hash map by ms609 · Pull Request #258 · ms609/TreeTools

ms609 · 2026-03-13T09:53:03Z

Faster match lookup (?)

_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 · 2026-03-13T11:10:21Z

⚠️ This benchmark result is outdated.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

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-0.77%	22.4 → 22.7, 22.5
`as.Splits(someTrees)`	⚪ NSD	2.14%	11.6 → 11.4, 11.1
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	0.85%	99.8 → 99.8, 98.1
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	0.14%	4.11 → 4.1, 4.11
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-1.16%	1.23 → 1.25, 1.23
`Consensus(forest21.260)`	⚪ NSD	-0.36%	1.25 → 1.26, 1.24
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	0%	2.99 → 3, 2.97
`DropTip(tr2000, 5)`	⚪ NSD	0.74%	17.7 → 17.6, 17.5
`DropTip(tr80, 5)`	⚪ NSD	-0.32%	0.107 → 0.107, 0.107
`DropTip(unlen2k, 5)`	⚪ NSD	1.69%	0.297 → 0.294, 0.291
`DropTip(unlen80, 5)`	⚪ NSD	0.22%	0.0405 → 0.0404, 0.0403
`lapply(bigSplits, as.phylo)`	🟣 ~same	2.11%	30 → 29.3, 29.4
`lapply(someSplits, as.phylo)`	🟣 ~same	4.73%	14.4 → 13.5, 13.7
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-0.2%	16.8 → 16.7, 17.1
`PathLengths(tr80, full = TRUE)`	⚪ NSD	-10.25%	0.0387 → 0.0419, 0.044
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	-5.79%	0.0411 → 0.0439, 0.0423
`RootTree(tr2000, 5)`	⚪ NSD	-0.18%	0.394 → 0.395, 0.396
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	0.33%	0.0711 → 0.071, 0.0707
`RootTree(tr80, "t3")`	⚪ NSD	-1.68%	0.0496 → 0.0504, 0.0504
`RootTree(tr80, "t30")`	⚪ NSD	-1.72%	0.0496 → 0.0503, 0.0505
`RootTree(unlen2k, 5)`	⚪ NSD	0.14%	0.33 → 0.33, 0.328
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-0.09%	0.0654 → 0.0657, 0.0651
`RootTree(unlen80, "t3")`	⚪ NSD	-1.55%	0.0428 → 0.0434, 0.0435
`RootTree(unlen80, "t30")`	⚪ NSD	-0.88%	0.0434 → 0.044, 0.0437
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	0.85%	16.2 → 15.9, 16.1
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-0.31%	3.29 → 3.28, 3.32
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	-1.42%	0.102 → 0.106, 0.1
`TreeTools:::postorder_order(bal40)`	⚪ NSD	0.51%	0.00176 → 0.00174, 0.00177
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	1.53%	0.436 → 0.43, 0.429
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-2.25%	0.00182 → 0.00183, 0.00188
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	-9.11%	2.19 → 2.39, 2.39
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	-17.94%	0.00263 → 0.00306, 0.00312
`TreeTools:::postorder_order(dpec40k)`	🟣 ~same	-5.93%	3410 → 3620, 3610
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	-25.85%	0.00411 → 0.00511, 0.00523
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-2.74%	0.00216 → 0.00216, 0.00225
`TreeTools:::postorder_order(nbal40k)`	🟠 Slower 🙁	-10.37%	2.19 → 2.42, 2.41
`TreeTools:::postorder_order(npec40)`	⚪ NSD	-15.78%	0.00292 → 0.00335, 0.0034
`TreeTools:::postorder_order(npec40k)`	🟠 Slower 🙁	-6.1%	3430 → 3640, 3630
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	-23.35%	0.00464 → 0.00567, 0.00575
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-1.16%	0.00173 → 0.00171, 0.00181
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	2.36%	0.437 → 0.425, 0.427
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	1.8%	0.00221 → 0.0021, 0.00223

