Marvin N. Wright

Full text links in publication list

2018-05-15T00:00:00+00:00

The publication list now includes a full text link for most papers (PDF links). For open access papers, this is just the link to the publisher’s version and some others are available on arXiv. A few papers are not freely available but for most of them I am allowed to share them privately (e.g. via email).

ranger out-of-bag proximity matrix

2017-12-14T00:00:00+00:00

I’ve created a function to compute an out-of-bag proximity matrix of a ranger object, based on edarf::extract_proximity:

extract_proximity_oob = function(fit, olddata) {
  pred = predict(fit, olddata, type = "terminalNodes")$predictions
  prox = matrix(NA, nrow(pred), nrow(pred))
  ntree = ncol(pred)
  n = nrow(prox)
  
  if (is.null(fit$inbag.counts)) {
    stop("call ranger with keep.inbag = TRUE")
  }
  
  # Get inbag counts
  inbag = simplify2array(fit$inbag.counts)
  
  for (i in 1:n) {
    for (j in 1:n) {
      # Use only trees where both obs are OOB
      tree_idx = inbag[i, ] == 0 & inbag[j, ] == 0
      prox[i, j] = sum(pred[i, tree_idx] == pred[j, tree_idx]) / sum(tree_idx)
    }
  }
  
  prox
}

(taken from https://github.com/imbs-hl/ranger/issues/234)

How are trees saved in ranger?

2017-12-14T00:00:00+00:00

A frequently asked question is: “How are trees saved in ranger objects?”

Answer (taken from https://github.com/imbs-hl/ranger/issues/147):

child.nodeIDs is a list containing two vectors for each tree. These are the child node IDs for each node in the tree. The left children in the first vector, the right children in the second vector. The nodeIDs are 0-indexed. However, since the root of a tree (ID 0) cannot be a child, the 0 is used for terminal nodes.

In split.varIDs there is a vector for each tree with the splitting variables for each node in the tree. These IDs are 0-indexed, too. If you use the formula interface, the 0-variable should be the outcome. Terminal nodes also have a 0 here.

In split.values the splitting values for all nodes are saved. In terminal nodes, the outcome for this node is saved in split.values.

Note: A 0 in split.varIDs is no sufficient condition for a terminal node. Check child.nodeIDs to be sure.