menu to select the trait in the closest corner.
setTraitNames(String[]) - Method in class Module: Set trait names.
setTraitRange(double, double, int) - Method in class Continuous: Set the trait minimum and maximum for trait trait.
setTraits(int[], int[]) - Method in class TraitMap
setTraits(int[], int[]) - Method in interface HasPhase2D.Data2Phase: Allows custom implementations to set the traits displayed on phase plane axes.
setTraitsAt(int, double[]) - Method in class IBSMCPopulation: Set the trait array of individual with index idx to array idxtraits.
setTrajectoryColor(Color) - Method in class Module: Sets color of trajectories.
setTransform(double, double, double, double, double, double) - Method in class AffineTransform: Sets this transform to the matrix specified by the 6 double precision values.
setTransform(AffineTransform) - Method in class AffineTransform: Sets this transform to a copy of the transform in the specified AffineTransform object.
setType(GeometryType) - Method in class AbstractGeometry: Update the geometry GeometryType.
setType(PopulationUpdate.Type) - Method in class PopulationUpdate: Sets the population update type.
setType(PlayerUpdate.Type) - Method in class PlayerUpdate: Sets the player update type.
setType(SpeciesUpdate.Type) - Method in class SpeciesUpdate: Sets the population update type.
setupCFitGraph(LineGraph) - Method in class Mean: Configure a graph style and colors for fitness in continuous models.
setupConsole(Logger) - Method in class EvoLudoWeb: Setup the EvoLudo console to display log messages.
setupContextMenuHandlers(ContextMenu) - Static method in class ContextMenu: Setup handlers to manage context menu visibility.
setupContextMenuLocation(ContextMenu) - Static method in class ContextMenu: Setup location of context menu in DOM.
setupCTraitGraph(LineGraph, int) - Method in class Mean: Configure a graph style and colors for a single continuous trait.
setupDFitGraph(LineGraph) - Method in class Mean: Configure a graph style and colors for fitness in discrete models.
setupDTraitGraph(LineGraph) - Method in class Mean: Configure a graph style and colors for a discrete module (multiple traits).
setupEngine() - Method in class EvoLudoWeb: Create EvoLudo engine and load modules.
setupLogger(EvoLudoGWT) - Method in class EvoLudoWeb: Retrieve the logger and setup the log handler.
setValue(double) - Method in class Slider: Set the value of slider taking its linear or logarithmic scaling into account.
setViewCorner(ParaGraph.ViewState, double, double) - Method in class ParaGraph: Clamp and apply the view corner for the provided state.
setVR(boolean) - Method in class PopGraph3D: Set the stereo effect for the 3D view.
setWindingRule(int) - Method in class Path2D: Sets the winding rule for this path to the specified value.
setWorldView(Camera) - Method in class Network3DGWT: Set the visual perspective of this network.
setX(double) - Method in class Point2D: Set the x-coordinate of this 2D point.
setX(double) - Method in class Point3D: Set the x-coordinate of this 3D point.
setXRange(int) - Method in class GraphStyle: Set the range of the horizontal axis to xSteps * xIncr.
setY(double) - Method in class Point2D: Set the y-coordinate of this 2D point.
setY(double) - Method in class Point3D: Set the y-coordinate of this 3D point.
setYRange(int) - Method in class GraphStyle: Set the range of the vertical axis to ySteps * yIncr.
setZ(double) - Method in class Point3D: Set the z-coordinate of this 3D point.
setZoom(boolean) - Method in class TrackballControls: Enable/disable zoom (default: enabled).
setZoomSpeed(double) - Method in class TrackballControls: Set zoom speed (default: 1.2).
sfExponent - Variable in class ScalefreeGeometry: Power-law exponent used when sampling the degree distribution.
SHA_EXCLUDE - Static variable in class TestEvoLudo: List of keys to exclude from test case comparisons.
SHA_PREFIX - Static variable in class TestEvoLudo: The prefix to mark the beginning of the SHA hash in the filename.
sha256(Plist, Collection) - Static method in class TestEvoLudo: Compute the SHA-256 hash of the plist, excluding the keys in exclude.
shake(double) - Method in interface Point: Randomly shake the position of this point by an amount scaled by quake.
shake(double) - Method in class Point2D
shake(double) - Method in class Point3D
shake(Network.LayoutListener, double) - Method in class Network: Shake the network by randomly shifting the position of all nodes by an amount of up to quake in any coordinate.
shakeMenu - Variable in class GenericPopGraph: The context menu item for rearranging networks through random shifts of node positions.
sharedContextMenu() - Static method in class ContextMenu: The context menu is added to the RootPanel of the GWT application and shared among all elements that sport a context menu.
sharedTooltip() - Static method in class Tooltip: The tooltip is added to the RootPanel of the GWT application and shared among all elements that sport tooltips.
shear(double, double) - Method in class AffineTransform: Concatenates this transform with a shearing transformation.
shift(double, double) - Method in class Line2D: Shift the line right by dx and up by dy.
shift(double, double) - Method in class Point2D: Shift the 2D point by dx, and dy in the x-, y-coordinates, respectively, to (x+dx,y+dy).
shift(double, double) - Method in class Rectangle2D: Shift/translate the rectangle.
shift(double, double) - Method in class Segment2D
shift(double, double, double) - Method in class Point3D: Shift the 3D point by dx, dy, and dz in the x-, y-, and z-coordinates, respectively, to (x+p.x,y+p.y,z+p.z).
shift(int, int) - Method in class AbstractGraph: Shift the (zoomed) graph within the view port by (dx, dy).
shift(int, int) - Method in interface AbstractGraph.Shifter: Shift the (zoomed) graph within the view port by (dx, dy).
shift(int, int) - Method in class LineGraph
shift(int, int) - Method in class ParaGraph
shift(int, int) - Method in class AbstractView: Default implementation for synchronized shifting of multiple graphs.
shift(Point2D) - Method in class Point2D: Shift the 2D point by p.x, and p.y in the x-, y-coordinates, respectively, to (x+p.x,y+p.y).
shift(Point3D) - Method in class Point3D: Shift the 3D point by p.x, p.y, and p.z in the x-, y-, and z-coordinates, respectively, to (x+p.x,y+p.y,z+p.z).
shifter - Variable in class AbstractGraph: The controller for shifting this graph.
shiftNodeBy(int, int, int) - Method in class PopGraph2D: Shift a single node with index nodeidx by (dx, dy).
show() - Method in class EvoLudoTrigger.LightboxPanel: Show the overlay.
show() - Method in class Console.Log: Show the log buffer in the HTML widget.
show() - Method in class Tooltip: Show tooltip.
showAltModeFromTouch() - Method in class KeyHandler: Marks Alt mode active for touch interactions so button labels update accordingly.
showAltTouchTimer - Variable in class EvoLudoWeb: On touch devices, the Init button changes to Reset for extended touches.
showAt(int, int) - Method in class ContextMenu: Show context menu (or submenu) at position (x, y) relative to browser window.
showAt(ContextMenu.Listener, int, int) - Method in class ContextMenu: Prepares context menu (or submenu) for showing at position (x, y) relative to browser window.
showDecoratedFrame - Variable in class GraphStyle: The flag to indicate whether to show decorations of the frame (ticks and labels).
showFrame - Variable in class GraphStyle: The flag to indicate whether to show the frame of the graph.
showHelp() - Method in class EvoLudoWeb: Show help in the console, EvoLudoWeb.viewConsole.
showHelp() - Method in class EvoLudo: Show help on command line options.
showHelp() - Method in class EvoLudoGWT
showLabel - Variable in class GraphStyle: The flag to indicate whether to show the graph label.
showXLabel - Variable in class GraphStyle: The flag to indicate whether to show the x-axis label.
showXLevels - Variable in class GraphStyle: The flag to indicate whether vertical levels are shown.
showXTickLabels - Variable in class GraphStyle: The flag to indicate whether to show tick labels along the horizontal axis.
showXTicks - Variable in class GraphStyle: The flag to indicate whether tick labels along the horizontal axis are shown.
showYAxisRight - Variable in class GraphStyle: The flag to indicate whether y-axis decorations are drawn on the right.
showYLabel - Variable in class GraphStyle: The flag to indicate whether to show the y-axis label.
showYLevels - Variable in class GraphStyle: The flag to indicate whether horizontal levels are shown.
showYTickLabels - Variable in class GraphStyle: The flag to indicate whether to show tick labels along the vertical axis.
showYTicks - Variable in class GraphStyle: The flag to indicate whether tick labels along the vertical axis are shown.
shrinkBuffer(int) - Method in class RingBuffer: Shrink buffer to capacity.
SHUTDOWN - Enum constant in enum class ChangeListener.PendingAction: GWT application unloaded (stop execution, unload model).
side - Variable in class PopGraph2D: The size of the graph for lattices.
sign(double) - Method in class simCDLP: The sign function.
simCDL - Class in org.evoludo.simulator.exec: Simulations to investigate the role of volunteering in public goods games.
simCDL(EvoLudo) - Constructor for class simCDL: Create a new simulation to investigate the role of volunteering in public goods games.
simCDL.simCDLIBS - Class in org.evoludo.simulator.exec: The simulation for the CDL module.
simCDLIBS(EvoLudo, CDL) - Constructor for class simCDL.simCDLIBS: Create a new simulation.
simCDLP - Class in org.evoludo.simulator.exec: Simulations to investigate peer punishment in the voluntary public goods game.
simCDLP(EvoLudo) - Constructor for class simCDLP: Create a new simulation to investigate the role of punishment in voluntary public goods games.
simCDLPQ - Class in org.evoludo.simulator.exec: Simulations of peer- versus pool-punishment in voluntary public goods games.
simCDLPQ(EvoLudo) - Constructor for class simCDLPQ: Create a new simulation to investigate the role of pool- versus peer-punishment in voluntary public goods games.
simMoran - Class in org.evoludo.simulator.exec: Simulations to investigate the Moran process on graph structured populations.
simMoran(EvoLudoJRE) - Constructor for class simMoran: Create a new simulation to investigate fixation probabilities and times in the Moran process.
SimpleKey(String, String) - Constructor for class CLOption.SimpleKey: Create a new key with the name key and title title.
simTBT - Class in org.evoludo.simulator.exec: Simulation of the two player, two trait model.
simTBT(EvoLudo) - Constructor for class simTBT: Create a new simulation to investigate the two player, two trait model.
simTraits - Class in org.evoludo.simulator.exec: Simulations to investigate individual based simulations versus stochastic differential equations for modelling the evolutionary dynamics of populations with pairwise interactions and d strategic traits.
simTraits(EvoLudo) - Constructor for class simTraits: Create a new simulation to compare the performance of individual based simulations versus stochastic differential equations.
simulation() - Method in class EvoLudo: Run simulation.
Simulation - Static variable in class CLOCategory: The category for simulation specific options.
SIR - Class in org.evoludo.simulator.modules: The SIR module implements the classic Susceptible-Infected-Recovered (SIR) model of disease dynamics.
SIR(EvoLudo) - Constructor for class SIR: Create a new SIR module with the given pacemaker.
SIR.IBSPop - Class in org.evoludo.simulator.modules: Population for individual based simulations of the SIR module.
SIR.ODE - Class in org.evoludo.simulator.modules: ODE model for the SIR module.
SIR.PDE - Class in org.evoludo.simulator.modules: PDE model for the SIR module.
SIR.SDE - Class in org.evoludo.simulator.modules: SDE model for the SIR module.
size - Variable in class AbstractGeometry: The number of nodes in the graph.
size() - Method in class Network
SIZE - Enum constant in enum class SpeciesUpdate.Type: Pick focal species based on population size.
sizeDemes - Variable in class DemesTBT: The size of each deme.
Sizing & Limits - Section in class org.evoludo.graphics.PopGraph2D
sketch(Path2D, boolean) - Method in class AbstractGraph: Draw or fill (if fill == true) the path path.
sketchCircle(double, double, double) - Method in class AbstractGraph: Helper method to create a path for a circle with the center at (x,y) and radius radius.
skewness(double[]) - Static method in class Distributions: Sample skewness of data points x[i] stored in double vector x.
skewness(double[], double) - Static method in class Distributions: Sample skewness of data points x[i] stored in double vector x with known mean m1.
skipComments() - Method in class PlistReader: Utility method to skip comments in plist-string.
skipSHA - Variable in class TestEvoLudo: The flag to indicate whether to skip SHA checks.
Slider - Class in org.evoludo.ui: A standard slider widget.
Slider() - Constructor for class Slider: Creates a slider ranging from 0.0 to 100.0 with 100 steps and initial value (0.0+100.0)/2.
Slider(double, double) - Constructor for class Slider: Creates a slider ranging from min to max with 100 steps and initial value (min+max)/2.
Slider(double, double, double, int) - Constructor for class Slider: Creates a slider ranging from min to max with steps increments and initial value init.
Slider(double, double, double, int, ChangeHandler) - Constructor for class Slider: Creates a slider ranging from min to max with steps increments and initial value init.
Slider(double, double, ChangeHandler) - Constructor for class Slider: Creates a slider ranging from min to max with 100 steps and initial value (min+max)/2 as well as a change handler.
Slider(int, int, int, int, ChangeHandler) - Constructor for class Slider: Creates a slider ranging from min to max with steps increments and initial value init as well as a change handler.
Slider(Element) - Constructor for class Slider: This constructor may be used by subclasses to explicitly use an existing element.
Slider(ChangeHandler) - Constructor for class Slider: Creates a slider ranging from 0.0 to 100.0 with 100 steps and initial value (0.0+100.0)/2 as well as a change handler.
SLIDER_MAX - Static variable in class Slider: Default maximum value of slider.
SLIDER_MIN - Static variable in class Slider: Default minimum value of slider.
SLIDER_STEPS - Static variable in class Slider: Default number of steps between minimum and maximum of slider.
smallScores - Variable in class IBSPopulation: Array to hold scores of individuals during payoff calculations for small groups (not all neighbours).
smallTrait - Variable in class IBSMCPopulation: Temporary storage for traits of individuals in small sub-group interactions.
snapDynamics(Model) - Method in class EvoLudoWeb: Helper method to process snap for dynamics mode.
snapinterval - Variable in class scanCSD: The interval for snapshots.
snapinterval - Variable in class simCDLPQ: The interval for saving snapshots.
snapinterval - Variable in class simTBT: The interval for saving snapshots.
snapLayoutTimeout - Variable in class EvoLudo: timeout for layout process of snapshots in msec.
snapmarker - Variable in class EvoLudoWeb: Marker element to indicate that a snapshot is ready.
snapNearZero(double) - Method in class ParaGraph: Snap small linear values to zero.
snapprefix - Variable in class simTBT: The prefix for snapshot filenames.
snapSamples(Model) - Method in class EvoLudoWeb: Helper method to process snap for statistics sample mode.
snapshotReady() - Method in class EvoLudoWeb: Prepare GUI to create a snapshot.
solidLine - Variable in class GraphStyle: The dashing pattern for a dashed line.
