Package: phyloatlas 0.1.0
Francisco Richter
phyloatlas: Access to the 'Phylo-Species Atlas' of Empirical Phylogenies
Provides convenience functions to fetch standardized phylogenetic trees and per-tree provenance metadata from the 'Phylo-Species Atlas' <https://github.com/franciscorichter/phylo-species-atlas> directly from R. The atlas is a curated collection of empirical species-level trees covering Bacteria, Archaea, and Eukaryota, organized into 62 partitions of life with tip labels normalized against a shared dictionary of standardized species identifiers. Functions load any of the standardized trees with species labels resolved from the dictionary, list available trees, and inspect per-tree provenance.
Authors:
phyloatlas_0.1.0.tar.gz
phyloatlas_0.1.0.tar.gz(r-4.7-any)phyloatlas_0.1.0.tar.gz(r-4.6-any)
phyloatlas_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
phyloatlas/json (API)
NEWS
| # Install 'phyloatlas' in R: |
| install.packages('phyloatlas', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/franciscorichter/phylo-species-atlas/issues
Last updated from:7a8673aadb. Checks:4 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 116 | ||
| source / vignettes | OK | 171 | ||
| linux-release-x86_64 | OK | 101 | ||
| wasm-release | OK | 108 |
Exports:atlas_clear_cacheatlas_infolist_treesload_atlas_tree
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Clear the in-memory cache | atlas_clear_cache |
| Get metadata for a single tree | atlas_info |
| List trees available in the Phylo-Species Atlas | list_trees |
| Load a tree from the Phylo-Species Atlas | load_atlas_tree |