Uses of Class
org.evoludo.simulator.modules.Module

Packages that use Module

Package	Description
org.evoludo	EvoLudo - A platform for the exploration of evolutionary models.
org.evoludo.graphics	The GWT graphics for rendering and visualizing evolutionary models.
org.evoludo.simulator	The toolkit to explore interactive evolutionary models.
org.evoludo.simulator.exec	Custom modules for running simulations on the command line.
org.evoludo.simulator.models	The models that generate evolutionary trajectories based on the specifications of each module.
org.evoludo.simulator.modules	The modules to implement various evolutionary models.
org.evoludo.simulator.ui
org.evoludo.simulator.views	The views to visualize results and interact with evolutionary models.

Uses of Module in org.evoludo

Fields in org.evoludo declared as Module

Modifier and Type	Field	Description
(package private) Module<?>	EvoLudoWeb.GUIState.module	The active module.

Uses of Module in org.evoludo.graphics

Fields in org.evoludo.graphics declared as Module

Modifier and Type	Field	Description
protected Module<?>	AbstractGraph.module	The module backing the graph.

Methods in org.evoludo.graphics that return Module

Modifier and Type	Method	Description
Module<?>	AbstractGraph.getModule()	Get the module that backs the graph.

Constructors in org.evoludo.graphics with parameters of type Module

Modifier	Constructor	Description
protected	AbstractGraph(AbstractView<?> view, Module<?> module)	Create the base class for graphs.
protected	GenericPopGraph(AbstractView<?> view, Module<?> module)	Create the base class for population graphs.
	HistoGraph(Histogram view, Module<?> module, int row)	Create new histogram graph for module running in view.
	LineGraph(Mean view, Module<?> module)	Create new line graph for view.
	ParaGraph(Phase2D view, Module<?> module)	Create new parametric graph for module running in view.
	PopGraph2D(AbstractView<?> view, Module<?> module)	Create a graph for graphically visualizing the structure of a network (or population).
	PopGraph3D(Pop3D view, Module<?> module)	Create a graph for graphically visualizing the structure of a network (or population).
	S3Graph(S3 view, Module<?> module, int role)	Create a new simplex \(S_3\) graph for module running in view with the specified role.

Uses of Module in org.evoludo.simulator

Fields in org.evoludo.simulator declared as Module

Modifier and Type	Field	Description
protected Module<?>	EvoLudo.activeModule	The active module.

Fields in org.evoludo.simulator with type parameters of type Module

Modifier and Type	Field	Description
protected HashMap<String, Module<?>>	EvoLudo.modules	The lookup table for all available modules.

Methods in org.evoludo.simulator that return Module

Modifier and Type	Method	Description
Module<?>	EvoLudo.getModule()	Gets the active Module.

Methods in org.evoludo.simulator with parameters of type Module

Modifier and Type	Method	Description
void	EvoLudo.addModule(Module<?> module)	Add module to lookup table of modules using the module's key.

Uses of Module in org.evoludo.simulator.exec

Subclasses of Module in org.evoludo.simulator.exec

Modifier and Type	Class	Description
class	scanCSD	Simulations of the evolution of continuous investement levels in social dilemmas.
class	simCDL	Simulations to investigate the role of volunteering in public goods games.
class	simCDLP	Simulations to investigate peer punishment in the voluntary public goods game.
class	simCDLPQ	Simulations of peer- versus pool-punishment in voluntary public goods games.
class	simMoran	Simulations to investigate the Moran process on graph structured populations.
class	simTBT	Simulation of the two player, two trait model.
class	simTraits	Simulations to investigate individual based simulations versus stochastic differential equations for modelling the evolutionary dynamics of populations with pairwise interactions and d strategic traits.

Uses of Module in org.evoludo.simulator.models

Classes in org.evoludo.simulator.models with type parameters of type Module

Modifier and Type	Class	Description
class	IBSPopulation<M extends Module<?>, P extends IBSPopulation<?,?>>	The core class for individual based simulations.

Fields in org.evoludo.simulator.models declared as Module

Modifier and Type	Field	Description
protected M	IBSPopulation.module	The module associated with this population.
protected Module<?>	PDE.module	Convenience variable: module associated with this model (useful as long as PDE models are restricted to single species).
protected Module<?>	SDE.module	Convenience variable: module associated with this model (useful as long as SDE models are restricted to single species).

Fields in org.evoludo.simulator.models with type parameters of type Module

Modifier and Type	Field	Description
protected List<? extends Module<?>>	Model.species	Short-cut to the list of species modules.

Methods in org.evoludo.simulator.models that return Module

Modifier and Type	Method	Description
Module<?>	Model.getSpecies(int id)	Return the species with ID id.

