RenumberTree(): numeric tipOrder

NEWS.md

@@ -1,6 +1,7 @@
 # TreeTools 2.0.0.9006 (development) #
 - `FirstMatchingSplit()`...
 - Support logical `pole` in `PolarizeSplits()`.
+- `RenumberTree()` supports numeric `tipOrder` input.
 
 # TreeTools 2.0.0.9004 (development) #
 - Support larger trees in `ClusterTable` objects.

R/tree_numbering.R

@@ -583,8 +583,9 @@ TntOrder.NULL <- function(tree) NULL
 #'
 #' @template treeParam
 #' @param tipOrder A character vector containing the values of
-#'        `tree[["tip.label"]]` in the desired sort order, or an object
-#'        (perhaps of class `phylo` or `Splits`) with tip labels.
+#' `tree[["tip.label"]]` in the desired sort order,
+#' an object (perhaps of class `phylo` or `Splits`) with tip labels,
+#' or a numeric specifying the desired order.
 #'
 #' @return `RenumberTips()` returns `tree`, with the tips' internal
 #' representation numbered to match `tipOrder`.
@@ -604,7 +605,11 @@ RenumberTips <- function(tree, tipOrder) UseMethod("RenumberTips")
 #' @export
 RenumberTips.phylo <- function(tree, tipOrder) {
   startOrder <- tree[["tip.label"]]
-  newOrder <- TipLabels(tipOrder, single = TRUE)
+  newOrder <- if (is.numeric(tipOrder)) {
+    startOrder[tipOrder]
+  } else {
+    TipLabels(tipOrder, single = TRUE)
+  }
   if (!identical(startOrder, newOrder)) {
     if (length(startOrder) != length(newOrder)) {
       startOnly <- setdiff(startOrder, newOrder)

tests/testthat/test-tree_numbering.R

@@ -22,6 +22,12 @@ test_that("RenumberTree() fails safely", {
   expect_error(RenumberTree(1:4, 1:4, 5:6))
 })
 
+test_that("RenumberTree() with numeric tipOrder", {
+  tr <- BalancedTree(6)
+  order <- c(6, 5, 4, 2, 3, 1)
+  expect_equal(RenumberTips(tr, order), RenumberTips(tr, TipLabels(order)))
+})
+
 test_that("RenumberTree() handles polytomies", {
   tr <- ape::read.tree(text = "(a, (b, d, c));")
   edge <- tr$edge