R/localLambda.R

In hferg/hfgr:

#' localLambda
#'
#' A function that transforms a tree according to lambda, or a portion of a tree according to lambda.
#' @param tree A tree of class phylo.
#' @param node A node number describing the clade(s) to be transformed.
#' @param lambda The value or values of lambda by which to transform the specified clade(s).

localLambda <- function(tree, node, lambda) {
    descs <- getDescs(tree, node)
    trans.edges <- which(tree$edge[ ,2] %in% descs & tree$edge[ ,2] > length(tree$tip.label))
    ht1 <- nodeHeights(tree)
    tree$edge.length[trans.edges] <- lambda * tree$edge.length[trans.edges]
    ht2 <- nodeHeights(tree)
    tree$edge.length[-trans.edges] <- tree$edge.length[-trans.edges] + ht1[-trans.edges, 2] - ht2[-trans.edges, 2]
    return(tree)
  }