`Cherries()` by ms609 · Pull Request #236 · ms609/TreeTools

ms609 · 2025-09-14T06:40:37Z

Counts the cherries in a binary tree

github-actions · 2025-09-14T06:51:33Z

⚠️ This benchmark result is outdated.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

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-1.76%	23 → 23.6, 23
`as.Splits(someTrees)`	⚪ NSD	0.8%	11.3 → 11, 11.3
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	2%	97.3 → 95.3, 98.7
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	1.25%	4.08 → 4.05, 4.01
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	0.42%	1.21 → 1.2, 1.21
`Consensus(forest21.260)`	⚪ NSD	0.25%	1.21 → 1.21, 1.2
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	0.93%	2.98 → 2.97, 2.94
`DropTip(tr2000, 5)`	⚪ NSD	-1.29%	19.8 → 20.1, 19.9
`DropTip(tr80, 5)`	⚪ NSD	1.22%	0.104 → 0.103, 0.103
`DropTip(unlen2k, 5)`	⚪ NSD	-2.49%	0.207 → 0.215, 0.21
`DropTip(unlen80, 5)`	⚪ NSD	1.48%	0.0411 → 0.0408, 0.0401
`lapply(bigSplits, as.phylo)`	🟣 ~same	-3.88%	27.7 → 28.7, 28.8
`lapply(someSplits, as.phylo)`	⚪ NSD	-2.46%	13.6 → 14, 13.8
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-0.33%	19 → 19.1, 19.5
`PathLengths(tr80, full = TRUE)`	🟢 Faster!	70.95%	0.103 → 0.1, 0.0296
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	-4.69%	0.0303 → 0.0311, 0.0318
`RootTree(tr2000, 5)`	⚪ NSD	1.9%	0.396 → 0.377, 0.394
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	0.48%	0.0708 → 0.0699, 0.0708
`RootTree(tr80, "t3")`	⚪ NSD	1.61%	0.0505 → 0.0486, 0.0502
`RootTree(tr80, "t30")`	⚪ NSD	1.19%	0.0505 → 0.0488, 0.0505
`RootTree(unlen2k, 5)`	⚪ NSD	-2.76%	0.325 → 0.338, 0.33
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-1.51%	0.0643 → 0.0656, 0.0651
`RootTree(unlen80, "t3")`	⚪ NSD	0%	0.0435 → 0.0435, 0.0434
`RootTree(unlen80, "t30")`	⚪ NSD	-0.32%	0.0438 → 0.0441, 0.0437
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	-1.07%	0.0905 → 0.0904, 0.0927
`TreeTools:::postorder_order(bal40)`	⚪ NSD	4.11%	0.0017 → 0.00163, 0.00163
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	0.92%	0.449 → 0.446, 0.444
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-1.73%	0.00173 → 0.00177, 0.00175
`TreeTools:::postorder_order(dbal40k)`	🟠 Slower 🙁	-10.78%	2.13 → 2.36, 2.36
`TreeTools:::postorder_order(dpec40)`	🟠 Slower 🙁	-18.73%	0.00251 → 0.00299, 0.00299
`TreeTools:::postorder_order(dpec40k)`	🟠 Slower 🙁	-6.57%	3390 → 3610, 3610
`TreeTools:::postorder_order(drnd80)`	🟠 Slower 🙁	-27.69%	0.00395 → 0.00503, 0.00507
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-0.01%	0.00211 → 0.00212, 0.00211
`TreeTools:::postorder_order(nbal40k)`	🟠 Slower 🙁	-11.25%	2.17 → 2.42, 2.41
`TreeTools:::postorder_order(npec40)`	🟠 Slower 🙁	-17.11%	0.00281 → 0.00328, 0.00331
`TreeTools:::postorder_order(npec40k)`	🟠 Slower 🙁	-6.52%	3410 → 3630, 3630
`TreeTools:::postorder_order(nrnd80)`	🟠 Slower 🙁	-24.45%	0.00451 → 0.0056, 0.00562
`TreeTools:::postorder_order(pec40)`	⚪ NSD	0.06%	0.00163 → 0.00163, 0.00163
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	-0.14%	0.428 → 0.429, 0.428
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	1.43%	0.00209 → 0.00205, 0.00207

