R/InternalSES.gee.R

In MXM: Feature Selection (Including Multiple Solutions) and Bayesian Networks

InternalSES.gee = function(target, reps, group, dataset, max_k = 3, threshold = 0.05, test = NULL, ini, wei = NULL, user_test = NULL, 
                                hash = FALSE, varsize, stat_hash, pvalue_hash, targetID, correl, se, ncores) {
  #univariate feature selection test
  if ( is.null(ini) ) {
    univariateModels = univariateScore.gee(target, reps, group, dataset, test, wei = wei, targetID = targetID, correl = correl, se = se, ncores = ncores);
  } else   univariateModels = ini
  
  pvalues = univariateModels$pvalue;
  stats = univariateModels$stat;
  stat_hash = univariateModels$stat_hash;
  pvalue_hash = univariateModels$pvalue_hash;
  #if we dont have any associations , return
  if ( min(pvalues , na.rm = TRUE) > threshold ) { 
    #cat('No associations!');
    results = NULL;
    results$selectedVars = c();
    class(results$selectedVars) = "numeric";
    results$selectedVarsOrder = c();
    class(results$selectedVarsOrder) = "numeric";
    results$queues = c();
    class(results$queues) = 'list';
    results$signatures = matrix(nrow=1,ncol=1);
    class(results$signatures) = 'matrix';
    results$hashObject = NULL;
    class(results$hashObject) = 'list';
    class(results$univ) = 'list';
    results$pvalues = pvalues;
    results$stats = stats;
    results$univ = univariateModels;
    results$max_k = max_k;
    results$threshold = threshold;
    results$correl = correl
    results$se = se
    results$n.tests = length(stats)
    
    return(results);
  }
  #Initialize the data structs
  selectedVars = numeric(varsize);
  selectedVarsOrder = numeric(varsize);
  queues = vector('list' , varsize);
  queues <- lapply(1:varsize , function(i){queues[[i]] = i;})
  #select the variable with the highest association
  selectedVar = which.max(stats)
  selectedVars[selectedVar] = 1
  selectedVarsOrder[selectedVar] = 1 #CHANGE
  #lets check the first selected var
  #remaining variables to be considered
  remainingVars = rep(1,varsize)
  remainingVars[selectedVar] = 0
  remainingVars[pvalues > threshold] = 0
  if (targetID > 0)   remainingVars[targetID] = 0
  ################ main ses loop ################
  #main SES loop
  #loop until there are not remaining vars
  loop = any(as.logical(remainingVars))
  
  while(loop)  {
    #lets find the equivalences
    IdEq_results <- IdentifyEquivalence.gee(queues, target, reps, group, dataset, test, wei, threshold, max_k, selectedVars, pvalues, stats, remainingVars, univariateModels, selectedVarsOrder, hash=hash, stat_hash=stat_hash, pvalue_hash=pvalue_hash, correl = correl, se = se)
    queues = IdEq_results$queues
    selectedVars = IdEq_results$selectedVars
    remainingVars = IdEq_results$remainingVars
    pvalues = IdEq_results$pvalues
    stats = IdEq_results$stats
    stat_hash=IdEq_results$stat_hash
    pvalue_hash=IdEq_results$pvalue_hash
    #lets find the variable with the max min association
    max_min_results = max_min_assoc.gee(target, reps, group, dataset, test, wei, threshold, max_k, selectedVars, pvalues, stats, remainingVars, univariateModels, selectedVarsOrder, hash=hash, stat_hash=stat_hash, pvalue_hash=pvalue_hash, correl = correl, se = se)
    selectedVar = max_min_results$selected_var
    selectedPvalue = max_min_results$selected_pvalue
    remainingVars = max_min_results$remainingVars
    pvalues = max_min_results$pvalues
    stats = max_min_results$stats
    stat_hash=max_min_results$stat_hash
    pvalue_hash=max_min_results$pvalue_hash
    #if the selected variable is associated with target , add it to the selected variables
    if (selectedPvalue <= threshold)  {
      selectedVars[selectedVar] = 1
      selectedVarsOrder[selectedVar] = max(selectedVarsOrder) + 1
      remainingVars[selectedVar] = 0
    }
    loop = any(as.logical(remainingVars))
  }
  
  #lets find the variables to be discarded
  IdEq_results <- IdentifyEquivalence.gee(queues, target, reps, group, dataset, test, wei, threshold, max_k, selectedVars, pvalues, stats, remainingVars, univariateModels, selectedVarsOrder, hash=hash, stat_hash=stat_hash, pvalue_hash=pvalue_hash, correl = correl, se = se)
  queues = IdEq_results$queues
  selectedVars = IdEq_results$selectedVars
  pvalues = IdEq_results$pvalues
  stats = IdEq_results$stats
  remainingVars = IdEq_results$remainingVars
  stat_hash=IdEq_results$stat_hash
  pvalue_hash=IdEq_results$pvalue_hash
  selectedVarsOrder[which(!selectedVars)] = varsize#
  numberofSelectedVars = sum(selectedVars)#
  selectedVarsOrder = sort(selectedVarsOrder)#
  #  selectedVars = selectedVarsOrder[1:numberofSelectedVars]
  # queues correctness
  all_queues = queues
  queues = queues[which(selectedVars==1)]
  queues <- lapply(1:length(queues) , function(i){ queues[[i]] = unique(queues[[i]]) })
  #adjusting the results
  if (targetID > 0)  {
    toAdjust <- which(selectedVars > targetID)
    selectedVars[toAdjust] = selectedVars[toAdjust] + 1
  }
  
  results = NULL
  results$selectedVars = which(selectedVars == 1)
  svorder = sort(pvalues[results$selectedVars] , index.return = TRUE)
  svorder = results$selectedVars[svorder$ix]
  results$selectedVarsOrder = svorder
  results$queues = queues
  results$signatures = as.matrix(do.call(expand.grid, results$queues))
  hashObject = NULL
  hashObject$stat_hash = stat_hash
  hashObject$pvalue_hash = pvalue_hash
  results$hashObject = hashObject
  class(results$hashObject) = 'list'
  results$pvalues = pvalues
  results$stats = stats
  results$univ = univariateModels
  results$max_k = max_k
  results$threshold = threshold
  results$correl = correl
  results$se = se
  results$n.tests = length(stats) + length( hashObject$stat_hash )
  
  return(results)
}