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.
install.packages("deSolve")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:
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:
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:
install.packages("MCSimMod.tar.gz", repos = NULL, type = "source")To learn about the MCSimMod package and how to use it, check out the vignettes.
browseVignettes(package = "MCSimMod")To report an issue with MCSimMod, please use the issue tracker.
GNU General Public License 3.0
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.
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.
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')"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.
# 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.
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