Compute.GeneTree_Likelihoods_SpeciesNetwork: Compute.GeneTree_Likelihoods_SpeciesNetwork: function to...

In radamsRHA/SpeciesTopoTestR: Likelihood-based tests of species topologies in R

Compute.GeneTree_Likelihoods_SpeciesNetwork: function to compute gene tree likelihoods using PhyloNet for a species topology and/or network

Description

This function returns a vector of gene tree likelihoods given a set of gene trees and a particular species tree (networks included)

Usage

Compute.GeneTree_Likelihoods_SpeciesNetwork(
  string.SpeciesNetwork,
  handle.GeneTrees,
  string.PathDir
)

Arguments

string.SpeciesNetwork	String of the species network in Rich newick format (can be read by dendroscope)
handle.GeneTrees	Phylo object of gene trees
string.PathDir	String of the path to a parent directory used for simulating gene trees

Value

vector.GeneTreeProbs Vector of gene tree likelihoods for each gene tree provided

Examples

################
# Load depends #
################
library(SpeciesTopoTestR)
library(ape)

####################################
# Generate example species network #
####################################
string.SpeciesNetwork <- "(((((C:1.0,D:1.0):1)#H1:0::0.25,A:1.0):2,B:1.0):2,#H1:0::0.75);"
string.SpeciesNetwork_2 <- "((A:1,B:1):1,(C:1,D:1):1);"


####################################################
# Simlate a set of gene trees for this species tree #
#####################################################
handle.SimulatedGeneTrees <- Simulate.GeneTrees_From_SpeciesNetwork(string.SpeciesNetwork = string.SpeciesNetwork,
                                                                    string.PathDir = '~/Desktop/',
                                                                    numeric.NumberOfGeneTrees = 100)

############################
# Optimize species network #
############################
handle.Optimized_Network1 <- Optimize.Network(string.SpeciesNetwork = string.SpeciesNetwork,
                                              handle.GeneTrees = handle.SimulatedGeneTrees,
                                              string.PathDir = '~/Desktop/')


#################################################################
# Compute gene tree likelihoods given optimized species network #
#################################################################
vector.GeneTreeLikelihoods_SpeciesNetwork <- Compute.GeneTree_Likelihoods_SpeciesNetwork(string.SpeciesNetwork = handle.Optimized_Network1$string.Optimized_SpeciesNetwork,
                                                                                         handle.GeneTrees = handle.SimulatedGeneTrees,
                                                                                         string.PathDir = '~/Desktop/')

radamsRHA/SpeciesTopoTestR documentation built on Sept. 5, 2022, 7:37 p.m.