Allows for fitting of maximum likelihood models using Markov chains on phylogenetic trees for analysis of discrete character data. Examples of such discrete character data include restriction sites, gene family presence/absence, intron presence/absence, and gene family size data. Hypothesis-driven user- specified substitution rate matrices can be estimated. Allows for biologically realistic models combining constrained substitution rate matrices, site rate variation, site partitioning, branch-specific rates, allowing for non-stationary prior root probabilities, correcting for sampling bias, etc.

Maintainer: Utkarsh J. Dang <udang at mcmaster.ca>

Author(s): Utkarsh J. Dang and G. Brian Golding

Install package and any missing dependencies by running this line in your R console:

install.packages("markophylo")

Depends R (>= 2.10)
Imports Rcpp(>=0.11.4), ape(>=3.2), numDeriv(>=2012.9.1), phangorn(>=1.99.13)
Suggests knitr(>=1.10), testthat(>=0.9.1)
Enhances
Linking to Rcpp, RcppArmadillo
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depends
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imports
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suggests
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enhances
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linking to

Package markophylo
Materials
URL
Task Views Phylogenetics
Version 1.0.4
Published 2015-12-31
License GPL (>= 2)
BugReports
SystemRequirements
NeedsCompilation yes
Citation
CRAN checks markophylo check results
Package source markophylo_1.0.4.tar.gz