Package: RevGadgets 1.2.1

Carrie Tribble

RevGadgets: Visualization and Post-Processing of 'RevBayes' Analyses

Processes and visualizes the output of complex phylogenetic analyses from the 'RevBayes' phylogenetic graphical modeling software.

Authors:Carrie Tribble [aut, cre], Michael R. May [aut], William A. Freyman [aut], Michael J. Landis [aut], Lim Jun Ying [aut], Joelle Barido-Sottani [aut], Andrew Magee [aut], Bjorn Tore Kopperud [aut], Sebastian Hohna [aut], Nagashima Kengo [ctb], Schliep Klaus [ctb], Ronja J. Billenstein [aut]

RevGadgets_1.2.1.tar.gz
RevGadgets_1.2.1.zip(r-4.7)RevGadgets_1.2.1.zip(r-4.6)RevGadgets_1.2.1.zip(r-4.5)
RevGadgets_1.2.1.tgz(r-4.6-any)RevGadgets_1.2.1.tgz(r-4.5-any)
RevGadgets_1.2.1.tar.gz(r-4.7-any)RevGadgets_1.2.1.tar.gz(r-4.6-any)
RevGadgets_1.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RevGadgets/json (API)
NEWS

# Install 'RevGadgets' in R:

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

Bug tracker:https://github.com/revbayes/revgadgets/issues

On CRAN:

6.22 score 14 stars 266 scripts 275 downloads 1 mentions 36 exports 122 dependencies

Last updated from:2a7ce495ae. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	189
source / vignettes	OK	251
linux-release-x86_64	OK	196
macos-release-arm64	OK	162
macos-oldrel-arm64	OK	357
windows-devel	OK	167
windows-release	OK	168
windows-oldrel	OK	260
wasm-release	OK	165

Exports:calculateShiftBayesFactor colFun combineTraces densiTreeWithBranchData dropTip geom_stepribbon GeomStepribbon getMAP matchNodes plotAncStatesMAP plotAncStatesPie plotDiversityOBDP plotDivRates plotFBDTree plotHiSSE plotMassExtinctions plotMuSSE plotPopSizes plotPostPredStats plotTrace plotTree posteriorSamplesToParametricPrior processAncStates processBranchData processDivRates processPopSizes processPostPredStats processSSE readOBDP readTrace readTrees removeBurnin rerootPhylo setMRFGlobalScaleHyperpriorNShifts simulateMRF summarizeTrace

Dependencies:ape aplot base64enc bslib cachem cli clusterGeneration coda codetools combinat commonmark cpp11 curl deeptime deeptimedata DEoptim digest doParallel dplyr evaluate expm farver fastmap fastmatch fontawesome fontBitstreamVera fontLiberation fontquiver foreach fs gdtools generics ggfittext ggforce ggfun ggh4x ggimage gginnards ggiraph ggplot2 ggplotify ggpp ggtree glue gridExtra gridGraphics gridtext grImport2 gtable highr htmltools htmlwidgets igraph isoband iterators jpeg jquerylib jsonlite knitr labeling lattice lazyeval lifecycle litedown lubridate magick magrittr maps markdown MASS Matrix memoise mime mnormt nlme numDeriv optimParallel patchwork phangorn phytools pillar pkgconfig plyr png polyclip polynom purrr quadprog R6 rappdirs RColorBrewer Rcpp reshape rlang rmarkdown S7 sass scales scatterplot3d shades stringi stringr systemfonts tibble tidyr tidyselect tidytree timechange tinytex treeio tweenr utf8 vctrs viridisLite withr xfun XML xml2 xts yaml yulab.utils zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Bayes Factors in support of a shift in diversification rates over a given time interval.	calculateShiftBayesFactor
Color Function	colFun
Combine traces	combineTraces
DensiTree-style plot with branch-specific data	densiTreeWithBranchData
dropTip	dropTip
plot geom stepribbon for diversification rates	GeomStepribbon geom_stepribbon
get MAP	getMAP
match Nodes	matchNodes
plot Ancestral States MAP	plotAncStatesMAP
plot Ancestral States Pie	plotAncStatesPie
Plot Diversity Distribution from OBDP Analysis	plotDiversityOBDP
Plot Diversification Rates	plotDivRates
Plot FBD tree	plotFBDTree
plotHiSSE	plotHiSSE
Plot Mass Extinction Support	plotMassExtinctions
plotMuSSE	plotMuSSE
Plot Population Sizes	plotPopSizes
plot Posterior Predictive Statistics	plotPostPredStats
Plot trace	plotTrace
Plot tree	plotTree
Plot Full tree	plotTreeFull
Priors from MCMC samples	posteriorSamplesToParametricPrior
Process Ancestral States	processAncStates
processBranchData	processBranchData
Process Diversification Rates	processDivRates
Process Population Sizes	processPopSizes
process Posterior Predictive Statistics	processPostPredStats
Title	processSSE
Read OBDP Outputs	readOBDP
Read trace	readTrace
Read trees	readTrees
Remove Burnin	removeBurnin
Reroot Phylo	rerootPhylo
RevGadgets	RevGadgets
Sets a global scale parameter for a GMRF or HSMRF model given a prior mean number of effective shifts.	setMRFGlobalScaleHyperpriorNShifts
Simulates a single Markov random field trajectory.	simulateMRF
Summarize trace	summarizeTrace