Resample.Bootstrap_GeneTree_Replicates_NP: Resample.Bootstrap_GeneTree_Replicates_NP: function to...

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

Resample.Bootstrap_GeneTree_Replicates_NP: function to conduct non-parametric bootstrapping (i.e., random sampling with replacement) for a set of input gene trees

Description

This function returns a list containing multiple replicate sets of gene trees (each replicate is a bootstrapped dataset)

Usage

Resample.Bootstrap_GeneTree_Replicates_NP(
  handle.GeneTrees,
  numeric.NumberOfReps
)

Arguments

handle.GeneTrees	MultiPhylo object of the input gene trees
numeric.NumberOfReps	Numeric number of bootstrap replicates

Value

list.BootStrap_GeneTree_ReplicateSets List containing sets of gene trees bootstrap replicates

Examples

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

#################################
# Generate example species tree #
#################################
handle.SpeciesTree <- read.tree(text = "(A:1.0,(B:0.5,(C:1.0,D:1.0):1.5):0.5);")

#####################################################
# Simlate a set of gene trees for this species tree #
#####################################################
handle.Simulated_GeneTrees <- Simulate.GeneTrees_From_SpeciesTree3(handle.SpeciesTree = handle.SpeciesTree, 
                                                                  string.PathDir = '~/Desktop/', 
                                                                  numeric.NumberOfGeneTrees = 10)

#################################################
# Resample from example simulated gene tree set #
#################################################
list.Bootstrapped_GeneTreesSets <- Resample.Bootstrap_GeneTree_Replicates_NP(handle.GeneTrees = handle.Simulated_GeneTrees, numeric.NumberOfReps = 10)

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