R Observatory: Metrics for BeastJar version 10.5.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BeastJar

10.5.1Package record

JAR Dependency for MCMC Using 'BEAST'

1packages depend

6.1Kdownloads / year

70.6%test coverage

13/13flavors OK

Overview

About

Maintained by Marc A. SuchardCRAN page ↗GitHub ↗

Provides JAR to perform Markov chain Monte Carlo (MCMC) inference using the popular Bayesian Evolutionary Analysis by Sampling Trees 'BEAST X' software library of Baele et al (2025) doi:10.1038/s41592-025-02751-x. 'BEAST X' supports auto-tuning Metropolis-Hastings, slice, Hamiltonian Monte Carlo and Sequential Monte Carlo sampling for a large variety of composable standard and phylogenetic statistical models using high performance computing. By placing the 'BEAST X' JAR in this package, we offer an efficient distribution system for 'BEAST X' use by other R packages using CRAN.

Changes in 10.5.1

Changes:

1. Update to BEAST X 'hmc-clock' to patch gradients

2. Add custom spell-check dictionary

3. Update copyright year

4. Reducce CPU vs elapsed time in examples

From NEWS.md in the release

Install

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

install.packages("BeastJar", 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("beast-dev/BeastJar")

Development version from beast-dev/BeastJar. 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-beastjar

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-BeastJar

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-BeastJar

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: 1.4 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-06
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-04

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 10.5.1

READMEYes · 46 wordsVignettesNoNEWSYes · 0% structured · mentions 10.5.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 3 (1 internal)includes a package overview page
Examples that run: 100%2 run in a plain check
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

6.1K

CRAN downloads in the past year

Rank #5,003 · ~17/day · ~506/mo

Releases R versions

Daily download trend is not available in this view yet.

57830 days

1.7K90 days

6.1K1 year

Compare downloads with other packages →

Also on318 r2u24 autocran144 c2d4u

How downloads are counted

Repository

beast-dev/beastjar ↗Organization: beast-dev

1Stars

1Forks

0Open issues

0Open PRs

0Releases

79Commits

1Commit identities

79 commits · Last activity 2025-07-20

Responsiveness

not measured

Stars over time

2020-08-29 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/beast-dev/beastjar on 2026-10-21.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

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

Coverage (1)

Coverage reporting

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing BeastJar adds 1 package (1 with compiled code, 624 KB of source tarballs). Heaviest: rJava 624 KB.

Depends (1)

R >= 3.5.0

Imports (1)

rJava

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

EvidenceSynthesis

How these are counted

Code & Tests

People & History

People (3)

Marc A. Suchard

Alexei J. Drummond

Copyright holder

Andrew Rambaut

Copyright holder

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
10.5.1Latest
record
2025-08-21 · current release · diff ↗
10.5.0
record
2025-07-20 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
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
1.10.6
record
2020-10-26 · diff ↗ ·
added 1 export
supportsJava8
1.10.5
record
2020-10-13
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-10-13
Total releases: 4 / 6 yrs
License: Apache License 2.0 OSI
Copyright: See file COPYRIGHTS
Minimum R: ≥ 3.5.0
Download size: 7.7 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BeastJar")

Format

Suchard, M. A., Drummond, A. J., & Rambaut, A. (2025). BeastJar: JAR Dependency for MCMC Using 'BEAST' (Version 10.5.1) [Computer software]. https://doi.org/10.32614/CRAN.package.BeastJar

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 BeastJar version 10.5.1 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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