R Observatory: Metrics for FSK2R version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

FSK2R

0.2.0Package record

An Interface Between the 'FSKX' Standard and 'R'

0packages depend

3.3Kdownloads / year

20.1%test coverage

13/13flavors OK

Overview

About

Maintained by Alberto GarreCRAN page ↗

Functions for importing, creating, editing and exporting 'FSK' files https://foodrisklabs.bfr.bund.de/fskx-food-safety-knowledge-exchange-format/ using the 'R' programming environment. Furthermore, it enables users to run simulations contained in the 'FSK' files and visualize the results.

Changes in 0.2.0

Major New Features

**Dynamic Script Detection**: import_fsk() now dynamically detects model and visualization script filenames from metadata.rdf instead of hardcoding "model.r" and "visualization.r". This enables support for FSKX files with non-standard script names.
**Complete Temporary Folder Execution**: run_simulation() now executes models in their unpacked temporary directory, solving file loading issues for models that depend on CSV, Excel, and other data files (e.g., QMRA models).
**Workspace Copying Functionality**: Added optional workspace copying with intelligent directory naming:
New parameters: copy_workspace and workspace_mode in run_simulation() and run_all_simulations()
Creates directories named: fsk_workspace_[model_name]_[simulation_name]/
Three copy modes: "all" (complete workspace), "generated" (new files only), "modified" (changed files only)
**Model Chaining Support**: Added inject_to_global parameter enabling seamless model chaining workflows:
New parameter: inject_to_global in run_simulation() and run_all_simulations()
When TRUE, simulation variables are injected directly into the user's global environment
Enables users to access simulation results directly without complex variable extraction
Facilitates model chaining: use results from Model A as inputs to Model B

Show all changes in 0.2.0Hide the rest of the changes in 0.2.0

Maintains backward compatibility (FALSE by default)

Bug Fixes and Improvements

Cross-platform line endings: All textual files exported into FSKX archives now use LF line endings on every OS (including Windows). This applies to:
README.txt, metaData.json, packages.json, manifest.xml, metadata.rdf
model and visualization scripts
workspace.r
sim.sedml and model.sbml
Other files: R scripts included via other_files are normalized to LF on export; other file types are copied unchanged.
Encoding: All textual exports are written as UTF-8 (no BOM).
Internal: Introduced write_text_lf() helper to normalize line endings and write via binary connections; XML writers now use binary connections; zipping uses utils::zip to preserve directory structure.
**File Loading Fix**: Models that load external files (CSV, Excel, etc.) now work correctly by executing in the proper temporary directory with automatic working directory restoration.
**Enhanced Return Values**: run_simulation() now returns all user-created variables with preserved data types (scalars, vectors, data frames, lists, matrices) .
**Improved Visualization Handling**: Enhanced automatic display of ggplot objects created by visualization scripts.
**Package Build Optimization**: Added comprehensive .Rbuildignore file to exclude development files (test projects, debug scripts, session artifacts) from package builds.
**Robust Error Handling**: Added proper error handling and cleanup for working directory management and workspace copying operations.
**Updated Documentation**: Enhanced function documentation to reflect new parameters and capabilities.

Breaking Changes

None - all changes are backward compatible with existing workflows.

From NEWS.md in the release

Install

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

install.packages("FSK2R", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-fsk2r

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-FSK2R

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.0

READMEYes · 113 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.2.0Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 61
Examples that run: 0%12 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 32%
Documented parameters: 100%
Return-value docs: 74%
Help pages citing references: 0%

Vignettes (1)

FSK2R: an interface between FSK-ML and R HTML

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #13,108 · ~9/day · ~278/mo

Releases R versions

Daily download trend is not available in this view yet.

33030 days

88490 days

3.3K1 year

Compare downloads with other packages →

Also on87 r2u

How downloads are counted

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing FSK2R adds 75 packages (47 with compiled code, 61 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, bslib 5.6 MB.

Depends (0)

none

Imports (14)

XML purrr dplyr tibble (>= 2.0.0)tidyr rlang readxl (>= 1.3.1)readtext xml2 jsonlite (>= 1.6.0)shinytoolsutilsR.utils

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (5)

Alberto Garre

Author, Maintainer since 0.1.1 (2020)

Pablo S. Fernandez

Author

Matthias Filter

Author

Thomas Schueler

Author · added in 0.2.0

Miguel de Alba Aparicio

Author

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.2.0Latest
record
2025-10-10 · current release · diff ↗ ·
added 21 exports
FSKAuthor, FSKCreator, FSKDataBackground, FSKGeneralInformation, FSKMetadata, FSKModelCategory, FSKModelMath, FSKParameter, FSKReference, FSKScope, clean_empty_values, read_R_model, read_fsk_json_metadata, read_fsk_manifest, read_fsk_model, read_fsk_packages, read_fsk_rdf_metadata, read_fsk_readme, read_fsk_sim, read_other_files, read_visualization
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
0.1.3
record
2022-02-25 · diff ↗ ·
removed 2 exports
download_metadata_schema, read_fsk_metadata
R
R 4.1.0 released · 2021-05-18
0.1.2
record
2020-10-06 · diff ↗
0.1.1
record
2020-05-13
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-05-13
Total releases: 4 / 6 yrs
License: GPL-3 OSI
Download size: 1.2 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("FSK2R")

The package provides a citation file, so citation() returns the authors' own entry.

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 FSK2R version 0.2.0 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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