R Observatory: Metrics for rtrees version 2.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rtrees

2.0.2Package record

Deriving Phylogenies from Synthesis Trees

0packages dependsuggested by 2

1.3Kdownloads / year

73.1%test coverage

13/13flavors OK

Overview

About

Maintained by Daijiang LiCRAN page ↗Website ↗

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 4.9 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-06-12

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.2

READMEYes · 1,074 wordsVignettesYes · 4 · dynamicNEWSNoCitation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 12 (2 internal)includes a package overview page
Examples that run: 100%4 run in a plain check
Exported functions with examples: 50%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (4)

How these are measured

Downloads

1.3K

CRAN downloads in the past year

Rank #15,250 · ~4/day · ~111/mo

Releases R versions

Daily download trend is not available in this view yet.

23230 days

80490 days

1.3K1 year

Compare downloads with other packages →

Also on93 r2u4 autocran

How downloads are counted

Repository

daijiang/rtrees ↗Account: daijiang

35Stars

12Forks

1Open issues

0Open PRs

0Releases

166Commits

2Commit identities

rrstatsr-packagephylogenetic-trees

License file reads as GPL-3.0 · 166 commits · Last activity 2026-10-23 · 0% stars, 30d · Default branch at 2.0.3, ahead of CRAN 2.0.2 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 0
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-07 · 352026-08-30 · 35

How these are measured

PracticesBeta

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

Checks run against github.com/daijiang/rtrees on 2026-10-21.

Continuous integration (1)

GitHub Actions

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-09-14 · The repository has a site deploy workflow

pkgdown site last built 2026-09-14

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-05-01
Named in .Rbuildignore: .claude
Named in .gitignore: .claude
Commits: at least 2 crediting it in the message

Models named in its commits

Claude Sonnet 4.62 commits · May 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing rtrees adds 41 packages (25 with compiled code, 38 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, megatrees 4.1 MB.

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

0direct

0indirect

Suggested by 2

Suggests, most downloaded first

prepR4pcm megatrees

How these are counted

Code & Tests

Datasets

People & History

People (1)

Daijiang Li

Author, Maintainer since 2.0.2 (2026)

Releases (1)

2.0.2Latest
record
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: 1.7 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("rtrees")

The package provides a citation file, so citation() returns the authors' own entry.

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 v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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