Large tree support: `SplitList` #241

ms609 · 2026-01-05T16:07:25Z

No description provided.

codecov · 2026-01-05T16:17:04Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.53%. Comparing base (7c3a13c) to head (37bb168).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #241      +/-   ##
==========================================
+ Coverage   96.46%   96.53%   +0.07%     
==========================================
  Files          74       74              
  Lines        5315     5337      +22     
==========================================
+ Hits         5127     5152      +25     
+ Misses        188      185       -3

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github-actions · 2026-01-05T16:17:06Z

⚠️ This benchmark result is outdated.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

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	🟠 Slower 🙁	-10.83%	21.8 → 24.8, 22.9
`as.Splits(someTrees)`	⚪ NSD	-1.4%	11.5 → 11.5, 11.7
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	-0.36%	98.2 → 98.6, 98.3
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	0.39%	4.13 → 4.14, 4.1
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	0.54%	1.23 → 1.22, 1.23
`Consensus(forest21.260)`	⚪ NSD	1.15%	1.22 → 1.21, 1.21
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	0.89%	3.03 → 3.01, 3
`DropTip(tr2000, 5)`	🟣 ~same	2.14%	20.8 → 20.4, 20.4
`DropTip(tr80, 5)`	⚪ NSD	-1.75%	0.104 → 0.106, 0.106
`DropTip(unlen2k, 5)`	⚪ NSD	0.91%	0.212 → 0.211, 0.21
`DropTip(unlen80, 5)`	⚪ NSD	1.17%	0.041 → 0.0406, 0.0406
`lapply(bigSplits, as.phylo)`	🟠 Slower 🙁	-8.56%	27.8 → 30.2, 30.2
`lapply(someSplits, as.phylo)`	🟣 ~same	-5.85%	13.6 → 14.3, 14.7
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-1.86%	19.7 → 19.9, 20.2
`PathLengths(tr80, full = TRUE)`	⚪ NSD	-223.17%	0.032 → 0.102, 0.105
`PathLengths(tr80Unif, full = TRUE)`	🟠 Slower 🙁	-216.33%	0.0331 → 0.105, 0.0407
`RootTree(tr2000, 5)`	⚪ NSD	-3.81%	0.376 → 0.399, 0.38
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-2.5%	0.0696 → 0.0712, 0.0715
`RootTree(tr80, "t3")`	⚪ NSD	-4.19%	0.0485 → 0.0503, 0.0507
`RootTree(tr80, "t30")`	⚪ NSD	-3.25%	0.049 → 0.0502, 0.0509
`RootTree(unlen2k, 5)`	⚪ NSD	-0.36%	0.337 → 0.333, 0.342
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-1.98%	0.0642 → 0.0647, 0.0662
`RootTree(unlen80, "t3")`	⚪ NSD	-3.01%	0.043 → 0.043, 0.045
`RootTree(unlen80, "t30")`	⚪ NSD	-3.13%	0.0432 → 0.0433, 0.0454
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-3.29%	15.3 → 15.8, 15.9
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-0.96%	3.2 → 3.22, 3.23
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	0.54%	0.0932 → 0.0908, 0.0951
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-3.16%	0.00161 → 0.00167, 0.00166
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-0.22%	0.45 → 0.449, 0.452
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-1.72%	0.00177 → 0.00182, 0.00178
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	-0.05%	2.38 → 2.37, 2.38
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	-0.33%	0.003 → 0.00303, 0.00299
`TreeTools:::postorder_order(dpec40k)`	⚪ NSD	0.08%	3610 → 3610, 3610
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	1.34%	0.00513 → 0.00506, 0.00506
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	-0.94%	0.00212 → 0.00214, 0.00213
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	0.27%	2.43 → 2.42, 2.42
`TreeTools:::postorder_order(npec40)`	⚪ NSD	-0.03%	0.00329 → 0.00329, 0.0033
`TreeTools:::postorder_order(npec40k)`	⚪ NSD	0.04%	3630 → 3630, 3620
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	0.55%	0.00564 → 0.00563, 0.00559
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-0.6%	0.00165 → 0.00167, 0.00164
`TreeTools:::postorder_order(pec40k)`	🟢 Faster!	19.44%	0.534 → 0.431, 0.43
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	1.89%	0.0021 → 0.0021, 0.00203