github-actions · 2025-09-14T07:01:33Z

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

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-3.14%	22.2 → 23.2, 21.2
`as.Splits(someTrees)`	⚪ NSD	2.45%	11.3 → 10.9, 11.1
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	-1.4%	94.7 → 96.7, 94.5
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-1.77%	3.97 → 4.08, 3.99
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-1%	1.19 → 1.21, 1.19
`Consensus(forest21.260)`	⚪ NSD	-0.63%	1.18 → 1.2, 1.18
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-1.61%	2.91 → 2.97, 2.94
`DropTip(tr2000, 5)`	⚪ NSD	1.1%	20.6 → 20, 20.5
`DropTip(tr80, 5)`	⚪ NSD	-0.32%	0.105 → 0.103, 0.106
`DropTip(unlen2k, 5)`	⚪ NSD	1.33%	0.212 → 0.209, 0.21
`DropTip(unlen80, 5)`	⚪ NSD	0.27%	0.0407 → 0.0405, 0.0407
`lapply(bigSplits, as.phylo)`	🟣 ~same	-4.64%	27.7 → 28.7, 29.1
`lapply(someSplits, as.phylo)`	🟢 Faster!	14.42%	16.5 → 14, 14.7
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-0.64%	19.5 → 19.8, 19.3
`PathLengths(tr80, full = TRUE)`	⚪ NSD	3.49%	0.105 → 0.101, 0.103
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	-207.73%	0.0333 → 0.102, 0.103
`RootTree(tr2000, 5)`	⚪ NSD	1.13%	0.378 → 0.374, 0.373
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	1.01%	0.0715 → 0.0713, 0.0702
`RootTree(tr80, "t3")`	⚪ NSD	0.56%	0.0503 → 0.0503, 0.0498
`RootTree(tr80, "t30")`	⚪ NSD	0.45%	0.0507 → 0.0508, 0.0501
`RootTree(unlen2k, 5)`	⚪ NSD	-1.46%	0.329 → 0.336, 0.332
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-0.69%	0.0654 → 0.0666, 0.0649
`RootTree(unlen80, "t3")`	⚪ NSD	0.56%	0.0445 → 0.0449, 0.0434
`RootTree(unlen80, "t30")`	⚪ NSD	0.29%	0.0449 → 0.0452, 0.0442
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	1.1%	0.0923 → 0.0914, 0.0911
`TreeTools:::postorder_order(bal40)`	⚪ NSD	3.6%	0.00166 → 0.00159, 0.00162
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-0.72%	0.447 → 0.455, 0.44
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-1.74%	0.00172 → 0.00173, 0.00177
`TreeTools:::postorder_order(dbal40k)`	🟠 Slower 🙁	-10.79%	2.13 → 2.36, 2.36
`TreeTools:::postorder_order(dpec40)`	🟠 Slower 🙁	-17.33%	0.00255 → 0.00298, 0.003
`TreeTools:::postorder_order(dpec40k)`	🟠 Slower 🙁	-6.58%	3390 → 3610, 3620
`TreeTools:::postorder_order(drnd80)`	🟠 Slower 🙁	-23.9%	0.00407 → 0.00504, 0.00504
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-1.91%	0.00209 → 0.0021, 0.00215
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	-7.57%	2.23 → 2.4, 2.4
`TreeTools:::postorder_order(npec40)`	🟠 Slower 🙁	-15.86%	0.00284 → 0.00328, 0.0033
`TreeTools:::postorder_order(npec40k)`	🟠 Slower 🙁	-6.38%	3410 → 3620, 3620
`TreeTools:::postorder_order(nrnd80)`	🟠 Slower 🙁	-22.56%	0.00457 → 0.0056, 0.0056
`TreeTools:::postorder_order(pec40)`	⚪ NSD	1.75%	0.00165 → 0.00161, 0.00164
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	0.74%	0.43 → 0.427, 0.428
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	3.31%	0.00211 → 0.00205, 0.00204

codecov · 2025-09-14T07:37:48Z

Codecov Report

❌ Patch coverage is 97.72727% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 96.46%. Comparing base (a169345) to head (b41fb49).
⚠️ Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
inst/include/TreeTools/n_cherries.h	96.55%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #236      +/-   ##
==========================================
+ Coverage   96.45%   96.46%   +0.01%     
==========================================
  Files          71       74       +3     
  Lines        5274     5318      +44     
==========================================
+ Hits         5087     5130      +43     
- Misses        187      188       +1

