Models of Trait Macroevolution on Trees

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Documentation for package ‘motmot’ version 2.1.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

motmot-package	Models Of Trait Macroevolution On Trees
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
mammals	Mammal data
mcmc.plot	plot the output from transformPhylo.MCMC
ML.RatePhylo	Maximum likelihood rate estimation for traits and phylogenies
motmot	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
RatePhylo.allCI	Confidence intervals for rate parameters
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
traitData.plot	plot a univariate continuous trait data on a phylogeny
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