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#' Path distance
#'
#' Calculate the path distance between rooted or unrooted trees.
#'
#' This function is a faster alternative to the function
#' \code{\link[phangorn:treedist]{path.dist()}} in the phangorn package,
#' which can crash if the internal representation of trees does not conform to
#' certain (unspecified) expectations, and which treats all trees as unrooted.
#'
#' The path distance is calculated by tabulating the cladistic difference (=
#' topological distance) between each pair of tips in each tree.
#' A precursor to the path distance \insertCite{Farris1969}{TreeDist}
#' took the mean squared
#' difference between the elements of each tree's tabulation (Farris, 1973);
#' the method used here is that proposed by
#' \insertCite{Steel1993;textual}{TreeDist}, which takes the square root of this
#' sum.
#' Other precursor measures are described in
#' \insertCite{Williams1971;textual}{TreeDist} and
#' \insertCite{Phipps1971;textual}{TreeDist}.
#'
#' If a root node is present, trees are treated as rooted.
#' To avoid counting the root edge twice, use `UnrootTree(tree)` before
#' calculating the path distance.
#'
#' Use of the path distance is discouraged as it emphasizes
#' shallow relationships at the expense of deeper (and arguably more
#' fundamental) relationships \insertCite{Farris1973}{TreeDist}.
#'
#' @template tree12ListParams
#'
#' @return `PathDist()` returns a vector or distance matrix of distances
#' between trees.
#'
#' @examples
#' library("TreeTools")
#'
#' # Treating the two edges to the root node as distinct
#' PathDist(BalancedTree(7), PectinateTree(7))
#'
#' # Counting those two edges once
#' PathDist(UnrootTree(BalancedTree(7)), UnrootTree(PectinateTree(7)))
#'
#' PathDist(BalancedTree(7), as.phylo(0:2, 7))
#' PathDist(as.phylo(0:2, 7), PectinateTree(7))
#'
#' PathDist(list(bal = BalancedTree(7), pec = PectinateTree(7)),
#' as.phylo(0:2, 7))
#'
#' PathDist(as.phylo(30:33, 8))
#'
#' @references \insertAllCited{}
#'
#' @template MRS
#' @family tree distances
#' @importFrom TreeTools Postorder
#' @export
PathDist <- function(tree1, tree2 = NULL) {
if (inherits(tree1, "phylo")) {
if (inherits(tree2, "phylo")) {
.PathDist11(tree1, tree2)
} else {
.PathDist1Many(tree1, tree2)
}
} else if (is.null(tree2)) {
.PathDistManySelf(tree1)
} else if (inherits(tree2, "phylo")) {
.PathDist1Many(tree2, tree1)
} else {
.PathDistManyMany(tree1, tree2)
}
}
.EuclideanDistance <- function(x) sqrt(sum(x * x))
.PathDist11 <- function(tree1, tree2) {
.EuclideanDistance(PathVector(tree1) - PathVector(RenumberTips(tree2, tree1)))
}
.PathDist1Many <- function(tree1, treeMany) {
v1 <- PathVector(tree1)
apply(v1 - vapply(RenumberTips(treeMany, tree1), PathVector, v1), 2,
.EuclideanDistance)
}
.PathDistManyMany <- function(trees1, trees2) {
nTip <- NTip(trees1[[1]])
v1 <- vapply(RenumberTips(trees1, trees1), PathVector,
integer(nTip * (nTip - 1) / 2))
v2 <- vapply(RenumberTips(trees2, trees1), PathVector,
integer(nTip * (nTip - 1) / 2))
vec_diff_euclidean(v1, v2)
}
.PathDistManySelf <- function(trees) {
nTip <- NTip(trees[[1]])
v1 <- vapply(RenumberTips(trees, trees), PathVector,
integer(nTip * (nTip - 1) / 2))
nTree <- length(trees)
ret <- structure(pair_diff_euclidean(v1),
Size = nTree, Diag = FALSE, Upper = FALSE,
class = "dist")
# Return:
ret
}
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