ms609 · Sep 8, 2026 · Jul 9, 2026 · Jul 9, 2026 · Jul 9, 2026 · Jul 9, 2026
diff --git a/.Rprofile b/.Rprofile
@@ -24,7 +24,7 @@ local({
 # when content changes).  Patching here intercepts every caller — devtools,
 # pkgbuild, RStudio auto-build — not just our manual wrapper script.
 local({
-  .normalise_lf <- function(pkgdir) {
+  .normalize_lf <- function(pkgdir) {
     for (f in file.path(pkgdir, c("src/RcppExports.cpp", "R/RcppExports.R"))) {
       if (!file.exists(f)) next
       lines <- readLines(f, warn = FALSE)
@@ -42,7 +42,7 @@ local({
     if (isTRUE(attr(orig, ".lf_patched"))) return()
     patched <- function(pkgdir = ".", verbose = getOption("verbose")) {
       result <- orig(pkgdir = pkgdir, verbose = verbose)
-      .normalise_lf(pkgdir)
+      .normalize_lf(pkgdir)
       invisible(result)
     }
     attr(patched, ".lf_patched") <- TRUE

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
@@ -113,26 +113,18 @@ jobs:
           # shinytest2 pulls chromote, whose declared system requirement is
           # `chromium`.  On Linux that makes pak add the ppa:xtradeb/apps PPA,
           # re-run `apt-get update`, and install Chromium and its GTK/X11
-          # dependency tree -- ~70 s on EVERY run, including cache hits, since
-          # the sysreqs pass is not cached.  Nothing here needs it: shinytest2
-          # is used only by inst/Parsimony/tests, which is .Rbuildignore'd and
-          # so absent from the tarball R CMD check sees, and those tests run in
-          # the dedicated `shiny` job on Windows.
+          # dependency tree -- ~70 s on every run, including cache hits, since
+          # the sysreqs pass is not cached.  Nothing here needs it.
+          #
           # Coreset isn't on CRAN, so without this pak fetches and compiles it
-          # from source on every cache miss -- ~67 s of the ~174 s dependency
-          # step (measured on this exact leg, run 30697330564). This URL is a
-          # prebuilt binary for this exact platform/R combo (aarch64,
-          # release), published by ms609/packages' build-maxmin workflow.
-          # The URL has no version/commit in it -- it always points at
-          # whatever Coreset build is current -- so it never needs updating
-          # here when Coreset changes.
+          # from source on every cache miss -- ~67 s. The URL is a prebuilt
+          # binary for this exact platform/R combo (aarch64, release),
+          # published by ms609/packages' build-maxmin workflow.
+          # 
+          # Remove ms609/TreeTools when >=2.4.1 reaches CRAN (exptd 2026-09-16)
           extra-packages: |
             shinytest2=?ignore
             url::https://ms609.github.io/packages/bin/linux/aarch64-release/Coreset_latest.tar.gz
-          # cache-version bumped to 2: the v1 caches were built while a
-          # project-level .Rprofile shadowed ~/.Rprofile, so every package
-          # in them was compiled from source.  Retire them once.
-          cache-version: 2
 
       - name: Check package
         uses: r-lib/actions/check-r-package@v2
@@ -252,10 +244,6 @@ jobs:
           # fails on Coreset by name; the branch only fires when pandoc is off
           # PATH, which is why only the non-Linux legs hit it.
           install-pandoc: true
-          # cache-version bumped to 2: the v1 caches were built while a
-          # project-level .Rprofile shadowed ~/.Rprofile, so every package
-          # in them was compiled from source.  Retire them once.
-          cache-version: 2
 
       - name: Set up R dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
@@ -278,10 +266,6 @@ jobs:
             shinytest2=?ignore
             ${{ matrix.config.r == '4.1' && 'url::https://ms609.github.io/packages/bin/linux/x86_64-4.1/Coreset_latest.tar.gz' || 'url::https://ms609.github.io/packages/bin/linux/aarch64-devel/Coreset_latest.tar.gz' }}
             ${{ matrix.config.r == '4.1' && 'url::https://cran.r-project.org/src/contrib/Archive/highs/highs_1.12.0-3.tar.gz' || '' }}
-          # cache-version bumped to 2: the v1 caches were built while a
-          # project-level .Rprofile shadowed ~/.Rprofile, so every package
-          # in them was compiled from source.  Retire them once.
-          cache-version: 2
 