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

github-actions · 2025-09-14T07:41:42Z

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

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-2.4%	21.6 → 22.2, 21.8
`as.Splits(someTrees)`	⚪ NSD	0.69%	11.1 → 10.9, 11.1
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	1.91%	97.5 → 96.2, 94.3
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	0.57%	4.05 → 4.07, 3.97
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-0.3%	1.21 → 1.22, 1.2
`Consensus(forest21.260)`	⚪ NSD	0.62%	1.2 → 1.21, 1.19
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	0.28%	2.98 → 3.03, 2.92
`DropTip(tr2000, 5)`	⚪ NSD	-0.86%	20 → 20.7, 20
`DropTip(tr80, 5)`	⚪ NSD	-0.52%	0.102 → 0.104, 0.102
`DropTip(unlen2k, 5)`	⚪ NSD	-25.1%	0.217 → 0.278, 0.21
`DropTip(unlen80, 5)`	⚪ NSD	1.08%	0.0407 → 0.0401, 0.0403
`lapply(bigSplits, as.phylo)`	⚪ NSD	0.07%	27.6 → 27.7, 27.6
`lapply(someSplits, as.phylo)`	⚪ NSD	-0.98%	13.5 → 13.8, 13.6
`PathLengths(tr2000, full = TRUE)`	🟣 ~same	2.59%	19.9 → 19.5, 19.2
`PathLengths(tr80, full = TRUE)`	⚪ NSD	2.25%	0.104 → 0.1, 0.102
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	-206.37%	0.0335 → 0.1, 0.105
`RootTree(tr2000, 5)`	⚪ NSD	-2.49%	0.378 → 0.379, 0.391
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	2.53%	0.0706 → 0.0692, 0.0685
`RootTree(tr80, "t3")`	⚪ NSD	1.56%	0.05 → 0.0488, 0.0495
`RootTree(tr80, "t30")`	⚪ NSD	2.25%	0.0508 → 0.0493, 0.0499
`RootTree(unlen2k, 5)`	⚪ NSD	-0.42%	0.33 → 0.333, 0.328
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	1.98%	0.0652 → 0.0635, 0.0643
`RootTree(unlen80, "t3")`	⚪ NSD	2.31%	0.0442 → 0.0432, 0.0432
`RootTree(unlen80, "t30")`	⚪ NSD	1.83%	0.0444 → 0.0434, 0.0436
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	1.51%	0.0923 → 0.0904, 0.0915
`TreeTools:::postorder_order(bal40)`	⚪ NSD	1.22%	0.00163 → 0.00162, 0.00161
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-0.17%	0.441 → 0.442, 0.442
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-2.33%	0.00171 → 0.00175, 0.00174
`TreeTools:::postorder_order(dbal40k)`	🟠 Slower 🙁	-12.45%	2.09 → 2.35, 2.35
`TreeTools:::postorder_order(dpec40)`	🟠 Slower 🙁	-18.78%	0.00251 → 0.00299, 0.00299
`TreeTools:::postorder_order(dpec40k)`	🟠 Slower 🙁	-9.28%	3300 → 3610, 3610
`TreeTools:::postorder_order(drnd80)`	🟠 Slower 🙁	-26.84%	0.004 → 0.00506, 0.00509
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-3.37%	0.00204 → 0.00211, 0.0021
`TreeTools:::postorder_order(nbal40k)`	🟠 Slower 🙁	-10.33%	2.17 → 2.39, 2.39
`TreeTools:::postorder_order(npec40)`	🟠 Slower 🙁	-16.72%	0.00282 → 0.00329, 0.00329
`TreeTools:::postorder_order(npec40k)`	🟠 Slower 🙁	-9.92%	3290 → 3610, 3620
`TreeTools:::postorder_order(nrnd80)`	🟠 Slower 🙁	-23.37%	0.00455 → 0.00561, 0.00561
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-1.23%	0.00162 → 0.00163, 0.00165
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	-0.03%	0.427 → 0.427, 0.428
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	0.48%	0.00209 → 0.00206, 0.0021

