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motmot.2.0 (version 1.1.2)

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 (2011) and include functions that allow for tests of variation in the rates of trait evolution.

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Version

Install

install.packages('motmot.2.0')

Monthly Downloads

3

Version

1.1.2

License

GPL (>= 2)

Maintainer

Mark Puttick

Last Published

January 10th, 2018

Functions in motmot.2.0 (1.1.2)

allCladeMembers

allCladeMembers (internal function)
ancState

Extimate ancestral state (internal function)
ML.RatePhylo

Maximum likelihood rate estimation for traits and phylogenies
RatePhylo.CI

Confidence intervals for rate parameters
make.anc

Create design matrix (internal function)
make.likRatePhylo

Internal function
nodeTimes

Get times for nodes and tips
optim.likRatePhylo

Maximum likelihood rate estimation for traits and phylogenies
anolis.data

Anolis phenotype data
name.check

Name check (internal function)
node.descendents

Identify nodes and tips descended from a node (internal function).
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)
traitMedusaSummary

Identify shifts in the rate of trait diversification
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
transformPhylo.ML

Maximum likelihood for models of trait evoluion
transformPhylo

Phylogenetic tree transformations
likRatePhylo

Log-likelihood rate estimation for traits and phylogenies
likTraitPhylo

Log-likelihood rate estimation for traits and phylogenies
phyloCovar

Calculation of Brownian (co)variance using independent contrasts.
phyloMean

Calculation of phylogenetically corrected mean.
sortTraitData

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

Identify shifts in the rate of trait diversification through time
transformPhylo.MCMC

Bayesian MCMC for models of trait evolution
RatePhylo.allCI

Confidence intervals for rate parameters
addFossilToPhy

add a fossil to an interior branch of a time-scaled phylogeny
dropTipPartial

Drop tips from a phylogenetic tree while preserving deleted nodes
fairProportions

Calculate fair proportions phylogenetic diversity metric
sampleHiddenSp

Sample hidden speciation events along branches of a tree (internal function)
sliceTree

Slice tree (internal function)
transformPhylo.ll

Log-likelhood for models of trait evolution.
transformPhylo.sim

Phylogenetic tree transformations
phyloVar

Calculation of Brownian variance.
pic.motmot

Phylogenetically independent contrasts (internal)
timeTravelPhy

timeTravelPhy (internal function)
traitData.plot

plot a univariate continuous trait data on a phylogeny
transformRateMatrix

Conversion among data and phylogeny objects