Package: motmot 2.1.4

motmot: Models of Trait Macroevolution on Trees

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

Authors:Mark Puttick [aut, cph], Gavin Thomas [aut, cph], Rob Freckleton [aut, cph], Magnus Clarke [ctb], Travis Ingram [ctb], David Orme [ctb], Emmanuel Paradis [ctb], Martin R. Smith [ctb, cre]

motmot_2.1.4.tar.gz
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motmot_2.1.4.tgz(r-4.6-x86_64)motmot_2.1.4.tgz(r-4.6-arm64)motmot_2.1.4.tgz(r-4.5-x86_64)motmot_2.1.4.tgz(r-4.5-arm64)
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motmot_2.1.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
motmot/json (API)

# Install 'motmot' in R:

install.packages('motmot', repos = c('https://ms609.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ms609/motmot/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

allopatric.data - Finch allopatric data
anolis.data - Anolis phenotype data
anolis.tree - Anolis phylogeny
finch.data - Finch phenotype data
finch.tree - Finch tree
sympatric.data - Pairwise sympatry matrix for finch species

On CRAN:

cpp

5.64 score 54 scripts 509 downloads 8 mentions 34 exports 18 dependencies

Last updated from:91f2841aad. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	192
linux-devel-x86_64	OK	156
source / vignettes	OK	217
linux-release-arm64	OK	160
linux-release-x86_64	OK	152
macos-release-arm64	OK	159
macos-release-x86_64	OK	331
macos-oldrel-arm64	OK	105
macos-oldrel-x86_64	OK	326
windows-devel	OK	144
windows-release	OK	113
windows-oldrel	OK	114
wasm-release	OK	107

Exports:addFossilToPhy as.rateData as.rateMatrix calcCutOff chr.disp.lrt chr.disp.param chr.disp.sim contemporaryPhy dropTipPartial fairProportions likRatePhylo likTraitPhylo mcmc.plot ML.RatePhylo node.descendents nodeTimes optim.likRatePhylo phyloCovar phyloMean phyloVar pic.pgls plot.timeSlice.ML plot.traitMedusa.model RatePhylo.allCI sampleShid sortTraitData summary.traitMedusa traitData.plot transformPhylo transformPhylo.ll transformPhylo.MCMC transformPhylo.ML transformPhylo.sim transformRateMatrix

Dependencies:ape caper coda digest FNN kernlab KernSmooth ks lattice MASS Matrix mclust mgcv multicool mvtnorm nlme pracma Rcpp

MOTMOT: Models Of Trait Macroevolution On Trees

Rendered frommotmot.vignette.Rmdusingknitr::rmarkdown

Last update: 2026-04-15
Started: 2019-02-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Models Of Trait Macroevolution On Trees	motmot-package motmot
add a fossil to an interior branch of a time-scaled phylogeny	addFossilToPhy
Finch allopatric data	allopatric.data
Anolis phenotype data	anolis.data
Anolis phylogeny	anolis.tree
Conversion among data and phylogeny objects	as.rateData
Conversion among data and phylogeny objects	as.rateMatrix
Blomberg's K Estimate Blomberg's K (Blomberg et al. 2003)	blomberg.k
Calculate multiple-test cut-off	calcCutOff
Character displacement likelihood ratio test	chr.disp.lrt
Simulate character displacement data wrapper	chr.disp.param
Simulate character displacement data	chr.disp.sim
prune tree and data to lineages present in a time bin in the past	contemporaryPhy
Drop tips from a phylogenetic tree while preserving deleted nodes	dropTipPartial
Calculate fair proportions phylogenetic diversity metric	fairProportions
Finch phenotype data	finch.data
Finch tree	finch.tree
Log-likelihood rate estimation for traits and phylogenies	likRatePhylo
Log-likelihood estimation for traits and phylogenies	likTraitPhylo
plot the output from transformPhylo.MCMC	mcmc.plot
Maximum likelihood rate estimation for traits and phylogenies	ML.RatePhylo
Identify nodes and tips descended from a node	node.descendents
Get times for nodes and tips	nodeTimes
Maximum likelihood rate estimation for traits and phylogenies	optim.likRatePhylo
Calculation of Brownian (co)variance using independent contrasts.	phyloCovar
Calculation of phylogenetically corrected mean.	phyloMean
Calculation of Brownian variance.	phyloVar
Fast PLGS estimation based on contrasts	pic.pgls
Identify shifts in the rate of trait diversification through time	plot.timeSlice.ML
Tree plotting for rates	plot.traitMedusa.model
Confidence intervals for rate parameters	RatePhylo.allCI
Sample hidden speciation events along branches of a tree	sampleShid
Sort data and remove missing entries for tree and trait data	sortTraitData
Identify shifts in the rate of trait diversification	summary.traitMedusa
Pairwise sympatry matrix for finch species	sympatric.data
plot a univariate continuous trait data on a phylogeny	traitData.plot
Phylogenetic tree transformations	transformPhylo
Log-likelhood for models of trait evolution.	transformPhylo.ll
Bayesian MCMC for models of trait evolution	transformPhylo.MCMC
Maximum likelihood for models of trait evoluion	transformPhylo.ML
Phylogenetic tree transformations	transformPhylo.sim
Conversion among data and phylogeny objects	transformRateMatrix