github-actions · 2025-09-14T07:49:20Z

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

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	0.95%	22.3 → 22.4, 21.3
`as.Splits(someTrees)`	⚪ NSD	-0.12%	11.2 → 11.2, 11.1
`Consensus(forest1k.888, check = FALSE)`	🟣 ~same	-3.93%	93.7 → 98, 97.4
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-1.76%	3.98 → 4.05, 4.04
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-1.81%	1.19 → 1.21, 1.21
`Consensus(forest21.260)`	⚪ NSD	-1.12%	1.18 → 1.19, 1.21
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-2.79%	2.91 → 2.98, 3
`DropTip(tr2000, 5)`	⚪ NSD	0.95%	19.7 → 19.4, 19.6
`DropTip(tr80, 5)`	⚪ NSD	-0.6%	0.103 → 0.103, 0.104
`DropTip(unlen2k, 5)`	🟢 Faster!	22.72%	0.274 → 0.213, 0.209
`DropTip(unlen80, 5)`	⚪ NSD	-0.33%	0.0402 → 0.0403, 0.0403
`lapply(bigSplits, as.phylo)`	⚪ NSD	-0.24%	27.7 → 27.8, 27.7
`lapply(someSplits, as.phylo)`	⚪ NSD	0.63%	13.6 → 13.5, 13.5
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-0.76%	18.8 → 18.8, 19
`PathLengths(tr80, full = TRUE)`	⚪ NSD	1.37%	0.0271 → 0.0261, 0.0276
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	1.04%	0.0288 → 0.028, 0.0288
`RootTree(tr2000, 5)`	⚪ NSD	0.17%	0.392 → 0.391, 0.392
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-2.18%	0.0686 → 0.0703, 0.07
`RootTree(tr80, "t3")`	⚪ NSD	-0.54%	0.0497 → 0.0498, 0.0502
`RootTree(tr80, "t30")`	⚪ NSD	0.28%	0.0501 → 0.0499, 0.05
`RootTree(unlen2k, 5)`	⚪ NSD	-2.09%	0.322 → 0.327, 0.33
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-3.93%	0.0628 → 0.064, 0.0662
`RootTree(unlen80, "t3")`	⚪ NSD	-1.59%	0.0427 → 0.0431, 0.0436
`RootTree(unlen80, "t30")`	⚪ NSD	-2.2%	0.0428 → 0.0433, 0.0441
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	0.27%	0.0889 → 0.088, 0.0893
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-0.61%	0.00163 → 0.00164, 0.00164
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-1.07%	0.44 → 0.447, 0.444
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-2.94%	0.0017 → 0.00175, 0.00176
`TreeTools:::postorder_order(dbal40k)`	🟠 Slower 🙁	-13.27%	2.08 → 2.35, 2.36
`TreeTools:::postorder_order(dpec40)`	🟠 Slower 🙁	-19.2%	0.00251 → 0.00298, 0.003
`TreeTools:::postorder_order(dpec40k)`	🟠 Slower 🙁	-7.66%	3350 → 3610, 3610
`TreeTools:::postorder_order(drnd80)`	🟠 Slower 🙁	-26.42%	0.00398 → 0.00501, 0.00504
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-3.97%	0.00204 → 0.00211, 0.00213
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	-9.19%	2.2 → 2.4, 2.4
`TreeTools:::postorder_order(npec40)`	🟠 Slower 🙁	-17.92%	0.0028 → 0.00329, 0.00331
`TreeTools:::postorder_order(npec40k)`	🟠 Slower 🙁	-7.62%	3360 → 3620, 3620
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	-21.81%	0.0046 → 0.00561, 0.0056
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-1.23%	0.00162 → 0.00163, 0.00165
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	3.98%	0.447 → 0.429, 0.428
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	1.44%	0.00208 → 0.00203, 0.00206

