Man pages for PuttickMacroevolution/motmot
Models of Trait Macroevolution on Trees

addFossilToPhyadd a fossil to an interior branch of a time-scaled phylogeny
allopatric.dataFinch allopatric data
anolis.dataAnolis phenotype data
anolis.treeAnolis phylogeny
as.rateDataConversion among data and phylogeny objects
as.rateMatrixConversion among data and phylogeny objects
blomberg.kBlomberg's K Estimate Blomberg's K (Blomberg et al. 2003)
calcCutOffCalculate multiple-test cut-off
chr.disp.lrtCharacter displacement likelihood ratio test
chr.disp.paramSimulate character displacement data wrapper
chr.disp.simSimulate character displacement data
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
finch.dataFinch phenotype data
finch.treeFinch tree
likRatePhyloLog-likelihood rate estimation for traits and phylogenies
likTraitPhyloLog-likelihood estimation for traits and phylogenies
mammalsMammal data
mcmc.plotplot the output from transformPhylo.MCMC
ML.RatePhyloMaximum likelihood rate estimation for traits and phylogenies
motmot-packageModels Of Trait Macroevolution On Trees
node.descendentsIdentify nodes and tips descended from a node
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.pglsFast PLGS estimation based on contrasts
plot.timeSlice.MLIdentify shifts in the rate of trait diversification through...
plot.traitMedusa.modelTree plotting for rates
RatePhylo.allCIConfidence intervals for rate parameters
sampleShidSample hidden speciation events along branches of a tree
sortTraitDataSort data and remove missing entries for tree and trait data
summary.traitMedusaIdentify shifts in the rate of trait diversification
traitData.plotplot a univariate continuous trait data on a phylogeny
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
PuttickMacroevolution/motmot documentation built on June 5, 2020, 7 p.m.