Package: motmot 2.1.3

motmot: 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.

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

motmot_2.1.3.tar.gz
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motmot.pdf |motmot.html✨
motmot/json (API)

# Install 'motmot' in R:
install.packages('motmot', repos = c('https://puttickmacroevolution.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

6.04 score 4 stars 34 scripts 177 downloads 8 mentions 34 exports 18 dependencies

Last updated 4 years agofrom:59299172fb. Checks:OK: 1 ERROR: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-win-x86_64ERRORNov 06 2024
R-4.5-linux-x86_64ERRORNov 06 2024
R-4.4-win-x86_64ERRORNov 06 2024
R-4.4-mac-x86_64ERRORNov 06 2024
R-4.4-mac-aarch64ERRORNov 06 2024
R-4.3-win-x86_64ERRORNov 06 2024
R-4.3-mac-x86_64ERRORNov 06 2024
R-4.3-mac-aarch64ERRORNov 06 2024

Exports:addFossilToPhyas.rateDataas.rateMatrixcalcCutOffchr.disp.lrtchr.disp.paramchr.disp.simcontemporaryPhydropTipPartialfairProportionslikRatePhylolikTraitPhylomcmc.plotML.RatePhylonode.descendentsnodeTimesoptim.likRatePhylophyloCovarphyloMeanphyloVarpic.pglsplot.timeSlice.MLplot.traitMedusa.modelRatePhylo.allCIsampleShidsortTraitDatasummary.traitMedusatraitData.plottransformPhylotransformPhylo.lltransformPhylo.MCMCtransformPhylo.MLtransformPhylo.simtransformRateMatrix

Dependencies:apecapercodadigestFNNkernlabKernSmoothkslatticeMASSMatrixmclustmgcvmulticoolmvtnormnlmepracmaRcpp

MOTMOT: Models Of Trait Macroevolution On Trees

Mark Puttick

Rendered frommotmot.vignette.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2019-11-21
Started: 2019-02-27

MOTMOT: Models Of Trait Macroevolution On Trees

Mark Puttick

Rendered frommotmot.vignette.pdf.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2019-11-21
Started: 2019-05-30

Readme and manuals

Help Manual

Help pageTopics
Models Of Trait Macroevolution On Treesmotmot-package motmot
add a fossil to an interior branch of a time-scaled phylogenyaddFossilToPhy
Finch allopatric dataallopatric.data
Anolis phenotype dataanolis.data
Anolis phylogenyanolis.tree
Conversion among data and phylogeny objectsas.rateData
Conversion among data and phylogeny objectsas.rateMatrix
Blomberg's K Estimate Blomberg's K (Blomberg et al. 2003)blomberg.k
Calculate multiple-test cut-offcalcCutOff
Character displacement likelihood ratio testchr.disp.lrt
Simulate character displacement data wrapperchr.disp.param
Simulate character displacement datachr.disp.sim
prune tree and data to lineages present in a time bin in the pastcontemporaryPhy
Drop tips from a phylogenetic tree while preserving deleted nodesdropTipPartial
Calculate fair proportions phylogenetic diversity metricfairProportions
Finch phenotype datafinch.data
Finch treefinch.tree
Log-likelihood rate estimation for traits and phylogenieslikRatePhylo
Log-likelihood estimation for traits and phylogenieslikTraitPhylo
Mammal datamammals
plot the output from transformPhylo.MCMCmcmc.plot
Maximum likelihood rate estimation for traits and phylogeniesML.RatePhylo
Identify nodes and tips descended from a nodenode.descendents
Get times for nodes and tipsnodeTimes
Maximum likelihood rate estimation for traits and phylogeniesoptim.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 contrastspic.pgls
Identify shifts in the rate of trait diversification through timeplot.timeSlice.ML
Tree plotting for ratesplot.traitMedusa.model
Confidence intervals for rate parametersRatePhylo.allCI
Sample hidden speciation events along branches of a treesampleShid
Sort data and remove missing entries for tree and trait datasortTraitData
Identify shifts in the rate of trait diversificationsummary.traitMedusa
plot a univariate continuous trait data on a phylogenytraitData.plot
Phylogenetic tree transformationstransformPhylo
Log-likelhood for models of trait evolution.transformPhylo.ll
Bayesian MCMC for models of trait evolutiontransformPhylo.MCMC
Maximum likelihood for models of trait evoluiontransformPhylo.ML
Phylogenetic tree transformationstransformPhylo.sim
Conversion among data and phylogeny objectstransformRateMatrix