github-actions · 2025-09-14T17:54:57Z

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

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-9.53%	20.6 → 21.6, 22.8
`as.Splits(someTrees)`	⚪ NSD	0.73%	11.3 → 11.2, 11.2
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	2.95%	97.3 → 95.1, 94.4
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	0.44%	4 → 3.97, 3.99
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	0.34%	1.2 → 1.19, 1.2
`Consensus(forest21.260)`	⚪ NSD	1.08%	1.2 → 1.18, 1.18
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	0.66%	2.95 → 2.93, 2.93
`DropTip(tr2000, 5)`	⚪ NSD	-0.25%	19.8 → 19.8, 19.9
`DropTip(tr80, 5)`	⚪ NSD	0.21%	0.104 → 0.103, 0.104
`DropTip(unlen2k, 5)`	⚪ NSD	-2.25%	0.206 → 0.209, 0.214
`DropTip(unlen80, 5)`	⚪ NSD	-0.72%	0.0402 → 0.04, 0.0409
`lapply(bigSplits, as.phylo)`	⚪ NSD	-0.6%	27.7 → 27.6, 28.7
`lapply(someSplits, as.phylo)`	⚪ NSD	1.21%	13.7 → 13.6, 13.6
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-0.17%	19.1 → 19.3, 19.1
`PathLengths(tr80, full = TRUE)`	🟠 Slower 🙁	-252.46%	0.0286 → 0.103, 0.099
`PathLengths(tr80Unif, full = TRUE)`	🟠 Slower 🙁	-255.24%	0.0287 → 0.104, 0.0424
`RootTree(tr2000, 5)`	⚪ NSD	0.85%	0.376 → 0.373, 0.372
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	1.1%	0.07 → 0.0694, 0.0691
`RootTree(tr80, "t3")`	⚪ NSD	0.99%	0.0494 → 0.0492, 0.0485
`RootTree(tr80, "t30")`	⚪ NSD	0.27%	0.0493 → 0.0493, 0.049
`RootTree(unlen2k, 5)`	⚪ NSD	-1.9%	0.328 → 0.334, 0.334
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	0.39%	0.0644 → 0.0644, 0.0638
`RootTree(unlen80, "t3")`	⚪ NSD	-0.07%	0.0433 → 0.0435, 0.0431
`RootTree(unlen80, "t30")`	⚪ NSD	0.3%	0.0436 → 0.0437, 0.0433
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	-0.65%	0.0899 → 0.0906, 0.0903
`TreeTools:::postorder_order(bal40)`	⚪ NSD	0.56%	0.00163 → 0.00163, 0.00161
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	0.15%	0.443 → 0.442, 0.443
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-3.46%	0.0017 → 0.00175, 0.00176
`TreeTools:::postorder_order(dbal40k)`	🟠 Slower 🙁	-11.54%	2.11 → 2.36, 2.35
`TreeTools:::postorder_order(dpec40)`	🟠 Slower 🙁	-18.29%	0.00252 → 0.00298, 0.00297
`TreeTools:::postorder_order(dpec40k)`	🟠 Slower 🙁	-6.95%	3380 → 3610, 3610
`TreeTools:::postorder_order(drnd80)`	🟠 Slower 🙁	-29.69%	0.00398 → 0.00526, 0.00504
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-3.9%	0.00205 → 0.00214, 0.00212
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	-10.27%	2.16 → 2.4, 2.34
`TreeTools:::postorder_order(npec40)`	🟠 Slower 🙁	-17.15%	0.00281 → 0.0033, 0.00329
`TreeTools:::postorder_order(npec40k)`	🟠 Slower 🙁	-7.15%	3380 → 3620, 3620
`TreeTools:::postorder_order(nrnd80)`	🟠 Slower 🙁	-23.27%	0.00456 → 0.00564, 0.0056
`TreeTools:::postorder_order(pec40)`	⚪ NSD	1.16%	0.00164 → 0.00163, 0.00162
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	-0.17%	0.428 → 0.433, 0.426
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	0.53%	0.00208 → 0.00207, 0.00205

