EcoEvo
The EcoEvo package facilitates the analysis of species- and trait-based ecological and eco-evolutionary models.
Project home:
https://github.com/cklausme/EcoEvo
Overall Principles
— general ideas behind EcoEvo package syntax and implementation
Model Structure
— details on parts of EcoEvo models
Example Models
— worked examples where different EcoEvo models are analyzed
Functions
​
EcoEvo Models
SetModel
— set current working model
UnsetModel
— clear current working model
ModelInfo
— summarize current working model
MatrixToPopComponents
,
MatrixToGuildComponents
— help set up a matrix model
WeightedAbundance
— totals components within species in a guild
TotalAbundance
,
TraitMean
,
TraitVariance
— moments of trait distributions

— number of species in a guild
ExtractTraits
 ▪
ExtractInteractions
 ▪
ExtractAttributes
​​
ExtractAuxs
 ▪
ExtractPops
 ▪
ExtractGuilds
 ▪
ExtractSpecies
 ▪
ExtractVariables
TraitsQ
 ▪
InteractionsQ
 ▪
AttributesQ
​​
VariablesQ
 ▪
AttributesAndVariablesQ
 ▪
ListOfVariablesQ
EcoEqns
 ▪
EvoEqns
ExtinctSpecies
 ▪
ExtantSpecies
ParameterValues
 ▪
ClearParameters
Ecological Functions
EcoSim
— simulate ecological dynamics
PlotEcoStreams
,
PlotEcoIsoclines
,
PlotEcoPhasePlane
— ecological phase plane analysis
SolveEcoEq
,
NSolveEcoEq
,
FindEcoEq
— find ecological equilibria
FindEcoCycle
— find ecological cycles
ValidQ
,
SelectValid
— select valid equilibria
EcoJacobian
,
EcoEigenvalues
,
EcoStableQ
,
SelectEcoStable
— ecological stability analysis
FindEcoAttractor
— find an ecological attractor
PlotEcoEq
— plot ecological equilibria
ImpactVector
 ▪
PlotImpactVector
 ▪
PlotZNGI
Invasion Analysis
Inv
— calculate invasion fitness
StablePopulationStructure
,
ReproductiveValues
— left and right eigenvectors
PlotInv
— plot fitness landscape
MaximizeInv
— maximize invasion fitness
GlobalESSQ
,
LocalESSQ
— check whether an eco-evolutionary equilibrium is invadable
Eco-Evolutionary Functions
PlotPIP
,
PlotMIP
,
PlotZIP
— pairwise, mutual, and zero invasibility plots
PlotEvoStreams
,
PlotEvoIsoclines
,
PlotEvoPhasePlane
— evolutionary phase plane analysis
DInv
,
NDInv
— derivatives of invasion fitness
SolveEvoEq
,
NSolveEvoEq
,
FindEvoEq
— find evolutionary equilibria
EvoJacobian
,
EvoEigenvalues
,
GlobalESSQ
— evolutionary stability analysis
EcoEvoSim
— simulate eco-evolutionary dynamics
FindEcoEvoEq
,
FindEcoEvoCycle
,
FindEcoCycleEvoEq
— find eco-evolutionary equilibria
TrackEcoEvoEq
— track an eco-evolutionary equilibrium over a parameter range
EcoEvoJacobian
,
EcoEvoEigenvalues
— eco-evolutionary stability analysis
Plots
PlotDynamics
— plot temporal dynamics
PlotTrajectory
— plot a two- or three-dimensional trajectory
RuleListPlot
— plot two- and three-dimensional rule lists
PlotGuild
— trait abundance distribution (static or temporal)
PrestonPlot
,
WhittakerPlot
— species abundance distributions
PlotInterpolatingFunction
— plot an interpolating function
Rule Lists
MakeRuleList
— construct a rule list
RuleListDistance
— distance between two rule lists
RuleListComplement
— complement of rule lists
RuleListInterpolation
— thread Interpolation through a list of rule lists
ArrayToRuleList
— convert an array to a doubly indexed rule lists
RuleListAdd
 ▪
RuleListSubtract
 ▪
RuleListMultiply
 ▪
RuleListDivide
 ▪
RuleListTweak
 ▪
RuleListSet
RuleListQ
 ▪
NumericRuleListQ
 ▪
SortRuleList
 ▪
JoinFirst
 ▪
SplitSpecies
Temporal Rule Lists
TemporalRuleListQ
Slice
— extract values from a temporal rule lists
InitialSlice
 ▪
FinalSlice
 ▪
FinalDerivatives
InitialTime
 ▪
FinalTime
TemporalMean
,
TemporalVariance
,
TemporalCovariance
— statistical moments of temporal rule lists
FindExtrema
,
FindMaxima
,
FindMinima
— find extrema
ExtremumValues
,
MaximumValues
,
MinimumValues
— find local extremum values
MaximumValue
,
MinimumValue
— find global extrema
RelativeAmplitude
,
AbsoluteAmplitude
— find amplitude
InterpolatingFunctionTake
— extract part of an InterpolatingFunction
InterpolatingFunctionFunctionQ
 ▪
TemporalDataFunctionQ
Reinterpolation
— combine functions of InterpolatingFunctions
Community Structure Metrics
WeightedAbundance
— combine components into a single measure of abundance
TotalAbundance
,
TraitMean
,
TraitVariance
— moments of trait-abundance distributions
TraitDistance
 ▪
FunctionalDistinctiveness
Miscellaneous Functions
NMin
 ▪
NMax
 ▪
NHeavisideTheta
 ▪
NEqual
CompoundAnd
 ▪
CompoundOr
NumericListQ
 ▪
NumericFlattenedListQ
ExtractPlotPoints
 ▪
MyStreamPlot
 ▪
AxisFlip
SortedEigensystem
 ▪
RouthHurwitzCriteria
 ▪
ListMultiplier
NumberedGridForm
 ▪
ClearCache
 ▪
RealSimplify
 ▪
ModPart
FindRoots