DESCRIPTION

Package: pepo
Type: Package
Title: Estimate Hemiplasy and Homoplasy on a Phylogeny
Version: 0.2
Author: Rafael Guerrero
Maintainer: Rafael Guerrero <rafguerr@indiana.edu>
Description: P(e):P(o) is a minimal package that implements methods to calculate 
    the probabilities of hemiplasy (trait evolution incongruent with species tree due to incomplete
    lineage sorting) and homoplasy (incongruent traits due to convergent mutations). In this first version, the
    package includes functions to estimate and plot the ratio of these two probabilities--the Hemiplasy Risk Factor (HRF)-- of all branches on a phylogeny, 
    provided a tree is in coalescent units and a mutation rate.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports:
    readr,
    purrr,
    dplyr,
    ape,
    phylobase,
    treeio,
Suggests:
    ggplot2,
    testthat,
    knitr,
    rmarkdown
RoxygenNote: 6.0.1
Collate:
    'data.R'
    'mutation_functions.R'
    'hrf_functions.R'
    'hrf_on_trees.R'
    'pepo.R'
    'pepo_utilities.R'
VignetteBuilder: knitr