       - name: Check package
         uses: r-lib/actions/check-r-package@v2
@@ -354,10 +338,6 @@ jobs:
           # (auto-detect's `pak::pkg_deps(".")` solve cannot see extra-packages).
           # `false` here: this job runs shinytest2, not vignettes.
           install-pandoc: false
-          # cache-version bumped to 2: the v1 caches were built while a
-          # project-level .Rprofile shadowed ~/.Rprofile, so every package
-          # in them was compiled from source.  Retire them once.
-          cache-version: 2
 
       - name: Run EasyTrees shinytest2 suite
         run: |
@@ -448,10 +428,6 @@ jobs:
           # pre-emptive, since whether a macOS runner ships pandoc on PATH is
           # exactly the condition that decides whether the bad branch fires.
           install-pandoc: true
-          # cache-version bumped to 2: the v1 caches were built while a
-          # project-level .Rprofile shadowed ~/.Rprofile, so every package
-          # in them was compiled from source.  Retire them once.
-          cache-version: 2
 
       - name: Check package
         uses: r-lib/actions/check-r-package@v2

diff --git a/AGENTS.md b/AGENTS.md
@@ -224,7 +224,7 @@ whose comment names a worktree is being worked there — often by the human deve
 Closing **without** a fix (not-a-bug, superseded design, negative result) needs more: close
 as *not planned* with `deferred`/`wontfix` **and** a comment carrying the reasoning and
 **what would make it live again**. A stated reopening condition is what let a later round
-recognise T-377 firing rather than re-hunt it. Long reasoning goes in `dev/benchmarks/*.md`,
+recognize T-377 firing rather than re-hunt it. Long reasoning goes in `dev/benchmarks/*.md`,
 linked.
 
 **Blocked on GHA, Hamilton or review?** Comment what you await, its reference, and the
@@ -261,7 +261,7 @@ Run these before committing whenever the trigger applies:
 |---------|---------|
 | Function signature or roxygen block changed | `Rscript -e "devtools::check_man()"` |
 | Documentation prose changed | `Rscript -e "spelling::spell_check_package()"` |
-| C++ signature changed | `Rscript .claude/tools/compile-attrs.R` (normalises LF + verifies `ts_rcpp.cpp` / `TreeSearch-init.c` arg counts) |
+| C++ signature changed | `Rscript .claude/tools/compile-attrs.R` (normalizes LF + verifies `ts_rcpp.cpp` / `TreeSearch-init.c` arg counts) |
 | Search behaviour changed (heuristics, scoring, stopping, pool) | Update `vignettes/search-algorithm.Rmd` |
 
 Full details: `.AGENTS/memory/r-package-conventions.md`.

