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MCSimMod

MCSimMod: An R Package for Working with Ordinary Differential Equation Models Encoded in the MCSim Model Specification Language - Published in JOSS (2025)

https://github.com/usepa/mcsimmod

Science Score: 93.0%

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    CITATION.cff file
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    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 4 DOI reference(s) in README and JOSS metadata
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    Academic publication links
    Links to: joss.theoj.org
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    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

ode ode-model pbpk pbpk-modeling r
Last synced: 6 months ago · JSON representation

Repository

MCSim Models in R

Basic Info
  • Host: GitHub
  • Owner: USEPA
  • License: gpl-3.0
  • Language: C
  • Default Branch: main
  • Homepage:
  • Size: 1.6 MB
Statistics
  • Stars: 8
  • Watchers: 5
  • Forks: 0
  • Open Issues: 1
  • Releases: 4
Topics
ode ode-model pbpk pbpk-modeling r
Created almost 2 years ago · Last pushed 6 months ago
Metadata Files
Readme License

README.md

MCSimMod: An R Package for Working with MCSim Models

Documentation DOI CRAN Version CRAN Downloads GitHub Release

MCSimMod is an R package that facilitates ordinary differential equation (ODE) modeling. Many physical and biological phenomena can be described using mathematical models based on ODEs, and several example ODE models are described in "vignettes" included with the MCSimMod package. MCSimMod allows one to perform simulations for ODE models that are encoded in the GNU MCSim model specification language using ODE solvers from the R package deSolve.

Documentation is available at https://usepa.github.io/MCSimMod.

To work with MCSimMod, the package deSolve must be installed. R install.packages("deSolve")

Installation

As a prerequisite for installation on a Windows operating system, be sure to install RTools. RTools includes utilities that compile C source code for use in R. Installation of RTools is not required when using MCSimMod on a Unix operating system.

To install the latest stable version of MCSimMod from CRAN, use the command:

R install.packages("MCSimMod")

For the latest development version, install from GitHub using devtools::install_github(). If the package devtools has not already been installed, use install.packages("devtools"). Then, install MCSimMod using the following command: R devtools::install_github("https://github.com/USEPA/MCSimMod.git", build_vignettes = TRUE)

Alternatively, one can install MCSimMod from a compressed "tarball" file. For example, if you have a compressed tarball file named MCSimMod.tar.gz, use the following command:

R install.packages("MCSimMod.tar.gz", repos = NULL, type = "source")

Getting Started

To learn about the MCSimMod package and how to use it, check out the vignettes. R browseVignettes(package = "MCSimMod")

Contact

To report an issue with MCSimMod, please use the issue tracker.

License

GNU General Public License 3.0

Developer Installation

If you wish to contribute to development of MCSimMod, first clone the MCSimMod repository. Then, start an R session and set the current working directory to a directory within the repository. To document, build, install, and test the package, use the following commands. R devtools::document() devtools::build() devtools::install() devtools::test() covr::report(file = "coverage_html/index.html")

You can also issue these commands from a Windows or Unix command line terminal as follows. bash R -e "devtools::document()" R -e "devtools::build()" R -e "devtools::install()" R -e "devtools::test()" R -e "covr::report(file = 'coverage_html/index.html')"

Code Formatting

To maintain a consistent format for all MCSimMod source code, we use the styler package to format R code. Note that we use a specific version of the package. ```R

Install version 1.10.3 of the styler package.

install.packages("styler", version = "1.10.3")

Apply styler format conventions to all files in the package.

styler::style_pkg(".") ```

A check is added in continuous integration to ensure that the code conforms to formatting conventions. If it does not, the style check will fail.

Disclaimer

The United States Environmental Protection Agency (EPA) GitHub project code is provided on an "as is" basis and the user assumes responsibility for its use. EPA has relinquished control of the information and no longer has responsibility to protect the integrity, confidentiality, or availability of the information. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by EPA. The EPA seal and logo shall not be used in any manner to imply endorsement of any commercial product or activity by EPA or the United States Government.

Owner

  • Name: U.S. Environmental Protection Agency
  • Login: USEPA
  • Kind: organization
  • Location: United States of America

JOSS Publication

MCSimMod: An R Package for Working with Ordinary Differential Equation Models Encoded in the MCSim Model Specification Language
Published
August 15, 2025
DOI
Volume 10, Issue 112, Page 8492
Authors
Dustin F. Kapraun ORCID
U.S. Environmental Protection Agency, U.S.A.
Todd J. Zurlinden ORCID
U.S. Environmental Protection Agency, U.S.A.
Ryan D. Friese ORCID
Pacific Northwest National Laboratory, U.S.A.
Andrew J. Shapiro ORCID
U.S. Environmental Protection Agency, U.S.A.
Editor
Daniel S. Katz ORCID
Tags
MCSim ordinary differential equations mathematical models initial value problems
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GitHub Events

Total
  • Create event: 19
  • Release event: 2
  • Issues event: 3
  • Watch event: 9
  • Delete event: 18
  • Issue comment event: 2
  • Push event: 80
  • Pull request review event: 41
  • Pull request review comment event: 35
  • Pull request event: 30
Last Year
  • Create event: 19
  • Release event: 2
  • Issues event: 3
  • Watch event: 9
  • Delete event: 18
  • Issue comment event: 2
  • Push event: 80
  • Pull request review event: 41
  • Pull request review comment event: 35
  • Pull request event: 30

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 3
  • Total pull requests: 52
  • Average time to close issues: 17 days
  • Average time to close pull requests: 8 days
  • Total issue authors: 3
  • Total pull request authors: 4
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.38
  • Merged pull requests: 46
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 38
  • Average time to close issues: 17 days
  • Average time to close pull requests: 5 days
  • Issue authors: 3
  • Pull request authors: 4
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.18
  • Merged pull requests: 34
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • rdfriese (1)
  • dfkapraun (1)
  • shapiromatron (1)
Pull Request Authors
  • dfkapraun (24)
  • shapiromatron (18)
  • tjzurlin (6)
  • rdfriese (4)
Top Labels
Issue Labels
bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 484 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
cran.r-project.org: MCSimMod

Working with 'MCSim' Models

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 484 Last month
Rankings
Dependent packages count: 26.8%
Dependent repos count: 33.0%
Average: 48.8%
Downloads: 86.7%
Maintainers (1)
kapraun.dustin@epa.gov
Last synced: 6 months ago

Dependencies

.github/workflows/main.yml actions
  • actions/checkout v4 composite
  • actions/configure-pages v5 composite
  • actions/deploy-pages v4 composite
  • actions/upload-artifact v4 composite
  • actions/upload-pages-artifact v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
  • r-lib/actions/setup-tinytex v2 composite
DESCRIPTION cran
  • methods * depends
  • tools * depends
  • deSolve * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests