aphylo: Statistical Inference and Prediction of Annotations in Phylogenetic Trees

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>. With a focus 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).

Version: 0.2-1
Depends: R (≥ 3.5.0), ape (≥ 5.0)
Imports: Rcpp (≥ 0.12.1), Matrix, methods, coda, fmcmc, utils, MASS, xml2
LinkingTo: Rcpp
Suggests: covr, knitr, tinytest, AUC, rmarkdown
Published: 2022-01-21
Author: George Vega Yon ORCID iD [aut, cre], National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02), USC Biostatistics [cph]
Maintainer: George Vega Yon <g.vegayon at gmail.com>
BugReports: https://github.com/USCbiostats/aphylo/issues
License: MIT + file LICENSE
URL: https://github.com/USCbiostats/aphylo
NeedsCompilation: yes
Classification/MSC: 90C35, 90B18, 91D30
Citation: aphylo citation info
Materials: NEWS ChangeLog
CRAN checks: aphylo results

Documentation:

Reference manual: aphylo.pdf
Vignettes: Simulation and Inference

Downloads:

Package source: aphylo_0.2-1.tar.gz
Windows binaries: r-devel: aphylo_0.2-1.zip, r-release: aphylo_0.2-1.zip, r-oldrel: aphylo_0.2-1.zip
macOS binaries: r-release (arm64): aphylo_0.2-1.tgz, r-release (x86_64): aphylo_0.2-1.tgz, r-oldrel: aphylo_0.2-1.tgz

Linking:

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