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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()These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.