Man pages for motmot.2.0
Models of Trait Macroevolution on Trees

addFossilToPhyadd a fossil to an interior branch of a time-scaled phylogeny
allCladeMembersallCladeMembers (internal function)
ancStateExtimate ancestral state (internal function)
anolis.dataAnolis phenotype data
anolis.treeAnolis phylogeny
as.rateDataConversion among data and phylogeny objects
as.rateMatrixConversion among data and phylogeny objects
cladeIdentityIdentify branches (including tips) descended from a node...
contemporaryPhyprune tree and data to lineages present in a time bin in the...
dropTipPartialDrop tips from a phylogenetic tree while preserving deleted...
fairProportionsCalculate fair proportions phylogenetic diversity metric
likRatePhyloLog-likelihood rate estimation for traits and phylogenies
likTraitPhyloLog-likelihood rate estimation for traits and phylogenies
make.ancCreate design matrix (internal function)
make.likRatePhyloInternal function
ML.RatePhyloMaximum likelihood rate estimation for traits and phylogenies
name.checkName check (internal function)
node.descendentsIdentify nodes and tips descended from a node (internal...
nodeTimesGet times for nodes and tips
optim.likRatePhyloMaximum likelihood rate estimation for traits and phylogenies
phyloCovarCalculation of Brownian (co)variance using independent...
phyloMeanCalculation of phylogenetically corrected mean.
phyloVarCalculation of Brownian variance.
pic.motmotPhylogenetically independent contrasts (internal)
plotPhylo.motmotTree plotting for rates Plots trees with colours based on...
RatePhylo.allCIConfidence intervals for rate parameters
RatePhylo.CIConfidence intervals for rate parameters
removeNonBinremove species occuring before time in the past (internal...
sampleHiddenSpSample hidden speciation events along branches of a tree...
sliceTreeSlice tree (internal function)
sortTraitDataSort data and remove missing entries for tree and trait data
timeSliceSummaryIdentify shifts in the rate of trait diversification through...
timeTravelPhytimeTravelPhy (internal function)
traitData.plotplot a univariate continuous trait data on a phylogeny
traitMedusaSummaryIdentify shifts in the rate of trait diversification
transformPhyloPhylogenetic tree transformations
transformPhylo.llLog-likelhood for models of trait evolution.
transformPhylo.MCMCBayesian MCMC for models of trait evolution
transformPhylo.MLMaximum likelihood for models of trait evoluion
transformPhylo.simPhylogenetic tree transformations
transformRateMatrixConversion among data and phylogeny objects
motmot.2.0 documentation built on Jan. 11, 2018, 1:03 a.m.