Methods in org.evoludo.simulator.models with parameters of type Module

Modifier and Type	Method	Description
private IBSPopulation<?,?>	IBS.createIBSPopulation(Module<?> mod)	Factory method to create an IBSPopulation instance for the provided module type.
private double	SDE.getEffectiveNoise(Module<?> mod, int skip)	Helper method to determine the effective demographic noise for a given module based on the current population size.
private boolean	ODEInitialize.processDensity(Module<?> pop, String iargs, int start)	Parse a density/frequency specification and append it to ODE.y0.
private boolean	ODEInitialize.processMutant(Module<?> pop, String iargs, int start)	Parse a mutant initialization specification and append it to ODE.y0.
protected double	ODE.updateBest(Module<?> mod, double[] state, double[] fitness, int nGroup, int index, double[] change)	Implementation of player update PlayerUpdate.Type.BEST.
protected double	ODE.updateBestResponse(Module<?> mod, double[] state, double[] fitness, int nGroup, int index, double[] change)	Implementation of the player update PlayerUpdate.Type.BEST_RESPONSE.
protected double	ODE.updateEcology(Module<?> mod, double[] state, double[] fitness, int nGroup, int index, double[] change)	Implementation of the player updates for modules with populations of variable size (density based or with vacant 'space', i.e.
protected double	ODE.updateImitate(Module<?> mod, double[] state, double[] fitness, int nGroup, int index, double[] change)	Implementation of the player update PlayerUpdate.Type.IMITATE.
protected double	ODE.updateImitateBetter(Module<?> mod, double[] state, double[] fitness, int nGroup, int index, double[] change)	Implementation of the player update PlayerUpdate.Type.IMITATE_BETTER.
protected double	ODE.updateProportional(Module<?> mod, double[] state, double[] fitness, int nGroup, int index, double[] change)	Implementation of the player update PlayerUpdate.Type.PROPORTIONAL.
private double	ODE.updateReplicate(Module<?> mod, double[] state, double[] fitness, int nGroup, int index, double[] change, double noise)	Helper method to calculate the rate of change for the standard replicator dynamics with different amounts of noise arising from the microscopic update rule.
protected double	ODE.updateThermal(Module<?> mod, double[] state, double[] fitness, int nGroup, int index, double[] change)	Implementation of the player update PlayerUpdate.Type.THERMAL.

Uses of Module in org.evoludo.simulator.modules

Classes in org.evoludo.simulator.modules with type parameters of type Module

Modifier and Type	Class	Description
class	Module<T extends Module<T>>	Parent class of all EvoLudo modules.

Subclasses of Module in org.evoludo.simulator.modules

Modifier and Type	Class	Description
class	ATBT	The module for investigating the evolutionary dynamics in asymmetric 2×2 games.
class	CDL	Cooperation in voluntary (non-linear) public goods interactions.
class	CDLP	Cooperation in voluntary (non-linear) public goods interactions with peer punishment.
class	CDLPQ	Cooperation in voluntary (non-linear) public goods interactions with peer and pool punishment.
class	Centipede	The Centipede class provides an EvoLudo module for the centipede game.
class	CLabour	The module for the evolution of two behavioural traits.
class	Continuous	Parent class of all EvoLudo modules with one or more continuous traits.
class	CSD	The module for investigating the evolutionary dynamics of the continuous snowdrift game, or more generally, interactions among pairs of individuals with continuous traits.
class	DemesTBT	Simulations of 2x2 games in deme structured populations.
class	Discrete	Parent class of all EvoLudo modules with discrete sets of traits.
class	EcoPGG	Cooperation in ecological public goods interactions.
class	LV	Lotka-Volterra module for EvoLudo.
class	Moran	The module for investigating the evolutionary dynamics in the classical Moran process with two types of individuals that have constant fitness values.
class	NetGames	Cooperation in dynamical networks.
(package private) class	Predator	Predator class representing the predator species in the Lotka-Volterra model.
class	RSP	Cyclical dynamics of the rock-scissors-paper game.
class	SIR	The SIR module implements the classic Susceptible-Infected-Recovered (SIR) model of disease dynamics.
class	TBT	The module for investigating the evolutionary dynamics in the classical 2×2 games.
class	Traits

Fields in org.evoludo.simulator.modules declared as Module

Modifier and Type	Field	Description
protected Module<?>	ATBT.ODE.module	Convenience variable: module associated with this model (useful for single species).
(package private) Module<?>	Map2Fitness.module	The module that is using this fitness mapping.
(package private) Module<?>	Mutation.module	The module using this mutation.
(package private) Module<?>	PlayerUpdate.module	The module that is using this player update.
(package private) Module<?>	SpeciesUpdate.module	The module that is using this species update.
(package private) T	Module.opponent	Reference to Module of opponent.

Constructors in org.evoludo.simulator.modules with parameters of type Module

Modifier	Constructor	Description
	CentiMutations(Module<?> module)	Constructs a new CentiMutations instance to deal with mutations in the Centipede game.
	Continuous(Module<?> module)	Construct mutator for continuous traits.
	Discrete(Module<?> module)	Construct mutator for discrete traits.
	Map2Fitness(Module<?> module, Map2Fitness.Map map)	Instantiate new map of type map for module.
protected	Mutation(Module<?> module)	Instantiate new mutation.
	PlayerUpdate(Module<?> module)	Instantiate new player update for use in module.
	SpeciesUpdate(Module<?> module)	Instantiate new population update for use in IBS models.

