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.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(AbstractGraph.Controller controller, Module module)	Create the base class for graphs.
	GenericPopGraph(GenericPopGraph.PopGraphController controller, Module module)	Create the base class for population graphs.
	HistoGraph(AbstractGraph.Controller controller, Module module, int row)	Create new histogram graph for module running in controller.
	LineGraph(AbstractGraph.Controller controller, Module module)	Create new line graph for controller.
	ParaGraph(AbstractGraph.Controller controller, Module module)	Create new parametric graph for module running in controller.
	PopGraph2D(GenericPopGraph.PopGraphController controller, Module module)	Create a graph for graphically visualizing the structure of a network (or population).
	PopGraph3D(GenericPopGraph.PopGraphController controller, Module module)	Create a graph for graphically visualizing the structure of a network (or population).
	S3Graph(AbstractGraph.Controller controller, Module module, int role)	Create a new simplex \(S_3\) graph for module running in controller 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.
Module	EvoLudo.loadModule(String newModuleKey)	Load new module with key newModuleKey.

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.
static boolean	Geometry.displayUniqueGeometry(Module module)	Checks whether a single graphical representation can be used for the interaction and competition graphs.

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

Modifier	Constructor	Description
	Geometry(EvoLudo engine, Module module)	Instantiates a new geometry for intra-species module module with pacemaker engine.
	Geometry(EvoLudo engine, Module popModule, Module oppModule)	Instantiates a new geometry for inter-species module popModule and opponent oppModule with pacemaker engine.

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

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

Modifier and Type	Field	Description
protected Module	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 ArrayList<? 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	IBSPopulation.getModule()	Gets the module associated with this population.
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 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.
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.

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

Modifier	Constructor	Description
protected	IBSPopulation(EvoLudo engine, Module module)	Creates a population of individuals for IBS simulations.

Uses of Module in org.evoludo.simulator.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) Module	Module.opponent	Reference to Module of opponent.

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

Modifier and Type	Field	Description
(package private) ArrayList<? extends Module>	Module.species	List with all species in module including this one.

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

Modifier and Type	Method	Description
Module	Module.getOpponent()	Gets the opponent of this module/population.
Module	Module.getSpecies(int idx)	Gets module of species at index idx.

Methods in org.evoludo.simulator.modules that return types with arguments of type Module

Modifier and Type	Method	Description
ArrayList<? extends Module>	Module.getSpecies()	Gets list with all species.

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

Modifier and Type	Method	Description
void	Module.setOpponent(Module opponent)	Sets the opponent of this module/population.

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	Module(EvoLudo engine, Module partner)	Instantiate a new Module with engine and partner.
	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.views

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

Modifier and Type	Method	Description
private boolean	Histogram.doFixtimeDistr(Module module)	Helper method to check whether to show the fixation time distribution or the fixation times for each node.