From fe21dfc3986e246b44c8976d02d0651d31103cf7 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Tue, 17 Mar 2026 11:36:44 +0000
Subject: [PATCH] Fix PhyDatToMatrix crash on zero-character phyDat

PhyDatToMatrix() crashed when given a phyDat with nr=0 (e.g. from a
star tree) because matrix() could not reconcile empty data with
non-empty dimnames. Add an early return for the nr=0 case, returning
a 0-column matrix with correct row names.

This also fixes AddUnconstrained() when passed such a phyDat, since
it delegates to PhyDatToMatrix() internally.
---
 DESCRIPTION                            |  2 +-
 NEWS.md                                |  6 ++++++
 R/parse_files.R                        |  4 ++++
 tests/testthat/test-ImposeConstraint.R | 21 +++++++++++++++++++++
 4 files changed, 32 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 55995a7f3..be6dff373 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: TreeTools
 Title: Create, Modify and Analyse Phylogenetic Trees
-Version: 2.1.0.9007
+Version: 2.1.0.9008
 Authors@R: c(
   person("Martin R.", 'Smith', role = c("aut", "cre", "cph"), 
          email = "martin.smith@durham.ac.uk",
diff --git a/NEWS.md b/NEWS.md
index cd6b20bbe..9eea28c4f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+# TreeTools 2.1.0.9008 (2026-03-17) #
+
+- `PhyDatToMatrix()` no longer crashes on zero-character `phyDat` objects
+  (e.g. from a star tree); returns a 0-column matrix with correct row names.
+- `AddUnconstrained()` handles zero-character `phyDat` input gracefully.
+
 # TreeTools 2.1.0.9007 (2026-03-13) #
 
 - `duplicated.Splits()` uses hash-based O(n) de-duplication, replacing
diff --git a/R/parse_files.R b/R/parse_files.R
index c1288b4db..8c6fa50f7 100644
--- a/R/parse_files.R
+++ b/R/parse_files.R
@@ -809,6 +809,10 @@ PhyDatToMatrix <- function(dataset, ambigNA = FALSE, inappNA = ambigNA,
   }
   
   at <- attributes(dataset)
+  if (at[["nr"]] == 0L) {
+    return(matrix(character(0), nrow = length(at[["names"]]), ncol = 0,
+                  dimnames = list(at[["names"]], NULL)))
+  }
   allLevels <- as.character(at[["allLevels"]])
   if (inappNA) {
     allLevels[allLevels == "-"] <- NA_character_
diff --git a/tests/testthat/test-ImposeConstraint.R b/tests/testthat/test-ImposeConstraint.R
index d4d2f67fe..4e28f291d 100644
--- a/tests/testthat/test-ImposeConstraint.R
+++ b/tests/testthat/test-ImposeConstraint.R
@@ -1,3 +1,24 @@
+test_that("AddUnconstrained() handles zero-character phyDat", {
+  star <- ape::read.tree(text = "(a,b,c,d);")
+  empty_pd <- MatrixToPhyDat(t(as.matrix(star)))
+
+  # PhyDatToMatrix returns a correctly-dimensioned 0-column matrix
+  mat <- PhyDatToMatrix(empty_pd)
+  expect_equal(dim(mat), c(4L, 0L))
+  expect_equal(rownames(mat), c("a", "b", "c", "d"))
+
+  # AddUnconstrained returns 0-character phyDat with extra taxa
+  result <- AddUnconstrained(empty_pd, c("e", "f", "g"))
+  expect_s3_class(result, "phyDat")
+  expect_equal(names(result), c("a", "b", "c", "d", "e", "f", "g"))
+  expect_equal(attr(result, "nr"), 0L)
+
+  # asPhyDat = FALSE returns a 0-column matrix
+  result_mat <- AddUnconstrained(empty_pd, c("e", "f", "g"), asPhyDat = FALSE)
+  expect_equal(dim(result_mat), c(7L, 0L))
+  expect_equal(rownames(result_mat), c("a", "b", "c", "d", "e", "f", "g"))
+})
+
 test_that("AddUnconstrained() works", {
   tips <- letters[1:9]
   constraint <- StringToPhyDat("0000?1111 000111111 0000??110", tips, FALSE)