From fe61a3e51d0390a93f22567af8b180eb4a8d5ba7 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Mon, 9 Feb 2026 06:41:43 +0000
Subject: [PATCH 1/2] RenumberTree() with numeric tipOrder

---
 NEWS.md                              |  1 +
 R/tree_numbering.R                   | 11 ++++++++---
 man/RenumberTips.Rd                  |  5 +++--
 tests/testthat/test-tree_numbering.R |  6 ++++++
 4 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index e7862cb4d..bcecccebc 100644
--- a/NEWS.md
+++ b/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.
diff --git a/R/tree_numbering.R b/R/tree_numbering.R
index 40a1fdc27..5b8bf4635 100644
--- a/R/tree_numbering.R
+++ b/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)
diff --git a/man/RenumberTips.Rd b/man/RenumberTips.Rd
index c7f48bfe5..b439c690b 100644
--- a/man/RenumberTips.Rd
+++ b/man/RenumberTips.Rd
@@ -22,8 +22,9 @@ RenumberTips(tree, tipOrder)
 \item{tree}{A tree of class \code{\link[ape:read.tree]{phylo}}.}
 
 \item{tipOrder}{A character vector containing the values of
-\code{tree[["tip.label"]]} in the desired sort order, or an object
-(perhaps of class \code{phylo} or \code{Splits}) with tip labels.}
+\code{tree[["tip.label"]]} in the desired sort order,
+an object (perhaps of class \code{phylo} or \code{Splits}) with tip labels,
+or a numeric specifying the desired order.}
 }
 \value{
 \code{RenumberTips()} returns \code{tree}, with the tips' internal
diff --git a/tests/testthat/test-tree_numbering.R b/tests/testthat/test-tree_numbering.R
index 14989d72c..ed75ee461 100644
--- a/tests/testthat/test-tree_numbering.R
+++ b/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

From e549c4c5666e8a6b7756447515afd077bf662a66 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 9 Feb 2026 09:33:20 +0000
Subject: [PATCH 2/2] Missing )

---
 tests/testthat/test-tree_numbering.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-tree_numbering.R b/tests/testthat/test-tree_numbering.R
index ed75ee461..e6164bdf0 100644
--- a/tests/testthat/test-tree_numbering.R
+++ b/tests/testthat/test-tree_numbering.R
@@ -26,7 +26,7 @@ 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));")