RunHybridCoal: RunHybridCoal: function to run HYBRID-COAL on a given species...

In radamsRHA/PSTDistanceR: Computing probabilistic distances between species tree models

Description

This function returns vector.GeneTreeProbabilities: a vector of gene tree probabilities for the species model (sum ~1.0)

Usage

RunHybridCoal(string.PathHybridCoal, handle.SpeciesTree,
  string.PathParentDir, string.SpeciesTree.ModelName)

Arguments

string.PathHybridCoal	Path to HYBRID-COAL executable
handle.SpeciesTree	Species tree
string.PathParentDir	Path to a parent directory that will be used for subdirectories
string.SpeciesTree.ModelName	String giving the name of the species model

Value

vector.GeneTreeProbabilities: vector containing a set of gene tree probabilities for the species tree model

Examples

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

RunHybridCoal(string.PathHybridCoal = '/Applications/hybrid-coal-v0.2.1-beta/hybrid-coal', 
   handle.SpeciesTree = handle.SpeciesTree.1a, 
   string.PathParentDir = '~/Desktop/EXAMPLE/SmallTree/', 
   string.SpeciesTree.ModelName = "Model1a")
   

radamsRHA/PSTDistanceR documentation built on March 4, 2020, 11:03 a.m.