The ospsuite-R package provides the functionality of loading, manipulating, and simulating the simulations created in the Open Systems Pharmacology Software tools PK-Sim and MoBi.
If you are reading this on GitHub README, please refer to the online documentation for more details on the package.
In particular, we would recommend that you read the articles in the following order:
- Get Started
- Loading a simulation and accessing entities
- Changing parameter and molecule start values
- Running a simulation
- Efficient calculations
- Creating individuals
- Population simulations
- PK Analysis
- Sensitivity analysis
- Table parameters
- Dimensions and Units
- Working with data sets and import from excel
- Working with
DataCombinedclass - Visualizations with
DataCombined
The ospsuite package is compatible with R version 4.x.x and can be used on Windows and Linux (Ubuntu) operating systems.
ospsuite is not available on CRAN and also depends on packages from
the OSP ecosystem that are not available on CRAN. Please follow the
instructions below to install the packages and all required
dependencies.
The package requires additional software installations:
- Latest Microsoft Visual C++ Redistributable for Visual Studio 2015, 2017, 2019 and 2022 available here
- .NET 8 runtime available here.
NB: These pre-requisites are already installed if the OSP Suite was installed before.
The latest released version of the package can be installed from GitHub
using the {pak} package. The code below will download and install all
the required dependencies.
install.packages("pak")
pak::pak("Open-Systems-Pharmacology/OSPSuite-R@*release")Get the latest development version with:
install.packages("pak")
pak::pak("Open-Systems-Pharmacology/OSPSuite-R")It is also possible to install manually from archive pre-built archive files provided with the release.
When installing from such files, the CRAN dependencies need to be installed manually first.
# Install dependencies (e.g. R6) which are on CRAN
install.packages("data.table")
install.packages("dplyr")
install.packages("ggplot2")
install.packages("ggtext")
install.packages("jsonlite")
install.packages("lifecycle")
install.packages("openxlsx")
install.packages("patchwork")
install.packages("purrr")
install.packages("R6")
install.packages("readr")
install.packages("rlang")
install.packages("stringr")
install.packages("tidyr")
install.packages("xml2")Each of the pre-built released packages are available as a a binary
*.zip. OSPSuite-R binary archive can be downloaded from
here.
The other non-CRAN dependencies needed for OSPSuite-R also have to be
downloaded and manually installed:
If you use RStudio IDE, you can use the
Install option in the Packages pane and select the option Install
from -> Package Archive File to install a package from binary *.zip
files.
NB: The CRAN dependencies of rSharp, ospuite.utils and tlf were already installed during the previous step.
# Install `{rSharp}` from local file
# (`pathTo_rSharp.zip` here should be replaced with the actual path to the `.zip` file)
install.packages(pathTo_rSharp.zip, repos = NULL)
# Install `{ospsuite.utils}` from local file
# (`pathTo_ospsuite.utils.zip` here should be replaced with the actual path to the `.zip` file)
install.packages(pathTo_ospsuite.utils.zip, repos = NULL)
# Install `{tlf}` from local file
# (`pathTo_tlf.zip` here should be replaced with the actual path to the `.zip` file)
install.packages(pathTo_tlf.zip, repos = NULL)
# Install `{ospsuite}` from local file
# (`pathToOSPSuite.zip` here should be replaced with the actual path to the `.zip` file)
install.packages(pathToOSPSuite.zip, repos = NULL)The ospsuite package has been tested under Linux distribution Ubuntu 22.04. Installation under Linux requires several prerequisites, the detailed instructions can be found in the Wiki:
For other Linux distributions Docker containers can be used (Docker container based on Ubuntu 22 is available under https://github.com/Open-Systems-Pharmacology/OSPSuite-R/releases)
You can clone the GIT repository and build the package from source.
The {ospsuite} package requires some shared libraries to get access to
PK-Sim functionality. To get the latest libraries(.dll on Windows or
.so on Linux), run the script file `update_core_files.R’ provided
with this package.
– On Windows, set
Settings > Language > Administrative language settings > Current language for non-Unicode programs
to English (United States) and reboot. – On Linux, set the environment
variable LC_ALL before starting R:
export LC_ALL=en_US.UTF-8
The ospsuite package uses the features implemented in PK-Sim and MoBi by
creating .NET objects (e.g. a simulation) and using them from R. These
objects cannot be saved as part of the workspace and reloaded on next
start. Upon restoring the workspace, the objects will be NULL and
cannot be re-used.
Everyone interacting in the Open Systems Pharmacology community (codebases, issue trackers, chat rooms, mailing lists etc.) is expected to follow the Open Systems Pharmacology code of conduct.
We encourage contribution to the Open Systems Pharmacology community. Before getting started please read the contribution guidelines. If you are contributing to the codebase, please be familiar with the R coding standards as well as the collaboration guide.
OSPSuite-R is released under the GPLv2 License.
All trademarks within this document belong to their legitimate owners.