Function reference • TreEvo

All functions
`TreEvo-package`	TreEvo--abc for comparative methods
`boxcoxTransformation()` `boxcoxTransformationMatrix()`	Box-Cox Transformation for Simulation Summary Values
`compareListIPD()`	Plot Interparticle Distance between Runs
`doRun_prc()` `doRun_rej()`	Run Approximate Bayesian Computation for Phylogenetic Comparative Methods
`doSimulation()`	Discrete-Time Character Simulation
`nullExtrinsic()` `nearestNeighborDisplacementExtrinsic()` `everyoneDisplacementExtrinsic()` `ExponentiallyDecayingPushExtrinsic()`	Extrinsic Character Evolution Models
`getBMRatePrior()`	Get Brownian Motion Rate Prior
`highestDensityInterval()`	Highest Density Interval
`nullIntrinsic()` `brownianIntrinsic()` `boundaryIntrinsic()` `boundaryMinIntrinsic()` `boundaryMaxIntrinsic()` `autoregressiveIntrinsic()` `maxBoundaryAutoregressiveIntrinsic()` `minBoundaryAutoregressiveIntrinsic()` `autoregressiveIntrinsicTimeSlices()` `autoregressiveIntrinsicTimeSlicesConstantMean()` `autoregressiveIntrinsicTimeSlicesConstantSigma()`	Intrinsic Character Evolution Models
`landscapeFPK_Intrinsic()` `getTraitBoundsFPK()` `plot_landscapeFPK_model()`	Intrinsic Trait Evolution Model for a Macroevolutionary Landscape on a Fokker-Planck-Kolmogorov Potential Surface (Boucher et al., 2018)
`returnPLSModel()` `PLSTransform()`	Fitting Univariate Partial Least Squares Models to Free Parameters in ABC
`multiOptimaIntrinsic()`	Single Evolutionary Regime Model with Multiple Optima
`pairwiseESS()`	Pairwise Effective Sample Size
`pairwiseKS()`	Pairwise Kolmogorov-Smirnov test
`parentOffspringPlots()`	Plotting Parent-Offspring Particles
`plotABC_3D()`	3D ABCplots
`plotPosteriors()`	Plot posterior distributions
`plotPrior()` `plotUnivariatePosteriorVsPrior()` `getUnivariatePriorCurve()` `getUnivariatePosteriorCurve()`	Plotting, Summarizing and Comparing the Prior and Posterior Distributions
`simRunExample`	Example Analysis Output of a Simulated Dataset
`simulateWithPriors()` `parallelSimulateWithPriors()`	Simulate data for initial TreEvo analysis
`summarizePosterior()`	Summarize Posterior Distribution for a Free Parameter
`testMultivarOutlierHDR()`	Test If an Outlier Is Within a Highest Density Region of a Multivariate Cloud of Data Points

Reference

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