# Visualization and Post-Processing of 'RevBayes' Analyses

## Documentation for package ‘RevGadgets’ version 1.2.1

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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