github-actions · 2026-03-13T11:29:30Z

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

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	🟠 Slower 🙁	-14.87%	21.8 → 23.7, 25.6
`as.Splits(someTrees)`	⚪ NSD	1.93%	11.7 → 11.6, 11.4
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	-0.4%	102 → 100, 105
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-1.54%	4.12 → 4.14, 4.25
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-0.66%	1.25 → 1.25, 1.26
`Consensus(forest21.260)`	⚪ NSD	-0.3%	1.27 → 1.27, 1.28
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-1.27%	3.03 → 3.01, 3.1
`DropTip(tr2000, 5)`	⚪ NSD	-2.75%	17.2 → 17.9, 17.3
`DropTip(tr80, 5)`	⚪ NSD	1.39%	0.107 → 0.106, 0.106
`DropTip(unlen2k, 5)`	⚪ NSD	-31.46%	0.216 → 0.211, 0.295
`DropTip(unlen80, 5)`	⚪ NSD	0.22%	0.0408 → 0.0403, 0.041
`lapply(bigSplits, as.phylo)`	⚪ NSD	-0.2%	29.6 → 29.5, 29.7
`lapply(someSplits, as.phylo)`	⚪ NSD	1.33%	14.1 → 14.1, 13.9
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	0.51%	16.7 → 16.8, 16.4
`PathLengths(tr80, full = TRUE)`	⚪ NSD	-3.04%	0.0451 → 0.0494, 0.0419
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	0.86%	0.048 → 0.0501, 0.0432
`RootTree(tr2000, 5)`	⚪ NSD	1.73%	0.395 → 0.397, 0.377
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	1.43%	0.0724 → 0.0709, 0.0717
`RootTree(tr80, "t3")`	⚪ NSD	0.51%	0.0506 → 0.0503, 0.0503
`RootTree(tr80, "t30")`	⚪ NSD	0.61%	0.051 → 0.0506, 0.0507
`RootTree(unlen2k, 5)`	⚪ NSD	0.28%	0.333 → 0.33, 0.334
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	0.02%	0.0662 → 0.0661, 0.0662
`RootTree(unlen80, "t3")`	⚪ NSD	0.2%	0.0439 → 0.0433, 0.0442
`RootTree(unlen80, "t30")`	⚪ NSD	0.13%	0.0443 → 0.0437, 0.0446
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-0.98%	16.1 → 16.1, 16.4
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-1.18%	3.28 → 3.3, 3.33
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	1.65%	0.109 → 0.109, 0.106
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-0.51%	0.00174 → 0.00174, 0.00175
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-0.32%	0.434 → 0.438, 0.434
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-0.54%	0.00184 → 0.00186, 0.00185
`TreeTools:::postorder_order(dbal40k)`	🟠 Slower 🙁	-10%	2.19 → 2.4, 2.41
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	-16.74%	0.00264 → 0.00308, 0.00309
`TreeTools:::postorder_order(dpec40k)`	🟠 Slower 🙁	-6.39%	3400 → 3610, 3610
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	-27.31%	0.00407 → 0.00518, 0.00518
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-1.33%	0.00219 → 0.0022, 0.00222
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	-10.77%	2.21 → 2.82, 2.44
`TreeTools:::postorder_order(npec40)`	⚪ NSD	-15.86%	0.00291 → 0.00339, 0.00337
`TreeTools:::postorder_order(npec40k)`	🟣 ~same	-5.81%	3440 → 3650, 3630
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	-22.01%	0.00465 → 0.00568, 0.00566
`TreeTools:::postorder_order(pec40)`	⚪ NSD	1.09%	0.00174 → 0.00173, 0.00171
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	0%	0.432 → 0.433, 0.431
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	0%	0.00219 → 0.0022, 0.00218

