ML.RatePhylo            Maximum likelihood rate estimation for traits
                        and phylogenies
RatePhylo.allCI         Confidence intervals for rate parameters
addFossilToPhy          add a fossil to an interior branch of a
                        time-scaled phylogeny
allopatric.data         Finch allopatric data
anolis.data             Anolis phenotype data
anolis.tree             Anolis phylogeny
as.rateData             Conversion among data and phylogeny objects
as.rateMatrix           Conversion among data and phylogeny objects
blomberg.k              Blomberg's K Estimate Blomberg's K (Blomberg et
                        al. 2003)
calcCutOff              Calculate multiple-test cut-off
chr.disp.lrt            Character displacement likelihood ratio test
chr.disp.param          Simulate character displacement data wrapper
chr.disp.sim            Simulate character displacement data
contemporaryPhy         prune tree and data to lineages present in a
                        time bin in the past
dropTipPartial          Drop tips from a phylogenetic tree while
                        preserving deleted nodes
fairProportions         Calculate fair proportions phylogenetic
                        diversity metric
finch.data              Finch phenotype data
finch.tree              Finch tree
likRatePhylo            Log-likelihood rate estimation for traits and
                        phylogenies
likTraitPhylo           Log-likelihood estimation for traits and
                        phylogenies
mcmc.plot               plot the output from transformPhylo.MCMC
motmot-package          Models Of Trait Macroevolution On Trees
node.descendents        Identify nodes and tips descended from a node
nodeTimes               Get times for nodes and tips
optim.likRatePhylo      Maximum likelihood rate estimation for traits
                        and phylogenies
phyloCovar              Calculation of Brownian (co)variance using
                        independent contrasts.
phyloMean               Calculation of phylogenetically corrected mean.
phyloVar                Calculation of Brownian variance.
pic.pgls                Fast PLGS estimation based on contrasts
plot.timeSlice.ML       Identify shifts in the rate of trait
                        diversification through time
plot.traitMedusa.model
                        Tree plotting for rates
sampleShid              Sample hidden speciation events along branches
                        of a tree
sortTraitData           Sort data and remove missing entries for tree
                        and trait data
summary.traitMedusa     Identify shifts in the rate of trait
                        diversification
sympatric.data          Pairwise sympatry matrix for finch species
traitData.plot          plot a univariate continuous trait data on a
                        phylogeny
transformPhylo          Phylogenetic tree transformations
transformPhylo.MCMC     Bayesian MCMC for models of trait evolution
transformPhylo.ML       Maximum likelihood for models of trait evoluion
transformPhylo.ll       Log-likelhood for models of trait evolution.
transformPhylo.sim      Phylogenetic tree transformations
transformRateMatrix     Conversion among data and phylogeny objects
