NEWS.md
In aptg: Automatic Phylogenetic Tree Generator

aptg 0.4.0

region.tree() now validates its arguments (taxon, location mode) before checking that rgbif is installed, so argument errors (e.g. missing location) are reported even when rgbif isn't available, instead of being masked by the "requires the 'rgbif' package" message.

region.tree() builds tree(s) for a clade within a geographic area, pulling the species list from GBIF (via rgbif) and handing off to taxa.tree(). Two modes:
Radius --- a circle of radius_km around (lat, lon); the WKT circle is built with geosphere and wound counter-clockwise as GBIF requires.
Admin area --- a GADM GID via gadm (worldwide), or a Canadian province/territory via province. All 13 Canadian provinces and territories are supported by name or postal code (AB, BC, MB, NB, NL, NT, NS, NU, ON, PE, QC, SK, YT).
GBIF species are found by occurrence faceting (no bulk download, no credentials); only georeferenced records without geospatial issues are counted. Note the result is occurrence-based and sampling-biased, not a curated checklist -- see ?region.tree.
New Suggests: rgbif, geosphere.

downto.tree()'s key argument now exports the NCBI Entrez key as the ENTREZ_KEY environment variable for the duration of the call, so both the get_uid and downstream requests use it (previously it reached only get_uid). The prior ENTREZ_KEY value is restored on exit. Setting ENTREZ_KEY yourself and leaving key = NULL works identically.

Major backend change to make the package installable and CRAN-eligible again after its original dependencies were archived.

Dropped brranching / Phylomatic backend. brranching was archived from CRAN (2023-02-24) and the Phylomatic web service it called (phylodiversity.net) was shut down. Both functions now build trees as induced subtrees of the Open Tree of Life synthetic tree via rotl.
Phylum safeguard. taxa.tree() groups taxa by phylum and returns one tree per phylum, so no induced tree ever spans above phylum. Mammals, angiosperms, arthropods, etc. come back as separate trees.
taxa.tree() and downto.tree() now return (invisibly) list(trees, unmatched), where trees is a list keyed by phylum and each element is list(tree, dist). (Earlier 0.2.0 drafts returned a single list(tree, dist, unmatched).)

Fish backend. source = "fish" builds a dated chronogram from the Fish Tree of Life (fishtree, in Suggests) for ray-finned fishes. Unlike the topology-only Open Tree backend, its distance matrix is patristic (time). Requires install.packages("fishtree").

Names that Open Tree cannot resolve, or that resolve but are absent from the synthetic tree, are reported in $unmatched instead of silently failing inside try().
downto.tree() resolves the taxon to a UID once (was queried repeatedly), runs non-interactively (ask = FALSE), and supports db = "gbif" / "itis" to avoid NCBI rate limits.
Because Open Tree subtrees are topology-only, unit branch lengths are assigned when absent so dist is well defined (edge counts).