# Generated by roxygen2: do not edit by hand

S3method(as.bammdata,credibleshiftset)
S3method(as.phylo,bammdata)
S3method(plot,bammdata)
S3method(plot,bammshifts)
S3method(plot,credibleshiftset)
S3method(print,bammdata)
S3method(print,credibleshiftset)
S3method(summary,bammdata)
S3method(summary,credibleshiftset)
export(BAMMlikelihood)
export(addBAMMlegend)
export(addBAMMshifts)
export(assignColorBreaks)
export(cohorts)
export(computeBayesFactors)
export(credibleShiftSet)
export(cumulativeShiftProbsTree)
export(distinctShiftConfigurations)
export(dtRates)
export(generateControlFile)
export(getBestShiftConfiguration)
export(getBranchShiftPriors)
export(getCladeRates)
export(getCohortMatrix)
export(getEventData)
export(getJenksBreaks)
export(getMarginalBranchRateMatrix)
export(getMeanBranchLengthTree)
export(getRateThroughTimeMatrix)
export(getShiftNodesFromIndex)
export(getTipRates)
export(getmrca)
export(marginalOddsRatioBranches)
export(marginalShiftProbsTree)
export(maximumShiftCredibility)
export(plot.bammdata)
export(plot.bammshifts)
export(plot.credibleshiftset)
export(plotPrior)
export(plotRateThroughTime)
export(ratesHistogram)
export(richColors)
export(samplingProbs)
export(setBAMMpriors)
export(speciesByRatesMatrix)
export(stepBF)
export(subsetEventData)
export(subtreeBAMM)
export(testTimeVariableBranches)
export(traitDependentBAMM)
export(transparentColor)
export(writeEventData)
import(ape)
importFrom(Rcpp,evalCpp)
importFrom(gplots,rich.colors)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,gray)
importFrom(grDevices,pdf)
importFrom(grDevices,rgb)
importFrom(grDevices,terrain.colors)
importFrom(graphics,abline)
importFrom(graphics,axTicks)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,box)
importFrom(graphics,grconvertX)
importFrom(graphics,grconvertY)
importFrom(graphics,image)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,locator)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,plot.new)
importFrom(graphics,plot.window)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,rect)
importFrom(graphics,segments)
importFrom(graphics,text)
importFrom(methods,hasArg)
importFrom(stats,cor.test)
importFrom(stats,dbinom)
importFrom(stats,density)
importFrom(stats,dgeom)
importFrom(stats,kruskal.test)
importFrom(stats,loess)
importFrom(stats,median)
importFrom(stats,optim)
importFrom(stats,qchisq)
importFrom(stats,quantile)
importFrom(stats,reorder)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,wilcox.test)
importFrom(utils,lsf.str)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(utils,write.csv)
importFrom(utils,write.table)
useDynLib(BAMMtools)
