motmot v2.1.3

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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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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

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