Compute.Probabilistic.SpeciesTree.Distances: Compute.Probabilistic.SpeciesTree.Distances: function to...

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

Description

This function returns a vector of length (3): representing the "Hellinger", "Kullback_Leibler", and "Jensen_Shannon" distances between to trees

Usage

Compute.Probabilistic.SpeciesTree.Distances(handle.SpeciesTree.Model1,
  handle.SpeciesTree.Model2, string.PathParentDir, string.PathHybridCoal)

Arguments

handle.SpeciesTree.Model1	Species Tree Model 1
handle.SpeciesTree.Model2	Species Tree Model 2
string.PathParentDir	Path to a parent directory that will be used for subdirectories
string.PathHybridCoal	Path to HYBRID-COAL executable

Value

vector.Probabilistic.SpeciesTree.Distances Vector containing the three PSTD measures

Examples

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/EXAMPLE/SmallTree/', 
   string.PathHybridCoal = '/Applications/hybrid-coal-v0.2.1-beta/hybrid-coal')

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