Visualization and Post-Processing of 'RevBayes' Analyses
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Documentation for package ‘RevGadgets’ version 1.2.1
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 |