phyloatlas

R access to the Phylo-Species Atlas — 49 datasets, 641,763 species, standardized Newick format.

Install

# install.packages("pak")
pak::pkg_install("franciscorichter/phylo-species-atlas/phyloatlas")

Use

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)

Functions

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

Notes

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()