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NNIDist(): score all pairs in one C++ call - #228
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Renumber and postorder each tree once, compute each tree's splits once, and score every pair in cpp_nni_distance_all_pairs(). Output identical to CompareAll(trees, NNIDist). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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| for (int32_t i = 0; i < n_edge - 1; ++i) { /* final edge is second root edge */ | ||
| const ptrdiff_t parent_row_i = (edge(i, 0) - 1) * n_bin; | ||
| const ptrdiff_t child_row_i = (edge(i, 1) - 1) * n_bin; | ||
| const ptrdiff_t parent_row_i = (tree.parent[i] - 1) * n_bin; |
| const ptrdiff_t parent_row_i = (edge(i, 0) - 1) * n_bin; | ||
| const ptrdiff_t child_row_i = (edge(i, 1) - 1) * n_bin; | ||
| const ptrdiff_t parent_row_i = (tree.parent[i] - 1) * n_bin; | ||
| const ptrdiff_t child_row_i = (tree.child[i] - 1) * n_bin; |
Performance benchmark results
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #228 +/- ##
==========================================
+ Coverage 97.74% 97.77% +0.02%
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Files 60 60
Lines 6575 6648 +73
==========================================
+ Hits 6427 6500 +73
Misses 148 148 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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NNIDist(trees)(one list, all pairs) now renumbers and postorders each tree once and scores every pair in a single C++ call (cpp_nni_distance_all_pairs()), instead ofCompareAll()→.NNIDistSingle()per pair. Each tree's splits are computed once; per pair only the split matching and scoring run.cpp_nni_distance()shares the same core (nni_tree(),nni_edge_to_splits(),nni_rf_matching(),nni_score()). Two-argumentNNIDist(tree1, tree2)is unchanged.Identity. Output is
identical()toCompareAll(trees, NNIDist)(old path) on all 945 7-leaf trees, unrooted 7-leaf trees, random 60–200-leaf trees with shuffled labels, 3-leaf trees, polytomies, and lists that mix rooted and unrooted trees with equal edge counts (a pair is scored under the first tree's rootedness, as before; the second tree's splits are recomputed in that case).Benchmark (release installs, min of N, single thread, local R-devel, same session):
Main's 945-tree time includes the multiPhylo indexing cost fixed in #227; this PR bypasses
CompareAll()so doesn't conflict with it. Recorded in.AGENTS/memory/Optimizations.md. At 200 leaves the O(s²) split matching now dominates; sorting canonical splits would allow a linear merge (follow-up).New R and C++ lines covered by
test-tree_distance_nni.R; NEWS entry added.🤖 Generated with Claude Code