motmot v2.1.3

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by Mark Puttick View Source

Models of Trait Macroevolution on Trees

Functions for fitting models of trait evolution on phylogenies for continuous traits. The majority of functions described in Thomas and Freckleton (2012) <doi:10.1111/j.2041-210X.2011.00132.x> and include functions that allow for tests of variation in the rates of trait evolution.

Functions in motmot

Name	Description
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
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Vignettes of motmot

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motmot.Rmd
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Details

Type	Package
Date	2019-11-21
License	GPL (>= 2)
Repository	CRAN
URL	https://puttickbiology.wordpress.com/motmot/
RoxygenNote	7.0.1
LazyData	true
VignetteBuilder	knitr
LinkingTo	Rcpp
Encoding	UTF-8
SystemRequirements	C++11
NeedsCompilation	yes
Packaged	2019-11-25 13:58:02 UTC; markputtick
Date/Publication	2019-11-25 17:10:07 UTC

depends	ape (>= 3.0-7) , R (>= 2.10.0)
imports	caper , coda , ks , methods , mvtnorm , Rcpp
suggests	formatR , knitr , rmarkdown
Contributors	Rob Freckleton, Emmanuel Paradis, David Orme, Gavin Thomas, Travis Ingram, Mark Puttick, Magnus Clarke