github-actions · 2026-01-05T17:05:57Z

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

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-6.03%	21.4 → 22.1, 22.9
`as.Splits(someTrees)`	⚪ NSD	-0.57%	11.4 → 11.6, 11.2
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	-0.65%	97.8 → 101, 98.3
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-1.37%	4.05 → 4.09, 4.12
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-0.52%	1.21 → 1.21, 1.22
`Consensus(forest21.260)`	⚪ NSD	-0.76%	1.19 → 1.2, 1.21
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	1.09%	3.03 → 2.96, 3.02
`DropTip(tr2000, 5)`	⚪ NSD	-0.63%	19.7 → 19.9, 19.8
`DropTip(tr80, 5)`	⚪ NSD	-1.93%	0.103 → 0.105, 0.104
`DropTip(unlen2k, 5)`	⚪ NSD	-0.67%	0.214 → 0.215, 0.215
`DropTip(unlen80, 5)`	⚪ NSD	-0.27%	0.0406 → 0.0407, 0.0408
`lapply(bigSplits, as.phylo)`	🟠 Slower 🙁	-9.89%	27.7 → 30.2, 30.5
`lapply(someSplits, as.phylo)`	⚪ NSD	-5.24%	13.5 → 14.3, 14.2
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	-0.27%	19.2 → 19.4, 18.8
`PathLengths(tr80, full = TRUE)`	🟠 Slower 🙁	-238.91%	0.03 → 0.105, 0.1
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	-9.99%	0.0319 → 0.0339, 0.102
`RootTree(tr2000, 5)`	⚪ NSD	-1.61%	0.37 → 0.377, 0.375
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-3%	0.0685 → 0.0698, 0.0712
`RootTree(tr80, "t3")`	⚪ NSD	-1.45%	0.049 → 0.0496, 0.0498
`RootTree(tr80, "t30")`	⚪ NSD	-2.85%	0.0489 → 0.0499, 0.0507
`RootTree(unlen2k, 5)`	⚪ NSD	-0.34%	0.333 → 0.334, 0.333
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-3.01%	0.0637 → 0.0649, 0.0662
`RootTree(unlen80, "t3")`	⚪ NSD	-2.21%	0.043 → 0.0434, 0.0444
`RootTree(unlen80, "t30")`	⚪ NSD	-2.7%	0.0434 → 0.0443, 0.0448
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-4.73%	14.9 → 15.6, 15.8
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-2.31%	3.16 → 3.22, 3.26
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	1.22%	0.093 → 0.0948, 0.0897
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-0.54%	0.00166 → 0.00166, 0.00168
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	-0.63%	0.442 → 0.445, 0.444
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	-0.01%	0.00177 → 0.00177, 0.00177
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	-1.42%	2.32 → 2.36, 2.35
`TreeTools:::postorder_order(dpec40)`	⚪ NSD	0%	0.003 → 0.003, 0.003
`TreeTools:::postorder_order(dpec40k)`	⚪ NSD	0.03%	3610 → 3610, 3610
`TreeTools:::postorder_order(drnd80)`	⚪ NSD	0.59%	0.00507 → 0.00508, 0.00501
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	0.04%	0.00212 → 0.0021, 0.00211
`TreeTools:::postorder_order(nbal40k)`	⚪ NSD	0.73%	2.42 → 2.41, 2.4
`TreeTools:::postorder_order(npec40)`	⚪ NSD	0.9%	0.00331 → 0.00328, 0.00329
`TreeTools:::postorder_order(npec40k)`	⚪ NSD	0.2%	3630 → 3630, 3620
`TreeTools:::postorder_order(nrnd80)`	⚪ NSD	0.18%	0.00563 → 0.00563, 0.00561
`TreeTools:::postorder_order(pec40)`	⚪ NSD	1.15%	0.00165 → 0.00163, 0.00164
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	-2.27%	0.426 → 0.535, 0.429
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	0.48%	0.00208 → 0.00208, 0.00207

