`duplicated.Splits()` by ms609 · Pull Request #260 · ms609/TreeTools

ms609 · 2026-03-13T10:42:35Z

No description provided.

_init.R: do.call(bench::mark, args) evaluates expressions before passing them, so bench stored the evaluated result (e.g. a phylo tree) instead of the call. Restored direct ... passthrough. _compare_results.R: Use deparse1() instead of as.character(unlist()) for expression extraction (the latter decomposes call objects into components). Also iterate by index to guard against NA names, and use res$change instead of outer-scope percentage_change.

github-actions · 2026-03-13T11:13:01Z

⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-0.91%	23.1 → 22.2, 23.9
`as.Splits(someTrees)`	⚪ NSD	-2.84%	11.2 → 11.7, 11.4
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	0%	99.5 → 102, 98.7
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	0.12%	4.14 → 4.11, 4.16
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	1.35%	1.25 → 1.23, 1.23
`Consensus(forest21.260)`	⚪ NSD	1.61%	1.27 → 1.25, 1.26
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	0.6%	3.04 → 3.04, 2.99
`DropTip(tr2000, 5)`	⚪ NSD	0.65%	17.3 → 17, 17.4
`DropTip(tr80, 5)`	⚪ NSD	0.36%	0.106 → 0.106, 0.106
`DropTip(unlen2k, 5)`	⚪ NSD	0.42%	0.285 → 0.294, 0.214
`DropTip(unlen80, 5)`	⚪ NSD	0.15%	0.0405 → 0.0408, 0.0401
`lapply(bigSplits, as.phylo)`	⚪ NSD	0.63%	29.9 → 29.6, 29.7
`lapply(someSplits, as.phylo)`	⚪ NSD	0.91%	14 → 13.8, 13.8
`PathLengths(tr2000, full = TRUE)`	🟣 ~same	-4.13%	16.5 → 17.4, 17
`PathLengths(tr80, full = TRUE)`	⚪ NSD	-15.19%	0.0404 → 0.0493, 0.042
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	-12.76%	0.0424 → 0.0498, 0.0436
`RootTree(tr2000, 5)`	⚪ NSD	5.41%	0.397 → 0.375, 0.375
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-1.47%	0.07 → 0.0711, 0.071
`RootTree(tr80, "t3")`	⚪ NSD	1%	0.0502 → 0.0498, 0.0496
`RootTree(tr80, "t30")`	⚪ NSD	0.56%	0.0503 → 0.0501, 0.0499
`RootTree(unlen2k, 5)`	⚪ NSD	-2.87%	0.326 → 0.335, 0.336
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-1.67%	0.0644 → 0.0652, 0.0657
`RootTree(unlen80, "t3")`	⚪ NSD	0.11%	0.0435 → 0.0436, 0.0433
`RootTree(unlen80, "t30")`	⚪ NSD	0.23%	0.044 → 0.0441, 0.0436
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	1.43%	16.3 → 16, 16.3
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	0.73%	3.37 → 3.33, 3.37
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	-5.03%	0.102 → 0.109, 0.106
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-1.16%	0.00173 → 0.00174, 0.00175
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	1.03%	0.434 → 0.429, 0.429
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-0.06%	0.00182 → 0.00182, 0.00182
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	1.34%	2.18 → 2.19, 2.12
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	0.76%	0.00262 → 0.00259, 0.00261
`TreeTools:::postorder_order(dpec40k)`	🟣 ~same	-3.16%	3300 → 3430, 3380
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	1.7%	0.00412 → 0.00407, 0.00404
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	0.46%	0.00218 → 0.00216, 0.00217
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	0.8%	2.2 → 2.21, 2.12
`TreeTools:::postorder_order(npec40)`	⚪ NSD	2.04%	0.00294 → 0.00287, 0.00288
`TreeTools:::postorder_order(npec40k)`	🟣 ~same	-3.01%	3320 → 3430, 3400
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	0.67%	0.00466 → 0.0046, 0.00465
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-1.16%	0.00172 → 0.00173, 0.00175
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	1.38%	0.432 → 0.425, 0.427
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	2.21%	0.00222 → 0.00217, 0.00218

