motmot.2.0 v1.1.2

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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 (2011) <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.2.0

Name	Description
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
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Vignettes of motmot.2.0

Name
motmot.2.0.vignette.Rmd
myref_small.bib
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Details

Type	Package
Date	2018-01-10
License	GPL (>= 2)
Repository	CRAN
URL	https://puttickbiology.wordpress.com/motmot/
RoxygenNote	6.0.1
LazyData	true
VignetteBuilder	knitr
NeedsCompilation	no
Packaged	2018-01-10 18:30:29 UTC; mp1728
Date/Publication	2018-01-10 18:51:44 UTC

depends	ape (>= 3.0-7) , caper , coda , MASS , mvtnorm , R (>= 2.10.0)
suggests	knitr , rmarkdown
Contributors	Rob Freckleton, Emmanuel Paradis, David Orme, Gavin Thomas, Travis Ingram, Mark Puttick