sorting - Variable in class PDE: In order to preserve symmetry the densities of neighbouring cells in the diffusion step need to be sorted.
source - Variable in class IBSDPopulation.Link: The index of the individual at the tail end of the link.
space - Variable in class PDE: AbstractGeometry representing the spatial dimensions of this PDE.
SPAN_CLOSE - Static variable in class Console: String constant for closing an HTML span.
SPAN_OPEN - Static variable in class Console: String constant for opening a colored HTML span.
species - Variable in class Model: Short-cut to the list of species modules.
species - Variable in class Module: List with all species in module including this one.
SPECIES_DELIMITER - Static variable in class CLOParser: The delimiter for separating options in multi-species models.
speciesUpdate - Variable in class IBS: Type of species update (multi-species models only).
SpeciesUpdate - Class in org.evoludo.simulator.modules: The implementation of population updates.
SpeciesUpdate(Module) - Constructor for class SpeciesUpdate: Instantiate new population update for use in IBS models.
SpeciesUpdate.Type - Enum Class in org.evoludo.simulator.modules: Types of species updates (only relevant for multi-species models): size focal species selected proportional to their size fitness focal species selected proportional to their total fitness turns one species is selected after another. sync simultaneous updates of all species (not yet implemented). For size and fitness selection is also proportional to the update rate of each species.
specs - Variable in class AbstractGeometry: Optional CLI specification used to configure this geometry.
spheres - Variable in class PopGraph3D: The colors of the nodes.
SPLIT_ARG_REGEX - Static variable in class CLOParser: The regular expression to split the command line arguments for parsing.
sqrt(double[]) - Static method in class ArrayMath: Element-wise square-root of double array a.
sqrt(float[]) - Static method in class ArrayMath: Element-wise square-root of float array a.
SQRT_2 - Static variable in class S3Graph: Constant for \(\sqrt{2}\).
SQUARE - Enum constant in enum class GeometryType: Square lattice, 2D.
SQUARE - Enum constant in enum class PDEInitialize.Type: Square in the center with uniform trait densities <d1,...dn>.
SQUARE_MOORE - Enum constant in enum class GeometryType: Square lattice (Moore neighbourhood).
SQUARE_NEUMANN - Enum constant in enum class GeometryType: Square lattice (von Neumann neighbourhood).
SQUARE_NEUMANN_2ND - Enum constant in enum class GeometryType: Square lattice.
SquareGeometry - Class in org.evoludo.simulator.geometries: Square lattice with arbitrary neighbourhood sizes.
SquareGeometry(EvoLudo) - Constructor for class SquareGeometry: Create a square lattice geometry tied to the given engine.
srccolors - Variable in class ColorMap.Index: This is currently only needed to pass something to ColorMap.Index.toGradient1D(int).
standalone - Variable in class SettingsController.Settings: true if the lab runs on a standalone ePub page.
STANDARD_SEED - Static variable in class MersenneTwister: The standard initial seed (looks like a birthday?!)
STAR - Enum constant in enum class GeometryType: Star graph, connectivity \(k=2(N-1)/N\).
StarGeometry - Class in org.evoludo.simulator.geometries: Star geometry with node 0 as the hub connected to all leaves.
StarGeometry(EvoLudo) - Constructor for class StarGeometry: Create a star geometry tied to the given engine.
start - Variable in class MersenneTwister.StopWatch: Starting time
start() - Method in class MersenneTwister.StopWatch: Start/reset chronometer.
startColor - Variable in class GraphStyle: The color to mark start of trajectory.
startCPUSample() - Method in class RunController: Start a CPU sampling measurement if no sample is active.
startStatistics() - Method in class simCDL: Start collecting statistics.
startStatistics() - Method in class simCDLP: Start collecting statistics.
startStatistics() - Method in class simCDLPQ: Start collecting statistics.
startStatistics() - Method in class DemesTBT.IBSPop: Start collecting statistics.
startStop() - Method in class EvoLudo: Start or stop EvoLudo model.
startStop() - Method in class RunController: Start or stop EvoLudo model.
state - Variable in class AffineTransform: This field keeps track of which components of the matrix need to be applied when performing a transformation.
state - Variable in class simCDL: Temporary state buffer for sampling.
state - Variable in class simCDLP: Temporary state buffer for sampling.
state - Variable in class simCDLPQ: Temporary state buffer for sampling.
state - Variable in class simTBT: Temporary variables for fixation probabilities and absorption times.
state - Variable in class Mean: The state of the model at the current time.
state - Variable in class Phase2D: The current state of the model.
state - Variable in class S3: The current state of the model.
STATE - Enum constant in enum class AbstractView.ExportType: Current state of simulation, plist
stateEncoder - Variable in class EvoLudo: Responsible for encoding/restoring state and handling version reporting.
StateEncoder - Class in org.evoludo.simulator: Encapsulates encoding and restoration of EvoLudo engine state, including version handling.
StateEncoder(EvoLudo) - Constructor for class StateEncoder: Create a state encoder for the supplied engine.
stateEquals(MersenneTwister) - Method in class MersenneTwister: Returns true if the MersenneTwister's current internal state is equal to another MersenneTwister.
stateError() - Method in class AffineTransform
stateX - Variable in class TraitMap: The array of trait indices that are mapped to the x-axis.
stateY - Variable in class TraitMap: The array of trait indices that are mapped to the y-axis.
STATIC - Enum constant in enum class Map2Fitness.Map: static baseline fitness, \(fit = b+w*score\)
staticBR(int) - Method in class IBSDPopulation: Best response update for static (i.e.
staticfit - Variable in class ODE: For Modules with static fitness, e.g.
staticmodule - Variable in class IBSPopulation: Convenience field for static modules to avoid casts.
Statistics(IBS) - Constructor for class IBS.Statistics: Instantiate new statistics settings for use in IBS models.
STATISTICS_FIXATION_PROBABILITY - Enum constant in enum class Data: Fixation probability: the data represents fixation probabilities.
STATISTICS_FIXATION_TIME - Enum constant in enum class Data: Fixation time: the data represents fixation times.
STATISTICS_SAMPLE - Enum constant in enum class Mode: Statistics: generate samples to create statistics of the model.
STATISTICS_STATIONARY - Enum constant in enum class Data: Stationary distribution.
STATISTICS_UPDATE - Enum constant in enum class Mode: Statistics: generate samples from single run to create statistics of the model reflecting the different states of the population.
statisticsSampleNew - Variable in class Model: The flag to indicate whether to start new statistics sample.
statisticsSettings - Variable in class IBS: The settings for statistics mode.
stattype - Variable in class IBS.Statistics: The statistics type.
status - Variable in class Network: The status of the network layout.
status - Variable in class Histogram: The status of the view.
Status() - Constructor for enum class Network.Status
stdev - Variable in class RNGDistribution.Normal: The standard deviation of the Normal distribution.
stdev(double[]) - Static method in class Distributions: (Sample) Standard deviation of data points x[i] stored in double vector x.
stdev(double[], double) - Static method in class Distributions: (Sample) Standard deviation of data points x[i] stored in double vector x.
step() - Method in class IBSPopulation: Perform a single IBS step, i.e.
step() - Method in class NetGames.IBSPop
steps - Variable in class LineGraph: The default number of (time) steps shown on this graph.
steps - Variable in class Slider: Number of steps between minimum and maximum value of slider.
stop() - Method in class EvoLudo: Requests halting of a running Model on the next opportunity.
stop() - Method in class RunController: Requests halting of a running Model on the next opportunity.
STOP - Enum constant in enum class ChangeListener.PendingAction: Stop execution.
StopWatch() - Constructor for class MersenneTwister.StopWatch: Construct new stop watch and start measuring time.
store(PlistReader, Plist, String, Object) - Static method in class PlistParser: Stores the key-value pair in the dictionary.
STRING_CLOSE - Static variable in class Plist: String constant for closing an string entry during plist generation.
STRING_OPEN - Static variable in class Plist: String constant for opening an string entry during plist generation.
stripBoundary(String) - Method in class AbstractLattice: Helper to strip f|F boundary markers from the argument string and store the result on the instance.
STRIPES - Enum constant in enum class IBSD.Init.Type: Stripes of different traits.
stripExport(String) - Method in class TestEvoLudo: Strip export option from command line options clo.
stripGroupVacancies(IBSGroup, int[], int[]) - Method in class IBSDPopulation: Eliminate vacant sites from the assembled group.
stripKey(String, String) - Static method in class CLOption: Strips the key from the argument.
stripKey(CLOption.Key, String) - Static method in class CLOption: Strips the name of the key from the argument.
stripVacancies(int[], int, int[], int[]) - Method in class IBSDPopulation: Process traits while excluding vacant sites.
stroke(Path2D) - Method in class AbstractGraph: Draw the path path.
strokeCircle(double, double, double) - Method in class AbstractGraph: Draw the circle with the center at (x,y) and radius radius.
strokeCircle(Node2D) - Method in class AbstractGraph: Draw the outline of the 2D node.
strokeCircle(Point2D, double) - Method in class AbstractGraph: Draw the outline of a circle at point with radius.
strokeLine(double, double, double, double) - Method in class AbstractGraph: Draw a line from point (sx,sy) to (ex,ey).
strokeLine(Point2D, Point2D) - Method in class AbstractGraph: Draw a line from point a to b).
strokeRect(double, double, double, double) - Method in class AbstractGraph: Draw the rectangle with origin at (x,y), width w and height h.
STRONG_AMPLIFIER - Enum constant in enum class GeometryType: Strong (undirected) amplifier.
STRONG_SUPPRESSOR - Enum constant in enum class GeometryType: Strong (undirected) suppressor.
StrongAmplifierGeometry - Class in org.evoludo.simulator.geometries: Strong undirected amplifier graph based on Giakkoupis (2016).
StrongAmplifierGeometry(EvoLudo) - Constructor for class StrongAmplifierGeometry: Create a strong amplifier geometry tied to the given engine.
StrongSuppressorGeometry - Class in org.evoludo.simulator.geometries: Geometry implementation for the strong suppressor graphs of Giakkoupis (2016).
StrongSuppressorGeometry(EvoLudo) - Constructor for class StrongSuppressorGeometry: Create a strong suppressor geometry tied to the given engine.
structure - Variable in class Module: The geometry of population (interaction and competition graphs are the same)
structuredBR(int[], int) - Method in class IBSDPopulation: Best response update for structured populations.
style - Variable in class AbstractGraph: The style of the graph.
style - Variable in class ContextMenu: Reference to style of context menu.
style - Variable in class Tooltip: Reference to style of tooltip.
Styling - Section in class org.evoludo.graphics.PopGraph2D
sub(double[], double[]) - Static method in class ArrayMath: Subtract double array sub from array dst.
sub(double[], double[], double[]) - Static method in class ArrayMath: Non-destructive array subtraction.
sub(double, double) - Method in class Vector2D: Subtract dx and dy from coordinates, i.e.
sub(double, double, double) - Method in class Vector3D: Subtract dx, dy and dz from the x-, y-, and z-coordinates, respectively.
sub(float[], float[]) - Static method in class ArrayMath: Subtract float array sub from array dst.
sub(float[], float[], float[]) - Static method in class ArrayMath: Non-destructive array subtraction.
sub(int[], int[]) - Static method in class ArrayMath: Subtract integer array sub from array dst.
sub(int[], int[], int[]) - Static method in class ArrayMath: Non-destructive array subtraction.
sub(long[], long[]) - Static method in class ArrayMath: Subtract long array sub from array dst.
sub(long[], long[], long[]) - Static method in class ArrayMath: Non-destructive array subtraction.
sub(Vector2D) - Method in class Vector2D: Subtract the 2D vector sub from this vector.
sub(Vector2D, Vector2D) - Method in class Vector2D: Subtract 2D vectors b from a and store result in this 2D vector.
sub(Vector3D) - Method in class Vector3D: Subtract the 3D vector sub from this vector.
sub(Vector3D, Vector3D) - Method in class Vector3D: Subtract 3D vectors b from a and store result in this 3D vector.
subType - Variable in class HierarchicalGeometry: The geometry of each hierarchical level.
sum(int, int) - Method in class IBSDPopulation: Helper method to determine the number of stripes required so that each trait shares at least one interface with every other trait: nStripes = nTraits + 2 * sum(2, nTraits - 2).
sumFitness - Variable in class IBSPopulation: The total fitness of the population.
SUPER_STAR - Enum constant in enum class GeometryType: Superstar graph (single hub, petals).
SuperstarGeometry - Class in org.evoludo.simulator.geometries: Directed super-star geometry with configurable petals and amplification.
SuperstarGeometry(EvoLudo) - Constructor for class SuperstarGeometry: Create a super-star geometry tied to the given engine.
supervisor - Variable in class PDE: The supervisor for the integration of the reaction-diffusion process.
Supported Geometry Types - Section in class org.evoludo.graphics.PopGraph2D
Supported initialization types - Section in class org.evoludo.simulator.models.PDEInitialize
SVG - Enum constant in enum class AbstractView.ExportType: Scalable vector graphics format, svg
swap(int[], int, int) - Static method in class ScalefreeGeometry: Swap two entries within an array.
SWAP_MENU - Static variable in class S3Graph: The prefix of the swap order menu item.
SWAP_MENU_ARROW - Static variable in class S3Graph: The arrow symbol used in the swap order menu item.
SWAP_MENU_LABEL - Static variable in class S3Graph: The label of the swap order menu item.
swapEdges(int, int, int, int) - Method in class AbstractGeometry: Utility method to swap edges (undirected links) between nodes: change link a-an to a-bn and b-bn to b-an.
swapOrder(int[], int, int) - Method in class S3Graph: Helper method to swap two entries in the order array.
swapOrderMenu - Variable in class S3Graph: The context menu item to swap the order of the traits along the closest edge.
swapScoresAt(int, int) - Method in class IBSPopulation: Swap the scores (and fitness) of individuals with indices idxa and idxb.
swapTraits(int, int) - Method in class IBSCPopulation
swapTraits(int, int) - Method in class IBSDPopulation
swapTraits(int, int) - Method in class IBSMCPopulation
swapTraits(int, int) - Method in class IBSPopulation: Swap traits of individuals with index a and index b.
swapTraits(int, int) - Method in class NetGames.IBSPop
symDiffMenu - Variable in class EvoLudoGWT: The context menu item for symmetrical diffusion (only applies to PDE models).
SYNC - Enum constant in enum class PopulationUpdate.Type: Synchronized population updates.
syncDelaySlider() - Method in class EvoLudoWeb: Syncs the delay slider with the engine's current delay.
syncFraction - Variable in class IBSPopulation: The fraction of the population that gets updated in synchronous updates.