github-actions · 2026-03-13T11:45:59Z

⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-8.53%	22.1 → 23.1, 24.3
`as.Splits(someTrees)`	⚪ NSD	-1.34%	11 → 11.2, 11.1
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	0.25%	96.5 → 96.5, 95.3
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	0%	4.03 → 4.04, 4.02
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	1.33%	1.23 → 1.21, 1.21
`Consensus(forest21.260)`	⚪ NSD	1.03%	1.24 → 1.23, 1.23
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	0.71%	2.98 → 2.96, 2.96
`DropTip(tr2000, 5)`	🟣 ~same	-1.59%	16.6 → 17, 16.8
`DropTip(tr80, 5)`	⚪ NSD	0.34%	0.105 → 0.105, 0.105
`DropTip(unlen2k, 5)`	⚪ NSD	3.23%	0.293 → 0.216, 0.289
`DropTip(unlen80, 5)`	⚪ NSD	-0.39%	0.0404 → 0.0402, 0.0407
`lapply(bigSplits, as.phylo)`	⚪ NSD	-0.17%	29.7 → 29.7, 29.7
`lapply(someSplits, as.phylo)`	⚪ NSD	0.1%	13.8 → 13.8, 13.9
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-1.28%	16 → 16.4, 16.1
`PathLengths(tr80, full = TRUE)`	⚪ NSD	1.07%	0.0435 → 0.0442, 0.0408
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	1.58%	0.0444 → 0.0444, 0.0424
`RootTree(tr2000, 5)`	⚪ NSD	0.32%	0.394 → 0.395, 0.391
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-1.13%	0.0697 → 0.0709, 0.0699
`RootTree(tr80, "t3")`	⚪ NSD	0.76%	0.0501 → 0.05, 0.0494
`RootTree(tr80, "t30")`	⚪ NSD	-0.3%	0.0499 → 0.0501, 0.05
`RootTree(unlen2k, 5)`	⚪ NSD	-1.58%	0.324 → 0.331, 0.327
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	0.19%	0.0649 → 0.0649, 0.0646
`RootTree(unlen80, "t3")`	⚪ NSD	-0.47%	0.0429 → 0.0432, 0.0431
`RootTree(unlen80, "t30")`	⚪ NSD	-0.58%	0.0433 → 0.0435, 0.0435
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-1.5%	15.6 → 15.8, 15.7
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-0.65%	3.25 → 3.27, 3.29
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	0.86%	0.105 → 0.106, 0.103
`TreeTools:::postorder_order(bal40)`	⚪ NSD	0.56%	0.00175 → 0.00174, 0.00174
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	1.36%	0.434 → 0.427, 0.428
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	0.6%	0.00182 → 0.0018, 0.00181
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	-0.12%	2.16 → 2.15, 2.17
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	0.38%	0.00264 → 0.00257, 0.00267
`TreeTools:::postorder_order(dpec40k)`	🟣 ~same	-4.08%	3290 → 3430, 3420
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	-0.75%	0.00412 → 0.00422, 0.00407
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	1.38%	0.00218 → 0.00214, 0.00216
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	0.46%	2.19 → 2.17, 2.18
`TreeTools:::postorder_order(npec40)`	⚪ NSD	1.04%	0.0029 → 0.00284, 0.00288
`TreeTools:::postorder_order(npec40k)`	🟣 ~same	-3.74%	3310 → 3450, 3420
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	2.13%	0.00469 → 0.00457, 0.00461
`TreeTools:::postorder_order(pec40)`	⚪ NSD	2.87%	0.00177 → 0.00171, 0.00173
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	1.17%	0.429 → 0.425, 0.421
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	1.37%	0.00218 → 0.00211, 0.00219

