cpp_edge_to_splits_batch

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: TreeTools
 Title: Create, Modify and Analyse Phylogenetic Trees
-Version: 2.2.0
+Version: 2.2.0.9001
 Authors@R: c(
   person("Martin R.", 'Smith', role = c("aut", "cre", "cph"), 
          email = "martin.smith@durham.ac.uk",

NEWS.md

@@ -1,3 +1,5 @@
+# TreeTools 2.2.0.9001 #
+
 # TreeTools 2.2.0 (2026-03-18) #
 
 ## New functionality

src/splits.cpp

@@ -31,37 +31,15 @@ inline void check_16_bit(double x) {
   }
 }
 
+// Core edge-to-splits computation; assumes validated inputs with n_tip >= 1.
 // Edges must be listed in 'strict' postorder, i.e. two-by-two
-// [[Rcpp::export]]
-Rcpp::RawMatrix cpp_edge_to_splits(const Rcpp::IntegerMatrix& edge,
-                                   const Rcpp::IntegerVector& order,
-                                   const Rcpp::IntegerVector& nTip) {
-
-  // Check input is valid
-  if (edge.cols() != 2) {
-    Rcpp::stop("Edge matrix must contain two columns");
-  }
-
+static Rcpp::RawMatrix edge_to_splits_impl(
+    const Rcpp::IntegerMatrix& edge,
+    const Rcpp::IntegerVector& order,
+    const uintx n_tip
+) {
   const uintx n_edge = edge.rows();
-  if (n_edge + 1 >= NOT_TRIVIAL) {
-    Rcpp::stop("Too many edges in tree for edge_to_splits: "                    // # nocov
-               "Contact maintainer for advice");                                // # nocov
-  }
-
-  if (nTip[0] < 1) {
-    if (nTip[0] == 0) {
-      return RawMatrix(0, 0);
-    } else {
-      Rcpp::stop("Tree must contain non-negative number of tips.");
-    }
-  }
-
-  if (n_edge != static_cast<uintx>(order.length())) {
-    Rcpp::stop("Length of `order` must equal number of edges");
-  }
-
   const uintx n_node = n_edge + 1;
-  const uintx n_tip = nTip[0];
   const uintx n_bin = ((n_tip - 1) / BIN_SIZE) + 1;
 
   if (n_edge == n_tip || n_tip < 4) {
@@ -140,6 +118,37 @@ Rcpp::RawMatrix cpp_edge_to_splits(const Rcpp::IntegerMatrix& edge,
   return ret;
 }
 
+// [[Rcpp::export]]
+Rcpp::RawMatrix cpp_edge_to_splits(const Rcpp::IntegerMatrix& edge,
+                                   const Rcpp::IntegerVector& order,
+                                   const Rcpp::IntegerVector& nTip) {
+
+  // Check input is valid
+  if (edge.cols() != 2) {
+    Rcpp::stop("Edge matrix must contain two columns");
+  }
+
+  const uintx n_edge = edge.rows();
+  if (n_edge + 1 >= NOT_TRIVIAL) {
+    Rcpp::stop("Too many edges in tree for edge_to_splits: "                    // # nocov
+               "Contact maintainer for advice");                                // # nocov
+  }
+
+  if (nTip[0] < 1) {
+    if (nTip[0] == 0) {
+      return RawMatrix(0, 0);
+    } else {
+      Rcpp::stop("Tree must contain non-negative number of tips.");
+    }
+  }
+
+  if (n_edge != static_cast<uintx>(order.length())) {
+    Rcpp::stop("Length of `order` must equal number of edges");
+  }
+
+  return edge_to_splits_impl(edge, order, static_cast<uintx>(nTip[0]));
+}
+
 // [[Rcpp::export]]
 LogicalVector duplicated_splits(const RawMatrix splits,
                                 const LogicalVector fromLast) {

tests/testthat/test-Splits.R

@@ -151,6 +151,21 @@ test_that("as.Splits.multiPhylo()", {
 
   expect_equal(as.Splits(randomTrees[[1]]),
                as.Splits(randomTrees)[[1]])
+
+  # asSplits = FALSE returns raw matrices
+  rawResults <- as.Splits(randomTrees, asSplits = FALSE)
+  for (i in seq_along(randomTrees)) {
+    expect_equal(rawResults[[i]],
+                 as.Splits(randomTrees[[i]], asSplits = FALSE))
+  }
+
+  # Trees with different tip label order handled correctly
+  relabelled <- randomTrees
+  relabelled[[1]] <- RenumberTips(relabelled[[1]], rev(seq_len(11L)))
+  fallbackResults <- as.Splits(relabelled)
+  expect_equal(as.Splits(relabelled[[2]],
+                          tipLabels = unique(unlist(TipLabels(relabelled)))),
+               fallbackResults[[2]])
 })
 
 test_that("as.Splits.Splits()", {