T

t - Variable in class TrackballControls: Timer for reseting the CSS styling after zooming.
t1(double, int) - Method in class Moran: The absorbtion time (in generations) of a single mutant in a population of constant size N (and N-1 residents).
tA1(int) - Method in class Moran: The conditional fixation time of a single mutant in a population of fixed size N (and N-1 residents) measured in generations.
TABLE_CELL_BULLET - Static variable in interface BasicTooltipProvider: Table cell bullet used to highlight categorical values in tooltips.
TABLE_CELL_NEXT - Static variable in interface BasicTooltipProvider: Table cell separator for tooltips.
TABLE_CELL_NEXT_COLOR - Static variable in interface BasicTooltipProvider: Table cell separator for tooltips with color.
TABLE_END - Static variable in interface BasicTooltipProvider: Table end for tooltips.
TABLE_ROW_END - Static variable in interface BasicTooltipProvider: Table row end for tooltips.
TABLE_ROW_START - Static variable in interface BasicTooltipProvider: Table row start for tooltips.
TABLE_ROW_START_COLOR - Static variable in interface BasicTooltipProvider: Table row start for tooltips, right aligned with color.
TABLE_ROW_START_RIGHT - Static variable in interface BasicTooltipProvider: Table row start for tooltips, right aligned.
TABLE_SEPARATOR - Static variable in interface BasicTooltipProvider: Table row separator for tooltips.
TABLE_STYLE - Static variable in interface BasicTooltipProvider: Table style for tooltips.
tag - Variable in class PlistReader: Next tag.
tag - Variable in class PlistTag: The name of <key> tag.
TAG_ARRAY - Static variable in class PlistParser: Tag for parsing a array entry in a string representing a plist file.
TAG_DICT - Static variable in class PlistParser: Tag for parsing a dict entry in a string representing a plist file.
TAG_FALSE - Static variable in class PlistParser: Tag for parsing a false entry in a string representing a plist file.
TAG_INTEGER - Static variable in class PlistParser: Tag for parsing a integer entry in a string representing a plist file.
TAG_KEY - Static variable in class PlistParser: Tag for parsing a key entry in a string representing a plist file.
TAG_PLIST - Static variable in class PlistParser: Tag for parsing a string representing a plist file.
TAG_PRE_CLOSE - Static variable in class EvoLudoWeb: Closing tag of pre-formatted text.
TAG_PRE_OPEN - Static variable in class EvoLudoWeb: Opening tag of pre-formatted text.
TAG_REAL - Static variable in class PlistParser: Tag for parsing a real entry in a string representing a plist file.
TAG_STRING - Static variable in class PlistParser: Tag for parsing a string entry in a string representing a plist file.
TAG_TRUE - Static variable in class PlistParser: Tag for parsing a true entry in a string representing a plist file.
tags - Variable in class IBSPopulation: The array of individual tags counts.
tAi - Variable in class Moran: Store fixation time of i individuals of type A.
tAi(int, int, double, double) - Method in class Moran: The conditional fixation time of i mutants in a population of fixed size N (and N-i residents) measured in generations.
tanh(double) - Static method in class Functions: Returns the hyperbolic tangent of a double value.
TANH_MAX_ARG - Static variable in class Functions: The maximum argument that the hyperbolic tangent can handle.
target - Variable in class TrackballControls: Target point eye is looking at.
taui - Variable in class Moran: Store absorption time of i individuals of type A.
TBT - Class in org.evoludo.simulator.modules: The module for investigating the evolutionary dynamics in the classical 2×2 games.
TBT(EvoLudo) - Constructor for class TBT: Create a new instance of the module for 2×2 games.
TBT.IBSPop - Class in org.evoludo.simulator.modules: The extension for IBS simulations specific to populations engaging in 2×2 games.
temperature - Variable in class Mutation: The flag to indicate whether mutations arise uniformly distributed (cosmic rays) or are tied to reproduction events (temperature mutations).
TEMPERATURE - Enum constant in enum class IBSD.Init.Type: Single mutant with trait m in otherwise homogeneous population with trait r.
TEMPERING_MASK_B - Static variable in class MersenneTwister: Tempering parameter used in the final transformation.
TEMPERING_MASK_C - Static variable in class MersenneTwister: Second tempering parameter.
test(File) - Method in class TestEvoLudo: Test all files in directory dir.
test(MersenneTwister, Logger, MersenneTwister.Chronometer) - Static method in class RNGDistribution.Binomial: Test Binomial distribution.
test(MersenneTwister, Logger, MersenneTwister.Chronometer) - Static method in class RNGDistribution.Exponential: Test Exponential distribution.
test(MersenneTwister, Logger, MersenneTwister.Chronometer) - Static method in class RNGDistribution.Geometric: Test Geometric distribution.
test(MersenneTwister, Logger, MersenneTwister.Chronometer) - Static method in class RNGDistribution.Gillespie: Test Gillespie algorithm for random weight distribution.
test(MersenneTwister, Logger, MersenneTwister.Chronometer) - Static method in class RNGDistribution.Normal: Test Normal distribution.
test(MersenneTwister, Logger, MersenneTwister.Chronometer) - Static method in class RNGDistribution.Uniform: Test Uniform distribution.
testCorrectness(Logger) - Static method in class MersenneTwister: Tests if generated random numbers comply with reference mt19937ar.c.
TestEvoLudo - Class in org.evoludo.simulator.exec: TestEvoLudo is a test suite for EvoLudo.
TestEvoLudo() - Constructor for class TestEvoLudo: Constructor for TestEvoLudo.
TestEvoLudo.ConsoleColors - Enum Class in org.evoludo.simulator.exec: The control codes for changing the style of the console output.
testSamples - Variable in class RNGDistribution: number of samples for tests.
testsDir - Variable in class TestEvoLudo: Directory containing tests or for storing generated tests.
testSpeed(Logger, MersenneTwister.Chronometer, int) - Static method in class MersenneTwister: Tests speed of MersenneTwister as compared to Random.
THERMAL - Enum constant in enum class PlayerUpdate.Type: Fermi/thermal update
threshold - Variable in class simCDLP: The threshold for qualifying as a corner state.
THRESHOLD_SIZE - Static variable in class RNGDistribution.Gillespie: The threshold for switching between the standard and the optimized version of the Gillespie algorithm.
thumbHorizontal() - Method in interface Resources: Get the GWT sprite for VerticalSplitPanel GUI elements.
thumbVertical() - Method in interface Resources: Get the GWT sprite for HorizontalSplitPanel GUI elements.
ti(int, int, double) - Method in class Moran: The absorbtion time (in generations) of i mutants in a population of constant size N (and N-i residents).
tickLength - Variable in class GraphStyle: The tick length in pixels.
ticksLabelFont - Variable in class GraphStyle: The font for the axes tick labels as a CSS string.
TIETZE - Enum constant in enum class GeometryType: Tietze's graph, size \(N=12\), connectivity \(k=3\).
TietzeGeometry - Class in org.evoludo.simulator.geometries: Geometry implementation for the Tietze graph (a cubic 12-node graph).
TietzeGeometry(EvoLudo) - Constructor for class TietzeGeometry: Create a Tietze geometry tied to the given engine.
time - Variable in class Model: Keeps track of the time elapsed, measured based on the rates with which events occur.
timeFixed - Variable in class FixationData: The time until fixation in realtime units.
timer - Variable in class EvoLudoGWT: Timer for running models.
timeRead - Variable in class FixationData: The flag indicating whether the fixation times have been read.
timeRelax - Variable in class Model: The relaxation time for simulations measured in generations.
timeReverseMenu - Variable in class EvoLudoGWT: The context menu item to reverse time.
timesamples - Variable in class simCDLP: The time to reach the punisher corner.
timestamp - Variable in class Network: The timestamp of the last time the layouting process has completed.
timestamp - Variable in class AbstractView: The timestamp of model at the last update of this view.
timeStep - Variable in class Model: Indicates the interval (measured in generations) after which models report updates on their current state.
timeStop - Variable in class Model: Running simulations are halted when time ≥ timeStop holds for the first time.
tip - Variable in class S3Map: Temporary storage for the simplex coordinates of the tooltip.
title - Variable in enum class GeometryType: Brief description of geometry type for GUI and help display.
title - Variable in enum class IBS.MigrationType: Brief description of migration type for GUI and help display.
title - Variable in enum class IBS.ScoringType: Brief description of population update type for GUI and help display.
title - Variable in enum class IBS.Statistics.Type: Brief description of statistics type for help display.
title - Variable in enum class IBSC.Init.Type: Brief description of initialization type for help display.
title - Variable in enum class IBSD.Init.Type: Brief description of initialization type for help display.
title - Variable in enum class IBSD.OptimizationType: Brief description of optimization type for help display.
title - Variable in enum class IBSGroup.SamplingType: Brief description of interaction type for GUI and help display.
title - Variable in enum class ModelType: Title/description of the model type.
title - Variable in enum class ODEInitialize.InitType: Brief description of initialization type for help display.
title - Variable in enum class PDEInitialize.Type: Brief description of initialization type for help display.
title - Variable in enum class PopulationUpdate.Type: Brief description of population update type for GUI and help display.
title - Variable in enum class Continuous.Benefits: The brief description of the benefit function for the help display.
title - Variable in enum class Continuous.ColorModelType: Brief description of the color model type for help display.
title - Variable in enum class Continuous.Costs: The brief description of the cost function for the help display.
title - Variable in enum class Map2Fitness.Map: Brief description of map for help display.
title - Variable in enum class Mutation.Continuous.Type: Brief description of player update for help display.
title - Variable in enum class Mutation.Discrete.Type: Brief description of player update for help display.
title - Variable in enum class PlayerUpdate.Type: Brief description of player update for help display.
title - Variable in enum class SpeciesUpdate.Type: Brief description of species update type for GUI and help display.
title - Variable in enum class AbstractView.ExportType: The title of the export type.
title - Variable in class Slider: Title of slider.
title - Variable in class CLOption.SimpleKey: The title of the command line option.
tmpCount - Variable in class IBSDPopulation: Temporary storage for the number of each trait in group interactions.
tmpGroup - Variable in class IBSDPopulation: Temporary storage for indices of individuals in group interactions.
tmpGroup - Variable in class IBSMCPopulation: Temporary storage for traits of individuals in group interactions.
tmpScore - Variable in class IBSDPopulation: Temporary storage for the scores of each trait prior to the group interactions.
tmpTraits - Variable in class IBSDPopulation: Temporary storage for traits of individuals in group interactions.
tmpTraitScore - Variable in class IBSDPopulation: Temporary storage for the scores of each trait in group interactions.
toArray() - Method in class Network2D
toArray() - Method in class Network3D
