In JanEngelstaedter/cophy: Constructing random cophylogenetic trees and analysing their statistics

knitr::opts_chunk$set(
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cophy

The aim of cophy is to generate, analyse and plot cophylogenies. By this we mean a phylogenetic tree of species ("hosts"), combined with another phylogenetic tree of species ("parasites"). Each branch of the parasite tree is linked to one particular host branch. Random generation of cophylogenies involves a number of evolutionary events, including host speciation and extinction, parasite host shifts (potentially with a preference for closely related hosts), parasite extinction, and others.

Example

Here is a simple example for how you can create a random cophylogeny, and plot it:

library(cophy)
set.seed(7)
cop<-rcophylo(tmax=20, K=30, beta = 2, gamma = 0.3, nu = 0.3)
cop
get_infectionStatistics(cop)
plot(cop)

Installation

To install cophy, you first need to install and load the latest version of the devtools package (available on CRAN). Then, run the following line of code:

devtools::install_github("JanEngelstaedter/cophy", build_opts = c("--no-resave-data", "--no-manual"))

JanEngelstaedter/cophy documentation built on Nov. 7, 2023, 9:37 a.m.