Uses of Module in org.evoludo.simulator.ui

Methods in org.evoludo.simulator.ui with parameters of type Module

Modifier and Type	Method	Description
private void	ViewController.addFitnessViews(Module<?> module, boolean isODESDE, Map<String, AbstractView<?>> oldViews)	Adds fitness-related views based on module capabilities.
private void	ViewController.addStatisticsViews(Module<?> module, Model model, Map<String, AbstractView<?>> oldViews)	Adds statistics-related views based on model permissions.
private void	ViewController.addStrategyViews(Module<?> module, boolean isODESDE, Map<String, AbstractView<?>> oldViews)	Adds strategy-related views according to module capabilities.
private void	ViewController.addStructureViews(Module<?> module, boolean isODESDE, Map<String, AbstractView<?>> oldViews)	Adds structure-related views when available.

Uses of Module in org.evoludo.simulator.views

Methods in org.evoludo.simulator.views with parameters of type Module

Modifier and Type	Method	Description
private void	Phase2D.addDisabledSpeciesName(Module<?> mod, ContextMenu menu)	Add a disabled menu entry used as species header.
private void	Mean.addLineGraph(Module<?> module)	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.
private void	GenericPop.appendFitnessTip(int node, Module<?> module, StringBuilder tip)	Append fitness (and payoffs if the module is using payoff-to-fitness mappings) as well as interaction count for modules implementing the Payoffs interface.
private void	GenericPop.appendPDEFitnessTip(int node, Module<?> module, G graph, StringBuilder tip)	Append fitness and payoff information for PDE models.
private void	GenericPop.appendPDETraitTip(int node, Module<?> module, G graph, StringBuilder tip)	Append trait and density information for PDE models.
private ColorMap<String>	Pop2D.createColorMap(Module<?> module)	Create the ColorMap for a given module/graph based on the current data type and model settings.
private ColorMap<MeshLambertMaterial>	Pop3D.createColorMap(Module<?> module)	Create the ColorMap for a given module/graph based on the current data type and model settings.
private ColorMap<String>	Pop2D.createFitnessColorMap(Module<?> module)	Helper to create color map for fitness data.
private ColorMap<MeshLambertMaterial>	Pop3D.createFitnessColorMap(Module<?> module)	Helper to create color map for fitness data.
private S3Graph	S3.createS3Graph(Module<?> module, int role)	Helper method to create and configure an S3Graph for a given role.
private ColorMap<String>	Pop2D.createTraitColorMapContinuous(Module<?> module)	Helper for continuous trait color maps.
private ColorMap<MeshLambertMaterial>	Pop3D.createTraitColorMapContinuous(Module<?> module)	Helper for continuous trait color maps.
private ColorMap<String>	Pop2D.createTraitColorMapDiscreteOrPDE(Module<?> module)	Helper for discrete and PDE trait color maps.
private ColorMap<MeshLambertMaterial>	Pop3D.createTraitColorMapDiscreteOrPDE(Module<?> module)	Helper for discrete and PDE trait color maps.
private boolean	Histogram.doFixtimeDistr(Module<?> module)	Helper method to check whether to show the fixation time distribution or the fixation times for each node.
private boolean	Histogram.handleDEGraph(HistoGraph graph, ModelType mt, Module<?> module)	Handle messaging for DE/PDE models; returns true if a message was set on the graph and further processing should be skipped.
private String	GenericPop.tooltipForIBS(int node, int nNodes, Module<?> module, G graph, StringBuilder tip)	Assemble tooltip for IBS models.
private String	GenericPop.tooltipForPDE(int node, int nNodes, AbstractGeometry geometry, Module<?> module, G graph, StringBuilder tip)	Assemble tooltip for PDE models.
private int	Mean.updateGraph(LineGraph graph, Module<?> module, int idx, double newtime)	Pull updated mean data for the supplied graph and append it to the data buffer.

Method parameters in org.evoludo.simulator.views with type arguments of type Module

Modifier and Type	Method	Description
private int	Histogram.addDegreeGraphs(List<? extends Module<?>> species, int nGraphs)	Add degree graphs for the given module.
private int	Histogram.addFitnessGraphs(List<? extends Module<?>> species, int nGraphs)	Add fitness graphs for the given module.
private int	Histogram.addFixationProbabilityGraphs(List<? extends Module<?>> species, int nGraphs)	Add fixation probability graphs for the given module.
private int	Histogram.addFixationTimeGraphs(List<? extends Module<?>> species, int nGraphs)	Add fixation time graphs for the given module.
private int	Histogram.addStationaryGraphs(List<? extends Module<?>> species, int nGraphs)	Add stationary distribution graphs for the given module.
private int	Histogram.addTraitGraphs(List<? extends Module<?>> species)	Add trait histogram for the given module.
private void	Phase2D.buildTraitMenus(ContextMenu parent, List<? extends Module<?>> species, boolean isMultispecies)	Build or update trait selection sub-menus for the X and Y axes.
private int	Phase2D.computeTotalTraits(List<? extends Module<?>> species, boolean isDensity)	Compute total number of trait entries that will appear in the trait menus.
private void	Phase2D.populateTraitItems(List<? extends Module<?>> species, boolean isMultispecies)	Populate the trait menu items and optional species headers.