corHMM: Analysis of Binary Character Evolution

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Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.

Author
Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Jeffrey C. Oliver <jeffreycoliver@gmail.com>, Brian O'Meara <bomeara@utk.edu>
Date of publication
2016-09-27 08:41:44
Maintainer
Jeremy Beaulieu <jbeaulieu@nimbios.org>
License
GPL (>= 2)
Version
1.20

View on CRAN

Man pages

ancRECON
Ancestral state reconstruction
corDISC
Correlated evolution binary traits
corHMM
Hidden Rates Model
corPAINT
Binary character evolution with tree painting
lewisMkv
Phylogenetic inference of morphology using mkv model
plotRECON
Plot ancestral state reconstructions
primates
Example datasets
rate.mat.maker
Rate matrix maker
rayDISC
Evolution of categorical traits
readNexusMorph
Reads morphological character data In NEXUS Format

Files in this package

corHMM
corHMM/NAMESPACE
corHMM/data
corHMM/data/primates.rda
corHMM/data/primates.paint.rda
corHMM/data/rayDISC.example.rda
corHMM/R
corHMM/R/ancRECON.R
corHMM/R/corDISC.R
corHMM/R/lewisMkv.R
corHMM/R/corPAINT.R
corHMM/R/rayDISC.R
corHMM/R/corHMM.R
corHMM/R/readNexusMorph.R
corHMM/R/plotRECON.R
corHMM/R/rate.mat.maker.R
corHMM/MD5
corHMM/DESCRIPTION
corHMM/man
corHMM/man/plotRECON.Rd
corHMM/man/corPAINT.Rd
corHMM/man/rayDISC.Rd
corHMM/man/lewisMkv.Rd
corHMM/man/readNexusMorph.Rd
corHMM/man/primates.Rd
corHMM/man/rate.mat.maker.Rd
corHMM/man/corHMM.Rd
corHMM/man/corDISC.Rd
corHMM/man/ancRECON.Rd