Optimize.NetworkSearch: Optimize.NetworkSearch: function to find the ML network...

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

Optimize.NetworkSearch: function to find the ML network topology using PhyloNet

Description

This function returns an optimized network topology and its maximized likelihood

Usage

Optimize.NetworkSearch(
  handle.GeneTrees,
  numeric.MaxReticulations,
  string.PathDir
)

Arguments

handle.GeneTrees	Phylo object containing a list of gene trees
numeric.MaxReticulations	Numeric defining the maximum number of reticulations for PhyloNet search
string.PathDir	String defining the path to a parent directory used for optimizing species tree
numeric.Stells_algorthm	Numeric defining with algorithm of STELLS to use: 0 or 1

Value

handle.Optimized_SpeciesTree Species tree with branch lengths (in coalescent units) that has been optimized with STELLS

numeric.MaximizedLnL Numeric containing the maximum likelihood given the optimized branch lengths of the species tree

Examples

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

#################################
# Generate example species trees #
#################################
string.SpeciesNetwork <- "(((((C:1.0,D:1.0):1)#H1:0::0.5,A:1.0):2,B:1.0):2,#H1:0::0.5);"
string.SpeciesNetwork_2 <- "(((((C:1.0,A:1.0):1)#H1:0::0.5,D:1.0):2,B:1.0):2,#H1:0::0.5);"

##########################
# Simulate gene tree set #
##########################
handle.Simulated_GeneTreeSet <- Simulate.GeneTrees_From_SpeciesNetwork(string.SpeciesNetwork = string.SpeciesNetwork,
                                                                       string.PathDir = '~/Desktop/',
                                                                       numeric.NumberOfGeneTrees = 5)

####################################
# Optimize network topology search #
####################################
handle.OptimizedNetwork_Topology <- Optimize.NetworkSearch(handle.GeneTrees = handle.Simulated_GeneTreeSet,
                                                           numeric.MaxReticulations = 1,
                                                           string.PathDir = '~/Desktop/')

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