Package: markophylo
Type: Package
Title: Markov Chain Models for Phylogenetic Trees
Version: 1.0.9
Date: 2023-09-14
Author: Utkarsh J. Dang and G. Brian Golding
Maintainer: Utkarsh J. Dang <utkarshdang@cunet.carleton.ca>
Description: 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. See Dang and Golding (2016)
        <doi:10.1093/bioinformatics/btv541> for more details.
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.4), ape (>= 3.2), numDeriv (>= 2012.9.1),
        phangorn (>= 1.99.13), geiger
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr (>= 1.10), testthat (>= 0.9.1), markdown (> 1.0)
Depends: R (>= 2.10)
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: yes
Packaged: 2026-07-05 01:18:50 UTC; root
Repository: https://cran.r-universe.dev
Date/Publication: 2023-09-19 14:31:31 UTC
RemoteUrl: https://github.com/cran/markophylo
RemoteRef: HEAD
RemoteSha: 82c21cfa0cae2dfe197cb095b2091338b3c9e788