Package: rwty 1.0.2

rwty: R We There Yet? Visualizing MCMC Convergence in Phylogenetics

Implements various tests, visualizations, and metrics for diagnosing convergence of MCMC chains in phylogenetics. It implements and automates many of the functions of the AWTY package in the R environment, as well as a host of other functions. Warren, Geneva, and Lanfear (2017), <doi:10.1093/molbev/msw279>.

Authors:Dan Warren [aut, cre], Anthony Geneva [aut], Rob Lanfear [aut], Luke Harmon [ctb], April Wright [ctb], Diego Mallo [ctb], Klaus Schliep [ctb], Kelly Luke [ctb], Kendall Michelle [ctb], Smith Martin [ctb]

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rwty.pdf |rwty.html✨
rwty/json (API)

# Install 'rwty' in R:
install.packages('rwty', repos = c('https://danlwarren.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/danlwarren/rwty/issues

Datasets:
  • fungus - MrBayes output from analysis of Hibbett et al. data
  • salamanders - MrBayes output from analysis of Williams et al. data

On CRAN:

7.32 score 30 stars 117 scripts 220 downloads 1 mentions 27 exports 129 dependencies

Last updated 3 years agofrom:58c235ba6b. Checks:1 OK, 7 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 18 2025
R-4.5-winWARNINGFeb 18 2025
R-4.5-macWARNINGFeb 18 2025
R-4.5-linuxWARNINGFeb 18 2025
R-4.4-winWARNINGFeb 18 2025
R-4.4-macWARNINGFeb 18 2025
R-4.3-winWARNINGFeb 18 2025
R-4.3-macWARNINGFeb 18 2025

Exports:analyze.rwtycheck.chainsclade.freqcombine.ptablescumulative.freqestimate.autocorr.mload.multiload.treesmakeplot.acsf.cumulativemakeplot.acsf.slidingmakeplot.all.paramsmakeplot.asdsfmakeplot.autocorrmakeplot.pairsmakeplot.parammakeplot.pseudo.essmakeplot.splitfreq.matrixmakeplot.splitfreqs.cumulativemakeplot.splitfreqs.slidingmakeplot.topologymakeplot.treespaceslide.freqtopological.approx.esstopological.autocorrtopological.pseudo.esstree.dist.matrixtreespace

Dependencies:apeaskpassaudiobase64encbeeprbitbit64bitopsbslibcachemclassclassIntclicodacolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdigestdplyrDTe1071evaluatefansifarverfastmapfastmatchfontawesomeforcatsfsgenericsGGallygganimateggdendroggplot2ggstatsgifskigluegridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvhttrigraphisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelpSolvemagickmagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpatchworkphangornpillarpkgconfigplotlyPlotToolsplyrpngprettyunitsprogresspromisesproxypurrrquadprogR.cacheR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRCurlRdpackreshape2rlangrmarkdowns2sassscalessfshinyshinyjssourcetoolsstringistringrsystibbletidyrtidyselecttinytextransformrTreeDistTreeToolstweenrunitsusedistutf8vctrsviridisviridisLitewithrwkxfunxtableyaml

Comparing RWTY plots: what am I looking at?

Dan Warren, Anthony Geneva, and Rob Lanfear

Rendered fromplot-comparisons.Rmdusingknitr::rmarkdownon Feb 18 2025.

Last update: 2021-08-27
Started: 2016-09-29

RWTY (R We There Yet): An R package for examining convergence of Bayesian phylogenetic analyses

Dan Warren, Anthony Geneva, and Rob Lanfear

Rendered fromrwty.Rmdusingknitr::rmarkdownon Feb 18 2025.

Last update: 2021-08-27
Started: 2016-09-19

Readme and manuals

Help Manual

Help pageTopics
analyze.rwty, the main interface for rwty analyses and plots.analyze.rwty
Function for checking suitability of chains for rwty analyses, auto-generating labels, etccheck.chains
Returns clade names and frequenciesclade.freq
Function for merging p tables for multiple MCMC chainscombine.ptables
Cumulative means of clade split frequencies.cumulative.freq
Calculate sampling interval based on exponential semivariogram model.estimate.autocorr.m
MrBayes output from analysis of Hibbett et al. datafungus
Load all matching files from a directory into a list of rwty.chain objectsload.multi
Custom functions to load tree lists so that rwty can do basic processing on the way in.load.trees
Plot the Change in Split Frequencies (CSF) in sliding windows over the course of an MCMC.makeplot.acsf.cumulative
Plot the Chaing in Split Frequencies (CSF) in sliding windows over the course of an MCMC.makeplot.acsf.sliding
Plotting all parametersmakeplot.all.params
Plot the Standard Deviation of Split Frequencies over the course of an MCMC.makeplot.asdsf
Make autocorrelation plots of tree topologies from MCMC analysesmakeplot.autocorr
Plotting parameters against each othermakeplot.pairs
Plotting parametersmakeplot.param
Plot the pseudo ESS of tree topologies from MCMC chains.makeplot.pseudo.ess
Plots a matrix of split frequency comparisons between multiple MCMC chains.makeplot.splitfreq.matrix
Plot cumulative split frequencies over the course of an MCMCmakeplot.splitfreqs.cumulative
Plot split frequencies in sliding windows over the course of an MCMCmakeplot.splitfreqs.sliding
Plotting parametersmakeplot.topology
Plot chains in treespace.makeplot.treespace
Rename clades for easy recallparse.clades
Function for printing rwty.chain objectsprint.rwty.chain
MrBayes output from analysis of Williams et al. datasalamanders
Sliding window measurements of clade split frequencies.slide.freq
Calculate the approximate Effective Sample Size (ESS) of tree topologiestopological.approx.ess
Calculate data for autocorrelation plots of tree topologies from MCMC analysestopological.autocorr
Calculate the pseudo Effective Sample Size (ESS) of tree topologiestopological.pseudo.ess
Tree distance matrix calculationtree.dist.matrix
MDS scaling of treespace for a single tree list.treespace