github-actions · 2025-09-14T18:08:09Z

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

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	2.54%	21.7 → 21.2, 20.9
`as.Splits(someTrees)`	⚪ NSD	-1.78%	11.2 → 11.4, 11.1
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	-1.36%	95.5 → 97.7, 95.2
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-0.6%	4.02 → 4.06, 4.03
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-0.59%	1.2 → 1.21, 1.19
`Consensus(forest21.260)`	⚪ NSD	-0.53%	1.18 → 1.2, 1.18
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-0.74%	2.94 → 2.98, 2.94
`DropTip(tr2000, 5)`	⚪ NSD	-1.31%	19.5 → 19.6, 19.9
`DropTip(tr80, 5)`	⚪ NSD	-0.39%	0.104 → 0.104, 0.104
`DropTip(unlen2k, 5)`	🟢 Faster!	24.29%	0.275 → 0.208, 0.209
`DropTip(unlen80, 5)`	⚪ NSD	-0.22%	0.0408 → 0.0409, 0.0409
`lapply(bigSplits, as.phylo)`	⚪ NSD	0.26%	27.6 → 27.5, 27.7
`lapply(someSplits, as.phylo)`	⚪ NSD	-11.23%	13.6 → 13.5, 17.3
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-1.82%	19.1 → 19.6, 19.1
`PathLengths(tr80, full = TRUE)`	⚪ NSD	68.02%	0.0995 → 0.102, 0.0314
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	-9.54%	0.0301 → 0.0296, 0.0335
`RootTree(tr2000, 5)`	⚪ NSD	-1.56%	0.377 → 0.375, 0.388
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-0.41%	0.0709 → 0.072, 0.0701
`RootTree(tr80, "t3")`	⚪ NSD	-0.22%	0.0506 → 0.0508, 0.0507
`RootTree(tr80, "t30")`	⚪ NSD	-0.53%	0.0507 → 0.0511, 0.0508
`RootTree(unlen2k, 5)`	⚪ NSD	0.39%	0.332 → 0.334, 0.326
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-0.24%	0.0655 → 0.0662, 0.065
`RootTree(unlen80, "t3")`	⚪ NSD	0.56%	0.0444 → 0.0445, 0.0437
`RootTree(unlen80, "t30")`	⚪ NSD	0.67%	0.0448 → 0.0447, 0.0442
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	-1.97%	0.0901 → 0.09, 0.0942
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-1.85%	0.00162 → 0.00165, 0.00164
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-3.76%	0.439 → 0.505, 0.443
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-3.51%	0.00171 → 0.00175, 0.00178
`TreeTools:::postorder_order(dbal40k)`	🟠 Slower 🙁	-9.83%	2.13 → 2.36, 2.33
`TreeTools:::postorder_order(dpec40)`	🟠 Slower 🙁	-19.25%	0.0025 → 0.00297, 0.00301
`TreeTools:::postorder_order(dpec40k)`	🟠 Slower 🙁	-6.65%	3380 → 3610, 3610
`TreeTools:::postorder_order(drnd80)`	🟠 Slower 🙁	-27.06%	0.004 → 0.00507, 0.00509
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-2.9%	0.00206 → 0.0021, 0.00214
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	-9.43%	2.19 → 2.41, 2.39
`TreeTools:::postorder_order(npec40)`	🟠 Slower 🙁	-17.57%	0.0028 → 0.00328, 0.0033
`TreeTools:::postorder_order(npec40k)`	🟠 Slower 🙁	-6.29%	3400 → 3620, 3620
`TreeTools:::postorder_order(nrnd80)`	🟠 Slower 🙁	-23.3%	0.00456 → 0.00562, 0.00563
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-1.23%	0.00162 → 0.00162, 0.00165
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	-1.37%	0.422 → 0.429, 0.428
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	-1.01%	0.00207 → 0.00209, 0.00209

