BeastJar

10.5.1

JAR Dependency for MCMC Using 'BEAST'

1packages depend

6.4Kdownloads / year

70.6%test coverage

12/13checks pass

Overview

About

Maintained by Marc A. SuchardFirst published 2020-10-134 releasesCRAN 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.

Install

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

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.

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

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 1.4 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.82

70.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-06
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-04
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 46 wordsVignettesNopkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: 100%
References docs: 0%

Downloads

6.4K

CRAN downloads in the past year

Rank #7,580 · ~18/day · ~535/mo

Releases R versions

Daily download trend is not available in this view yet.

40430 days

1.3K90 days

6.4K1 year

Compare downloads with other packages →

Also on418 r2u46 c2d4u

Repository

GitHub ↗ beast-dev/beastjar

1Stars

1Forks

0Open issues

0Open PRs

0Releases

79Commits

1Contributors

79 commits · Last activity 2025-07-20 · 0% stars, 30d

Stars over time

2020-08-29 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/beast-dev/beastjar on 2026-08-02.

Continuous integration (2)

GitHub ActionsTravis CI

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

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

EvidenceSynthesis

Code & Tests

People & History

People (3)

Maintainer (1)

Marc A. Suchard

Author, Maintainer, Copyright holder

Authors (1)

Marc A. Suchard

Author, Maintainer, Copyright holder

Marc A. Suchard

Author, Maintainer, Copyright holder

Alexei J. Drummond

Andrew Rambaut

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
10.5.1Latest
2025-08-21 · current release · diff ↗
10.5.0
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
2020-10-26 · diff ↗
1.10.5
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
Minimum R: ≥ 3.5.0
Download size: 7.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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