motmot.2.0 v1.1.2

0

Monthly downloads

0th

Percentile

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
No Results!

Vignettes of motmot.2.0

Name
motmot.2.0.vignette.Rmd
myref_small.bib
No Results!

Last month downloads

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

Include our badge in your README

[![Rdoc](http://www.rdocumentation.org/badges/version/motmot.2.0)](http://www.rdocumentation.org/packages/motmot.2.0)