github-actions · 2025-09-23T07:17:09Z

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

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	2.89%	21.9 → 21.5, 20.8
`as.Splits(someTrees)`	⚪ NSD	-0.06%	11.1 → 11.2, 11
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	-1.79%	94 → 100, 94.2
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-1.47%	3.97 → 4.05, 3.97
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-1.15%	1.19 → 1.21, 1.2
`Consensus(forest21.260)`	⚪ NSD	-1.36%	1.18 → 1.21, 1.19
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-1.97%	2.91 → 2.99, 2.93
`DropTip(tr2000, 5)`	⚪ NSD	0.68%	20 → 19.5, 19.9
`DropTip(tr80, 5)`	⚪ NSD	0.69%	0.103 → 0.101, 0.103
`DropTip(unlen2k, 5)`	⚪ NSD	2.78%	0.215 → 0.207, 0.213
`DropTip(unlen80, 5)`	⚪ NSD	2.71%	0.0407 → 0.0396, 0.0396
`lapply(bigSplits, as.phylo)`	⚪ NSD	-0.11%	27.7 → 27.6, 27.8
`lapply(someSplits, as.phylo)`	⚪ NSD	-0.41%	13.5 → 13.6, 13.5
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-1.27%	19.1 → 19.7, 18.8
`PathLengths(tr80, full = TRUE)`	⚪ NSD	3.95%	0.106 → 0.0998, 0.103
`PathLengths(tr80Unif, full = TRUE)`	🟢 Faster!	9.36%	0.0335 → 0.0301, 0.0304
`RootTree(tr2000, 5)`	⚪ NSD	1.18%	0.375 → 0.372, 0.37
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-0.73%	0.0685 → 0.0694, 0.0687
`RootTree(tr80, "t3")`	⚪ NSD	0.89%	0.0494 → 0.0486, 0.0493
`RootTree(tr80, "t30")`	⚪ NSD	0.99%	0.0498 → 0.0492, 0.0494
`RootTree(unlen2k, 5)`	⚪ NSD	-1.46%	0.329 → 0.333, 0.335
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-0.86%	0.0637 → 0.0637, 0.0648
`RootTree(unlen80, "t3")`	⚪ NSD	1.45%	0.0437 → 0.0425, 0.0435
`RootTree(unlen80, "t30")`	⚪ NSD	2.36%	0.0441 → 0.0426, 0.0434
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	3.59%	0.0937 → 0.0893, 0.0915
`TreeTools:::postorder_order(bal40)`	⚪ NSD	1.2%	0.00167 → 0.00164, 0.00165
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	0.09%	0.444 → 0.443, 0.443
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-3.46%	0.00173 → 0.00182, 0.00178
`TreeTools:::postorder_order(dbal40k)`	🟠 Slower 🙁	-11.39%	2.13 → 2.38, 2.38
`TreeTools:::postorder_order(dpec40)`	🟠 Slower 🙁	-17.44%	0.00253 → 0.00298, 0.00299
`TreeTools:::postorder_order(dpec40k)`	🟠 Slower 🙁	-7.93%	3340 → 3610, 3610
`TreeTools:::postorder_order(drnd80)`	🟠 Slower 🙁	-25.41%	0.00402 → 0.00503, 0.00505
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-2.9%	0.00207 → 0.00212, 0.00213
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	-8.88%	2.2 → 2.4, 2.4
`TreeTools:::postorder_order(npec40)`	🟠 Slower 🙁	-16.71%	0.00283 → 0.00331, 0.0033
`TreeTools:::postorder_order(npec40k)`	🟠 Slower 🙁	-6.3%	3410 → 3630, 3620
`TreeTools:::postorder_order(nrnd80)`	🟠 Slower 🙁	-23.35%	0.00455 → 0.0056, 0.00563
`TreeTools:::postorder_order(pec40)`	⚪ NSD	2.39%	0.00167 → 0.00162, 0.00164
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	-0.93%	0.427 → 0.429, 0.436
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	1.43%	0.0021 → 0.00206, 0.00208