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -51,15 +51,17 @@ Imports:
   Rdpack (>= 0.7),
   stats,
   TreeDist (>= 2.6.3),
-  TreeTools (>= 2.3.0.9002),
+  TreeTools (>= 2.4.0.9002),
   utils,
+Remotes: ms609/TreeTools,
 Suggests:
   cluster,
   Coreset,
   future,
   highs,
   knitr,
   phangorn (>= 2.2.1),
+  pkgload,
   PlotTools,
   promises,
   protoclust,
@@ -90,11 +92,12 @@ Config/Needs/website:
   pkgdown,
   remotes,
   shinylive,
-Config/roxygen2/version: 8.0.0
+Config/roxygen2/version: 8.1.0
 Config/testthat/edition: 3
 Collate:
   'AdditionTree.R'
   'Bootstrap.R'
+  'Bremer.R'
   'CharacterHierarchy.R'
   'ClusterStrings.R'
   'Concordance.R'
@@ -122,6 +125,7 @@ Collate:
   'recode_hierarchy.R'
   'SPR.R'
   'ScoreSpectrum.R'
+  'SuboptimalTrees.R'
   'SuccessiveApproximations.R'
   'TBR.R'
   'TaxonInfluence.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -25,6 +25,7 @@ export(.NonDuplicateRoot)
 export(.UniqueExceptHits)
 export(AdditionTree)
 export(BootstrapTree)
+export(Bremer)
 export(Carter1)
 export(CharacterHierarchy)
 export(CharacterLength)
@@ -111,6 +112,7 @@ export(SingleCharData)
 export(SingleCharMorphy)
 export(StepInformation)
 export(StopUnlessBifurcating)
+export(SuboptimalTrees)
 export(Suboptimality)
 export(SuccessiveApproximations)
 export(SuccessiveWeights)
@@ -135,99 +137,119 @@ export(is.morphyPtr)
 export(mc_fitch_scores)
 importFrom(Rcpp,compileAttributes)
 importFrom(Rdpack,reprompt)
-importFrom(TreeDist,ClusteringEntropy)
-importFrom(TreeDist,ClusteringInfo)
-importFrom(TreeDist,ClusteringInfoDistance)
-importFrom(TreeDist,Entropy)
-importFrom(TreeDist,MutualClusteringInfo)
-importFrom(TreeDist,SharedPhylogeneticInfo)
-importFrom(TreeDist,entropy_int)
-importFrom(TreeTools,AddUnconstrained)
-importFrom(TreeTools,CharacterInformation)
-importFrom(TreeTools,CladeSizes)
-importFrom(TreeTools,CladisticInfo)
-importFrom(TreeTools,CompatibleSplits)
-importFrom(TreeTools,Consensus)
-importFrom(TreeTools,DescendantEdges)
-importFrom(TreeTools,DescendantTips)
-importFrom(TreeTools,DoubleFactorial)
-importFrom(TreeTools,EdgeAncestry)
-importFrom(TreeTools,KeepTip)
-importFrom(TreeTools,LnUnrooted)
-importFrom(TreeTools,Log2DoubleFactorial)
-importFrom(TreeTools,Log2Unrooted)
-importFrom(TreeTools,Log2UnrootedMult)
-importFrom(TreeTools,LogDoubleFactorial)
-importFrom(TreeTools,MakeTreeBinary)
-importFrom(TreeTools,MatchStrings)
-importFrom(TreeTools,MatrixToPhyDat)
-importFrom(TreeTools,NRooted)
-importFrom(TreeTools,NSplits)
-importFrom(TreeTools,NTip)
-importFrom(TreeTools,NUnrooted)
-importFrom(TreeTools,NUnrootedMult)
-importFrom(TreeTools,NexusTokens)
-importFrom(TreeTools,PaintTree)
-importFrom(TreeTools,PectinateTree)
-importFrom(TreeTools,PhyDatToMatrix)
-importFrom(TreeTools,PolarizeSplits)
-importFrom(TreeTools,Postorder)
-importFrom(TreeTools,PostorderOrder)
-importFrom(TreeTools,Preorder)
-importFrom(TreeTools,RandomTree)
-importFrom(TreeTools,Renumber)
-importFrom(TreeTools,RenumberEdges)
-importFrom(TreeTools,RenumberTips)
-importFrom(TreeTools,RenumberTree)
-importFrom(TreeTools,RootNode)
-importFrom(TreeTools,RootTree)
-importFrom(TreeTools,SampleOne)
