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motmot (version 2.1.3)

Models of Trait Macroevolution on Trees

Description

Functions for fitting models of trait evolution on phylogenies for continuous traits. The majority of functions described in Thomas and Freckleton (2012) and include functions that allow for tests of variation in the rates of trait evolution.

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Version

Install

install.packages('motmot')

Monthly Downloads

172

Version

2.1.3

License

GPL (>= 2)

Maintainer

Mark Puttick

Last Published

November 25th, 2019

Functions in motmot (2.1.3)

chr.disp.lrt

Character displacement likelihood ratio test
chr.disp.param

Simulate character displacement data wrapper
phyloVar

Calculation of Brownian variance.
chr.disp.sim

Simulate character displacement data
pic.pgls

Fast PLGS estimation based on contrasts
node.descendents

Identify nodes and tips descended from a node
motmot-package

Models Of Trait Macroevolution On Trees
contemporaryPhy

prune tree and data to lineages present in a time bin in the past
RatePhylo.allCI

Confidence intervals for rate parameters
finch.tree

Finch tree
finch.data

Finch phenotype data
likRatePhylo

Log-likelihood rate estimation for traits and phylogenies
fairProportions

Calculate fair proportions phylogenetic diversity metric
dropTipPartial

Drop tips from a phylogenetic tree while preserving deleted nodes
nodeTimes

Get times for nodes and tips
sortTraitData

Sort data and remove missing entries for tree and trait data
sampleShid

Sample hidden speciation events along branches of a tree
phyloCovar

Calculation of Brownian (co)variance using independent contrasts.
summary.traitMedusa

Identify shifts in the rate of trait diversification
traitData.plot

plot a univariate continuous trait data on a phylogeny
phyloMean

Calculation of phylogenetically corrected mean.
transformPhylo

Phylogenetic tree transformations
optim.likRatePhylo

Maximum likelihood rate estimation for traits and phylogenies
transformPhylo.ll

Log-likelhood for models of trait evolution.
likTraitPhylo

Log-likelihood estimation for traits and phylogenies
transformPhylo.MCMC

Bayesian MCMC for models of trait evolution
transformPhylo.ML

Maximum likelihood for models of trait evoluion
plot.traitMedusa.model

Tree plotting for rates
plot.timeSlice.ML

Identify shifts in the rate of trait diversification through time
transformRateMatrix

Conversion among data and phylogeny objects
mcmc.plot

plot the output from transformPhylo.MCMC
transformPhylo.sim

Phylogenetic tree transformations
mammals

Mammal data
anolis.data

Anolis phenotype data
allopatric.data

Finch allopatric data
addFossilToPhy

add a fossil to an interior branch of a time-scaled phylogeny
anolis.tree

Anolis phylogeny
ML.RatePhylo

Maximum likelihood rate estimation for traits and phylogenies
as.rateData

Conversion among data and phylogeny objects
blomberg.k

Blomberg's K Estimate Blomberg's K (Blomberg et al. 2003)
as.rateMatrix

Conversion among data and phylogeny objects
calcCutOff

Calculate multiple-test cut-off