Package: aphylo
Title: Statistical Inference and Prediction of Annotations in
        Phylogenetic Trees
Authors@R: c(person("George", "Vega Yon", role=c("aut","cre"),
         email="g.vegayon@gmail.com", comment = c(ORCID = "0000-0002-3171-0844")),
         person("National
         Cancer Institute (NCI)", role = "fnd", comment = "Grant Number
         5P01CA196569-02"),
         person("USC Biostatistics", role = "cph")
         )
Version: 0.3-6
Description: Implements a parsimonious evolutionary model to analyze
        and predict gene-functional annotations in phylogenetic trees
        as described in Vega Yon et al. (2021)
        <doi:10.1371/journal.pcbi.1007948>. Focusing on computational
        efficiency, 'aphylo' makes it possible to estimate pooled
        phylogenetic models, including thousands (hundreds) of
        annotations (trees) in the same run. The package also provides
        the tools for visualization of annotated phylogenies,
        calculation of posterior probabilities (prediction) and
        goodness-of-fit assessment featured in Vega Yon et al. (2021).
Depends: R (>= 3.5.0), ape (>= 5.0)
LazyData: true
Imports: Rcpp (>= 0.12.1), Matrix, methods, coda, fmcmc, utils, MASS,
        xml2
Suggests: covr, knitr, tinytest, AUC, rmarkdown,
VignetteBuilder: knitr
LinkingTo: Rcpp
RoxygenNote: 7.3.3
Encoding: UTF-8
URL: https://github.com/USCbiostats/aphylo
BugReports: https://github.com/USCbiostats/aphylo/issues
Classification/MSC: 90C35, 90B18, 91D30
License: MIT + file LICENSE
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: libxml2-dev
Repository: https://uscbiostats.r-universe.dev
Date/Publication: 2026-09-11 05:45:08 UTC
RemoteUrl: https://github.com/uscbiostats/aphylo
RemoteRef: HEAD
RemoteSha: ee7612a8b305e54117180d0245f15f8e47de5efe
NeedsCompilation: yes
Packaged: 2026-10-11 10:24:04 UTC; root
Author: George Vega Yon [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3171-0844>),
  National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02),
  USC Biostatistics [cph]
Maintainer: George Vega Yon <g.vegayon@gmail.com>