github-actions · 2026-03-13T12:09:34Z

⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-3.1%	23.6 → 22.5, 26
`as.Splits(someTrees)`	⚪ NSD	-0.38%	11 → 11, 11.1
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	-1.6%	95.7 → 97.6, 96.9
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-1.55%	4.03 → 4.1, 4.08
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-1.29%	1.22 → 1.23, 1.23
`Consensus(forest21.260)`	⚪ NSD	-1.78%	1.23 → 1.25, 1.25
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-2.3%	2.93 → 2.99, 3
`DropTip(tr2000, 5)`	⚪ NSD	-1.37%	16.6 → 16.7, 17
`DropTip(tr80, 5)`	⚪ NSD	-1.41%	0.104 → 0.105, 0.105
`DropTip(unlen2k, 5)`	⚪ NSD	-35.46%	0.209 → 0.218, 0.288
`DropTip(unlen80, 5)`	⚪ NSD	-0.13%	0.0401 → 0.0405, 0.0398
`lapply(bigSplits, as.phylo)`	⚪ NSD	-0.3%	29.6 → 29.4, 30.1
`lapply(someSplits, as.phylo)`	⚪ NSD	-0.48%	13.6 → 13.6, 14
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	1.12%	16.2 → 16, 16
`PathLengths(tr80, full = TRUE)`	⚪ NSD	-1.8%	0.0381 → 0.0392, 0.0382
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	-1.54%	0.0403 → 0.041, 0.0409
`RootTree(tr2000, 5)`	⚪ NSD	2.78%	0.397 → 0.376, 0.394
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-1.06%	0.07 → 0.0716, 0.0693
`RootTree(tr80, "t3")`	⚪ NSD	-2.61%	0.0491 → 0.0509, 0.0498
`RootTree(tr80, "t30")`	⚪ NSD	-1.4%	0.0499 → 0.0512, 0.05
`RootTree(unlen2k, 5)`	⚪ NSD	-1.25%	0.328 → 0.334, 0.328
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-0.86%	0.0649 → 0.0661, 0.0648
`RootTree(unlen80, "t3")`	⚪ NSD	-2.93%	0.0431 → 0.0452, 0.0432
`RootTree(unlen80, "t30")`	⚪ NSD	-3.45%	0.0433 → 0.0456, 0.0435
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-0.8%	15.5 → 15.7, 15.5
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-0.05%	3.27 → 3.32, 3.24
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	0.27%	0.102 → 0.101, 0.102
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-0.63%	0.00174 → 0.00178, 0.00174
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	0.77%	0.432 → 0.427, 0.431
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	0.61%	0.00181 → 0.00179, 0.00181
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	-0.44%	2.09 → 2.16, 2.1
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	1.14%	0.00263 → 0.00258, 0.00261
`TreeTools:::postorder_order(dpec40k)`	🟣 ~same	-3.68%	3290 → 3420, 3400
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	1.46%	0.00411 → 0.00407, 0.00404
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	0.91%	0.0022 → 0.00217, 0.00219
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	-5.39%	2.11 → 2.22, 2.22
`TreeTools:::postorder_order(npec40)`	⚪ NSD	0.69%	0.00291 → 0.00288, 0.0029
`TreeTools:::postorder_order(npec40k)`	🟣 ~same	-3.42%	3310 → 3410, 3450
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	1.29%	0.00466 → 0.0046, 0.00459
`TreeTools:::postorder_order(pec40)`	⚪ NSD	0.07%	0.00173 → 0.00171, 0.00174
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	0.74%	0.431 → 0.424, 0.431
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	3.16%	0.00221 → 0.00218, 0.00212

again(¬)

