Allow a function as lengths in tree-generation functions

[ms609]

Summary

• RandomTree(), YuleTree(), PectinateTree(), BalancedTree(), StarTree(), and SingleTaxonTree() now accept a function as the lengths argument; the function is called with the number of edges as its sole argument.
• This allows e.g. RandomTree(8, lengths = runif) instead of RandomTree(8, lengths = runif(14)).
• A private helper .EdgeLengths(lengths, nEdge) consolidates the dispatch (function vs vector) across all six functions.
• Docs updated (both GenerateTree.Rd and TrivialTree.Rd regenerated); example RandomTree(8, lengths = runif) added.
• Tests extended with seq_len-based assertions that verify the function is called with the exact edge count.

Test plan

• devtools::test(filter = "tree_generation") — 121 tests, 0 failures
• Inspect man/GenerateTree.Rd and man/TrivialTree.Rd for updated lengths description

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.18%. Comparing base (49179ea) to head (de710c1).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #273      +/-   ##
==========================================
- Coverage   96.19%   96.18%   -0.01%     
==========================================
  Files          81       81              
  Lines        6039     6033       -6     
==========================================
- Hits         5809     5803       -6     
  Misses        230      230              

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[github-actions]

Performance benchmark results

Call	Status	Change	Time (ms)
as.Splits(bigTrees)	⚪ NSD	-16.51%	22.2 → 27.8, 22.7
as.Splits(someTrees)	⚪ NSD	-3.16%	11.5 → 11.9, 11.5
Consensus(forest1k.888, check = FALSE)	⚪ NSD	3.45%	106 → 100, 105
Consensus(forest201.80, check = FALSE)	⚪ NSD	-5.38%	4.12 → 4.45, 4.21
Consensus(forest21.260, 0.5, FALSE)	⚪ NSD	0.45%	1.24 → 1.24, 1.23
Consensus(forest21.260)	⚪ NSD	0.62%	1.25 → 1.25, 1.25
Consensus(forestMaj, 0.5, FALSE)	⚪ NSD	0.27%	3.24 → 3.27, 3.23
DropTip(tr2000, 5)	⚪ NSD	-2.87%	16.8 → 17.6, 17
DropTip(tr80, 5)	⚪ NSD	-0.47%	0.106 → 0.107, 0.106
DropTip(unlen2k, 5)	⚪ NSD	0.53%	0.21 → 0.213, 0.206
DropTip(unlen80, 5)	⚪ NSD	-0.79%	0.0408 → 0.0415, 0.0407
lapply(bigSplits, as.phylo)	⚪ NSD	-0.31%	29.5 → 29.6, 29.5
lapply(someSplits, as.phylo)	⚪ NSD	-1.04%	14 → 14.3, 13.9
PathLengths(tr2000, full = TRUE)	⚪ NSD	-1.8%	16.5 → 17, 16.5
PathLengths(tr80, full = TRUE)	⚪ NSD	-0.76%	0.102 → 0.104, 0.102
PathLengths(tr80Unif, full = TRUE)	⚪ NSD	-1.12%	0.104 → 0.106, 0.104
RootTree(tr2000, 5)	⚪ NSD	-1.06%	0.4 → 0.406, 0.403
RootTree(tr80, c("t3", "t36"))	⚪ NSD	-3.53%	0.0713 → 0.0748, 0.0729
RootTree(tr80, "t3")	⚪ NSD	-3.05%	0.051 → 0.0533, 0.0516
RootTree(tr80, "t30")	⚪ NSD	-2.15%	0.0511 → 0.0527, 0.0517
RootTree(unlen2k, 5)	⚪ NSD	7.11%	0.357 → 0.334, 0.33
RootTree(unlen80, c("t3", "t36"))	⚪ NSD	-0.3%	0.0676 → 0.0682, 0.0675
RootTree(unlen80, "t3")	⚪ NSD	0.67%	0.0452 → 0.0451, 0.0447
RootTree(unlen80, "t30")	⚪ NSD	0.72%	0.0457 → 0.0458, 0.045
TreeDist::RobinsonFoulds(forest201.80)	⚪ NSD	-2.36%	16.8 → 17.6, 16.5
TreeDist::RobinsonFoulds(forest21.888)	⚪ NSD	-1.21%	3.55 → 3.64, 3.42
TreeTools:::path_lengths(tr80$edge, tr80$edge.length, FALSE)	⚪ NSD	-0.68%	0.0924 → 0.0943, 0.0918
TreeTools:::postorder_order(bal40)	⚪ NSD	-0.06%	0.00169 → 0.0017, 0.00169
TreeTools:::postorder_order(bal40k)	⚪ NSD	-0.07%	0.548 → 0.549, 0.548
TreeTools:::postorder_order(dbal40)	⚪ NSD	1.08%	0.00176 → 0.00174, 0.00175
TreeTools:::postorder_order(dbal40k)	⚪ NSD	1.15%	2.16 → 2.12, 2.14
TreeTools:::postorder_order(dpec40)	⚪ NSD	0.35%	0.00257 → 0.00256, 0.00257
TreeTools:::postorder_order(dpec40k)	⚪ NSD	-0.06%	3300 → 3300, 3300
TreeTools:::postorder_order(drnd80)	⚪ NSD	0.24%	0.0041 → 0.00413, 0.00406
TreeTools:::postorder_order(nbal40)	⚪ NSD	0.43%	0.00209 → 0.00207, 0.00208
TreeTools:::postorder_order(nbal40k)	⚪ NSD	-1.34%	2.2 → 2.23, 2.22
TreeTools:::postorder_order(npec40)	⚪ NSD	-1.05%	0.00286 → 0.00288, 0.00289
TreeTools:::postorder_order(npec40k)	⚪ NSD	-0.08%	3320 → 3330, 3320
TreeTools:::postorder_order(nrnd80)	⚪ NSD	0.65%	0.00465 → 0.00461, 0.00463
TreeTools:::postorder_order(pec40)	⚪ NSD	0.59%	0.00168 → 0.00167, 0.00167
TreeTools:::postorder_order(pec40k)	⚪ NSD	19.17%	0.547 → 0.548, 0.435
TreeTools:::postorder_order(rnd80)	⚪ NSD	1.4%	0.00214 → 0.00213, 0.0021