Conduct.SOWH_2N: Conduct.SOWH_2N: function to conduct the SOWH_2N STAR test...

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

Conduct.SOWH_2N: function to conduct the SOWH_2N STAR test given a species network topology

Description

This function returns a list containing p-values of the SOWH_1 STAR test

Usage

Conduct.SOWH_2N(
  string.SpeciesNetwork_1,
  handle.InputGeneTrees,
  numeric.NumberOfReps,
  numeric.MaxReticulations,
  string.PathDir
)

Arguments

string.SpeciesNetwork_1	String defining the first species topology (can be network or bifurcating)
numeric.NumberOfReps	Number of bootstrap replicates to analyze
numeric.MaxReticulations	Numeric defining the maximum number of reticulations for PhyloNet search
string.PathDir	String defining the path to a parent directory used for conduct SOWH_1 STAR test
handle.GeneTrees	Phylo object containing a list of the input gene trees

Value

List Returns a list containing (1) vector.Null_BS_Delta_Stat, (2) numeric.pValue, and (3) numeric.Delta_Observed

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 = 4)



#####################################
# Conduct SOWH_2 STAR using network #
#####################################
Conduct.SOWH_2N(string.SpeciesNetwork_1 = string.SpeciesNetwork_2,
                handle.InputGeneTrees = handle.Simulated_GeneTreeSet,
                numeric.NumberOfReps = 3,
                numeric.MaxReticulations = 1,
                string.PathDir = '~/Desktop/')

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