Fix PhyDatToMatrix crash on zero-character phyDat (#261)

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.

Author: ms609

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",

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

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_

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)