Conduct.KH_2N: Conduct.KH_2N: function to conduct the KH_2N STAR test given...

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

Conduct.KH_2N: function to conduct the KH_2N STAR test given two distinct species topologies (one or both are networks) and a set of input gene trees

Description

This function returns a list containing p-values of the KH_2N STAR test for two input species tree topologies

Usage

Conduct.KH_2N(
  string.SpeciesNetwork1,
  string.SpeciesNetwork2,
  handle.InputGeneTrees,
  numeric.NumberOfReps,
  string.PathDir
)

Arguments

string.SpeciesNetwork1	String defining the first species topology (can be network or bifurcating)
string.SpeciesNetwork2	String defining the first species topology (can be network or bifurcating)
numeric.NumberOfReps	Number of bootstrap replicates to analyze
string.PathDir	String defining the path to a parent directory used for conduct KH_1 STAR test
handle.GeneTrees	Phylo object containing a list of the input gene trees

Value

List Returns a list containing (1) twosided pvalue, (2) upper p-values, (3) lower p-values, and (4) a vector of the bootstrapped test statistics delta

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 = 5)

Conduct.KH_2N(string.SpeciesNetwork1 = string.SpeciesNetwork,
              string.SpeciesNetwork2 = string.SpeciesNetwork_2,
              handle.InputGeneTrees = handle.SimulatedGeneTrees,
              numeric.NumberOfReps = 3,
              string.PathDir = '~/Desktop/')

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