Package: CoalescentPhylo
Title: Phylogenetics via Root Distances Method Under the Coalescent
Version: 0.1.0
Authors@R: c(
    person("Arindam", "RoyChoudhury", , "arr2014@med.cornell.edu", role = c("aut", "cre", "cph")),
    person("Ying", "Li", role = "aut")
  )
Description: Estimates phylogenetic trees from allele count data using
        the root distance method under the Coalescent Model. Given a
        matrix of allele counts across taxa and loci, the package
        estimates pairwise root distances under the Coalescent Model
        using maximum likelihood estimation. Then, it estimates a
        labeled phylogenetic tree from the estimated root distances.
        See Peng et al. (2021) <doi:10.1016/j.ympev.2021.107142>.
License: AGPL-3
URL: https://github.com/ArindamRoyChoudhury/CoalescentPhylo
BugReports: https://github.com/ArindamRoyChoudhury/CoalescentPhylo/issues
Depends: R (>= 3.5.0)
Imports: ape, parallel, pbapply, phangorn, rootSolve
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.3
Config/pak/sysreqs: libglpk-dev libxml2-dev
Repository: https://arindamroychoudhury.r-universe.dev
Date/Publication: 2026-05-19 13:56:54 UTC
RemoteUrl: https://github.com/arindamroychoudhury/coalescentphylo
RemoteRef: HEAD
RemoteSha: 1ad35a9ade63710282de71255a18a6fec738e2d1
NeedsCompilation: no
Packaged: 2026-07-18 04:30:21 UTC; root
Author: Arindam RoyChoudhury [aut, cre, cph],
  Ying Li [aut]
Maintainer: Arindam RoyChoudhury <arr2014@med.cornell.edu>