ML.RatePhylo            Maximum likelihood rate estimation for traits
                        and phylogenies
RatePhylo.CI            Confidence intervals for rate parameters
RatePhylo.allCI         Confidence intervals for rate parameters
addFossilToPhy          add a fossil to an interior branch of a
                        time-scaled phylogeny
allCladeMembers         allCladeMembers (internal function)
ancState                Extimate ancestral state (internal function)
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
cladeIdentity           Identify branches (including tips) descended
                        from a node (internal function).
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
likRatePhylo            Log-likelihood rate estimation for traits and
                        phylogenies
likTraitPhylo           Log-likelihood rate estimation for traits and
                        phylogenies
make.anc                Create design matrix (internal function)
make.likRatePhylo       Internal function
name.check              Name check (internal function)
node.descendents        Identify nodes and tips descended from a node
                        (internal function).
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.motmot              Phylogenetically independent contrasts
                        (internal)
plotPhylo.motmot        Tree plotting for rates Plots trees with
                        colours based on rates of trait evolution. Also
                        provides simple coloured plotting for trait
                        values using the "ace" function in the ape
                        library.
removeNonBin            remove species occuring before time in the past
                        (internal function)
sampleHiddenSp          Sample hidden speciation events along branches
                        of a tree (internal function)
sliceTree               Slice tree (internal function)
sortTraitData           Sort data and remove missing entries for tree
                        and trait data
timeSliceSummary        Identify shifts in the rate of trait
                        diversification through time
timeTravelPhy           timeTravelPhy (internal function)
traitData.plot          plot a univariate continuous trait data on a
                        phylogeny
traitMedusaSummary      Identify shifts in the rate of trait
                        diversification
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