github-actions · 2026-03-13T14:20:39Z

⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	🟠 Slower 🙁	-15.84%	22.3 → 26.7, 24.8
`as.Splits(someTrees)`	⚪ NSD	-2.9%	11.1 → 11.5, 11.1
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	4.69%	101 → 97.2, 96
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	2.72%	4.2 → 4.06, 4.11
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	1.57%	1.24 → 1.22, 1.23
`Consensus(forest21.260)`	⚪ NSD	1.13%	1.25 → 1.23, 1.24
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	0.71%	3.04 → 3.01, 3.02
`DropTip(tr2000, 5)`	⚪ NSD	-0.97%	17.1 → 17.7, 16.9
`DropTip(tr80, 5)`	⚪ NSD	0.43%	0.106 → 0.105, 0.105
`DropTip(unlen2k, 5)`	⚪ NSD	-2.09%	0.285 → 0.295, 0.288
`DropTip(unlen80, 5)`	⚪ NSD	-0.18%	0.04 → 0.0405, 0.0395
`lapply(bigSplits, as.phylo)`	⚪ NSD	1.04%	30.1 → 29.7, 29.8
`lapply(someSplits, as.phylo)`	⚪ NSD	-1.09%	13.9 → 14, 14.1
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	2.51%	16.8 → 16.6, 16.2
`PathLengths(tr80, full = TRUE)`	⚪ NSD	4.26%	0.0437 → 0.0429, 0.0405
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	7.27%	0.0465 → 0.0433, 0.043
`RootTree(tr2000, 5)`	⚪ NSD	-2.15%	0.379 → 0.396, 0.375
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-0.83%	0.0696 → 0.071, 0.0691
`RootTree(tr80, "t3")`	⚪ NSD	-1.47%	0.049 → 0.0501, 0.0492
`RootTree(tr80, "t30")`	⚪ NSD	-0.67%	0.0496 → 0.0505, 0.0493
`RootTree(unlen2k, 5)`	⚪ NSD	-0.97%	0.332 → 0.334, 0.337
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-1.23%	0.0643 → 0.066, 0.064
`RootTree(unlen80, "t3")`	⚪ NSD	0.02%	0.0434 → 0.0439, 0.0429
`RootTree(unlen80, "t30")`	⚪ NSD	-1.38%	0.0435 → 0.0446, 0.0436
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-1.41%	15.8 → 15.8, 16.1
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-1.56%	3.25 → 3.31, 3.26
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	3.19%	0.107 → 0.103, 0.103
`TreeTools:::postorder_order(bal40)`	⚪ NSD	0.63%	0.00175 → 0.00174, 0.00174
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-0.01%	0.433 → 0.434, 0.433
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	5.22%	0.00191 → 0.00182, 0.0018
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	-0.69%	2.16 → 2.18, 2.16
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	1.52%	0.00264 → 0.00261, 0.00259
`TreeTools:::postorder_order(dpec40k)`	🟣 ~same	-2.26%	3290 → 3400, 3350
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	0.73%	0.00412 → 0.0041, 0.00407
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	1.84%	0.00223 → 0.0022, 0.00216
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	-0.41%	2.17 → 2.19, 2.18
`TreeTools:::postorder_order(npec40)`	⚪ NSD	1.4%	0.00293 → 0.0029, 0.00287
`TreeTools:::postorder_order(npec40k)`	🟣 ~same	-3.08%	3310 → 3380, 3440
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	1.28%	0.0047 → 0.00466, 0.00463
`TreeTools:::postorder_order(pec40)`	⚪ NSD	1.7%	0.00176 → 0.00174, 0.00171
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	0.04%	0.432 → 0.432, 0.432
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	0.95%	0.00222 → 0.0022, 0.00218

codecov · 2026-03-13T14:20:44Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.36%. Comparing base (2eb1042) to head (2a6c0b0).
⚠️ Report is 3 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #260      +/-   ##
==========================================
- Coverage   96.36%   96.36%   -0.01%     
==========================================
  Files          78       78              
  Lines        5780     5774       -6     
==========================================
- Hits         5570     5564       -6     
  Misses        210      210

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github-actions · 2026-03-13T14:22:14Z

⚠️ This benchmark result is outdated. See the latest comment below.

