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treespace

ANALYTICS
Velocity0.0

Statistical Exploration of Landscapes of Phylogenetic Trees

github.com/thibautjombart/treespace ↗

treespace ships once every year or two, and only when CRAN or a user forces it.

phylogeneticstransmission-treescran-compliancemaintenance-modeepidemiology
◆Current state
treespace explores and compares sets of phylogenetic and transmission trees, including the tree-distance measures used in outbreak reconstruction. Its release history is entirely reactive: five updates across five years, each triggered by a CRAN policy change, an upstream package removal, or a bug someone reported. The most recent is an Rd cross-reference format patch plus a maintainer email change.
◆Where it's heading
The package is stable and lightly staffed rather than abandoned — bugs that affect correctness do get fixed, and CRAN deadlines are met. But the 2023 update is the telling one: rather than vendor or replace adephylo when it faced removal, the maintainers disabled two tree-vector methods and marked the loss as hopefully temporary. Two years on, nothing in the feed indicates they came back.
◆Prediction
The next entry will most likely be another CRAN-compliance patch, on the pattern of four of the last five releases. Whether the Abouheif and sumDD methods ever return is not something these entries give any signal on.

◆Recent moves

  1. 11mo ago

    treespace patches Rd cross-references for CRAN

    Rd cross-reference formatting updated to meet new CRAN standards, plus a maintainer email change. Purely a compliance release, and the only activity in two years.

    View source ↗
  2. 2y ago

    treespace disables Abouheif and sumDD as adephylo exits CRAN

    Functionality removed under upstream pressure: with adephylo facing CRAN removal, the Abouheif and sumDD methods for defining a tree as a vector were disabled to drop the dependency. Users of those methods lost them, and the notes' hope that it is temporary has not yet been revisited.

    View source ↗
  3. 3y ago

    treespace fixes vignette build on NA tree names

    A vignette compilation bug involving NA row names, plus citation and test housekeeping in line with CRAN suggestions. No effect on tree comparison results.

    View source ↗
  4. 5y ago

    treespace fixes dist indexing that broke its tests

    An internal indexing correction after stats::as.dist() objects stopped accepting d[[i]]. It surfaced through the test suite rather than through users.

    View source ↗
  5. 5y ago

    treespace corrects tip label handling in transmission distances

    A user-reported error in how tip labels were handled when computing transmission tree distances — a bug class that yields plausible but wrong numbers rather than an error. Credited to outside researchers and covered by a new test, which is the right response to a silent-correctness issue.

    View source ↗