Small trees in root_on_node

ms609 · Jun 28, 2024 · 90d3f00 · 90d3f00
1 parent f9c7241
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: TreeTools
 Title: Create, Modify and Analyse Phylogenetic Trees
-Version: 1.11.1.9001
+Version: 1.11.1.9002
 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
@@ -1,3 +1,8 @@
+# TreeTools 1.11.1.9002 (2024-06-28) #
+
+- `root_on_node()` handles trees with < 2 leaves.
+
+
 # TreeTools 1.11.1.9001 (2024-06-19) #
 
 - `J1Index()` computes the robust, universal tree balance measure of 

diff --git a/inst/include/TreeTools/root_tree.h b/inst/include/TreeTools/root_tree.h
@@ -18,24 +18,27 @@ namespace TreeTools {
     const Rcpp::IntegerVector child,
     const Rcpp::DoubleVector weight);
 
-  // #TODO Write test cases
   // edge must be BINARY
   // edge must be in preorder
+  // 
   // Benchmarking at 2024-02-23 established that this is consistently twice
   // as fast as root_on_node, so is worth retaining,
   // despite some overlap in code.
+  // 
+  // #TODO Write test cases
+  // 
   // [[Rcpp::export]]
   inline Rcpp::IntegerMatrix root_binary(const Rcpp::IntegerMatrix edge,
                                          const int outgroup) {
 
-    if (edge(0, 1) == outgroup) return edge;
-
     const intx n_edge = edge.nrow(),
       n_node = n_edge / 2,
       n_tip = n_node + 1,
       root_node = n_tip + 1,
       max_node = n_node + n_tip;
-
+
+    if (!n_edge || !n_node || n_tip < 2) return edge;
+    if (edge(0, 1) == outgroup) return edge;
     if (outgroup < 1) {
       Rcpp::stop("`outgroup` must be a positive integer");
     }
@@ -102,8 +105,9 @@ namespace TreeTools {
       n_tip = max_node - n_node,
       root_node = n_tip + 1
     ;
-    const bool weighted = phy.containsElementNamed("edge.length");
+    if (!n_edge || !n_node || n_tip < 2) return phy;
 
+    const bool weighted = phy.containsElementNamed("edge.length");
     if (weighted) {
       Rcpp::List reweighted = preorder_weighted(
         edge(Rcpp::_, 0),

diff --git a/tests/testthat/test-root_tree.h.R b/tests/testthat/test-root_tree.h.R
@@ -21,6 +21,17 @@ test_that("Big trees don't fail", {
                PectinateTree(2^14 + 1))
 })
 
+test_that("Small trees are rootable", {
+  ztt <- ZeroTaxonTree()
+  expect_equal(root_on_node(ztt, 1), ztt)
+  expect_equal(root_binary(ztt[["edge"]], 1), ztt$edge)
+  expect_equal(root_on_node(ztt, 999), ztt)
+
+  stt <- SingleTaxonTree()
+  expect_equal(root_on_node(stt, 1), stt)
+  expect_equal(root_on_node(stt, 2), root_on_node(stt, 1))
+})
+
 test_that("Binary trees are rootable", {
   Test <- function(tree, root) {
     expect_equal(Preorder(ApeRoot(tree, tree$tip.label[root]))$edge,
@@ -33,6 +44,7 @@ test_that("Binary trees are rootable", {
   ed9 <- PectinateTree(9)$edge
   expect_equal(root_binary(ed9, 10), ed9)
   expect_equal(root_binary(ed9, 1), ed9)
+  expect_error(root_binary(ed9, 9999), "exceeds number of nodes")
 })
 
 test_that("Polytomous trees are rootable", {
@@ -78,6 +90,7 @@ test_that("Rooted trees report preorder accurately", {
 
   expect_preorder(root_binary(edge, 2))
   expect_preorder(root_binary(edge, 6))
+  expect_error(root_binary(edge, 999), "exceeds number of nodes")
 
   tree <- structure(list(edge = edge,
                          Nnode = nTips - 1L,