This package is considered a duplicate. The official version of this package is found at:https://revbayes.r-universe.dev/RevGadgets

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-4.5)RevGadgets_1.2.1.zip(r-4.4)RevGadgets_1.2.1.zip(r-4.3)
RevGadgets_1.2.1.tgz(r-4.4-any)RevGadgets_1.2.1.tgz(r-4.3-any)
RevGadgets_1.2.1.tar.gz(r-4.5-noble)RevGadgets_1.2.1.tar.gz(r-4.4-noble)
RevGadgets_1.2.1.tgz(r-4.4-emscripten)RevGadgets_1.2.1.tgz(r-4.3-emscripten)
RevGadgets.pdf |RevGadgets.html✨
RevGadgets/json (API)
NEWS

# Install 'RevGadgets' in R:

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

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

On CRAN:

6.08 score 13 stars 207 scripts 274 downloads 1 mentions 36 exports 103 dependencies

Last updated 1 years agofrom:2a7ce495ae. Checks:OK: 7. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 24 2024
R-4.5-win	OK	Nov 24 2024
R-4.5-linux	OK	Nov 24 2024
R-4.4-win	OK	Nov 24 2024
R-4.4-mac	OK	Nov 24 2024
R-4.3-win	OK	Nov 24 2024
R-4.3-mac	OK	Nov 24 2024

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 cli clusterGeneration coda codetools colorspace combinat commonmark cpp11 curl deeptime deeptimedata DEoptim digest doParallel dplyr expm fansi farver foreach fs generics ggfittext ggforce ggfun ggh4x ggimage gginnards ggplot2 ggplotify ggpp ggtree glue gridExtra gridGraphics gridtext grImport2 gtable igraph isoband iterators jpeg jsonlite labeling lattice lazyeval lifecycle lubridate magick magrittr maps markdown MASS Matrix mgcv mnormt munsell nlme numDeriv optimParallel patchwork phangorn phytools pillar pkgconfig plyr png polyclip polynom purrr quadprog R6 RColorBrewer Rcpp RcppArmadillo RcppEigen reshape rlang scales scatterplot3d shades stringi stringr systemfonts tibble tidyr tidyselect tidytree timechange treeio tweenr utf8 vctrs viridisLite withr xfun XML xml2 xts 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