…ocation (#242) Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>

github-actions · 2026-01-06T07:41:11Z

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

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	-9.38%	22.6 → 22.5, 26.2
`as.Splits(someTrees)`	⚪ NSD	0.4%	11.3 → 11.3, 11.2
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	0.1%	97 → 95.6, 97.7
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	0.37%	4.06 → 4.02, 4.06
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-1.5%	1.2 → 1.21, 1.22
`Consensus(forest21.260)`	⚪ NSD	-1.05%	1.19 → 1.2, 1.21
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	-0.71%	2.95 → 2.95, 2.98
`DropTip(tr2000, 5)`	🟣 ~same	1.77%	20.7 → 20.3, 20.3
`DropTip(tr80, 5)`	⚪ NSD	0.44%	0.106 → 0.106, 0.105
`DropTip(unlen2k, 5)`	⚪ NSD	3.34%	0.217 → 0.209, 0.211
`DropTip(unlen80, 5)`	⚪ NSD	0.24%	0.041 → 0.0408, 0.041
`lapply(bigSplits, as.phylo)`	🟠 Slower 🙁	-12.38%	27.8 → 31.5, 31
`lapply(someSplits, as.phylo)`	⚪ NSD	-5.11%	13.5 → 14.1, 14.2
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	1.13%	19.8 → 19.7, 19.6
`PathLengths(tr80, full = TRUE)`	🟠 Slower 🙁	-246.8%	0.0297 → 0.102, 0.104
`PathLengths(tr80Unif, full = TRUE)`	🟠 Slower 🙁	-238.22%	0.0312 → 0.105, 0.106
`RootTree(tr2000, 5)`	⚪ NSD	3.01%	0.395 → 0.385, 0.381
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-2.35%	0.0701 → 0.073, 0.0694
`RootTree(tr80, "t3")`	⚪ NSD	-1.07%	0.0504 → 0.0518, 0.0492
`RootTree(tr80, "t30")`	⚪ NSD	-0.9%	0.051 → 0.0526, 0.0495
`RootTree(unlen2k, 5)`	⚪ NSD	-0.79%	0.33 → 0.335, 0.331
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-2.44%	0.0653 → 0.0684, 0.0644
`RootTree(unlen80, "t3")`	⚪ NSD	-3.91%	0.0434 → 0.046, 0.0434
`RootTree(unlen80, "t30")`	⚪ NSD	-4.05%	0.0435 → 0.0462, 0.0439
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	1.13%	15.7 → 15.6, 15.4
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-2.4%	3.17 → 3.25, 3.24
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	0.32%	0.0919 → 0.0907, 0.0927
`TreeTools:::postorder_order(bal40)`	⚪ NSD	-0.61%	0.00165 → 0.00168, 0.00165
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	0.69%	0.445 → 0.443, 0.441
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	3.38%	0.0018 → 0.00175, 0.00173
`TreeTools:::postorder_order(dbal40k)`	⚪ NSD	9.27%	2.33 → 2.15, 2.1
`TreeTools:::postorder_order(dpec40)`	🟢 Faster!	15.06%	0.003 → 0.00255, 0.00252
`TreeTools:::postorder_order(dpec40k)`	🟢 Faster!	6.52%	3610 → 3360, 3390
`TreeTools:::postorder_order(drnd80)`	🟢 Faster!	20.59%	0.00506 → 0.00403, 0.004
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	1.42%	0.00211 → 0.00208, 0.00208
`TreeTools:::postorder_order(nbal40k)`	🟢 Faster!	7.81%	2.37 → 2.19, 2.18
`TreeTools:::postorder_order(npec40)`	🟢 Faster!	14.33%	0.00329 → 0.00282, 0.00282
`TreeTools:::postorder_order(npec40k)`	🟣 ~same	5.9%	3620 → 3410, 3410
`TreeTools:::postorder_order(nrnd80)`	🟢 Faster!	18.72%	0.00562 → 0.00457, 0.00457
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-0.61%	0.00163 → 0.00165, 0.00163
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	0.85%	0.433 → 0.428, 0.433
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	-1.94%	0.00206 → 0.0021, 0.0021

