Models of Trait Macroevolution on Trees


[Up] [Top]

Documentation for package ‘motmot.2.0’ version 1.1.2

Help Pages

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
ML.RatePhylo Maximum likelihood rate estimation for traits and phylogenies
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.
RatePhylo.allCI Confidence intervals for rate parameters
RatePhylo.CI Confidence intervals for rate parameters
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.ll Log-likelhood for models of trait evolution.
transformPhylo.MCMC Bayesian MCMC for models of trait evolution
transformPhylo.ML Maximum likelihood for models of trait evoluion
transformPhylo.sim Phylogenetic tree transformations
transformRateMatrix Conversion among data and phylogeny objects