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-1.53%	23.3 → 24.4, 22.1
`as.Splits(someTrees)`	⚪ NSD	-4.37%	11.4 → 12, 11.2
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	-6.16%	98.1 → 105, 103
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-5.9%	4.23 → 4.7, 4.08
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-0.51%	1.25 → 1.28, 1.23
`Consensus(forest21.260)`	⚪ NSD	-0.92%	1.27 → 1.31, 1.25
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-5.21%	2.99 → 3.26, 3
`DropTip(tr2000, 5)`	⚪ NSD	5.27%	18.2 → 19, 17.1
`DropTip(tr80, 5)`	⚪ NSD	1.25%	0.109 → 0.109, 0.106
`DropTip(unlen2k, 5)`	⚪ NSD	-31.26%	0.218 → 0.222, 0.291
`DropTip(unlen80, 5)`	⚪ NSD	-0.62%	0.0408 → 0.0417, 0.0404
`lapply(bigSplits, as.phylo)`	⚪ NSD	0.31%	29.9 → 30.1, 29.6
`lapply(someSplits, as.phylo)`	⚪ NSD	-1.32%	14.1 → 14.4, 13.6
`PathLengths(tr2000, full = TRUE)`	🟢 Faster!	6.35%	18 → 16.7, 17.1
`PathLengths(tr80, full = TRUE)`	⚪ NSD	9.33%	0.0453 → 0.0421, 0.0402
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	4.89%	0.0471 → 0.0437, 0.0467
`RootTree(tr2000, 5)`	⚪ NSD	-3.52%	0.382 → 0.409, 0.379
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	0.64%	0.0721 → 0.0733, 0.0703
`RootTree(tr80, "t3")`	⚪ NSD	0.95%	0.0514 → 0.0521, 0.0498
`RootTree(tr80, "t30")`	⚪ NSD	-0.33%	0.0512 → 0.0527, 0.0502
`RootTree(unlen2k, 5)`	⚪ NSD	0.24%	0.339 → 0.337, 0.339
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	0.98%	0.0667 → 0.0663, 0.0659
`RootTree(unlen80, "t3")`	⚪ NSD	1.34%	0.0454 → 0.0445, 0.0451
`RootTree(unlen80, "t30")`	⚪ NSD	0.51%	0.045 → 0.0445, 0.045
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	3.07%	16.3 → 15.9, 15.6
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	0.08%	3.3 → 3.32, 3.28
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	0.93%	0.105 → 0.105, 0.103
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-0.65%	0.00171 → 0.00173, 0.00172
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	0.36%	0.435 → 0.436, 0.432
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	1.09%	0.00182 → 0.00181, 0.0018
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	-0.79%	2.15 → 2.14, 2.17
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	0.38%	0.00262 → 0.00262, 0.0026
`TreeTools:::postorder_order(dpec40k)`	🟣 ~same	-3.12%	3290 → 3390, 3390
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	0.24%	0.00407 → 0.00407, 0.00406
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	2.27%	0.0022 → 0.00216, 0.00214
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	-0.13%	2.18 → 2.15, 2.19
`TreeTools:::postorder_order(npec40)`	⚪ NSD	-0.32%	0.00288 → 0.0029, 0.00288
`TreeTools:::postorder_order(npec40k)`	🟣 ~same	-3.41%	3310 → 3420, 3420
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	0.45%	0.00466 → 0.00465, 0.00463
`TreeTools:::postorder_order(pec40)`	⚪ NSD	0%	0.00172 → 0.00173, 0.00171
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	0%	0.432 → 0.434, 0.43
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	-3.26%	0.00212 → 0.00219, 0.00217

