R/survival_forest_matrix.R

In luyouepiusf/ClusteringTree4: Supervised clustering with survival outcomes

survival_forest_matrix<-function(
  time,
  event,
  matrix_numeric,
  matrix_factor,
  weights=rep(1,length(time)),
  significance=0.05,
  min_weights=50,
  missing="omit",
  test_type="univariate",
  nboot=100,
  seed=0){
  
  # check [missing], [test_type]
  if(!missing%in%c("majority","omit","weighted"))stop("Invalid 'missing' argument.")
  if(!test_type%in%c("univariate",p.adjust.methods))stop("Invalid 'test_type' argument.")
  
  ndim_numeric<-ncol(matrix_numeric)
  ndim_factor<-ncol(matrix_factor)
  nind<-length(time)
  
  # check dimensions
  if(nrow(matrix_numeric)!=nind)stop("Dimension mismatch between 'matrix_numeric' and 'time'.")
  if(nrow(matrix_factor)!=nind)stop("Dimension mismatch between 'matrix_factor' and 'time'.")
  if(any(is.na(time))|any(is.na(event)))stop("Missing values in 'time' or 'event'.")
  
  # create names
  if(is.null(colnames(matrix_numeric))&ndim_numeric>=1)colnames(matrix_numeric)<-paste0("numeric",1:ncol(matrix_numeric),sep="")
  if(is.null(colnames(matrix_factor))&ndim_factor>=1)colnames(matrix_factor)<-paste0("factor",1:ncol(matrix_factor),sep="")
  variable_names<-c(colnames(matrix_numeric),colnames(matrix_factor))
  
  # convert matrix_factor to an integer matrix
  # factor_dictionary<-list()
  # matrix_factor_int<-matrix(NA,nind,ndim_factor)
  # if(ncol(matrix_factor)>0){
  #   colnames(matrix_factor_int)<-colnames(matrix_factor)
  #   for(idx in 1:ncol(matrix_factor)){
  #     aname<-colnames(matrix_factor)[idx]
  #     a_dictionary<-create_dictionary(matrix_factor[,idx])
  #     factor_dictionary[[aname]]<-a_dictionary
  #     matrix_factor_int[,idx]<-a_dictionary[matrix_factor[,aname]]
  #   }
  # }
  # matrix_factor<-matrix_factor_int
  
  a_survival_forest<-list()
  set.seed(seed)
  for(boot_idx in 1:nboot){
    cat(boot_idx)
    shuffle<-sample(1:nind,nind,replace=T)
    time_boot<-time[shuffle]
    event_boot<-event[shuffle]
    matrix_numeric_boot<-matrix_numeric[shuffle,]
    matrix_factor_boot<-matrix_factor[shuffle,]
    weights_boot<-weights[shuffle]
    
    a_survival_tree<-survival_tree_matrix(
      time=time_boot,
      event=event_boot,
      matrix_numeric=matrix_numeric_boot,
      matrix_factor=matrix_factor_boot,
      weights=weights_boot,
      significance=significance,
      min_weights=min_weights,
      missing=missing,
      test_type=test_type)
    cat(" - ")
    a_survival_forest[[boot_idx]]<-a_survival_tree
  }
  
  return(list(
    variable_names=variable_names,
    ndim_numeric=ndim_numeric,
    ndim_factor=ndim_factor,
    survival_forest=a_survival_forest))
}