-importFrom(TreeTools,SplitConflicts)
-importFrom(TreeTools,SplitFrequency)
-importFrom(TreeTools,StringToPhyDat)
-importFrom(TreeTools,Subsplit)
-importFrom(TreeTools,SupportColour)
-importFrom(TreeTools,TipLabels)
-importFrom(TreeTools,TreeIsRooted)
-importFrom(TreeTools,as.Splits)
-importFrom(TreeTools,as.multiPhylo)
+importFrom(TreeDist,
+  ClusteringEntropy,
+  ClusteringInfo,
+  ClusteringInfoDistance,
+  Entropy,
+  MutualClusteringInfo,
+  SharedPhylogeneticInfo,
+  entropy_int
+)
+importFrom(TreeTools,
+  AddUnconstrained,
+  CharacterInformation,
+  CladeSizes,
+  CladisticInfo,
+  CompatibleSplits,
+  Consensus,
+  DescendantEdges,
+  DescendantTips,
+  DoubleFactorial,
+  EdgeAncestry,
+  KeepTip,
+  LnUnrooted,
+  Log2DoubleFactorial,
+  Log2Unrooted,
+  Log2UnrootedMult,
+  LogDoubleFactorial,
+  MakeTreeBinary,
+  MatchStrings,
+  MatrixToPhyDat,
+  NRooted,
+  NSplits,
+  NTip,
+  NUnrooted,
+  NUnrootedMult,
+  NexusTokens,
+  PaintTree,
+  PectinateTree,
+  PhyDatToMatrix,
+  PolarizeSplits,
+  Postorder,
+  PostorderOrder,
+  Preorder,
+  RandomTree,
+  Renumber,
+  RenumberEdges,
+  RenumberTips,
+  RenumberTree,
+  RootNode,
+  RootTree,
+  SampleOne,
+  SplitConflicts,
+  SplitFrequency,
+  StringToPhyDat,
+  Subsplit,
+  SupportColour,
+  TipLabels,
+  TreeIsRooted,
+  as.Splits,
+  as.multiPhylo
+)
 importFrom(abind,abind)
-importFrom(ape,consensus)
-importFrom(ape,keep.tip)
-importFrom(ape,nodelabels)
-importFrom(ape,plot.phylo)
-importFrom(ape,read.nexus)
-importFrom(ape,root)
-importFrom(ape,write.nexus)
-importFrom(cli,cli_alert)
-importFrom(cli,cli_alert_info)
-importFrom(cli,cli_alert_success)
-importFrom(cli,cli_alert_warning)
-importFrom(cli,cli_h1)
-importFrom(cli,cli_progress_bar)
-importFrom(cli,cli_progress_update)
-importFrom(colorspace,hex)
-importFrom(colorspace,max_chroma)
-importFrom(colorspace,polarLUV)
-importFrom(fastmatch,"%fin%")
-importFrom(fastmatch,fmatch)
-importFrom(grDevices,col2rgb)
-importFrom(grDevices,convertColor)
-importFrom(grDevices,rgb)
-importFrom(graphics,abline)
-importFrom(graphics,image)
-importFrom(graphics,mtext)
-importFrom(graphics,par)
-importFrom(stats,as.dist)
-importFrom(stats,cophenetic)
-importFrom(stats,cutree)
-importFrom(stats,dnorm)
-importFrom(stats,median)
-importFrom(stats,runif)
-importFrom(stats,sd)
-importFrom(stats,setNames)
-importFrom(stats,weighted.mean)
-importFrom(utils,adist)
-importFrom(utils,combn)
-importFrom(utils,head)
+importFrom(ape,
+  consensus,
+  keep.tip,
+  nodelabels,
+  plot.phylo,
+  read.nexus,
+  root,
+  write.nexus
+)
+importFrom(cli,
+  cli_alert,
+  cli_alert_info,
+  cli_alert_success,
+  cli_alert_warning,
+  cli_h1,
+  cli_progress_bar,
+  cli_progress_update
+)
+importFrom(colorspace,
+  hex,
+  max_chroma,
+  polarLUV
+)
+importFrom(fastmatch,
+  "%fin%",
+  fmatch
+)
+importFrom(grDevices,
+  col2rgb,
+  convertColor,
+  rgb
+)
+importFrom(graphics,
+  abline,
+  image,
+  mtext,
+  par
+)
+importFrom(stats,
+  as.dist,
+  cophenetic,
+  cutree,
+  dnorm,
+  median,
+  runif,
+  sd,
+  setNames,
+  weighted.mean
+)
+importFrom(utils,
+  adist,
+  combn,
+  head
+)
 useDynLib(TreeSearch, .registration = TRUE)