toggleSettings() - Method in class EvoLudoWeb: Helper method to toggle the visibility of EvoLudoWeb.evoludoCLOPanel to view or modify the parameter settings.
toggleState(int[], ContextMenuCheckBoxItem[]) - Method in class Phase2D.TraitCommand: Toggle the inclusion of traits that are selected in items on the current axis.
toggleView - Variable in class KeyHandler: Previously active view before switching to console view.
toGradient1D(int) - Method in class ColorMap.GradientND: Convert the N-dimensional color map into a 1D gradient with a total of nIncr shades.
toGradient1D(int) - Method in class ColorMap.Index: Convert the index colors into a 1D gradient with a total of nIncr shades.
toGradient1D(int) - Method in class ColorMap3D.GradientND
toGradient1D(int) - Method in class ColorMap3D.Index
toGradient1D(int) - Method in class ColorMapCSS.GradientND
toGradient1D(int) - Method in class ColorMapCSS.Index
tooltip - Variable in class AbstractGraph: The reference to the (shared) tooltip.
tooltip - Static variable in class Tooltip: Shared instance of tooltip.
Tooltip - Class in org.evoludo.ui: Tooltip extension to GWT's user interface.
Tooltip() - Constructor for class Tooltip: Create new tooltip.
TOOLTIP_DEFAULT_DELAY_HIDE - Static variable in class Tooltip: Default time until tooltip expires and closes (in milliseconds).
TOOLTIP_DEFAULT_DELAY_SHOW - Static variable in class Tooltip: Default delay before showing the tooltip (in milliseconds) after the pointer started to hover over (part of) element that supplies tooltip.
Tooltip.Provider - Interface in org.evoludo.ui: Provider interface for classes that are responsible for supplying the contents of the tooltip.
Tooltip.Registration - Class in org.evoludo.ui: Manage registrations of listener widgets, their tooltip providers and the corresponding event handlers.
tooltipForIBS(int, int, Module, G, StringBuilder) - Method in class GenericPop: Assemble tooltip for IBS models.
tooltipForPDE(int, int, AbstractGeometry, Module, G, StringBuilder) - Method in class GenericPop: Assemble tooltip for PDE models.
tooltipProvider - Variable in class AbstractGraph: The provider for tooltips.
TooltipProvider - Interface in org.evoludo.graphics: Views that provide more sophisticated tooltips should implement this interface.
TooltipProvider.Index - Interface in org.evoludo.graphics: Views that provide extended tooltips for specific locations that go beyond the capabilities of the BasicTooltipProvider should implement this interface.
TooltipProvider.Parametric - Interface in org.evoludo.graphics: Views that provide extended tooltips for specific (scaled) coordinates (x,y) on a parametric plot that go beyond the capabilities of the BasicTooltipProvider should implement this interface.
TooltipProvider.Simplex - Interface in org.evoludo.graphics: Views that provide extended tooltips for specific (scaled) coordinates (x,y) on a simplex plot that go beyond the capabilities of the BasicTooltipProvider should implement this interface.
Tooltips and context menu - Section in class org.evoludo.graphics.AbstractGraph
top - Variable in class Rectangle2D: The top segment of the rectangle.
toString() - Method in class AffineTransform: Returns a String that represents the value of this Object.
toString() - Method in class Line2D
toString() - Method in class Node2D
toString() - Method in class Node3D
toString() - Method in class Path2D
toString() - Method in class Point2D
toString() - Method in class Point3D
toString() - Method in class Rectangle2D
toString() - Method in class Segment2D
toString() - Method in class Vector2D
toString() - Method in class Vector3D
toString() - Method in enum class TestEvoLudo.ConsoleColors
toString() - Method in enum class GeometryType
toString() - Method in enum class Data
toString() - Method in class FixationData
toString() - Method in enum class IBS.MigrationType
toString() - Method in enum class IBS.ScoringType
toString() - Method in class IBS.Statistics
toString() - Method in enum class IBS.Statistics.Type
toString() - Method in class IBSD.Init
toString() - Method in enum class IBSD.OptimizationType
toString() - Method in enum class IBSGroup.SamplingType
toString() - Method in enum class Mode
toString() - Method in enum class ModelType
toString() - Method in enum class ODEInitialize.InitType
toString() - Method in enum class PDEInitialize.Type
toString() - Method in enum class PopulationUpdate.Type
toString() - Method in enum class Continuous.Benefits
toString() - Method in enum class Continuous.ColorModelType
toString() - Method in enum class Continuous.Costs
toString() - Method in enum class Map2Fitness.Map
toString() - Method in enum class Mutation.Continuous.Type
toString() - Method in enum class Mutation.Discrete.Type
toString() - Method in class PlayerUpdate
toString() - Method in enum class PlayerUpdate.Type
toString() - Method in class SpeciesUpdate
toString() - Method in enum class SpeciesUpdate.Type
toString() - Method in enum class AbstractView.ExportType
totDx - Variable in class LineGraph: The total shift in the x-direction.
totDy - Variable in class LineGraph: The total shift in the y-direction.
totFitnessNoVacant(int) - Method in class IBSPopulation: Compute total fitness of neighbours of individual me assuming no vacant sites.
totFitnessSkipVacant(int) - Method in class IBSPopulation: Compute total fitness of neighbours of individual me assuming vacant sites.
TOUCH_SHIFT_X - Static variable in class Tooltip: Horizontal offset for tooltip placement relative to tap that triggered it.
TOUCH_SHIFT_Y - Static variable in class Tooltip: Vertical offset for tooltip placement relative to tap that triggered it.
touchCancelHandler - Variable in class ContextMenu.Registration: The reference to the touch cancel event handler.
touchEndHandler - Variable in class AbstractGraph: The handler for TouchEndEvents.
touchEndHandler - Variable in class ContextMenu.Registration: The reference to the touch end event handler.
touchEndHandler - Variable in class Tooltip.Registration: Reference to touch end event handler for handling tooltips registered with the listener widget.
touchEndHandler - Variable in class TrackballControls: Reference to touch end event handler for interacting with 3D view.
touchEndRegistration - Variable in class Slider: The touch end event handler registration.
touchEndTime - Variable in class AbstractGraph: The time when the previous touch ended.
touchEvent - Variable in class Tooltip: true if touch events are processed.
touchEventsGWTHandler() - Method in interface Resources: Get the JavaScript file for patching the macOS patch for Apple Books (iBooks) on devices without touch.
touchMoveHandler - Variable in class AbstractGraph: The handler for TouchMoveEvents.
touchMoveHandler - Variable in class ContextMenu.Registration: The reference to the touch move event handler.
touchMoveHandler - Variable in class Tooltip.Registration: Reference to touch move event handler for handling tooltips registered with the listener widget.
touchMoveHandler - Variable in class TrackballControls: Reference to touch move event handler for interacting with 3D view.
touchMoveRegistration - Variable in class Slider: The touch move event handler registration.
touchSlider(TouchEvent) - Method in class Slider: Helper function to update the slider value based on touch events.
touchStartHandler - Variable in class AbstractGraph: The handler for TouchStartEvents.
touchStartHandler - Variable in class ContextMenu.Registration: The reference to the touch start event handler.
touchStartHandler - Variable in class Tooltip.Registration: Reference to touch start event handler for handling tooltips registered with the listener widget.
touchStartHandler - Variable in class TrackballControls: Reference to touch start event handler for interacting with 3D view.
touchStartRegistration - Variable in class Slider: The touch start event handler registration.
touchTimer - Variable in class ContextMenu: Timer for handling touch events that are scheduled to trigger context menu.
TouchTimer() - Constructor for class ContextMenu.TouchTimer: Create a timer to handle delayed touch-triggered context menus.
touchX - Variable in class ContextMenu.TouchTimer: Horizontal position of touch event scheduled to trigger context menu (relative to browser window).
touchY - Variable in class ContextMenu.TouchTimer: Vertical position of touch event scheduled to trigger context menu (relative to browser window).
Tplus(int, int) - Method in class Moran: Transition probability to go from i to i+1 mutants in a population of size N.
TrackballControls - Class in org.evoludo.ui: Trackball controls for 3D views adapted from Parallax and threejs
TrackballControls(Object3D, Widget) - Constructor for class TrackballControls: Creates a new instance of TrackballControls for the 3D scene displayed in widget as seen from the camera.
trait - Variable in class ColorMap.Gradient1D: The index of the trait that this gradient refers to (or -1 if not applicable).
trait - Variable in class Phase2D.TraitCommand: The index of the trait to show on the axis.
TRAIT - Enum constant in enum class Data: Trait: the data represents traits.
TRAIT_DELIMITER - Static variable in class CLOParser: The delimiter for separating options in continuous models with multiple traits.
TRAIT_MEAN - Static variable in class scanCSD: The index of the mean trait.
TRAIT_SDEV - Static variable in class scanCSD: The index of the standard deviation.
trait1 - Variable in class ColorMap.Gradient2D: The index of the color for the first trait.
trait2 - Variable in class ColorMap.Gradient2D: The index of the color for the second trait.
traitColor - Variable in class Module: The array with trait colors.
TraitCommand(int, int) - Constructor for class Phase2D.TraitCommand: Construct a new command to toggle the inclusion of a trait on either one of the phase plane axes.
TraitCommand(ContextMenuCheckBoxItem[], int, int) - Constructor for class Distribution.TraitCommand: Construct a new command to toggle the inclusion of a trait on either one of the phase plane axes.
traitItems - Variable in class Distribution.TraitCommand: The list of traits to toggle.
TraitMap - Class in org.evoludo.graphics: Default mapping of data to the phase plane or phase plane projections.
TraitMap(ParaGraph) - Constructor for class TraitMap: Construct a TraitMap for the given ParaGraph.
traitMax - Variable in class Continuous: The trait maxima.
traitMin - Variable in class Continuous: The trait minima.
traitName - Variable in class Module: Names of traits.
traitRangeMax - Variable in class IBSMCPopulation: The array with the maximal values for each trait.
traitRangeMin - Variable in class IBSMCPopulation: The array with the minimal values for each trait.
traits - Variable in class ColorMap.GradientND: Reference to trait colors that provide the basis to generate gradient colors.
traits - Variable in class IBSDPopulation: The array of individual traits.
traits - Variable in class IBSMCPopulation: The array of individual traits.
TRAITS - Enum constant in enum class Continuous.ColorModelType: Each trait refers to a color channel.
traits2payoff - Variable in class Continuous: The map to translate traits of interacting individuals into payoffs.
Traits2Payoff() - Constructor for class Continuous.Traits2Payoff: Create a payoff translator bound to the enclosing module.
traitsCount - Variable in class IBSDPopulation: The array with the total number of individuals of each trait.
traitsNext - Variable in class IBSDPopulation: The array for temporarily storing traits during updates.
traitsNext - Variable in class IBSMCPopulation: The array for temporarily storing traits during updates.
