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: 2023-09-19 11:28:03 UTC; udang
Repository: CRAN
Date/Publication: 2023-09-19 12:20:03 UTC
Built: R 4.6.0; aarch64-apple-darwin23; 2026-04-26 08:36:02 UTC; unix
Archs: markophylo.so.dSYM
