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 |