for expect_no_error

github-actions · 2025-09-23T09:31:48Z

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-1.1%	22.2 → 22.6, 21.5
`as.Splits(someTrees)`	⚪ NSD	1.28%	11.6 → 11.4, 11.4
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	-2.19%	95.7 → 101, 97.8
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-1.7%	4.02 → 4.1, 4.08
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-1.36%	1.19 → 1.21, 1.21
`Consensus(forest21.260)`	⚪ NSD	-1.1%	1.19 → 1.2, 1.2
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-0.73%	2.99 → 3, 3.02
`DropTip(tr2000, 5)`	⚪ NSD	-0.43%	19.7 → 19.6, 19.9
`DropTip(tr80, 5)`	⚪ NSD	1.84%	0.106 → 0.103, 0.104
`DropTip(unlen2k, 5)`	⚪ NSD	-0.38%	0.208 → 0.207, 0.211
`DropTip(unlen80, 5)`	⚪ NSD	-2.34%	0.0398 → 0.0406, 0.0409
`lapply(bigSplits, as.phylo)`	⚪ NSD	0.26%	27.9 → 27.8, 27.9
`lapply(someSplits, as.phylo)`	⚪ NSD	0.21%	13.9 → 14.2, 13.7
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	0.56%	19.3 → 19.1, 19.3
`PathLengths(tr80, full = TRUE)`	⚪ NSD	2.49%	0.105 → 0.102, 0.102
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	5.18%	0.0325 → 0.0324, 0.0301
`RootTree(tr2000, 5)`	🟣 ~same	5.88%	0.399 → 0.379, 0.373
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-0.53%	0.0701 → 0.071, 0.07
`RootTree(tr80, "t3")`	⚪ NSD	2.64%	0.0509 → 0.0493, 0.0497
`RootTree(tr80, "t30")`	⚪ NSD	1.03%	0.0506 → 0.05, 0.0501
`RootTree(unlen2k, 5)`	⚪ NSD	-2.64%	0.327 → 0.336, 0.335
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-1.71%	0.0648 → 0.0661, 0.0658
`RootTree(unlen80, "t3")`	⚪ NSD	0.3%	0.0438 → 0.0437, 0.0437
`RootTree(unlen80, "t30")`	⚪ NSD	-0.04%	0.0443 → 0.0445, 0.0441
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	2.37%	0.0927 → 0.0909, 0.0902
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-1.29%	0.00162 → 0.00165, 0.00164
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-0.14%	0.446 → 0.448, 0.444
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-2.96%	0.00172 → 0.00178, 0.00177
`TreeTools:::postorder_order(dbal40k)`	🟠 Slower 🙁	-11.09%	2.1 → 2.36, 2.26
`TreeTools:::postorder_order(dpec40)`	🟠 Slower 🙁	-18.45%	0.0025 → 0.00296, 0.00298
`TreeTools:::postorder_order(dpec40k)`	🟠 Slower 🙁	-6.46%	3390 → 3610, 3610
`TreeTools:::postorder_order(drnd80)`	🟠 Slower 🙁	-27.41%	0.00395 → 0.00504, 0.00501
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-2.97%	0.00205 → 0.00211, 0.00212
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	-7.73%	2.23 → 2.4, 2.42
`TreeTools:::postorder_order(npec40)`	🟠 Slower 🙁	-17.11%	0.00281 → 0.00329, 0.00329
`TreeTools:::postorder_order(npec40k)`	🟠 Slower 🙁	-6.25%	3410 → 3630, 3620
`TreeTools:::postorder_order(nrnd80)`	🟠 Slower 🙁	-23.67%	0.00453 → 0.0056, 0.00561
`TreeTools:::postorder_order(pec40)`	⚪ NSD	0.61%	0.00163 → 0.00162, 0.00162
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	1.74%	0.431 → 0.43, 0.415
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	1.93%	0.00206 → 0.00204, 0.002

Cherries()

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ms609 marked this pull request as ready for review September 14, 2025 06:40

Merge branch 'main' into cherries

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Hmisc@5.0-0

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Initialize root_internal_found

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std::unique_ptr<bool[]>

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code coverage

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Merge branch 'main' into cherries

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+R4.0

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skip_if_not_installed("testthat", "3.1.5")

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for expect_no_error

try testthat@3.1.5

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sp

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Merge branch 'deprecations' into cherries

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