R Observatory: Metrics for BacArena version 1.8.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2022-11-20. Its history is shown below.

Reason: requires archived package 'sybil'

Details below reflect version 1.8.2, its last release before removal.

BacArena

1.8.2

Modeling Framework for Cellular Communities in their Environments

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Johannes Zimmermann9 releasesCRAN page ↗

Can be used for simulation of organisms living in communities (Bauer and Zimmermann (2017) doi:10.1371/journal.pcbi.1005544). Each organism is represented individually and genome scale metabolic models determine the uptake and release of compounds. Biological processes such as movement, diffusion, chemotaxis and kinetics are available along with data analysis techniques.

Install

R (source archive)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/BacArena/BacArena_1.8.2.tar.gz"
pkgFile <- "BacArena_1.8.2.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.8.2) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-bacarena

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

16

Dependencies · direct

Documentation

READMEYes · 294 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 98%
Documented parameters: 98%
Return-value docs: 47%
References docs: 0%

Downloads

BacArena Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on366 r2u

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (5)

R >= 3.5.0sybil ReacTran deSolveMatrix

Imports (12)

methodsutilsstatsgraphicsggplot2 reshape2 glpkAPI plyr Rcpp igraph stringr R.matlab

LinkingTo (3)

Rcpp RcppArmadillo RcppEigen

Suggests (3)

parallelknitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Johannes Zimmermann

Author, Maintainer

Authors (2)

Johannes Zimmermann

Author, Maintainer

Eugen Bauer

Author

Package Timeline

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

R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2022-11-20
requires archived package 'sybil'
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.8.2
2020-05-20 · diff ↗
unarchivedReturned to CRAN
2020-05-20
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-04-09
check problems were not corrected despite reminders
1.8.1
2019-12-17 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.8
2019-02-15 · diff ↗
1.7
2018-05-09 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.6
2017-05-23 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.5.1
2016-07-25 · diff ↗

Show 5 earlier events

1.5.0
2016-07-14 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.0.1
2016-01-06 · diff ↗
1.0
2015-12-08
R
R 3.2.0 released · 2015-04-16

Package metadata

Total releases: 9
License: GPL-3 | file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 687 KB / 2 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BacArena")

Format

Bauer, E., & Zimmermann, J. (n.d.). BacArena: Modeling Framework for Cellular Communities in their Environments (Version 1.8.2) [Computer software]. Retrieved August 13, 2026, from https://CRAN.R-project.org/package=BacArena

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 BacArena version 1.8.2 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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