R Observatory: Metrics for atlantistools version 0.4.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2019-03-22. Its history is shown below.

Reason: check problems were not corrected in time

Details below reflect version 0.4.3, its last release before removal.

atlantistools

0.4.3

Process and Visualise Output from Atlantis Models

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Alexander Keth3 releasesCRAN page ↗GitHub ↗

Atlantis is an end-to-end marine ecosystem modelling framework. It was originally developed in Australia by E.A. Fulton, A.D.M. Smith and D.C. Smith (2007) and has since been adopted in many marine ecosystems around the world (http://atlantis.cmar.csiro.au). The output of an Atlantis simulation is stored in various file formats like .netcdf and .txt and different output structures are used for the output variables like e.g. productivity or biomass. This package is used to convert the different output types to a unified format according to the "tidy-data" approach by H. Wickham (2014) DOI:10.18637/jss.v059.i10. Additionally, ecological metrics like for example spatial overlap of predator and prey or consumption can be calculated and visualised with this package. Due to the unified data structure it is very easy to share model output with each other and perform model comparisons.

Install

R (source archive)pak (dev)

url <- "https://cran.r-project.org/src/contrib/Archive/atlantistools/atlantistools_0.4.3.tar.gz"
pkgFile <- "atlantistools_0.4.3.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 (0.4.3) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("alketh/atlantistools")

Development version from alketh/atlantistools. Installs pak first if it is not already available.

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.29

not tracked

Coverage

99%

Documentation · exports

16

Dependencies · direct

Documentation

READMEYes · 237 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 82%
Documented parameters: 99%
Return-value docs: 94%
References docs: 0%

Downloads

atlantistools Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.2.3

Imports (16)

dplyr magrittr RNetCDF stringr lazyeval tidyr ggplot2 proj4 gridExtra scales circlize RColorBrewer purrr rvest xml2 tibble

LinkingTo (0)

none

Suggests (5)

testthat knitr rmarkdown vdiffr rfishbase

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Alexander Keth

Author, Maintainer

Authors (1)

Alexander Keth

Author, Maintainer

Package Timeline

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

R
R 3.6.0 released · 2019-04-26
archivedRemoved from CRAN
2019-03-22
check problems were not corrected in time
R
R 3.5.0 released · 2018-04-23
0.4.3
2017-08-16 · diff ↗
0.4.2
2017-05-18 · diff ↗
0.4.1
2017-05-09
R
R 3.4.0 released · 2017-04-21

Package metadata

Total releases: 3
License: GPL-3 OSI
Minimum R: ≥ 3.2.3
Bundled data: 568 KB / 17 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("atlantistools")

Format

Keth, A. (n.d.). atlantistools: Process and Visualise Output from Atlantis Models (Version 0.4.3) [Computer software]. Retrieved August 15, 2026, from https://CRAN.R-project.org/package=atlantistools

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 atlantistools version 0.4.3 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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