phyloatlas

0.1.0

Access to the 'Phylo-Species Atlas' of Empirical Phylogenies

0packages depend

543downloads / year

83.8%test coverage

13/13checks pass

Overview

About

Maintained by Francisco RichterFirst published 2026-06-041 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("phyloatlas", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("franciscorichter/phylo-species-atlas")

Development version from franciscorichter/phylo-species-atlas. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-phyloatlas

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-phyloatlas

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-phyloatlas

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 1.0 min · r-release-windows-x86_64

Code health

Yes

Tests · ratio 0.90

83.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
11 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
10 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-05
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 109 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 50%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

543

CRAN downloads in the past year

Rank #21,099 · ~1/day · ~45/mo

Releases R versions

Daily download trend is not available in this view yet.

17430 days

54390 days

5431 year

Compare downloads with other packages →

Also on1 r2u2 autocran

Repository

GitHub ↗ franciscorichter/phylo-species-atlas

0Stars

0Forks

0Open issues

0Open PRs

8Releases

108Commits

1Contributors

License CC-BY-4.0 · 108 commits · Last activity 2026-07-05

Releases over time

2026-05-11 · 22026-07-07 · 8

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/franciscorichter/phylo-species-atlas on 2026-07-30.

Continuous integration (1)

GitHub Actions

Research and citation (2)

CITATION.cffZenodo

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0

Imports (2)

apeutils

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown testthat withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Francisco Richter

Author, Maintainer

Authors (1)

Francisco Richter

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

0.1.0Latest
2026-06-04 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-04
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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