corHMM: Analysis of Binary Character Evolution
Version 1.20

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.

Browse man pages Browse package API and functions Browse package files

AuthorJeremy M. Beaulieu <jbeaulieu@nimbios.org>, Jeffrey C. Oliver <jeffreycoliver@gmail.com>, Brian O'Meara <bomeara@utk.edu>
Date of publication2016-09-27 08:41:44
MaintainerJeremy Beaulieu <jbeaulieu@nimbios.org>
LicenseGPL (>= 2)
Version1.20
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("corHMM")

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

Functions

AddTaxonEverywhere Source code
DiscreteGamma Source code
FactorDataLewis Source code
FindAmpsLewis Source code
FormatForLikelihood Source code
GetSiteLikelihoods Source code
GetTotalLikelihood Source code
LikelihoodCalculation Source code
RogersSwoffordish Source code
ancRECON Man page Source code
ancRECON.paint Source code
corDISC Man page Source code
corHMM Man page Source code
corPAINT Man page Source code
dev.cordisc Source code
dev.corhmm Source code
dev.corpaint Source code
dev.raydisc Man page Source code
factorData Source code
findAmps Source code
lewisMkv Man page Source code
match.tree.data Source code
plotRECON Man page Source code
primates Man page
primates.paint Man page
print.cordisc Source code
print.corhmm Source code
print.corpaint Source code
print.lewis.mkv Source code
print.raydisc Source code
rate.cat.set.corHMM Source code
rate.cat.set.rayDISC Source code
rate.mat.maker Man page Source code
rate.mat.set Source code
rate.mat.set.paint Source code
rate.par.drop Man page Source code
rate.par.eq Man page Source code
rayDISC Man page Source code
rayDISC.example Man page
readNexusMorph Man page Source code

Files

NAMESPACE
data
data/primates.rda
data/primates.paint.rda
data/rayDISC.example.rda
R
R/ancRECON.R
R/corDISC.R
R/lewisMkv.R
R/corPAINT.R
R/rayDISC.R
R/corHMM.R
R/readNexusMorph.R
R/plotRECON.R
R/rate.mat.maker.R
MD5
DESCRIPTION
man
man/plotRECON.Rd
man/corPAINT.Rd
man/rayDISC.Rd
man/lewisMkv.Rd
man/readNexusMorph.Rd
man/primates.Rd
man/rate.mat.maker.Rd
man/corHMM.Rd
man/corDISC.Rd
man/ancRECON.Rd
corHMM documentation built on May 29, 2017, 12:20 p.m.