PSTDistanceR

PSTDistanceR: R package for computing probabilistic distances between species tree models under the multispecies coalscent

The R package PSTDistanceR is freely available to download and distribute from github https://github.com/radamsRHA/PSTDistanceR/. To install and load PSTDistanceR, you must first install the R packages phangorn, distory, Rcpp, and the program hybrid-coal-v0.2.1-beta.

install.packages("devtools")
install.packages("distory")
install.packages("phangorn")

Now using devtools we can install PSTDistanceR from github:

library(devtools)
install_github("radamsRHA/PSTDistanceR")
library(PSTDistanceR) # Load package ThetaMater

Here's an example usage of PSTDistanceR for computing the distance between two species trees:

library(PSTDistanceR)
library(phangorn)

string.SpeciesTree.1a <- "(((A:1,B:1):1,C:2):1,D:3);"
handle.SpeciesTree.1a <- read.tree(text = string.SpeciesTree.1a)

string.SpeciesTree.1b <- "(((A:1,C:1):1,B:2):1,D:3);"
handle.SpeciesTree.1b <- read.tree(text = string.SpeciesTree.1b)


Compute.Probabilistic.SpeciesTree.Distances(handle.SpeciesTree.Model1 = handle.SpeciesTree.1a, 
   handle.SpeciesTree.Model2 = handle.SpeciesTree.1b, 
   string.PathParentDir = '~/Desktop/', 
   string.PathHybridCoal = '/Applications/hybrid-coal-v0.2.1-beta/hybrid-coal')