R/Conduct.KH_2.R

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
#'
#' This function returns a list containing p-values of the KH_2 STAR test for two input species tree topologies
#' @param handle.SpeciesTree1 Phylogenetic tree defining the first species topology
#' @param handle.SpeciesTree2 Phylogenetic tree defining the second species topology
#' @param handle.GeneTrees Phylo object containing a list of the input gene trees
#' @param numeric.NumberOfReps Number of bootstrap replicates to analyze
#' @param string.PathDir String defining the path to a parent directory used for conduct KH_1 STAR test
#' @keywords Species tree, multispecies coalescent, phylogenetics, phylogenomics
#' @return 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
#' @export
#' @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/')

################
# Conduct.KH_2 #
################
Conduct.KH_2 <- function(handle.SpeciesTree1, handle.SpeciesTree2, handle.InputGeneTrees, numeric.NumberOfReps, string.PathDir){

  ###################
  # Summarize input #
  ###################
  numeric.NumberOfGeneTrees <- length(handle.InputGeneTrees)

  ####################################################
  # Define directory used for conduct KH_1 STAR test #
  ####################################################
  string.CurrentDir <- getwd()
  string.Path_Directory_KH2 = paste(string.PathDir, '/Conduct.KH_2_', Sys.Date(), sep = "")
  unlink(string.Path_Directory_KH2, recursive = T)
  dir.create(string.Path_Directory_KH2, showWarnings = T, recursive = T)

  #################################################################################
  # Define subdirectory used for comput likelihoods given optimized species tree1 #
  #################################################################################
  string.Path_Directory_KH2_GeneTreeLikes_SpeciesTree1 = paste(string.Path_Directory_KH2, '/GeneTreeLikes_Optimized_SpeciesTree1', sep = "")
  unlink(string.Path_Directory_KH2_GeneTreeLikes_SpeciesTree1, recursive = T)
  dir.create(string.Path_Directory_KH2_GeneTreeLikes_SpeciesTree1, showWarnings = T, recursive = T)

  #################################################################################
  # Define subdirectory used for comput likelihoods given optimized species tree2 #
  #################################################################################
  string.Path_Directory_KH2_GeneTreeLikes_SpeciesTree2 = paste(string.Path_Directory_KH2, '/GeneTreeLikes_Optimized_SpeciesTree2', sep = "")
  unlink(string.Path_Directory_KH2_GeneTreeLikes_SpeciesTree2, recursive = T)
  dir.create(string.Path_Directory_KH2_GeneTreeLikes_SpeciesTree2, showWarnings = T, recursive = T)

  #########################################################
  # Define subdirectory used for optimizing species tree1 #
  #########################################################
  string.Path_Directory_KH2_SpeciesTree1 = paste(string.Path_Directory_KH2, '/Optimized_SpeciesTree1', sep = "")
  unlink(string.Path_Directory_KH2_SpeciesTree1, recursive = T)
  dir.create(string.Path_Directory_KH2_SpeciesTree1, showWarnings = T, recursive = T)

  ######################################################################################
  # Compute observed test statistic for the differences in LnLs for the two topologies #
  ######################################################################################
  setwd(dir = string.Path_Directory_KH2_SpeciesTree1)
  handle.Optimized_SpeciesTree1_OBSERVED <- Optimize.BranchLengths(handle.SpeciesTree = handle.SpeciesTree1,
                                                                   handle.GeneTrees = handle.InputGeneTrees,
                                                                   string.PathDir = string.Path_Directory_KH2_SpeciesTree1,
                                                                   numeric.Stells_algorthm = 1)
  numeric.LnL_SpeciesTree1_OBSERVED <- handle.Optimized_SpeciesTree1_OBSERVED$numeric.MaximizedLnL


  #########################################################
  # Define subdirectory used for optimizing species tree2 #
  #########################################################
  string.Path_Directory_KH2_SpeciesTree2 = paste(string.Path_Directory_KH2, '/Optimized_SpeciesTree2', sep = "")
  unlink(string.Path_Directory_KH2_SpeciesTree2, recursive = T)
  dir.create(string.Path_Directory_KH2_SpeciesTree2, showWarnings = T, recursive = T)

