Conduct.KH_2: Conduct.KH_2: function to conduct the KH_2 STAR test given...

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

Conduct.KH_2: function to conduct the KH_2 STAR test given two distinct species topologies and a set of input gene trees

Description

This function returns a list containing p-values of the KH_2 STAR test for two input species tree topologies

Usage

Conduct.KH_2(
  handle.SpeciesTree1,
  handle.SpeciesTree2,
  handle.InputGeneTrees,
  numeric.NumberOfReps,
  string.PathDir
)

Arguments

handle.SpeciesTree1	Phylogenetic tree defining the first species topology
handle.SpeciesTree2	Phylogenetic tree defining the second species topology
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 trees #
#################################
handle.SpeciesTree1 <- read.tree(text = "(A:1.0,(B:0.5,(C:1.0,D:1.0):1.5):0.5);")
handle.SpeciesTree1$edge.length <- handle.SpeciesTree1$edge.length*0.01
handle.SpeciesTree2 <- read.tree(text = "(C:1.0,(B:0.5,(A:1.0,D:1.0):1.5):0.5);")

#################################################
# Simlate a set of gene trees for species tree1 #
#################################################
handle.Simulated_GeneTrees <- Simulate.GeneTrees_From_SpeciesTree(handle.SpeciesTree = handle.SpeciesTree1,
                                                                  string.PathDir = '~/Desktop/',
                                                                  numeric.NumberOfGeneTrees = 100)

##############################################################
# Conduct KH_2 STAR test for the two species tree topologies #
##############################################################
Conduct.KH_2(handle.SpeciesTree1 = handle.SpeciesTree1,
             handle.SpeciesTree2 = handle.SpeciesTree2,
             handle.InputGeneTrees = handle.Simulated_GeneTrees,
             numeric.NumberOfReps = 100,
             string.PathDir = '~/Desktop/')

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