LoginSign Up
← Back to all sparks
R

rotl

ANALYTICS
Velocity0.0

Interface to the Open Tree of Life API for retrieving phylogenetic trees in R

github.com/ropensci/rotl ↗

rotl's whole release history is keeping name matching honest against a moving taxonomy.

open-tree-of-lifetaxonomic-matchingreproducibilityapi-trackingdormant
◆Current state
Nearly every entry concerns `tnrs_match_names()`, the function that maps user-supplied names onto Open Tree taxonomy ids. 3.1.0 changed which taxon wins a multi-way match — highest matching score rather than lowest OTT id, reversing the rule 3.0.4 introduced. 3.0.12 defaulted `context_name` to 'All life' so a context inferred from the first name could not silently skew later ones. 3.0.11 made a total failure to match return an empty tibble with a warning instead of an error. The rest are small fixes tracking Open Tree API changes.
◆Where it's heading
The recurring problem is ambiguity: names match several taxa, and the package has changed its tie-breaking rule twice while making failures and edge cases return predictable objects rather than errors. Nothing here expands what rotl can retrieve; it makes what it retrieves reproducible. The feed also stops in mid-2023, so the package appears dormant.
◆Prediction
Nothing in the window suggests new capability. If a release comes, the pattern says it will follow an Open Tree API change or another matching-behaviour correction.

◆Recent moves

  1. 3y ago

    rotl 3.1.0 matches on score instead of lowest OTT id

    Changes `tnrs_match_names()` to return the highest-scoring taxon rather than the lowest OTT id, reversing the rule set in 3.0.4. Existing scripts can silently resolve to different taxa.

    View source ↗
  2. 4y ago

    rotl 3.0.12 defaults matching context to All life

    Defaults `context_name` to 'All life' so a context inferred from the first supplied name can no longer distort the rest of a batch. Another correction to the same ambiguity problem.

    View source ↗
  3. 5y ago

    rotl 3.0.11 returns empty tibble when no names match

    Returns an empty tibble with a warning when nothing matches, instead of erroring out. Makes the function behave consistently in scripted use.

    View source ↗
  4. 6y ago

    rotl 3.0.10 tracks Open Tree API updates

    Small fixes following Open Tree API updates, with no user-visible change, plus a documentation update for `tol_node_info()` output.

    View source ↗
  5. 7y ago

    rotl 3.0.9 tracks Open Tree API updates

    Another round of small fixes tracking Open Tree API changes. The package's most common release type.

    View source ↗
  6. 7y ago

    rotl 3.0.7 updates vignette for TNRS endpoint change

    A vignette update noting that the Open Tree TNRS endpoint no longer accepts underscores in taxon names. Documentation only.

    View source ↗