github-actions · 2026-01-06T07:42:08Z

Performance benchmark results

Call	Status	Change	Time (ms)
`as.Splits(bigTrees)`	⚪ NSD	3.38%	23.6 → 22.5, 22.9
`as.Splits(someTrees)`	⚪ NSD	2.05%	11.6 → 11.4, 11.4
`Consensus(forest1k.888, check = FALSE)`	⚪ NSD	0.93%	99 → 97.4, 98.7
`Consensus(forest201.80, check = FALSE)`	⚪ NSD	-0.97%	4.13 → 4.28, 4.12
`Consensus(forest21.260, 0.5, FALSE)`	⚪ NSD	-0.42%	1.21 → 1.22, 1.22
`Consensus(forest21.260)`	⚪ NSD	-0.2%	1.21 → 1.21, 1.21
`Consensus(forestMaj, 0.5, FALSE)`	⚪ NSD	0.87%	3.04 → 2.96, 3.04
`DropTip(tr2000, 5)`	⚪ NSD	1.52%	20.7 → 20.4, 20.4
`DropTip(tr80, 5)`	⚪ NSD	0.76%	0.106 → 0.105, 0.106
`DropTip(unlen2k, 5)`	⚪ NSD	2.89%	0.217 → 0.212, 0.21
`DropTip(unlen80, 5)`	⚪ NSD	1.03%	0.0411 → 0.0403, 0.0409
`lapply(bigSplits, as.phylo)`	🟠 Slower 🙁	-11.9%	27.9 → 31.5, 30.9
`lapply(someSplits, as.phylo)`	⚪ NSD	-3.48%	14.1 → 14.7, 14.5
`PathLengths(tr2000, full = TRUE)`	⚪ NSD	2.75%	19.9 → 19.3, 19.9
`PathLengths(tr80, full = TRUE)`	⚪ NSD	64.24%	0.101 → 0.103, 0.0357
`PathLengths(tr80Unif, full = TRUE)`	⚪ NSD	-25.91%	0.0305 → 0.105, 0.0378
`RootTree(tr2000, 5)`	⚪ NSD	3.12%	0.394 → 0.378, 0.385
`RootTree(tr80, c("t3", "t36"))`	⚪ NSD	-0.34%	0.0707 → 0.0707, 0.0711
`RootTree(tr80, "t3")`	⚪ NSD	0.59%	0.0498 → 0.0496, 0.0493
`RootTree(tr80, "t30")`	⚪ NSD	1.27%	0.0504 → 0.0494, 0.05
`RootTree(unlen2k, 5)`	⚪ NSD	-1.28%	0.328 → 0.33, 0.334
`RootTree(unlen80, c("t3", "t36"))`	⚪ NSD	-0.96%	0.065 → 0.0647, 0.0663
`RootTree(unlen80, "t3")`	⚪ NSD	0.18%	0.0434 → 0.043, 0.0437
`RootTree(unlen80, "t30")`	⚪ NSD	-0.84%	0.0436 → 0.0436, 0.0444
`TreeDist::RobinsonFoulds(forest201.80)`	⚪ NSD	-0.06%	16 → 16.2, 15.9
`TreeDist::RobinsonFoulds(forest21.888)`	⚪ NSD	-0.45%	3.25 → 3.28, 3.24
`TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)`	⚪ NSD	-5.81%	0.0901 → 0.0914, 0.0985
`TreeTools:::postorder_order(bal40)`	⚪ NSD	0.6%	0.00166 → 0.00163, 0.00166
`TreeTools:::postorder_order(bal40k)`	⚪ NSD	0.27%	0.451 → 0.463, 0.446
`TreeTools:::postorder_order(dbal40)`	⚪ NSD	1.68%	0.00178 → 0.00174, 0.00177
`TreeTools:::postorder_order(dbal40k)`	🟢 Faster!	10.51%	2.37 → 2.09, 2.13
`TreeTools:::postorder_order(dpec40)`	🟢 Faster!	15.39%	0.003 → 0.0025, 0.00255
`TreeTools:::postorder_order(dpec40k)`	🟢 Faster!	8.53%	3610 → 3320, 3300
`TreeTools:::postorder_order(drnd80)`	🟢 Faster!	21.99%	0.0051 → 0.00398, 0.00399
`TreeTools:::postorder_order(nbal40)`	⚪ NSD	0.95%	0.0021 → 0.00207, 0.0021
`TreeTools:::postorder_order(nbal40k)`	🟢 Faster!	10.33%	2.41 → 2.12, 2.17
`TreeTools:::postorder_order(npec40)`	🟢 Faster!	14.35%	0.00328 → 0.00279, 0.00283
`TreeTools:::postorder_order(npec40k)`	🟢 Faster!	8.86%	3630 → 3300, 3330
`TreeTools:::postorder_order(nrnd80)`	🟢 Faster!	18.71%	0.00562 → 0.00456, 0.00458
`TreeTools:::postorder_order(pec40)`	⚪ NSD	-0.61%	0.00164 → 0.00163, 0.00166
`TreeTools:::postorder_order(pec40k)`	⚪ NSD	-0.78%	0.429 → 0.431, 0.436
`TreeTools:::postorder_order(rnd80)`	⚪ NSD	0%	0.00208 → 0.00208, 0.00207

ms609 added 6 commits January 5, 2026 14:38

Gemini3pro first draft

8559f4a

Revision 2

dc49b35

sp

ae4d297

Guard against stack overflow

3cfe76a

Update version & news

d020acd

Restore simplementation

9c71008

ms609 added 2 commits January 5, 2026 16:47

Promote to int32

4970633

Coverage

02a4947

Copilot AI and others added 2 commits January 6, 2026 07:30

Remove 2048 leaf limit in splits_to_edge() with hybrid stack/heap all…

d80b95c

…ocation (#242) Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>

Update SplitInformation.Rd

37bb168

ms609 merged commit d7ba9f5 into main Jan 6, 2026
19 of 20 checks passed

ms609 deleted the large-trees branch January 6, 2026 07:49

ms609 mentioned this pull request Jan 6, 2026

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github-actions bot commented Jan 6, 2026

Performance benchmark results

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Large tree support: `SplitList` #241

Large tree support: `SplitList` #241

codecov bot commented Jan 5, 2026 •

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github-actions bot commented Jan 5, 2026 •

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github-actions bot commented Jan 6, 2026 •

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