R Observatory: Metrics for babette version 2.3.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

babette

2.3.4

Control 'BEAST2'

1packages depend

6.2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Richèl J.C. BilderbeekFirst published 2020-01-119 releasesCRAN page ↗GitHub ↗

'BEAST2' (https://www.beast2.org) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is commonly accompanied by 'BEAUti 2', 'Tracer' and 'DensiTree'. 'babette' provides for an alternative workflow of using all these tools separately. This allows doing complex Bayesian phylogenetics easily and reproducibly from 'R'.

Install

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

install.packages("babette", 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/babette")

Development version from ropensci/babette. 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-babette

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-babette

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-babette

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

Health

CRAN checks

13OK

Slowest check: 2.0 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

8

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-06
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-04
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

6.2K

CRAN downloads in the past year

Rank #7,907 · ~17/day · ~517/mo

Releases R versions

Daily download trend is not available in this view yet.

33930 days

1.1K90 days

6.2K1 year

Compare downloads with other packages →

Also on158 r2u4 autocran

Repository

GitHub ↗ ropensci/babette

46Stars

7Forks

7Open issues

0Open PRs

17Releases

982Commits

8Contributors

rr-packagerstatsphylogeneticsbeast2bayesian-inference

License GPL-3.0 · 982 commits · Last activity 2026-07-16 · 0% stars, 30d

Stars over time

2025-02-24 · 452026-07-07 · 46

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/ropensci/babette on 2026-08-16.

Continuous integration (2)

GitHub ActionsAppVeyor

Research and citation (2)

CITATION.cffcodemeta.json

Lint, format, editor (1)

RStudio project

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (5)

R >= 3.5.0beautier beastier mauricer tracerer

Imports (4)

phangorn rlang stringr xml2

LinkingTo (0)

none

Suggests (9)

ape ggplot2 knitr lintr nLTT rappdirs rmarkdown spelling testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

mcbette

Code & Tests

People & History

People (6)

Maintainer (1)

Richèl J.C. Bilderbeek

Author, Maintainer

Authors (1)

Richèl J.C. Bilderbeek

Author, Maintainer

Contributors (3)

Jason Griffiths

Contributor · added in 2.3

Giovanni Laudanno

Contributor

Olivier Roy

Contributor · added in 2.3.4

Reviewers (2)

Joëlle Barido-Sottani

Reviewer

David Winter

Reviewer

Package Timeline

9 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
2.3.4Latest
2024-06-25 · current release · diff ↗
unarchivedReturned to CRAN
2024-06-25
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2023-10-24
requires archived package 'assertive.properties'
2.3.3
2023-09-27 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.3.2
2022-08-12 · diff ↗
unarchivedReturned to CRAN
2022-08-12
archivedRemoved from CRAN
2022-08-08
requires archived package 'beautier'
2.3.1
2022-06-21 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.3
2021-09-27 · diff ↗
unarchivedReturned to CRAN
2021-09-27
archivedRemoved from CRAN
2021-07-13
requires archived package 'beastier'

Show 9 earlier events

R
R 4.1.0 released · 2021-05-18
2.2
2020-11-06 · diff ↗
2.1.4
2020-08-11 · diff ↗
unarchivedReturned to CRAN
2020-08-11
archivedRemoved from CRAN
2020-07-31
required archived package 'assertive'
R
R 4.0.0 released · 2020-04-24
2.1.2
2020-02-01 · diff ↗
2.1.1
2020-01-11
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-01-11
Total releases: 9 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 2.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("babette")

The authors publish a CITATION.cff, so they have said how they want this cited. Run citation() and use what it gives you.

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 babette version 2.3.4 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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