R Observatory: Metrics for treebase version 0.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

treebase

0.1.5Package record

Discovery, Access and Manipulation of 'TreeBASE' Phylogenies

0packages depend

5.2Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by Carl BoettigerCRAN page ↗GitHub ↗Website ↗Issues ↗

Interface to the API for 'TreeBASE' http://treebase.org from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic trees (of species, population, or genes) and the data used to create them.

Changes in 0.1.5

Re-roxygenize docs

From NEWS in the release

Install

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

install.packages("treebase", 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("ropensci/treebase")

Development version from ropensci/treebase. 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-treebase

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-treebase

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-treebase

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: 1.5 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.5

READMEYes · 144 wordsVignettesYes · 1 · staticNEWSYes · 67% structured · mentions 0.1.5Citation fileNoWebsiteYes · pkgdown

Help pages: 17 (9 internal)
Examples that run: 0%5 never run
Exported functions with examples: 71%
Documented parameters: 97%
Return-value docs: 86%
Help pages citing references: 0%

Vignettes (1)

Treebase Tutorial HTML

How these are measured

Downloads

5.2K

CRAN downloads in the past year

Rank #5,916 · ~14/day · ~437/mo

Releases R versions

Daily download trend is not available in this view yet.

37630 days

1.4K90 days

5.2K1 year

Compare downloads with other packages →

Also on148 r2u9 autocran903 conda_forge207 c2d4u

How downloads are counted

Repository

ropensci/treebase ↗Organization: ropensci

10Stars

4Forks

7Open issues

0Open PRs

0Releases

228Commits

4Commit identities

rrstatsr-package

License file reads as CC0-1.0 · 228 commits · Last activity 2024-02-16 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 8
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2024-04-10 · 102026-07-07 · 10

How these are measured

PracticesBeta

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

Checks run against github.com/ropensci/treebase on 2026-10-11.

Continuous integration (4)

GitHub ActionsR CMD check workflowTravis CI (config file)AppVeyor

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Code of conduct (inherited from ropensci)

Docs source (1)

GitHub Pages site last deployed 2018-11-05

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing treebase adds 14 packages (12 with compiled code, 8.0 MB of source tarballs). Heaviest: Rcpp 1.8 MB, ape 1.4 MB, openssl 1.1 MB.

Depends (2)

R >= 2.15ape

Imports (5)

XML RCurlmethodsutilshttr

LinkingTo (0)

none

Suggests (3)

testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Carl Boettiger

Author, Maintainer since 0.0-3 (2011)

Duncan Temple Lang

Author

Listed in earlier versions (1)

Duncan Temple-Lang

no longer listed · 0.0-3 to 0.0-4

Releases (11)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.1.5Latest
record
2024-02-16 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
0.1.4
record
2017-02-06 · diff ↗
0.1.3
record
2016-09-05 · diff ↗
R
R 3.3.0 released · 2016-05-03
0.1.2
record
2015-10-14 · diff ↗
0.1.1
record
2015-06-16 · diff ↗

Show 12 earlier eventsHide 12 earlier events

0.1.0
record
2015-06-15 · diff ↗
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
0.0-7.1
record
2014-02-21 · diff ↗
R
R 3.0.0 released · 2013-04-03
0.0-6
record
2012-06-27 · diff ↗ ·
removed 3 exports
get_study, get_study_id, search_metadata

added 1 export
download_metadata
R
R 2.15.0 released · 2012-03-30
0.0-5
record
2012-03-03 · diff ↗ ·
added 3 exports
cache_treebase, drop_nontrees, have_branchlength
0.0-4
record
2011-11-15 · diff ↗ ·
added 1 export
get_study
R
R 2.14.0 released · 2011-10-31
0.0-3
record
2011-10-25
R
R 2.13.0 released · 2011-04-13

Package metadata

First published: 2011-10-25
Total releases: 11 / 15 yrs
License: CC0 · relicensed from GPL (>= 2) in 0.0-5
Minimum R: ≥ 2.15
Bundled data: 4.0 MB / 3 files
Download size: 4.0 MB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("treebase")

Format

Boettiger, C., & Temple Lang, D. (2024). treebase: Discovery, Access and Manipulation of 'TreeBASE' Phylogenies (Version 0.1.5) [Computer software]. https://doi.org/10.32614/CRAN.package.treebase

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 treebase version 0.1.5 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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