traitXIdx - Variable in class Distribution: The index of the trait to be shown along the x-axis.
traitXItems - Variable in class Distribution: The context menu for selecting traits to display on the horizontal axis.
traitXItems - Variable in class Phase2D: The context menu for selecting traits to display on the horizontal axis.
traitXMenu - Variable in class Distribution: The context menu trigger for selecting traits to display on the horizontal axis.
traitXMenu - Variable in class Phase2D: The context menu trigger for selecting traits to display on the horizontal axis.
traitYIdx - Variable in class Distribution: The index of the trait to be shown along the y-axis.
traitYItems - Variable in class Distribution: The context menu for selecting traits to display on the vertical axis.
traitYItems - Variable in class Phase2D: The context menu for selecting traits to display on the vertical axis.
traitYMenu - Variable in class Distribution: The context menu trigger for selecting traits to display on the vertical axis.
traitYMenu - Variable in class Phase2D: The context menu trigger for selecting traits to display on the vertical axis.
trajColor - Variable in class GraphStyle: The color of trajectories.
trajectoryColor - Variable in class Module: Color for trajectories.
transform(double[], int, double[], int, int) - Method in class AffineTransform: Transforms an array of double precision coordinates by this transform.
transform(AffineTransform) - Method in class Path2D: Transforms the geometry of this path using the specified AffineTransform.
transform(Point2D[], int, Point2D[], int, int) - Method in class AffineTransform: Transforms an array of point objects by this transform.
transform(Point2D, Point2D) - Method in class AffineTransform: Transforms the specified ptSrc and stores the result in ptDst.
translate(double) - Method in class ColorMap.Gradient: Translate the double value data to a color gradient.
translate(double) - Method in class ColorMap.Gradient1D
translate(double[]) - Method in class ColorMap.Gradient2D
translate(double[]) - Method in class ColorMap: Translate the multi-trait double[] array data to a color.
translate(double[]) - Method in class ColorMap3D.GradientND: Translate the multi-trait double[] array data to a color.
translate(double[]) - Method in class ColorMapCSS.GradientND: Translate the multi-trait double[] array data to a color.
translate(double[][], double[][], T[]) - Method in class ColorMap.Gradient1D: Translate the data1 and data2 arrays of double[] multi-trait values to colors and store the results in the color array.
translate(double[][], double[][], T[]) - Method in class ColorMap: Translate the data1 and data2 arrays of double[] multi-trait values to colors and store the results in the color array.
translate(double[][], T[]) - Method in class ColorMap.Gradient1D: Translate the data array of double[] multi-trait values to colors and store the results in the color array.
translate(double[][], T[]) - Method in class ColorMap.Gradient2D: Translate the data array of double[] multi-trait values to colors and store the results in the color array.
translate(double[][], T[]) - Method in class ColorMap.GradientND: Translate the data array of double[] multi-trait values to colors and store the results in the color array.
translate(double[][], T[]) - Method in class ColorMap: Translate the data array of double[] multi-trait values to colors and store the results in the color array.
translate(double[], T[]) - Method in class ColorMap.Gradient1D: Translate the data array of double values to colors and store the results in the color array.
translate(double[], T[]) - Method in class ColorMap.Gradient2D: Translate the data array of double values to colors and store the results in the color array.
translate(double[], T[]) - Method in class ColorMap.GradientND: Translate the data array of double values to colors and store the results in the color array.
translate(double[], T[]) - Method in class ColorMap: Translate the data array of double values to colors and store the results in the color array.
translate(double, double) - Method in class AffineTransform: Concatenates this transform with a translation transformation.
translate(double, double) - Method in class Path2D: Translate path.
translate(int[], T[]) - Method in class ColorMap.Index
translate(int[], T[]) - Method in class ColorMap: Translate the data array of int values to colors and store the results in the color array.
Tratio(int) - Method in class Moran: The ratio of transition probabilities to go from i to i+1 mutants over the reverse, i.e.
TRIANGULAR - Enum constant in enum class GeometryType: Triangular lattice, connectivity \(k=3\).
TriangularGeometry - Class in org.evoludo.simulator.geometries: Triangular (hexagonal) lattice geometry supporting periodic or fixed boundaries.
TriangularGeometry(EvoLudo) - Constructor for class TriangularGeometry: Create a triangular (hexagonal tiling) geometry linked to the given engine.
trimToSize() - Method in class Path2D: Trim excessive storage of Path2D.
tryConnectOrRewire(int, int, int[], int, int) - Method in class AbstractNetwork: Attempt to connect two nodes, rewiring existing edges if necessary.
tsFit - Variable in class TBT.IBSPop: Timestamp for the last fitness calculation.
tsFits - Variable in class TBT.IBSPop: The trait fitnesses for the two sublattices for GeometryType.SQUARE_NEUMANN_2ND.
tsMean - Variable in class TBT.IBSPop: Timestamp for the last mean trait calculation.
tsTraits - Variable in class TBT.IBSPop: The trait frequencies for the two sublattices for GeometryType.SQUARE_NEUMANN_2ND.
TURNS - Enum constant in enum class SpeciesUpdate.Type: Pick species sequentially.
twist() - Method in class MersenneTwister: The twister: core mechanism for generating pseudo random numbers.
TWO_TO_27 - Static variable in class MersenneTwister: Constant: 2^27.
TWO_TO_31_FLOAT - Static variable in class MersenneTwister: Constant: 2^31.
TWO_TO_31M1 - Static variable in class MersenneTwister: Constant: 2^31 - 1.
TWO_TO_32 - Static variable in class MersenneTwister: Constant: 2^32.
TWO_TO_53 - Static variable in class MersenneTwister: Constant: 2^53.
TWO_TO_NEG24 - Static variable in class MersenneTwister: Constant: 2^-24.
TWO_TO_NEG25 - Static variable in class MersenneTwister: Constant: 2^-25.
TWO_TO_NEG27 - Static variable in class MersenneTwister: Constant: 2^-27.
TWO_TO_NEG31 - Static variable in class MersenneTwister: Constant: 1/2^-31.
TWO_TO_NEG31_FLOAT - Static variable in class MersenneTwister: Constant: 2^-31.
TWO_TO_NEG52 - Static variable in class MersenneTwister: Constant: 2^-52.
TWO_TO_NEG53 - Static variable in class MersenneTwister: Constant: 2^-53.
TWOPI - Static variable in class AbstractGraph: Constant representing the numerical value of \(2 \pi\)
TWOPI - Static variable in class SIR: Useful constant for converting between angular frequency and period.
type - Variable in class AffineTransform: This field caches the current transformation type of the matrix.
type - Variable in class AbstractGeometry: Current geometry type handled by this instance.
type - Variable in class IBSC.Init: The population update type.
type - Variable in class IBSD.Init: The population update type.
type - Variable in class Model: The type of the model: IBS, ODE, SDE, or PDE.
type - Variable in class PopulationUpdate: The population update type.
type - Variable in class Mutation: Mutation type.
type - Variable in class PlayerUpdate: The player update type.
type - Variable in class SpeciesUpdate: The species update type.
type - Variable in class AbstractView: The type of data shown in this graph.
type - Variable in class CLOption: The type of the command line option with no, optional, or required argument.
Type(String, String) - Constructor for enum class IBS.Statistics.Type: Instantiate new statistics type.
Type(String, String) - Constructor for enum class IBSD.Init.Type: Instantiate new initialization type.
Type(String, String) - Constructor for enum class PDEInitialize.Type: Instantiate new initialization type.
Type(String, String) - Constructor for enum class PopulationUpdate.Type: Instantiate new type of population update.
Type(String, String) - Constructor for enum class Mutation.Continuous.Type: Instantiates a new type of player update type.
Type(String, String) - Constructor for enum class Mutation.Discrete.Type: Instantiates a new type of player update type.
Type(String, String) - Constructor for enum class PlayerUpdate.Type: Instantiates a new type of player update type.
Type(String, String) - Constructor for enum class SpeciesUpdate.Type: Instantiate new species update type.
Type(String, String, int) - Constructor for enum class IBSC.Init.Type: Instantiate new initialization type.
TYPE - Static variable in class FullscreenChangeEvent: Event type for fullscreenchange events.
TYPE - Static variable in class InputEvent: Event type for input events.
TYPE_ALTRUIST - Static variable in class NetGames: The color index of altruists.
TYPE_EGOIST - Static variable in class NetGames: The color index of egoists.
TYPE_FAIR - Static variable in class NetGames: The color index of fair players.
TYPE_FLIP - Static variable in class AffineTransform: This flag bit indicates that the transform defined by this object performs a mirror image flip about some axis which changes the normally right handed coordinate system into a left handed system in addition to the conversions indicated by other flag bits.
TYPE_GENERAL_ROTATION - Static variable in class AffineTransform: This flag bit indicates that the transform defined by this object performs a rotation by an arbitrary angle in addition to the conversions indicated by other flag bits.
TYPE_GENERAL_SCALE - Static variable in class AffineTransform: This flag bit indicates that the transform defined by this object performs a general scale in addition to the conversions indicated by other flag bits.
TYPE_GENERAL_TRANSFORM - Static variable in class AffineTransform: This constant indicates that the transform defined by this object performs an arbitrary conversion of the input coordinates.
TYPE_IDENTITY - Static variable in class AffineTransform: This constant indicates that the transform defined by this object is an identity transform.
TYPE_MASK_ROTATION - Static variable in class AffineTransform: This constant is a bit mask for any of the rotation flag bits.
TYPE_MASK_SCALE - Static variable in class AffineTransform: This constant is a bit mask for any of the scale flag bits.
TYPE_QUADRANT_ROTATION - Static variable in class AffineTransform: This flag bit indicates that the transform defined by this object performs a quadrant rotation by some multiple of 90 degrees in addition to the conversions indicated by other flag bits.
TYPE_TRANSLATION - Static variable in class AffineTransform: This flag bit indicates that the transform defined by this object performs a translation in addition to the conversions indicated by other flag bits.
TYPE_UNIFORM_SCALE - Static variable in class AffineTransform: This flag bit indicates that the transform defined by this object performs a uniform scale in addition to the conversions indicated by other flag bits.
TYPE_UNKNOWN - Static variable in class AffineTransform
typeColor - Variable in class NetGames: The colors for altruists, fair players, and egoists.
typeFitness - Variable in class IBSPopulation: Optimization: the lookup table for fitness in well-mixed populations.
typeFixed - Variable in class FixationData: The trait that reached fixation.
typeIdx - Variable in class Path2D.Iterator
typeScores - Variable in class IBSPopulation: Optimization: the lookup table for scores in well-mixed populations.
typeScores - Variable in class Moran: The array with the scores for each trait.

