phyloatlas 0.1.1

• load_atlas_tree() stops with an error that gives the address of the source when the requested tree is one the atlas does not redistribute because its source states no licence (data release v1.1.3: cephalopods, frogs, gastropods, insects, primates, seed_plants, sharks, sponges). The list is read from the atlas’s registers/withheld_trees.csv; when the atlas named by phyloatlas.base_url has no such register, the copy bundled with the package (inst/extdata/withheld_trees.csv) is used.

phyloatlas 0.1.0

• Initial CRAN release.
• Four user-facing functions:
  • load_atlas_tree() — fetch a standardized Newick tree from the Phylo-Species Atlas, optionally resolving integer tip IDs to species names via the shared dictionary.
  • list_trees() — data frame of every tree in the atlas with provenance fields (study, year, journal, DOI, coverage).
  • atlas_info() — single-row provenance for a tree by name.
  • atlas_clear_cache() — drop the in-session dictionary/metadata cache.
• In-memory caching of the dictionary and metadata files so repeated calls in a session don’t re-download.
• Fork / mirror support via the phyloatlas.base_url option.
• Bundled offline demo data under inst/extdata/ so examples and tests run without network access.