github-actions · 2026-03-13T11:45:21Z

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-6.12%	21.9 → 23.7, 22.1
`as.Splits(someTrees)`	⚪ NSD	-3.58%	11.2 → 11.8, 11.1
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	0.85%	98.2 → 97.9, 97
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-2.6%	3.99 → 4.16, 4.05
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-0.75%	1.22 → 1.23, 1.24
`Consensus(forest21.260)`	⚪ NSD	-1.11%	1.24 → 1.25, 1.25
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-2.13%	2.93 → 2.98, 2.99
`DropTip(tr2000, 5)`	⚪ NSD	0.1%	17.3 → 17.7, 16.9
`DropTip(tr80, 5)`	⚪ NSD	0.78%	0.107 → 0.107, 0.104
`DropTip(unlen2k, 5)`	⚪ NSD	25.19%	0.292 → 0.217, 0.22
`DropTip(unlen80, 5)`	⚪ NSD	2.82%	0.0419 → 0.041, 0.0405
`lapply(bigSplits, as.phylo)`	⚪ NSD	-1.72%	29.1 → 29.9, 29.3
`lapply(someSplits, as.phylo)`	⚪ NSD	-0.67%	13.9 → 14, 13.8
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-1.72%	16.3 → 17.1, 16
`PathLengths(tr80, full = TRUE)`	⚪ NSD	-1.65%	0.0402 → 0.0418, 0.04
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	-1.53%	0.042 → 0.044, 0.041
`RootTree(tr2000, 5)`	⚪ NSD	0.26%	0.386 → 0.392, 0.375
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-1.5%	0.0695 → 0.0703, 0.0708
`RootTree(tr80, "t3")`	⚪ NSD	0.5%	0.0504 → 0.05, 0.0502
`RootTree(tr80, "t30")`	⚪ NSD	0.52%	0.0504 → 0.0503, 0.0499
`RootTree(unlen2k, 5)`	⚪ NSD	-1.53%	0.324 → 0.326, 0.33
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-1.54%	0.0639 → 0.0646, 0.0651
`RootTree(unlen80, "t3")`	⚪ NSD	-1.16%	0.043 → 0.0432, 0.0438
`RootTree(unlen80, "t30")`	⚪ NSD	-1.04%	0.0434 → 0.0435, 0.0442
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-0.37%	16.5 → 16.8, 16.3
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-1.43%	3.27 → 3.32, 3.32
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	-1.8%	0.103 → 0.106, 0.104
`TreeTools:::postorder_order(bal40)`	⚪ NSD	0.57%	0.00174 → 0.00174, 0.00172
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	0.96%	0.432 → 0.428, 0.428
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-3.3%	0.00181 → 0.00187, 0.00187
`TreeTools:::postorder_order(dbal40k)`	🟠 Slower 🙁	-9.61%	2.17 → 2.38, 2.38
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	-18.92%	0.0026 → 0.00309, 0.00309
`TreeTools:::postorder_order(dpec40k)`	🟠 Slower 🙁	-7.18%	3370 → 3620, 3610
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	-26.33%	0.00407 → 0.00517, 0.0051
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-1.87%	0.00219 → 0.00222, 0.00225
`TreeTools:::postorder_order(nbal40k)`	🟠 Slower 🙁	-10.77%	2.17 → 2.42, 2.39
`TreeTools:::postorder_order(npec40)`	⚪ NSD	-17.71%	0.00289 → 0.00338, 0.00342
`TreeTools:::postorder_order(npec40k)`	🟠 Slower 🙁	-7.12%	3390 → 3630, 3630
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	-22.73%	0.00463 → 0.00569, 0.00566
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-0.58%	0.00173 → 0.00174, 0.00174
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	0.73%	0.43 → 0.428, 0.426
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	1.37%	0.00219 → 0.00221, 0.0021

codecov · 2026-03-13T11:50:52Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.37%. Comparing base (0d7feda) to head (e5977aa).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #258      +/-   ##
==========================================
+ Coverage   96.33%   96.37%   +0.03%     
==========================================
  Files          77       77              
  Lines        5758     5761       +3     
==========================================
+ Hits         5547     5552       +5     
+ Misses        211      209       -2

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ms609 added 6 commits March 13, 2026 09:45

c++ for normalize splits.

a688e95

hash map

789a418

branches: ["*"]

9968668

sp

bf14733

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

faa75a5

Base automatically changed from batch-as-splits to main March 13, 2026 11:26

Merge branch 'main' into posit-9006

e5977aa

ms609 merged commit a221fac into main Mar 13, 2026
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ms609 deleted the posit-9006 branch March 13, 2026 11:51

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hash map#258

hash map#258
ms609 merged 8 commits intomainfrom
posit-9006

ms609 commented Mar 13, 2026

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