# NAMESPACE is maintained by hand (roxygen tags in R/ are not
# consistently in sync with it); do not regenerate with roxygen2
# without first auditing all @export tags.

S3method(plot,phyloscaled)
S3method(print,anccond)
export(AncCond)
export(CalcD)
export(CalcPopD)
export(FuzzyMatch)
export(GetTipRates)
export(Mode)
export(ReOrderAlignment)
export(ResSel)
export(SampleTrees)
export(SlidingWindow)
export(SuperMatrix)
export(WinCalcD)
export(countTrees)
export(fix.simmap)
export(getNe)
export(make.simmap2)
export(pSAF)
export(scaleTreeRates)
importFrom(RColorBrewer,brewer.pal)
importFrom(ape,Ntip)
importFrom(ape,all.equal.phylo)
importFrom(ape,drop.tip)
importFrom(ape,is.binary)
importFrom(ape,is.ultrametric)
importFrom(ape,matexpo)
importFrom(ape,multi2di)
importFrom(ape,plot.phylo)
importFrom(ape,read.dna)
importFrom(ape,read.nexus)
importFrom(ape,read.tree)
importFrom(ape,reorder.phylo)
importFrom(ape,write.dna)
importFrom(ape,write.nexus)
importFrom(ape,write.tree)
importFrom(castor,asr_mk_model)
importFrom(expm,expm)
importFrom(graphics,abline)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(igraph,graph_from_data_frame)
importFrom(igraph,shortest_paths)
importFrom(methods,hasArg)
importFrom(phytools,fastAnc)
importFrom(phytools,fitMk)
importFrom(phytools,make.simmap)
importFrom(phytools,matchNodes)
importFrom(phytools,nodeHeights)
importFrom(phytools,rstate)
importFrom(phytools,to.matrix)
importFrom(seqinr,read.alignment)
importFrom(seqinr,read.fasta)
importFrom(seqinr,write.fasta)
importFrom(stats,dgamma)
importFrom(stats,lm)
importFrom(stats,logLik)
importFrom(stats,nlminb)
importFrom(stats,optim)
importFrom(stats,optimize)
importFrom(stats,pnorm)
importFrom(stats,rbinom)
importFrom(stats,reorder)
importFrom(stats,rexp)
importFrom(stats,rgamma)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(utils,adist)
importFrom(utils,flush.console)
importFrom(utils,write.csv)
importFrom(viridis,viridis)
