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:
rwty_1.0.3.tar.gz
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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
- fungus - MrBayes output from analysis of Hibbett et al. data
- salamanders - MrBayes output from analysis of Williams et al. data
Last updated 5 days agofrom:a72560d561. Checks:9 OK. Indexed: yes.
Target | Result | Latest binary |
---|---|---|
Doc / Vignettes | OK | Mar 27 2025 |
R-4.5-win | OK | Mar 27 2025 |
R-4.5-mac | OK | Mar 27 2025 |
R-4.5-linux | OK | Mar 27 2025 |
R-4.4-win | OK | Mar 27 2025 |
R-4.4-mac | OK | Mar 27 2025 |
R-4.4-linux | OK | Mar 27 2025 |
R-4.3-win | OK | Mar 27 2025 |
R-4.3-mac | OK | Mar 27 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:apebase64encbitbit64bitopsbslibcachemclicodacolorspacecommonmarkcpp11crayondigestdplyrfansifarverfastmapfastmatchfontawesomeforcatsfsgenericsGGallyggdendroggplot2ggstatsgluegridExtragtablehmshtmltoolshttpuvigraphisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepatchworkphangornpillarpkgconfigPlotToolsplyrprettyunitsprogresspromisespurrrquadprogR.cacheR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRCurlRdpackreshape2rlangsassscalesshinyshinyjssourcetoolsstringistringrtibbletidyrtidyselectTreeDistTreeToolsutf8vctrsviridisviridisLitewithrxtable
Comparing RWTY plots: what am I looking at?
Rendered fromplot-comparisons.Rmd
usingknitr::rmarkdown
on Mar 27 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
Rendered fromrwty.Rmd
usingknitr::rmarkdown
on Mar 27 2025.Last update: 2021-08-27
Started: 2016-09-19