R/helpers.R

In nicolas-robette/moreparty: A Toolbox for Conditional Inference Trees and Random Forests

simplify_rule <- function(x) {
  df <- data.frame(rule = unlist(strsplit(x, " & ")))
  df$rang <- 1:nrow(df)
  df$variable <- sapply(df$rule, function(x) strsplit(x, " ")[[1]][1])
  df$type_cat <- grepl(" in ", df$rule)
  df <- df[order(df$rang, decreasing = TRUE),]
  df$id <- with(df, ave(seq_along(variable), variable, FUN=seq_along))
  df <- df[df$type_cat == FALSE | (df$type_cat == TRUE & df$id == 1),]
  df <- df[order(df$rang),]
  res <- paste(df$rule, collapse = " & ")
  return(res)
}







# unexported function from partykit

list.rules.party <- function(x, i = NULL, ...) {
  if (is.null(i)) {
    i <- partykit::nodeids(x, terminal = TRUE)
  }
  if (length(i) > 1) {
    ret <- sapply(i, list.rules.party, x = x)
    names(ret) <- if (is.character(i)) {
      i
    } else {
      names(x)[i]
    }
    return(ret)
  }
  if (is.character(i) && !is.null(names(x))) {
    i <- which(names(x) %in% i)
  }
  stopifnot(length(i) == 1 & is.numeric(i))
  stopifnot(i <= length(x) & i >= 1)
  i <- as.integer(i)
  dat <- partykit::data_party(x, i)
  if (!is.null(x$fitted)) {
    findx <- which("(fitted)" == names(dat))[1]
    fit <- dat[, findx:ncol(dat), drop = FALSE]
    dat <- dat[, -(findx:ncol(dat)), drop = FALSE]
    if (ncol(dat) == 0) {
      dat <- x$data
    }
  }
  else {
    fit <- NULL
    dat <- x$data
  }
  rule <- c()
  recFun <- function(node) {
    if (partykit::id_node(node) == i) {
      return(NULL)
    }
    kid <- sapply(partykit::kids_node(node), partykit::id_node)
    whichkid <- max(which(kid <= i))
    split <- partykit::split_node(node)
    ivar <- partykit::varid_split(split)
    svar <- names(dat)[ivar]
    index <- partykit::index_split(split)
    if (is.factor(dat[, svar])) {
      if (is.null(index)) {
        index <- ((1:nlevels(dat[, svar])) > partykit::breaks_split(split)) +
          1
      }
      slevels <- levels(dat[, svar])[index == whichkid]
      srule <- paste(svar, " %in% c(\"", paste(slevels,
                                               collapse = "\", \"", sep = ""
      ), "\")", sep = "")
    }
    else {
      if (is.null(index)) {
        index <- 1:length(kid)
      }
      breaks <- cbind(c(-Inf, partykit::breaks_split(split)), c(
        partykit::breaks_split(split),
        Inf
      ))
      sbreak <- breaks[index == whichkid, ]
      right <- partykit::right_split(split)
      srule <- c()
      if (is.finite(sbreak[1])) {
        srule <- c(srule, paste(svar, ifelse(right, ">",
                                             ">="
        ), sbreak[1]))
      }
      if (is.finite(sbreak[2])) {
        srule <- c(srule, paste(svar, ifelse(right, "<=",
                                             "<"
        ), sbreak[2]))
      }
      srule <- paste(srule, collapse = " & ")
    }
    rule <<- c(rule, srule)
    return(recFun(node[[whichkid]]))
  }
  node <- recFun(partykit::node_party(x))
  paste(rule, collapse = " & ")
}





