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.
R access to the Phylo-Species Atlas — 49 datasets, 641,763 species, standardized Newick format.
# install.packages("pak")
pak::pkg_install("franciscorichter/phylo-species-atlas/phyloatlas")
library(phyloatlas)
# Browse available trees
trees <- list_trees()
head(trees)
# Load one
tree <- load_atlas_tree("mammals")
plot(tree, show.tip.label = FALSE)
# Provenance for a single tree
atlas_info("birds")
Trees larger than ~10k tips download faster with resolve_labels = FALSE, which skips the 18 MB species dictionary:
tree <- load_atlas_tree("seed_plants", resolve_labels = FALSE)
| Function | Purpose |
|---|---|
load_atlas_tree(name) |
Load a tree by name, with standardized labels |
list_trees() |
Data frame of every tree + provenance |
atlas_info(name) |
One-row metadata for a single tree |
atlas_clear_cache() |
Force re-download of cached metadata/dictionary |
Dictionary and metadata are cached in memory once per R session. To point at a fork or local mirror:
options(phyloatlas.base_url = "https://raw.githubusercontent.com/yourfork/phylo-species-atlas/main")
atlas_clear_cache()