10Repetition.R

source('importDP.R')


  
  
  ### Remove The Past 
  rm(list = ls())
  #################################### SIMULATED DATA PROPERTIES ####################################################
  ## Number of points
  ptm <- proc.time()
  
  N.test = 100
  N.train =100
  
  ## Number of Clusters
  F = 3
  
  ## Distribution of the points within three clusters
  
  p.dist = c(0.4,0.3,0.3)
  
  ## Total Number of features D
  
  D = 10
  
  ## Total Percentage of irrelevant feature
  
  prob.noise.feature = 0.6
  
  
  ## Overlap between Cluster of molecular Data of the relevant features
  
  prob.overlap = 0.01
  
  ###### Get the Data #####################################
  
  ## Initialize the Training Data
  source('simulateDPMM.R')
  simulateDPMM()
  
  
  
  ############################# PARAMETERS for GIBB's SAMPLING ####
  iter = 100
  iter.burnin = 10*D
  iter.thin  =5
  k =3
  
  ########################### Initialize the functions ############
  
  
  
  ######################### Initialize the Parameters ################
  source('initializeDPMM.R')
  initializeDPMM()
  
  
  ######### Ground Truth ##############################
  ###source('SIMgroundtruth.R')
  ###SIMgroundtruth()
  
  
  
  ########### Train the Model #########################################
  source('burninDPMM.R')
  burninDPMM()
  
  
  source('gibbsDPMM.R')
  gibbsDPMM()
  
  ########## Analyze the fit ##########################################
  source('SIManalyzeDPMM.R')
  SIManalyzeDPMM()
  
  
  ######## Predict on New Data Set #####################################
  source('predictCLASS.R')
  predictCLASS(Y.new, time.new)
  ## Check how much concordance is there
  test.randindex <- adjustedRandIndex(apply(posteriorprob,1,which.max),c.true.new)
  
  source('predictchineseAFTtime.R')
  predictchineseAFTtime(Y.new)
  ## Do a Non parametric test
  predicted.close.pvalue <- wilcox.test(as.vector(time.real.new), as.vector(post.time.avg), paired = TRUE)$p.value
  ### Check of the Predicted C-index ## 91% concordance
  predicted.cindex <- survConcordance(Surv(time.new,censoring.new) ~ exp(-post.time.avg))[1]
  
  x = 4
  
  filename <- paste("/home/bit/ashar/ExpressionSets/Simulations/D10K30Crep",x,".RData",sep = "")
  save(list =ls(), file = filename)

  proc.time() - ptm