U

uiBinder - Static variable in class EvoLudoWeb: GWT magic to create GUI elements (see EvoLudoWeb.ui.xml).
UNDEFINED - Enum constant in enum class Data: Undefined: the data type is not defined/unknown.
UNDEFINED - Enum constant in enum class PopulationUpdate.Type: No population update selected.
UNDIRECTED - Static variable in class ColorMap3D: The color of undirected links.
Uniform() - Constructor for class RNGDistribution.Uniform: Creates uniform random distribution in interval [0,1) with new instance of MersenneTwister.
Uniform(double, double) - Constructor for class RNGDistribution.Uniform: Creates uniform random distribution in interval [min, max) with new instance of MersenneTwister.
Uniform(MersenneTwister, double, double) - Constructor for class RNGDistribution.Uniform: Creates uniform random distribution in interval [min, max) with random number generator rng.
UNIFORM - Enum constant in enum class IBSC.Init.Type: Uniform distribution of traits covering entire trait interval (default).
UNIFORM - Enum constant in enum class IBSD.Init.Type: Uniform random distribution of traits.
UNIFORM - Enum constant in enum class ODEInitialize.InitType: Uniform initial frequencies of traits.
UNIFORM - Enum constant in enum class PDEInitialize.Type: Uniform/homogeneous distribution of trait densities <d1,...dn>.
UNIFORM - Enum constant in enum class Mutation.Continuous.Type: Mutate to any trait value.
UNIFORM - Enum constant in enum class SpeciesUpdate.Type: Pick focal species uniformly at random.
unitSize - Variable in class IBSGroup.HierarchyUnit: Size of a full hierarchy unit (leaf count).
UNITY - Enum constant in enum class ODEInitialize.InitType: Uniform initial trait densities of one.
UNIVERSE_RADIUS - Static variable in class Network3D: The baseline size of the 3D universe.
unload() - Method in class IBS
unload() - Method in class IBSD
unload() - Method in class Model: Milestone: Unload this model and free resources (if applicable).
unload() - Method in class ODE
unload() - Method in class PDE
unload() - Method in class PDESupervisor: Unload the supervisor and free resources.
unload() - Method in class PDESupervisorGWT
unload() - Method in class RungeKutta
unload() - Method in class SDE
unload() - Method in class ATBT
unload() - Method in class CDL
unload() - Method in class CLabour
unload() - Method in class Continuous
unload() - Method in class Discrete
unload() - Method in class LV
unload() - Method in class Module: Unload module and free all resources.
unload() - Method in class Moran
unload() - Method in class NetGames
unload() - Method in class RSP
unload() - Method in class TBT
unload() - Method in class WebListener: Unregisters this listener from the engine.
unload() - Method in class AbstractView: Unload the view.
unload() - Method in class GenericPop
unload() - Method in class Histogram
unload() - Method in class Phase2D
unload() - Method in class S3
unload() - Method in class TrackballControls: Remove mouse and touch handlers.
unloadModel() - Method in class EvoLudo: Unload model framework.
unloadModel() - Method in class LifecycleController: Unload model framework.
unloadModel(boolean) - Method in class EvoLudo: Unload model framework and, if requested, notifies all registered LifecycleListeners.
unloadModel(boolean) - Method in class LifecycleController: Unload model framework and, if requested, notifies all registered LifecycleListeners.
unloadModule() - Method in class EvoLudo: Unload current module to free up resources.
unloadModule() - Method in class LifecycleController: Unload current module to free up resources.
unloadViews(HashMap) - Method in class ViewController: Unload and remove all views except the console.
unregister() - Method in class KeyHandler: Unregisters the handler and removes listeners when no handlers remain.
unregisterGlobal(KeyHandler) - Static method in class KeyHandler: Unregisters a handler from global key event handling.
update() - Method in class IBS
update() - Method in class Model: Update this model.
update() - Method in class ODE
update() - Method in class PDE: Update this model.
update() - Method in class PDESupervisor: Called after a change of parameters.
update() - Method in class AbstractView: Called when the view needs updating.
update() - Method in class Slider: Updates the logRange if needed as well as the tooltip of the slider.
update() - Method in class Tooltip: Update tooltip if visible.
update() - Method in class TrackballControls: Update the view of the 3D scene.
update(boolean) - Method in class GenericPopGraph: Update the graph.
update(boolean) - Method in class PopGraph2D
update(boolean) - Method in class AbstractView: Called when the view needs updating.
update(boolean) - Method in class Console
update(boolean) - Method in class Distribution
update(boolean) - Method in class GenericPop
update(boolean) - Method in class Histogram
update(boolean) - Method in class Mean
update(boolean) - Method in class Phase2D
update(boolean) - Method in class S3
update(double, double, double, double, double) - Method in class ParaGraph.ViewState: Update the cached view state for the provided base ranges and zoom factor.
updateAutoscale() - Method in class ParaGraph: Update autoscale ranges based on the most recent buffered point.
updateBest(Module, double[], double[], int, int, double[]) - Method in class ODE: Implementation of player update PlayerUpdate.Type.BEST.
updateBestResponse(Module, double[], double[], int, int, double[]) - Method in class ODE: Implementation of the player update PlayerUpdate.Type.BEST_RESPONSE.
updateCanvas() - Method in class AbstractGraph: Update the canvas size and coordinate space dimensions.
updateCFitGraph() - Method in class Mean: Build the data array for continuous fitness graphs (mean +/- stddev).
updateCLO() - Method in class CLOParser: Updates current collection of options by contacting all registered providers.
updateCLOControls(boolean) - Method in class SettingsController: Updates the command-line option controls to reflect whether editing is allowed.
updateCounter() - Method in class EvoLudoWeb: Helper method to update counter of GUI.
updateCTraitGraph(int, int) - Method in class Mean: Build the data array for a continuous-trait graph (mean +/- stddev).
updateData() - Method in class AbstractView: Update view-specific data even when GUI rendering is throttled.
updateData() - Method in class Histogram
updateDegree() - Method in class Histogram: Update degree histograms, delegating to getDegreeHistogramData where needed.
updateDensity(double[], double[], double[]) - Method in class PDE: Update minimum, maximum and mean density during to reaction step.
updateDFitGraph(int) - Method in class Mean: Build the data array for discrete fitness graphs.
updateDomain() - Method in class ParaGraph: Return the current domain limits for zooming and shifting.
updateDropHandlers() - Method in class EvoLudoWeb: Update drag-and-drop handlers after UI toggles changed the layout.
updateDTraitGraph(int) - Method in class Mean: Build the data array for a discrete-trait graph.
updateDynamicsMode() - Method in class ODE: Determine whether the current setup should use density- or frequency-based dynamics and refresh dependent indices accordingly.
updateEcology(Module, double[], double[], int, int, double[]) - Method in class ODE: Implementation of the player updates for modules with populations of variable size (density based or with vacant 'space', i.e.
updateEffScoreRange(int, double, double) - Method in class IBSPopulation: Keep track of highest score through a reference to the corresponding individual.
updateFailed(int, int, double, double, double) - Method in class IBSPopulation: Handle failed adoption decision and log diagnostic details before aborting.
updateFitness() - Method in class Histogram: Update fitness histograms.
updateFitness(double[], double[], double[]) - Method in class PDE: Update minimum, maximum and mean fitnesses during to reaction step.
updateFitnessAt(int) - Method in class IBSPopulation: Update the fitness of the individual with index idx by mapping its current score.
updateFitnessMean() - Method in class NetGames.IBSPop: Update the mean, minimum, and maximum fitness of individuals.
updateFromModelAt(int, int) - Method in class IBSDPopulation
updateFromModelAt(int, int) - Method in class IBSMCPopulation
updateFromModelAt(int, int) - Method in class IBSPopulation: Update individual with index me and adopt the trait of individual with index you.
updateGraph(LineGraph, Module, int, double) - Method in class Mean: Pull updated mean data for the supplied graph and append it to the data buffer.
updateGUI() - Method in class EvoLudoWeb: Update GUI for running/stopped model.
updateImitate(Module, double[], double[], int, int, double[]) - Method in class ODE: Implementation of the player update PlayerUpdate.Type.IMITATE.
updateImitateBetter(Module, double[], double[], int, int, double[]) - Method in class ODE: Implementation of the player update PlayerUpdate.Type.IMITATE_BETTER.
updateKeys() - Method in class EvoLudoWeb: The Alt-key toggles the button labels for controlling the EvoLudo lab.
updateMaxRate() - Method in class IBSDPopulation: Computes the maximum ecological event rate for this species given the current set of rates.
updateMaxRate() - Method in class IBSPop
updateMinMaxScores() - Method in class IBSDPopulation
updateMinMaxScores() - Method in class IBSPopulation: Retrieve and store extremal scores and fitnesses to reduce calls to Module.
updateMixedHierarchy() - Method in class IBSDPopulation: Calculate scores in hierarchical structures with well-mixed units.
updateMixedMeanfield() - Method in class IBSDPopulation: Calculate scores in well-mixed populations.
updateMixedScores() - Method in class IBSDPopulation: Calculate scores in well-mixed populations as well as hierarchical structures with well-mixed units.
updateModifierStates(String) - Method in class KeyHandler: Updates the modifier key states when keys are released.
updateOnce() - Method in class IBSPopulation: Update all individuals in the population once asynchronously.
updatePlayerAsync() - Method in class IBSPopulation: Perform a single, asynchronous update of the trait of a randomly selected individual.
updatePlayerAsyncAt(int) - Method in class IBSPopulation: Update the trait of the focal individual with index me.
updatePlayerAt(int) - Method in class IBSPopulation: Perform a single update of the individual with index me.
updatePlayerAt(int) - Method in class ATBT.ATBTPop
updatePlayerAt(int, int[], int) - Method in class IBSPopulation: Perform a single update of the individual with index me using the rGroupSize models in the array refGroup.
updatePlayerAt(int, int[], int) - Method in class SIR.IBSPop
updatePlayerBest(int, int[], int) - Method in class IBSPopulation: Updates the focal individual with index me by adopting the trait of the best performing reference individual among the rGroupSize models in the array refGroup.
updatePlayerBestHalf(int, int[], int) - Method in class IBSPopulation: Updates the focal individual with index me by adopting the trait of the best performing reference individual among the the rGroupSize models in the array refGroup.
updatePlayerBestResponse(int, int[], int) - Method in class IBSDPopulation: Best-response update.
updatePlayerBestResponse(int, int[], int) - Method in class IBSPopulation: Best-response update.
updatePlayerBestResponse(int, int[], int) - Method in class NetGames.IBSPop
updatePlayerEcology() - Method in class IBSPopulation: Perform a single ecological update of an individual selected uniformly at random.
updatePlayerEcologyAt(int) - Method in class IBSDPopulation: Perform a single ecological update of the individual with index me: Focal individual dies with probability proportional to the death rate.
updatePlayerEcologyAt(int) - Method in class IBSPopulation: Perform a single ecological update of the site with index index.
updatePlayerIndividual(int) - Method in class NetGames.IBSPop: Update the focal individual with index focal by probabilistically removing links from more successful and less cooperative individuals, adding links to more successful and more cooperative individuals.
updatePlayerMoranBirthDeath() - Method in class IBSDPopulation: Perform a single, Moran (Birth-death) update for a random individual selected with a probability proportional to fitness.
updatePlayerMoranBirthDeath() - Method in class IBSPopulation: Perform a single, Moran (Birth-death) update for a random individual selected with a probability proportional to fitness.
updatePlayerMoranBirthDeathAt(int) - Method in class IBSPopulation: Perform a Moran (Birth-death) update for the focal individual with index parent to produce a clonal offspring and replace one of the parent's neighbours selected uniformly at random.
updatePlayerMoranBirthDeathAt(int) - Method in class DemesTBT.IBSPop
updatePlayerMoranDeathBirth() - Method in class IBSDPopulation
updatePlayerMoranDeathBirth() - Method in class IBSPopulation: Perform a single Moran (death-Birth) update for a site selected uniformly at random.
updatePlayerMoranDeathBirth(boolean) - Method in class IBSDPopulation: The optimized Moran process for death-Birth and imitation updatating.
updatePlayerMoranDeathBirthAt(int) - Method in class IBSPopulation: Perform a single Moran (death-Birth) update for the focal site with index vacant.
updatePlayerMoranImitate() - Method in class IBSDPopulation
updatePlayerMoranImitate() - Method in class IBSPopulation: Perform a single, Moran (imitate) update for a site selected uniformly at random.
updatePlayerMoranImitateAt(int) - Method in class IBSPopulation: Update the focal individual with index imitator by comparing its own payoff and those of its neighbors.
updatePlayerSwap(int, int) - Method in class IBSPopulation: Swap players in locations a and b.
updateProgressAfterConnect(int[], int[], int[], int, int, int) - Method in class AbstractNetwork: Update the progress after successfully connecting two nodes.
updateProportional(Module, double[], double[], int, int, double[]) - Method in class ODE: Implementation of the player update PlayerUpdate.Type.PROPORTIONAL.
updateProportionalAbs(int, int[], int) - Method in class IBSPopulation: Updates the focal individual with index me by adopting the trait of one reference individual (including itself) among the the rGroupSize models in the array refGroup with a probability proportional to their scores.
updateReplicate(Module, double[], double[], int, int, double[], double) - Method in class ODE: Helper method to calculate the rate of change for the standard replicator dynamics with different amounts of noise arising from the microscopic update rule.
updateReplicator(int, int[], int, boolean) - Method in class IBSPopulation: Helper method for replicator type updates.
updateReplicatorHalf(int, int[], int) - Method in class IBSPopulation: Updates the focal individual with index me by adopting the trait of one reference individual among the the rGroupSize models in the array refGroup.
updateReplicatorNeutral(int, int[], int, boolean) - Method in class IBSPopulation: Replicator type update in the neutral case.
updateReplicatorNoise(int[], int, double, boolean) - Method in class IBSPopulation: Replicator type update with noise.
updateReplicatorNoNoise(int[], int, double, boolean) - Method in class IBSPopulation: Replicator type update without noise.
updateReplicatorPlus(int, int[], int) - Method in class IBSPopulation: Updates the focal individual with index me by adopting the trait of one reference individual among the the rGroupSize models in the array refGroup.
updates - Variable in class IBS: Keeps track of the time elapsed, measured in number of updates.
updateScheduled - Variable in class AbstractView: The flag to indicate whether an update is already scheduled.
updateScoreAt(int, boolean) - Method in class IBSPopulation: Update the scores of the focal individual with index me.
updateScoreAt(int, double) - Method in class IBSPopulation: Update the score of the individual with index index by adding newscore from single interaction.
updateScoreAt(int, double, int) - Method in class IBSDPopulation
updateScoreAt(int, double, int) - Method in class IBSPopulation: Update the score of the individual with index index by adding (incr > 0 or removing, incr < 0) newscore as the result of incr interactions.
updateScores() - Method in class IBS: For synchronous updates, updates the scores for all populations, checks convergence across all species and returns the total update rate.
updateScores() - Method in class IBSDPopulation: Update the scores of all individuals in the population.
updateScores() - Method in class IBSPopulation: Update the scores of all individuals in the population.
updateScores() - Method in class DemesTBT.IBSPop: Update the scores of all individuals in the population.
updateScores() - Method in class NetGames.IBSPop
updatesFixed - Variable in class FixationData: The number of updates until fixation was reached.
updateState() - Method in class AffineTransform: Manually recalculates the state of the transform when the matrix changes too much to predict the effects on the state.
updateStationary() - Method in class Histogram: Update stationary statistics histograms.
updateStatistics(double) - Method in class simCDL: Update statistics.
updateStatistics(double) - Method in class simCDLP: Update statistics.
updateStatistics(double) - Method in class simCDLPQ: Update statistics.
updateStatistics(double) - Method in class DemesTBT.IBSPop: Update statistics.
updateStatus() - Method in class EvoLudoWeb: Helper method to update status of GUI.
updateSyncAll() - Method in class IBSPopulation: Update all individuals in the population synchronously.
updateSyncFraction() - Method in class IBSPopulation: Update a fraction of individuals in the population synchronously.
updateThermal(int, int[], int) - Method in class IBSPopulation: Updates the focal individual with index me by adopting the trait of one reference individual among the the rGroupSize models in the array refGroup.
updateThermal(Module, double[], double[], int, int, double[]) - Method in class ODE: Implementation of the player update PlayerUpdate.Type.THERMAL.
updateThermalNoise(int, int[], int) - Method in class IBSPopulation: Thermal update with noise.
updateThermalNoNoise(int, int[], int) - Method in class IBSPopulation: Thermal update without noise.
updatetime - Variable in class EvoLudoWeb: Time of last GUI update
updatetimeStatus - Variable in class AbstractView: Time of last status update.
updatetimeView - Variable in class AbstractView: Time of last GUI update
updateTitle() - Method in class Slider: Updates the tooltip of the slider.
updateTooltip() - Method in class Tooltip: Helper method: update contents and visibility of tooltip.
updateTrait() - Method in class Histogram: Update trait histograms (continuous models).
updateTraitCount() - Method in class IBSDPopulation: Update the count of each trait.
updateXRangeFromBuffer() - Method in class LineGraph: Update the x-axis range to show all buffered data (latest segment only).
updateXTickOffset() - Method in class LineGraph: Update the x-axis tick label offset to the most recent finite time value.
updateYRangeFromBuffer(boolean, boolean) - Method in class LineGraph: Update the y-axis range based on buffered data.
UPPER_MASK - Static variable in class MersenneTwister: Mask isolating the most significant w-r bits.
usage() - Method in class AbstractGeometry: Get the usage description for the command line option --geometry.
Usage - Section in class org.evoludo.EvoLudoWeb
Usage - Section in class org.evoludo.graphics.PopGraph2D
Usage - Section in class org.evoludo.simulator.models.PDEInitialize
Usage - Section in class org.evoludo.simulator.views.Phase2D
Usage and integration - Section in class org.evoludo.simulator.views.Pop2D
Usage and integration - Section in class org.evoludo.simulator.views.Pop3D
Usage example (conceptual): - Section in class org.evoludo.graphics.LineGraph
Usage notes: - Section in class org.evoludo.graphics.ParaGraph
Usage notes and important constraints - Section in class org.evoludo.graphics.HistoGraph
useCompression - Variable in class TestEvoLudo: The flag to indicate whether to use compression for the generated test files.
useScheduling() - Method in class Model: GWT models run asynchronously and long running tasks require scheduling to maintain responsive user interface.
useScheduling() - Method in class PDE
useScheduling() - Method in class PDESupervisor: Indicates whether scheduling is used to advance the PDE model.
useScheduling() - Method in class PDESupervisorGWT
Utilities & Helper classes - Section in class org.evoludo.graphics.AbstractGraph