github-actions · 2026-03-16T13:38:50Z

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	0.92%	28.8 → 27.9, 29
`as.Splits(someTrees)`	⚪ NSD	-0.31%	10 → 10, 10
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	1.99%	88.3 → 86.8, 86.1
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	2.98%	4.05 → 3.92, 3.94
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	2.54%	1.15 → 1.11, 1.12
`Consensus(forest21.260)`	⚪ NSD	1.94%	1.14 → 1.11, 1.12
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	4.88%	2.99 → 2.86, 2.83
`DropTip(tr2000, 5)`	⚪ NSD	2.14%	26.3 → 25.2, 26.2
`DropTip(tr80, 5)`	⚪ NSD	-0.76%	0.0897 → 0.0904, 0.0904
`DropTip(unlen2k, 5)`	⚪ NSD	1.05%	0.192 → 0.19, 0.191
`DropTip(unlen80, 5)`	⚪ NSD	0.22%	0.0341 → 0.0339, 0.0341
`lapply(bigSplits, as.phylo)`	⚪ NSD	0.2%	27.8 → 27.7, 27.8
`lapply(someSplits, as.phylo)`	⚪ NSD	0.64%	11.7 → 11.6, 11.5
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-1.73%	24.7 → 24.8, 25.2
`PathLengths(tr80, full = TRUE)`	⚪ NSD	1.94%	0.0407 → 0.0391, 0.0404
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	-0.28%	0.0414 → 0.0414, 0.0419
`RootTree(tr2000, 5)`	⚪ NSD	-0.75%	0.288 → 0.291, 0.289
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	0.29%	0.0562 → 0.0559, 0.0562
`RootTree(tr80, "t3")`	⚪ NSD	0.15%	0.0396 → 0.0395, 0.0395
`RootTree(tr80, "t30")`	⚪ NSD	0.67%	0.0396 → 0.0394, 0.0394
`RootTree(unlen2k, 5)`	⚪ NSD	6.16%	0.276 → 0.258, 0.26
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-0.48%	0.0521 → 0.0522, 0.0524
`RootTree(unlen80, "t3")`	⚪ NSD	-0.04%	0.035 → 0.0349, 0.0351
`RootTree(unlen80, "t30")`	⚪ NSD	-0.24%	0.0352 → 0.0353, 0.0353
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	1%	14.8 → 14.6, 14.7
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-0.21%	2.91 → 2.93, 2.91
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	0.45%	0.0696 → 0.0687, 0.0699
`TreeTools:::postorder_order(bal40)`	⚪ NSD	2.57%	0.0014 → 0.00133, 0.00137
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	0.35%	0.316 → 0.315, 0.315
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	2.19%	0.00155 → 0.0015, 0.00153
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	-0.58%	2.27 → 2.28, 2.28
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	0.43%	0.00234 → 0.00232, 0.00233
`TreeTools:::postorder_order(dpec40k)`	⚪ NSD	0.18%	4460 → 4450, 4450
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	-1.35%	0.00384 → 0.0038, 0.00393
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	1.46%	0.00192 → 0.00189, 0.00188
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	9.7%	2.71 → 2.44, 2.47
`TreeTools:::postorder_order(npec40)`	⚪ NSD	-0.34%	0.00265 → 0.00266, 0.00265
`TreeTools:::postorder_order(npec40k)`	⚪ NSD	0.34%	4470 → 4430, 4530
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	-0.67%	0.00451 → 0.00459, 0.00448
`TreeTools:::postorder_order(pec40)`	⚪ NSD	4.03%	0.00139 → 0.00134, 0.00133
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	-0.3%	0.312 → 0.312, 0.313
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	2.57%	0.00164 → 0.0016, 0.00159

ms609 added 10 commits March 13, 2026 09:45

c++ for normalize splits.

a688e95

hash map

789a418

branches: ["*"]

38ee89a

branches: ["*"]

9968668

NodeDepth c++

de0f4ae

duplicated.Splits()

53d399f

sp

bf14733

ms609 added 3 commits March 13, 2026 11:17

Merge branch 'batch-as-splits' into posit-9006

faa75a5

Merge branch 'posit-9006' into posit-9k6

4a706b2

Merge branch 'posit-9k6' into posit-9007

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ms609 added 2 commits March 13, 2026 11:53

Merge branch 'main' into posit-9k6

3fab4ba

Merge branch 'posit-9k6' into posit-9007

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Base automatically changed from posit-9k6 to main March 13, 2026 14:05

ms609 added 2 commits March 13, 2026 14:05

Merge branch 'main' into posit-9007

d6c6e19

de-duplication

9218163

again(¬)

Merge branch 'main' into posit-9007

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ms609 merged commit 5bb40b8 into main Mar 16, 2026
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ms609 deleted the posit-9007 branch March 16, 2026 13:28

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`duplicated.Splits()`#260

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