R/getCompFeatures.R

In rgmantovani/MfeatExtractor: Extract meta-features from classification datasets

# -------------------------------------------------------------------------------------------------
# -------------------------------------------------------------------------------------------------

# R Code
# DCoL Library
# Ho and Basu 2002 Ho et al. 2006 and Orriols-Puig et al. 2010
# A set of measures designed to characterize the apparent complexity of data sets

# *** Reminder: nominal or categorical attributes must be numerically coded and treated 
# as continuous. This restriction is because most of the complexity measures rely on distance 
# functions between attributes.

# -------------------------------------------------------------------------------------------------
# -------------------------------------------------------------------------------------------------

cxName = function(data) {
  name = paste(".", paste(sample(letters, 20, replace=TRUE), collapse=""), sep="")
  RWeka::write.arff(data, paste(DIR, "/", name, ".arff", sep=""))
  return(name)
}

# -------------------------------------------------------------------------------------------------
# -------------------------------------------------------------------------------------------------

cxExecute = function(name) {
  exe = paste(DIR, "/src/./dcol -i ",DIR,"/",name,".arff -o ",DIR,"/",name," -A",sep="")
  system(paste(exe, sep=""), ignore.stdout=TRUE, ignore.stderr=TRUE)
  vet = read.table(paste(DIR, "/", name, ".txt", sep=""), skip=18)[,-1]
  names(vet) = COMPLEX
  return(vet)	
}

# -------------------------------------------------------------------------------------------------
# -------------------------------------------------------------------------------------------------

cxReplace = function(name) {
  exe = paste(DIR, "/src/./dcol -i ", DIR, "/", name, ".arff -o ", DIR, "/", name, 
    " -F 1v -L 1 -L 2 -L 3 -d", sep="")
  system(paste(exe, sep=""), ignore.stdout=TRUE, ignore.stderr=TRUE)
  vet = colMeans(read.table(paste(DIR, "/", name, ".txt", sep=""), skip=8)[,-1])
  names(vet) = REPLACE
  return(vet)
}

# -------------------------------------------------------------------------------------------------
# -------------------------------------------------------------------------------------------------

cxRemove = function(name) {
  system(paste("rm ", DIR, "/", name, ".* ", sep=""))
}

# -------------------------------------------------------------------------------------------------
# -------------------------------------------------------------------------------------------------

getCompFeatures = function(data) {

  name = cxName(data)
  dcol = cxExecute(name)
  if(nlevels(data$Class) > 2){
    dcol[,REPLACE] = cxReplace(name)
  }
  cxRemove(name)
  return(dcol)
}

# -------------------------------------------------------------------------------------------------
# -------------------------------------------------------------------------------------------------