V

VACANT - Static variable in class EcoPGG: The trait (and index) value of defectors.
VACANT - Static variable in class LV: The index of vacant sites.
VACANT_COLOR - Static variable in class Module: The default name of the vacant type (empty site).
VACANT_NAME - Static variable in class Module: The default name of the vacant type (empty site).
vacantIdx - Variable in class IBSPopulation: The index of vacant sites or -1 if module does not support vacancies.
vacantIdx - Variable in class Module: The index for the vacant type (empty site) or -1 if Module does not admit empty sites.
valid - Variable in class ParaGraph.ViewState: Cached validity flag.
validateRewiring() - Method in class AbstractGeometry: Ensure rewiring parameters are feasible for the current connectivity and adjust them if needed.
value - Variable in class PlistTag: The value associated with tag.
valueOf(String) - Static method in enum class TestEvoLudo.ConsoleColors: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class GeometryType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ChangeListener.PendingAction: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class Data: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class IBS.Event: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class IBS.MigrationType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class IBS.ScoringType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class IBS.Statistics.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class IBSC.Init.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class IBSD.Init.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class IBSD.OptimizationType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class IBSGroup.SamplingType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class Mode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ModelType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ODEInitialize.InitType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class PDEInitialize.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class PopulationUpdate.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class Continuous.Benefits: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class Continuous.ColorModelType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class Continuous.Costs: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class Map2Fitness.Map: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class Mutation.Continuous.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class Mutation.Discrete.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class PlayerUpdate.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class SpeciesUpdate.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class Network.Status: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class AbstractView.ExportType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class CLOption.Argument: Returns the enum constant of this class with the specified name.
values() - Static method in enum class TestEvoLudo.ConsoleColors: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class GeometryType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ChangeListener.PendingAction: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class Data: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class IBS.Event: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class IBS.MigrationType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class IBS.ScoringType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class IBS.Statistics.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class IBSC.Init.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class IBSD.Init.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class IBSD.OptimizationType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class IBSGroup.SamplingType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class Mode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ModelType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ODEInitialize.InitType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class PDEInitialize.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class PopulationUpdate.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class Continuous.Benefits: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class Continuous.ColorModelType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class Continuous.Costs: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class Map2Fitness.Map: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class Mutation.Continuous.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class Mutation.Discrete.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class PlayerUpdate.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class SpeciesUpdate.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class Network.Status: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class AbstractView.ExportType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class CLOption.Argument: Returns an array containing the constants of this enum class, in the order they are declared.
var - Variable in class simTBT: Temporary variables for fixation probabilities and absorption times.
variance - Variable in class simCDL: Temporary running variance for fixation probabilities.
variance - Variable in class simCDLP: Temporary running variance for fixation probabilities.
variance - Variable in class simCDLPQ: Temporary running variance for fixation probabilities.
variance(double[]) - Static method in class Distributions: Sample variance of data points x[i] stored in double vector x using one-pass algorithm based on Welford's algorithm.
variance(double[], double) - Static method in class Distributions: Sample variance of data points x[i] stored in double vector x with known mean.
vBorder() - Method in interface Resources: Get the vertical border for GWT GUI elements.
vec - Variable in class Network2D: Temporary storage for the directional vector connecting two nodes.
vec - Variable in class Network3D: Temporary storage for the directional vector connecting two nodes.
VECTOR_DELIMITER - Static variable in class CLOParser: The delimiter for separating entries when passing a vector as an option.
VECTOR_DELIMITER - Static variable in class Formatter: Delimiter between vector elements.
Vector2D - Class in org.evoludo.geom: Utility class for 2D vector manipulations.
Vector2D() - Constructor for class Vector2D: Create a new 2D vector (0,0).
Vector2D(double, double) - Constructor for class Vector2D: Create a new 2D vector with coordinates (x,y).
Vector2D(Point2D) - Constructor for class Vector2D: Create a new 2D vector from point/vector p.
Vector3D - Class in org.evoludo.geom: Utility class for 3D vector manipulations.
Vector3D() - Constructor for class Vector3D: Create a new 3D vector (0,0,0).
Vector3D(double, double, double) - Constructor for class Vector3D: Create a new 3D vector with coordinates (x,y,z).
Vector3D(Vector3D) - Constructor for class Vector3D: Create a new 3D vector from point p.
verbose - Variable in class TestEvoLudo: The flag to indicate whether to run in verbose mode.
verbose() - Method in class Plist: Set verbose mode to report all differences.
vertical() - Method in class Line2D: Check if the line is vertical.
view - Variable in class EvoLudoWeb.GUIState: The active view.
view - Variable in class AbstractGraph: The view of this graph.
viewConsole - Variable in class EvoLudoWeb: Console view requires slightly special treatment to ensure results of early feature detection get reported.
viewController - Variable in class EvoLudoWeb: Controller managing all data views and the EvoLudoWeb.evoludoDeck.
ViewController - Class in org.evoludo.simulator.ui: Controller that manages the set of AbstractView instances displayed in the EvoLudo web client.
ViewController(EvoLudoGWT, DeckLayoutPanel, ListBox, Console, Runnable) - Constructor for class ViewController: Create a controller instance.
viewCorner - Variable in class AbstractGraph: The coordinates of the lower left corner visible on the canvas.
viewCornerXForMin(double) - Method in class ParaGraph.ViewState: Compute a view corner value that aligns the visible minimum with desiredMin.
viewCornerYForMax(double) - Method in class ParaGraph.ViewState: Compute a view corner value that aligns the visible maximum with desiredMax.
Views and Display - Section in class org.evoludo.EvoLudoWeb
viewState - Variable in class ParaGraph: Reusable view state for zooming and shifting calculations.
ViewState() - Constructor for class ParaGraph.ViewState: Private constructor for the ViewState class.
VonNeumannGeometry - Class in org.evoludo.simulator.geometries: Square lattice with von Neumann neighbourhood (four nearest neighbours).
VonNeumannGeometry(EvoLudo) - Constructor for class VonNeumannGeometry: Create a von Neumann square lattice geometry tied to the given engine.
vrMenu - Variable in class Pop3D: The context menu item for selecting stereo projection of the 3D space for a virtual reality representation of the graph.

