Package: TreEvo 0.22.1

Brian C. OMeara

TreEvo: Using ABC to Understand Trait Evolution

Various functions for estimating parameters of trait evolution in comparative analyses using Approximate Bayesian Computation.

Authors:Brian O'Meara [aut], David Bapst [aut, cre], Barb Banbury [aut]

TreEvo_0.22.1.tar.gz
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TreEvo.pdf |TreEvo.html✨
TreEvo/json (API)

# Install 'TreEvo' in R:

install.packages('TreEvo', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bomeara/treevo/issues

Datasets:

ancStateExample - Example Analysis Output of a Simulated Dataset
genRateExample - Example Analysis Output of a Simulated Dataset
resultsBMExample - Example Analysis Output of a Simulated Dataset
resultsBoundExample - Example Analysis Output of a Simulated Dataset
simCharExample - Example Analysis Output of a Simulated Dataset
simPhyExample - Example Analysis Output of a Simulated Dataset

On CRAN:

42 exports 1 stars 0.61 score 102 dependencies 65 scripts

Last updated 1 years agofrom:f0e13d5bb4. Checks:OK: 1 WARNING: 6. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Aug 23 2024
R-4.5-win	WARNING	Aug 23 2024
R-4.5-linux	WARNING	Aug 23 2024
R-4.4-win	WARNING	Aug 23 2024
R-4.4-mac	WARNING	Aug 23 2024
R-4.3-win	WARNING	Aug 23 2024
R-4.3-mac	WARNING	Aug 23 2024

Exports:autoregressiveIntrinsic autoregressiveIntrinsicTimeSlices autoregressiveIntrinsicTimeSlicesConstantMean autoregressiveIntrinsicTimeSlicesConstantSigma boundaryIntrinsic boundaryMaxIntrinsic boundaryMinIntrinsic boxcoxTransformation boxcoxTransformationMatrix brownianIntrinsic compareListIPD doRun_prc doRun_rej doSimulation everyoneDisplacementExtrinsic ExponentiallyDecayingPushExtrinsic getBMRatePrior getTraitBoundsFPK getUnivariatePosteriorCurve getUnivariatePriorCurve highestDensityInterval landscapeFPK_Intrinsic maxBoundaryAutoregressiveIntrinsic minBoundaryAutoregressiveIntrinsic multiOptimaIntrinsic nearestNeighborDisplacementExtrinsic nullExtrinsic nullIntrinsic pairwiseESS pairwiseKS parallelSimulateWithPriors parentOffspringPlots plot_landscapeFPK_model plotABC_3D plotPosteriors plotPrior plotUnivariatePosteriorVsPrior PLSTransform returnPLSModel simulateWithPriors summarizePosterior testMultivarOutlierHDR

Dependencies:ape askpass base64enc bslib cachem cli clusterGeneration coda codetools colorspace combinat corpcor covr cpp11 crayon curl DEoptim digest doParallel evaluate expm fansi farver fastmap fastmatch fontawesome foreach fs future future.apply generics ggplot2 ggseqlogo globals glue gmp gtable highr htmltools htmlwidgets httr igraph isoband iterators jquerylib jsonlite knitr labeling lattice lazyeval lifecycle listenv magrittr maps MASS mathjaxr Matrix memoise mgcv mime mnormt munsell mvtnorm nlme numDeriv openssl optimParallel parallelly partitions phangorn phylolm phytools pillar pkgconfig pls polynom quadprog R6 rappdirs rbibutils RColorBrewer Rcpp RcppGSL RcppZiggurat Rdpack rex rgl rlang rmarkdown sass scales scatterplot3d sets sys tibble tinytex utf8 vctrs viridisLite withr xfun yaml

Analyzing Trait Evolution with Approximate Bayesian Computation in TreEvo

David W. Bapst

Rendered fromtreevo_ABC_vignette.Rmdusingknitr::rmarkdownon Aug 23 2024.

Last update: 2020-08-20
Started: 2017-12-01

Citation

Development and contributors

Readme and manuals

Help Manual

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