## Unexported function
## taken from varImp package
## https://github.com/PhilippPro/varImp


# create_cond_list
#
# create the list of variables to condition on for the current variable of interest, xname,
create_cond_list = function(cond, threshold, xname, input) {
  stopifnot(is.logical(cond))
  if (!cond) return(NULL)
  if (threshold > 0 & threshold < 1) {
    ctrl = ctree_control(teststat = "quad", testtype = "Univariate", stump = TRUE)
    xnames = names(input)
    xnames = xnames[xnames != xname]
    ct = party::ctree(as.formula(paste(xname, "~", paste(xnames, collapse = "+"), collapse = "")),
               data = input, controls = ctrl)
    crit = ct@tree$criterion[[2]]
    crit[which(is.na(crit))] = 0
    return(xnames[crit > threshold])
  }
  stop()
}

### extract ID of _all_ variables the tree uses for splitting
varIDs = function(node) {
  
  v = c()
  foo = function(node) {
    if (node[[4]]) return(NULL)
    v <<- c(v, node[[5]][[1]])
    foo(node[[8]])
    foo(node[[9]])
  }
  foo(node)
  return(v)
}

conditional_perm = function(cond, xnames, input, tree, oob) {
  
  ## intitial partitioning => all observations in one partition
  parts = rep(1, length(oob))
  
  ## develop partitioning by going over all the conditiong variables
  for (condVar in cond) {
    
    ## varID is variable index or column number of input (predictor matrix) 
    ## not variable name!
    varID = which(xnames == condVar)
    
    ## if conditioning variable is not used for splitting in current tree
    ## proceed with next conditioning variable
    cl = cutpoints_list(tree, varID)
    if (is.null(cl)) next
    
    ## proceed cutpoints for different types of variables
    x = input[, varID]
    xclass = class(x)[1]
    if (xclass == "integer") xclass = "numeric"
    
    block = switch(xclass, "numeric" = cut(x, breaks = c(-Inf, sort(unique(cl)), Inf)),
                   "ordered" = cut(as.numeric(x), breaks =  c(-Inf, sort(unique(cl)), Inf)),
                   "factor" = {
                     CL = matrix(as.logical(cl), nrow = nlevels(x))                            
                     rs = rowSums(CL)
                     dlev = (1:nrow(CL))[rs %in% rs[duplicated(rs)]]
                     fuse = c()
                     for (ii in dlev) {
                       for (j in dlev[dlev > ii]) {
                         if (all(CL[ii,] == CL[j,])) fuse = rbind(fuse, c(ii, j))
                       }
                     }
                     xlev = 1:nlevels(x)
                     newl = nlevels(x) + 1
                     block = as.integer(x)
                     for (l in xlev) {
                       if (NROW(fuse) == 0) break
                       if (any(fuse[, 1] == l)) {
                         f = c(l, fuse[fuse[, 1] == l, 2])
                         fuse = fuse[!fuse[,1] %in% f, , drop = FALSE]
                         block[block %in% f] = newl
                         newl = newl + 1
                       }
                     }
                     as.factor(block)
                   })
    ## add partitioning based on the split points the variable to the 
    ## current partitioning
    parts = interaction(parts, as.numeric(block), drop = TRUE, sep = "")
  }
  
  ## if none of the conditioning variables are used in the tree
  if (!length(levels(parts)) > 1) {
    perm = sample(which(oob))
    return(perm)
  } else {
    ## one conditional permutation
    perm = 1:nrow(input)
    for(part in levels(parts)){
      index = which(parts == part & oob)
      if (length(index) > 1)
        perm[index] = index[sample.int(length(index))]
    }
    return(perm[oob])
  }
}

# cutpoints_list() returns:
# - vector of cutpoints (length=number of cutpoints) 
#   if variable is continuous
# - vector of indicators (length=number of categories x number of cutpoints)
#   if variable is categorical (nominal or ordered)
cutpoints_list = function(tree, variableID) {
  
  cutp = function(node) {
    if (node[[4]]) return(NULL)
    cp = NULL
    if (node[[5]][[1]] == variableID)
      cp = node[[5]][[3]]
    nl = cutp(node[[8]])
    nr = cutp(node[[9]])
    return(c(cp, nl, nr))
  }
  return(cutp(tree))
}