W

w - Variable in class ParaGraph.ViewState: Cached frame width in pixels.
warn(String) - Method in class AbstractGeometry: Log a warning message using the geometry-conditioned label.
warnIfConnectivityProvided(String) - Method in class SquareGeometry: Emit a warning if the user attempts to specify connectivity for a fixed stencil.
WE_EXP - Enum constant in enum class Continuous.Benefits: Saturating benefit function following an exponential (sum of focal, \(x\), and opponent, \(y\), traits): \(B(x,y)=b_0 \left(1-e^{-b_1\,(x+y)}\right)\).
WE_LINEAR - Enum constant in enum class Continuous.Benefits: Linear benefit function (sum of focal, \(x\), and opponent, \(y\), traits): \(B(x,y)=b_0\,(x+y)\).
WE_LINEAR - Enum constant in enum class Continuous.Costs: Linear cost function (sum of focal, \(x\), and opponent, \(y\), traits): \(C(x,y)=c_0 (x+y)\).
WE_LOG - Enum constant in enum class Continuous.Benefits: Saturating benefit function following a logarithm (sum of focal, \(x\), and opponent, \(y\), traits): \(B(x,y)=b_0\log{b_1\,(x+y)+1}\).
WE_QUAD - Enum constant in enum class Continuous.Benefits: Quadratic benefit function (sum of focal, \(x\), and opponent, \(y\), traits): \(B(x,y)=b_0\,(x+y)+\b_1\,(x+y)^2\).
WE_QUAD - Enum constant in enum class Continuous.Costs: Quadratic cost function (sum of focal, \(x\), and opponent, \(y\), traits): \(C(x,y)=c_0 (x+y)+c_1 (x+y)^2\).
WE_QUARTIC - Enum constant in enum class Continuous.Costs: Quartic cost function (sum of focal, \(x\), and opponent, \(y\), traits): \(C(x,y)=c_0 (x+y)+c_1 (x+y)^2+c_2 (x+y)^3+c_3 (x+y)^4\).
WE_QUBIC - Enum constant in enum class Continuous.Costs: Cubic cost function (sum of focal, \(x\), and opponent, \(y\), traits): \(C(x,y)=c_0 (x+y)+c_1 (x+y)^2+c_2 (x+y)^3\).
WE_SQRT - Enum constant in enum class Continuous.Benefits: Saturating benefit function following a square root (sum of focal, \(x\), and opponent, \(y\), traits): \(B(x,y)=b_0\sqrt{x+y}\).
webListener - Variable in class EvoLudoWeb: Controller managing Lifecycle, Run, Sample, and Change events.
WebListener - Class in org.evoludo.simulator.ui: Centralizes all engine listener callbacks for EvoLudoWeb.
WebListener(EvoLudoWeb, EvoLudoGWT, KeyHandler) - Constructor for class WebListener: Creates a new web listener.
weights - Variable in class ColorMap.GradientND: Temporary variable to store the weights of each color component.
WELLMIXED - Enum constant in enum class GeometryType: Mean-field/well-mixed population.
wellMixedBR(int) - Method in class IBSDPopulation: Best response update for well-mixed populations.
WellmixedGeometry - Class in org.evoludo.simulator.geometries: Geometry implementation for well-mixed (mean-field) populations.
WellmixedGeometry(EvoLudo) - Constructor for class WellmixedGeometry: Create a well-mixed (mean-field) geometry tied to the supplied engine.
WHEEL - Enum constant in enum class GeometryType: Wheel graph, connectivity \(k=4(N-1)/N\).
WheelGeometry - Class in org.evoludo.simulator.geometries: Wheel geometry: ring lattice plus central hub node 0 connected to every rim node.
WheelGeometry(EvoLudo) - Constructor for class WheelGeometry: Create a wheel (cycle with hub) geometry tied to the given engine.
WHITE - Enum constant in enum class TestEvoLudo.ConsoleColors: White color.
WHITE_BACKGROUND - Enum constant in enum class TestEvoLudo.ConsoleColors: White background color.
WHITE_BACKGROUND_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: White high intensity background.
WHITE_BOLD - Enum constant in enum class TestEvoLudo.ConsoleColors: White color.
WHITE_BOLD_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: White high intensity color.
WHITE_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: White high intensity color.
WHITE_UNDERLINED - Enum constant in enum class TestEvoLudo.ConsoleColors: White color.
width - Variable in class Rectangle2D: The width of the rectangle.
WIND_EVEN_ODD - Static variable in class Path2D: An even-odd winding rule for determining the interior of a path.
WIND_EVEN_ODD - Static variable in interface PathIterator: The winding rule constant for specifying an even-odd rule for determining the interior of a path.
WIND_NON_ZERO - Static variable in class Path2D: A non-zero winding rule for determining the interior of a path.
WIND_NON_ZERO - Static variable in interface PathIterator: The winding rule constant for specifying a non-zero rule for determining the interior of a path.
windingRule - Variable in class Path2D
WindowGlobal - Class in org.evoludo.ui: JSInterop bridge exposing the global window object.
WindowGlobal() - Constructor for class WindowGlobal: Utility class – prevent instantiation.
Work in progress... - Section in interface org.evoludo.geom.Node
Work in progress... - Section in interface org.evoludo.geom.Point
worldView - Variable in class Network3DGWT: The Camera controlling the view of the network.
wrap(Element) - Static method in class Slider: Creates a Slider widget that wraps an existing <input> element.
wrapper - Variable in class AbstractGraph: The wrapper element which displays the canvas.
wrapper - Variable in class AbstractView: The GWT widget that contains the graphical representations of the data.
writeFooter() - Method in class EvoLudo: Concluding words for report (currently JRE only).
writeHeader() - Method in class EvoLudo: Write header of report to output (currently JRE only).

X

x - Variable in class Point2D: The x-coordinate of the point.
x - Variable in class Point3D: The x-coordinate of the point.
x - Variable in class HistoGraph.Marker: The x-coordinate of the marker.
x - Variable in class Tooltip: x-coordinates of current tooltip location (relative to listener widget.
X_AXIS - Static variable in class Distribution.TraitCommand: The index of the horizontal axis.
X_AXIS - Static variable in class Phase2D.TraitCommand: The index of the horizontal axis.
x2bin(double) - Method in class HistoGraph: Convert x-coordinate to bin index.
xIncr - Variable in class GraphStyle: The x-axis increments.
xLabel - Variable in class GraphStyle: The x-axis label of the graph (if any).
xMax - Variable in class GraphStyle: The maximum value of the x-axis.
xMin - Variable in class GraphStyle: The minimum value of the x-axis.
XML_TAG - Static variable in class PlistReader: Tag identifying start of XML declaration.
XMLCoder - Class in org.evoludo.util: Encode and decode XML strings.
XMLCoder() - Constructor for class XMLCoder: Suppresses default constructor, ensuring non-instantiability.
XMLDecode - Static variable in class XMLCoder: Lookup table for decoding XML strings.
XMLEncode - Static variable in class XMLCoder: Lookup table for encoding XML strings.
XMLLogFormatter - Class in org.evoludo.util: Formats LogRecords into XML/XHTML compliant text
XMLLogFormatter(boolean) - Constructor for class XMLLogFormatter: Construct a new formatter for log messages without XML/XHTML encoding.
XMLLogFormatter(boolean, boolean) - Constructor for class XMLLogFormatter: Construct a new formatter for log messages with XML/XHTML encoding, provided that isHTML is false.
xTickOffset - Variable in class GraphStyle: The offset added to x-axis tick labels when GraphStyle.offsetXTickLabels is enabled.

Y

y - Variable in class Point2D: The y-coordinate of the point.
y - Variable in class Point3D: The y-coordinate of the point.
y - Variable in class Tooltip: y-coordinates of current tooltip location (relative to listener widget.
y(double) - Method in class Line2D: Return the y-value, y = m*x+b, for given the x-value.
Y_AXIS - Static variable in class Distribution.TraitCommand: The index of the vertical axis.
Y_AXIS - Static variable in class Phase2D.TraitCommand: The index of the vertical axis.
y0 - Variable in class ODE: The initial frequencies/densities of the ODE.
yalpGroupGameAt(IBSGroup) - Method in class IBSCPopulation: Counterpart of IBSPopulation.playGroupGameAt(IBSGroup), IBSPopulation.playGameAt(int) and/or IBSPopulation.playGameSyncAt(int).
yalpGroupGameAt(IBSGroup) - Method in class IBSDPopulation
yalpGroupGameAt(IBSGroup) - Method in class IBSMCPopulation: Counterpart of IBSPopulation.playGroupGameAt(IBSGroup), IBSPopulation.playGameAt(int) and/or IBSPopulation.playGameSyncAt(int).
yalpGroupGameAt(IBSGroup) - Method in class IBSPopulation: Counterpart of IBSPopulation.playGroupGameAt(IBSGroup), IBSPopulation.playGameAt(int) and/or IBSPopulation.playGameSyncAt(int).
yalpGroupGameAt(IBSGroup) - Method in class NetGames.IBSPop
YELLOW - Enum constant in enum class TestEvoLudo.ConsoleColors: Yellow color.
YELLOW_BACKGROUND - Enum constant in enum class TestEvoLudo.ConsoleColors: Yellow background color.
YELLOW_BACKGROUND_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Yellow high intensity background.
YELLOW_BOLD - Enum constant in enum class TestEvoLudo.ConsoleColors: Yellow color.
YELLOW_BOLD_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Yellow high intensity color.
YELLOW_BRIGHT - Enum constant in enum class TestEvoLudo.ConsoleColors: Yellow high intensity color.
YELLOW_UNDERLINED - Enum constant in enum class TestEvoLudo.ConsoleColors: Yellow color.
yerr - Variable in class RungeKutta: Helper variables and temporary storage for errors, states and fitness when calculating derivatives for different steps.
yIncr - Variable in class GraphStyle: The x-axis increments.
yLabel - Variable in class GraphStyle: The y-axis label of the graph (if any).
yMax - Variable in class GraphStyle: The maximum value of the y-axis.
yMin - Variable in class GraphStyle: The minimum value of the y-axis.
you - Variable in class CLabour: Temporary storage for the traits of the opponent.
YOU_EXP - Enum constant in enum class Continuous.Benefits: Saturating benefit function following an exponential (independent of focal): \(B(x,y)=b_0 \left(1-e^{-b_1\,y}\right)\).
YOU_LINEAR - Enum constant in enum class Continuous.Benefits: Linear benefit function (independent of focal): \(B(x,y)=b_0\,y\).
YOU_LOG - Enum constant in enum class Continuous.Benefits: Saturating benefit function following a logarithm (independent of focal): \(B(x,y)=b_0\log{b_1\,y+1}\).
YOU_QUAD - Enum constant in enum class Continuous.Benefits: Quadratic benefit function (independent of focal): \(B(x,y)=b_0\,y+\b_1\,y^2\).
YOU_SQRT - Enum constant in enum class Continuous.Benefits: Saturating benefit function following a square root (independent of focal): \(B(x,y)=b_0\sqrt{y}\).
yout - Variable in class ODE: The previous frequencies/densities of the ODE.
yt - Variable in class ODE: The current frequencies/densities of the ODE.
ytmp - Variable in class RungeKutta

Z

z - Variable in class Point3D: The z-coordinate of the point.
zip() - Method in interface Resources: Get the JavaScript file for accepting compressed files for restoring states through drag'n'drop.
zoom - Variable in class AbstractGraph.ZoomCommand: The adjustment factor of the zoom level.
zoom() - Method in class AbstractGraph: Reset zoom.
zoom() - Method in interface AbstractGraph.Zooming: Reset zoom.
zoom() - Method in class LineGraph
zoom() - Method in class ParaGraph
zoom() - Method in class PopGraph3D.Pop3DScene: Reset zoom level.
zoom() - Method in class TrackballControls: Reset zoom.
zoom(double) - Method in class AbstractGraph: Adjust zoom level by the factor zoom.
zoom(double) - Method in interface AbstractGraph.Zooming: Adjust zoom level by the factor zoom.
zoom(double) - Method in class ParaGraph
zoom(double) - Method in class PopGraph3D.Pop3DScene: Adjust zoom level by the factor zoom.
zoom(double) - Method in class PopGraph3D
zoom(double) - Method in class TrackballControls: Set zoom factor.
zoom(double, double, double) - Method in class AbstractGraph: Helper method to adjust zoom level with the zoom center at the scaled coordinates (fx, fy), specified as a fraction of the view port in horizontal and vertical directions, respectively.
zoom(double, double, double) - Method in class LineGraph
zoom(double, int, int) - Method in class AbstractGraph: Adjust zoom level by the factor zoom with the center at coordinates (x,y) (in display coordinates as provided by event listeners).
zoom(double, int, int) - Method in interface AbstractGraph.Zoomer: Adjust zoom level by the factor zoom with the center at coordinates (x,y) (in display coordinates as provided by event listeners).
zoom(double, int, int) - Method in class ParaGraph
zoom(double, int, int) - Method in class AbstractView: Default implementation for synchronized zooming of multiple graphs.
ZOOM_FIT_MARGIN - Static variable in class LineGraph: Padding applied when fitting the y-axis to visible data.
ZOOM_INCR - Static variable in interface AbstractGraph.Zooming: The factor for increasing/decreasing the zoom level on MouseWheelEvent or TouchMoveEvents.
ZOOM_INCR - Static variable in class TrackballControls: Default increments of zoom factor (multiplicative).
ZOOM_MAX - Static variable in interface AbstractGraph.Zooming: The maximum zoom level.
zoomCamera() - Method in class TrackballControls: Update eye and target for zooming.
zoomChange - Variable in class TrackballControls: Utility variable to keep track of changes of zoom factor while zooming.
ZoomCommand(double) - Constructor for class AbstractGraph.ZoomCommand: Create a new zoom command with an adjustment factor of zoom.
zoomer - Variable in class AbstractGraph: The controller for zooming this graph.
zoomFactor - Variable in class AbstractGraph: The current zoom level.
zoomFitMenu - Variable in class LineGraph: The context menu item to fit the y-axis to the visible data.
zoomFitMenu - Variable in class ParaGraph: The context menu item to zoom to fit the buffered data.
zoomInertiaTimer - Variable in class AbstractGraph: The timer to remove the CSS classes .evoludo-cursorZoomIn or .evoludo-cursorZoomIn, respectively, from the graph element after the inertia of zooming has worn off.
zoomInMenu - Variable in class AbstractGraph: The context menu item to zoom in (enlarge) by a factor of 2.
zoomMenu - Variable in class AbstractGraph: The context menu holding zoom actions.
zoomOutMenu - Variable in class AbstractGraph: The context menu item to zoom out (reduce) by a factor of 1/2.
zoomResetMenu - Variable in class AbstractGraph: The context menu item to reset the zoom level.
zoomSpeed - Variable in class TrackballControls: Speed for zoom.
zoomToFit() - Method in class ParaGraph: Set axis ranges to fit the full buffered trajectory and reset zoom factor.
zoomX - Variable in class ParaGraph.ViewState: Cached x-axis zoom factor.
zoomY - Variable in class ParaGraph.ViewState: Cached y-axis zoom factor.

_

_matround(double) - Static method in class AffineTransform

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