addFossilToPhy	addFossilToPhy
allCladeMembers	allCladeMembers
ancState	ancState
anolis.data	anolis.data
anolis.tree	anolis.tree
as.rateData	as.rateData
as.rateMatrix	as.rateMatrix
cladeIdentity	cladeIdentity
contemporaryPhy	contemporaryPhy
dropTipPartial	dropTipPartial
fairProportions	fairProportions
likRatePhylo	likRatePhylo
likTraitPhylo	likTraitPhylo
make.anc	make.anc
make.likRatePhylo	make.likRatePhylo
ML.RatePhylo	ML.RatePhylo
name.check	name.check
node.descendents	node.descendents
nodeTimes	nodeTimes
optim.likRatePhylo	optim.likRatePhylo
phyloCovar	phyloCovar
phyloMean	phyloMean
phyloVar	phyloVar
pic.motmot	pic.motmot
plotPhylo.motmot	plotPhylo.motmot
RatePhylo.allCI	RatePhylo.allCI
RatePhylo.CI	RatePhylo.CI
removeNonBin	removeNonBin
sampleHiddenSp	sampleHiddenSp
sliceTree	sliceTree
sortTraitData	sortTraitData
timeSliceSummary	timeSliceSummary
timeTravelPhy	timeTravelPhy
traitData.plot	traitData.plot
traitMedusaSummary	traitMedusaSummary
transformPhylo	transformPhylo
transformPhylo.ll	transformPhylo.ll
transformPhylo.MCMC	transformPhylo.MCMC
transformPhylo.ML	transformPhylo.ML
transformPhylo.sim	transformPhylo.sim
transformRateMatrix	transformRateMatrix
