R Observatory: Metrics for rtrees version 2.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rtrees

2.0.2

Deriving Phylogenies from Synthesis Trees

2packages depend

604downloads / year

73.1%test coverage

13/13checks pass

Overview

About

Maintained by Daijiang LiFirst published 2026-06-111 releasesCRAN page ↗

Provides tools to derive species-level phylogenies from large synthesis mega-trees for a wide range of taxonomic groups, including plants, birds, mammals, amphibians, reptiles, fish, bees, butterflies, and sharks. When a queried species is absent from the mega-tree, it is grafted onto the tree using one of two placement strategies: attachment at the basal node of the most closely related genus or family ('at_basal_node'), or random attachment below that basal node with probability proportional to branch length ('random_below_basal'). See Li (2023) doi:10.1111/ecog.06643 for details. Multiple species from a genus not represented in the mega-tree are placed as a polytomy to preserve clade coherence. The package interfaces with the 'megatrees' data package, which bundles or downloads on demand curated mega-trees. Users can also provide their own mega-trees.

Install

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

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

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

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-rtrees

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-rtrees

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-rtrees

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

Health

CRAN checks

13OK

Slowest check: 4.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.70

73.1%

Coverage · measured lines

100%

Documentation · exports

12

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-12
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,074 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

604

CRAN downloads in the past year

Rank #17,624 · ~2/day · ~50/mo

Releases R versions

Daily download trend is not available in this view yet.

20030 days

60490 days

6041 year

Compare downloads with other packages →

Also on50 r2u

Repository

GitHub ↗ daijiang/rtrees

36Stars

12Forks

1Open issues

0Open PRs

0Releases

165Commits

2Contributors

rrstatsr-packagephylogenetic-trees

License GPL-3.0 · 165 commits · Last activity 2026-06-05 · 0% stars, 30d

Stars over time

2025-08-07 · 352026-07-07 · 36

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/daijiang/rtrees on 2026-08-03.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

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

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: claude on 2026-05-01

claude

Most recent: claude on 2026-05-01

Evidence

claude: on or before 2026-05-01 · evidence B, D

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (12)

ape tidytree dplyr tibbleutilscastor furrr future megatrees fastmatch data.table Rcpp

LinkingTo (1)

Rcpp

Suggests (6)

knitr rmarkdown testthat piggyback R.rsp ggplot2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

megatrees prepR4pcm

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Daijiang Li

Author, Maintainer

Authors (1)

Daijiang Li

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

2.0.2Latest
2026-06-11 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-11
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 302 KB / 2 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rtrees")

Format

Li, D. (2026). rtrees: Deriving Phylogenies from Synthesis Trees (Version 2.0.2) [Computer software]. https://doi.org/10.32614/CRAN.package.rtrees

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for rtrees version 2.0.2 [Data set]. HJJB, LLC. Data release v2026-08-09. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-09, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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