ComputePSTD: ComputeDistancesPSTD

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

Description

Function to compute the probabililistic distance between two gene tree probabilities for the Hellinger (dH, first), KL (dKL, second), and JS (dJS, third) distance measures of Garba et al 2018

IMPORTANT: This function assumes that the two gene tree probability vectors (vectorM1 and vectorM2) are sorted by to be the same. That is, the first gene tree in vectorM1 is also the first gene tree in vectorM2, and so on... The gene tree probability output files of HYBRID-COAL are sorted automatically.

Usage

ComputePSTD(vectorM1, vectorM2)

Arguments

vectorM1	Vector of the gene tree probabilities for M1
vectorM2	Vector of the gene tree probabilities for M2

Details

ComputeDistancesPSTD Computes the probabilistic distances between two probability distributions

Examples

vector.GeneTreeProbs.M1 <- Read.GeneTree.Probabilities(string.PathToGeneTreeProbs = '~/Desktop/EXAMPLE/SmallTree/M1.prob')
vector.GeneTreeProbs.M2 <- Read.GeneTree.Probabilities(string.PathToGeneTreeProbs = '~/Desktop/EXAMPLE/SmallTree/M2.prob')

ComputePSTD(vectorM1 = vector.GeneTreeProbs.M1, vectorM2 = vector.GeneTreeProbs.M2)

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