Package: rwty 1.0.3

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]

rwty_1.0.3.tar.gz
rwty_1.0.3.zip(r-4.7)rwty_1.0.3.zip(r-4.6)rwty_1.0.3.zip(r-4.5)
rwty_1.0.3.tgz(r-4.6-any)rwty_1.0.3.tgz(r-4.5-any)
rwty_1.0.3.tar.gz(r-4.7-any)rwty_1.0.3.tar.gz(r-4.6-any)
rwty_1.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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:

Conda:

7.47 score 33 stars 148 scripts 291 downloads 1 mentions 27 exports 84 dependencies

Last updated from:a72560d561. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK244
source / vignettesOK460
linux-release-x86_64OK248
macos-release-arm64OK250
macos-oldrel-arm64OK221
windows-develOK146
windows-releaseOK124
windows-oldrelOK121
wasm-releaseOK133

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:apebase64encbitbit64bslibcachemclicodacolorspacecommonmarkcpp11crayondigestdplyrfarverfastmapfastmatchfontawesomeforcatsfsgenericsGGallyggdendroggplot2ggstatsgluegridExtragtablehmshtmltoolshttpuvigraphisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemimenlmeotelpatchworkphangornpillarpkgconfigPlotToolsplyrprettyunitsprogresspromisespurrrquadprogR6rappdirsrbibutilsRColorBrewerRcppRdpackreshape2rlangS7sassscalesshinyshinyjssourcetoolsstringistringrtibbletidyrtidyselectTreeDistTreeToolsutf8vctrsviridisviridisLitewithrxtable

Comparing RWTY plots: what am I looking at?
RWTY produces a number of different plots and statistics for evaluating the performance of MCMC chains. These plots can help to illustrate problems with convergence in idividual chains as well as explore differences between chains built from different sequence data. Here we're going to explore some of these plots in detail, comparing well-behaved to poorly-behaved chains when appropriate. | Running RWTY | Parameter plots | Topology trace plots and histograms | Split frequency plots | Pairs plots | Average Change in Split Frequency (ACSF) plots | Treespace plots | Autocorrelation plots | Pseudo-ESS plots | Split frequency matrix plots | ASDSF plots | Citations
Rendered fromplot-comparisons.Rmdusingknitr::rmarkdown

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

RWTY (R We There Yet): An R package for examining convergence of Bayesian phylogenetic analyses
RWTY: R We There Yet? | Plot comparisons - what does it all mean? | Installation | Installing from GitHub using devtools | Install from zip file | Setting the number of cores | Interacting with RWTY | load.trees() | load.multi() | analyze.rwty() | makeplot.x() | topological.approx.ess() | RWTY outputs | Parameter trace plots | Parameter correlation plots | Tree topology trace plot | Autocorrelation plots | Treespace plots | Sliding window and cumulative split frequency plots | Sliding window and cumulative average change in split frequency (ACSF) plots | Multiple chains only | Average Standard Deviation of Split Frequency (ASDSF) plot | Split frequency scatterplot matrix | ASDSF tree
Rendered fromrwty.Rmdusingknitr::rmarkdown

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
Rename clades for easy recallparse.slide.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