# Models of Trait Macroevolution on Trees

## 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