  ######################################################################################
  # Compute observed test statistic for the differences in LnLs for the two topologies #
  ######################################################################################
  setwd(dir = string.Path_Directory_KH2_SpeciesTree1)
  handle.Optimized_SpeciesTree2_OBSERVED <- Optimize.BranchLengths(handle.SpeciesTree = handle.SpeciesTree2,
                                                                   handle.GeneTrees = handle.InputGeneTrees,
                                                                   string.PathDir = string.Path_Directory_KH2_SpeciesTree2,
                                                                   numeric.Stells_algorthm = 1)
  numeric.LnL_SpeciesTree2_OBSERVED <- handle.Optimized_SpeciesTree2_OBSERVED$numeric.MaximizedLnL

  ##################################
  # Step 1: Compute observed delta #
  ##################################
  numeric.Delta_Observed <- numeric.LnL_SpeciesTree1_OBSERVED - numeric.LnL_SpeciesTree2_OBSERVED

  ###########################################################################
  # Step 2.1: Compute gene tree likelihoods for each optimized species tree #
  ###########################################################################
  vector.GeneTree_Likelihoods_SpeciesTree1 <- Compute.GeneTree_Likelihoods(handle.SpeciesTree = handle.Optimized_SpeciesTree1_OBSERVED$handle.Optimized_SpeciesTree,
                                                                           handle.GeneTrees = handle.InputGeneTrees,
                                                                           string.PathDir = string.Path_Directory_KH2_GeneTreeLikes_SpeciesTree1)
                                                                           
  vector.GeneTree_Likelihoods_SpeciesTree2 <- Compute.GeneTree_Likelihoods(handle.SpeciesTree = handle.Optimized_SpeciesTree2_OBSERVED$handle.Optimized_SpeciesTree,
                                                                           handle.GeneTrees = handle.InputGeneTrees,
                                                                           string.PathDir = string.Path_Directory_KH2_GeneTreeLikes_SpeciesTree2)

  ##########################
  # Compute observed delta #
  ##########################
  vector.ObservedDelta <- vector.GeneTree_Likelihoods_SpeciesTree1 - vector.GeneTree_Likelihoods_SpeciesTree2

  ###############################################################################
  # Step 2.2: Conducting RELL bootstrap resampling of the gene tree likelihoods #
  ###############################################################################
  vector.Delta_BootstrapReplicates_RELL <- rep(NA, numeric.NumberOfReps)

  ###########################
  # Loop through replicates #
  ###########################
  for (i in 1:numeric.NumberOfReps){

    vector.BootstrapReplicate_i <- sample(x = vector.ObservedDelta, size = numeric.NumberOfGeneTrees, replace = T)
    vector.Delta_BootstrapReplicates_RELL[i] <- sum(vector.BootstrapReplicate_i)

  }

  ###############################################
  # Step 3: Center the delta LnLs by their mean #
  ###############################################
  vector.Delta_BootstrapReplicates <- vector.Delta_BootstrapReplicates_RELL[!is.na(vector.Delta_BootstrapReplicates_RELL)]
  vector.Centered_Delta_BootstrapReplicates <- vector.Delta_BootstrapReplicates - mean(vector.Delta_BootstrapReplicates)

  ###############################
  # Step 5: Compute signficance #
  ###############################
  numeric.Upper_Pvalue <- length(vector.Centered_Delta_BootstrapReplicates[vector.Centered_Delta_BootstrapReplicates>=numeric.Delta_Observed])/length(vector.Centered_Delta_BootstrapReplicates)
  numeric.Lower_Pvalue <- length(vector.Centered_Delta_BootstrapReplicates[vector.Centered_Delta_BootstrapReplicates<=numeric.Delta_Observed])/length(vector.Centered_Delta_BootstrapReplicates)

  numeric.MinPvalue <- min(c(numeric.Upper_Pvalue, numeric.Lower_Pvalue))
  numeric.TwoSided_Pvalue <- numeric.MinPvalue*2

  ##########################################
  # Return to directory and return results #
  ##########################################
  setwd(dir = string.CurrentDir)
  return(list(TwoSided_Pvalue = numeric.TwoSided_Pvalue,
              Upper_Pvalue = numeric.Upper_Pvalue,
              Lower_Pvalue = numeric.Lower_Pvalue,
              Observed_Delta = numeric.Delta_Observed,
              BS_Delta = vector.Delta_BootstrapReplicates))

}