The ospsuite.reportingframework , which is based on the {esqlabsR package}, is a robust tool designed to systematically define simulation scenarios, their inputs and outputs, and standardize data import and matching processes. These functionalities allow for easy and automatable model execution and plot generation, ultimately facilitating the generation of customizable reports for OSP physiologically-based pharmacokinetic (PBPK) models. As a result, this framework significantly enhances reporting efficiency, enabling researchers to create clear, tailored reports that effectively communicate complex modeling results.
Pharmacology ecosystem:
This is the beta release of the ospsuite.reportingframework. We welcome your feedback as we refine its features and performance.
OSPSuite.ReportingFramework
Framework to create R workflows which configures simulations, runs them plots results and creates a report
Installation
The ospsuite.reportingframework package is compatible with version 2.10 and higher of R. Please follow the installation instructions below:
From GitHub 
You can install the development version of ospsuite.reportingframework from GitHub with:
# install.packages("remotes")
remotes::install_github("Open-Systems-Pharmacology/OSPSuite.ReportingFramework")Required packages
ospsuite.reportingframework requires following packages to be installed:
- From the Open Systems Pharmacology ecosystem:
| Package | Version | Installation Instructions |
|---|---|---|
{ospsuite.plots} |
latest | Download and install package bundle here 📦 |
{ospsuite} |
latest | Download and install package bundle here 📦 Instructions are available here 📖 ⚠ Visit {ospsuite} Documentation to install its dependencies ⚠ |
{ospsuite.utils} |
latest | Download and install package bundle here 📦 |
- From the esqLABS ecosystem:
| Package | Version | Installation Instructions |
|---|---|---|
{esqlabsR} |
latest | Download and install package bundle here 📦 |
Once the bundles downloaded, you can install the packages by using the code below:
# bundlePath <- path/to/osp/bundles
install.packages(file.path(bundlePath,"ospsuite.plots.zip"), repos = NULL)
install.packages(file.path(bundlePath,"ospsuite.zip"), repos = NULL)
install.packages(file.path(bundlePath,"ospsuite.utils.zip"), repos = NULL)
install.packages(file.path(bundlePath,"esqlabsR.zip"), repos = NULL)- Required packages from CRAN: > Some of these packages may already be installed as dependencies of the Open Systems Pharmacology ecosystem
- Optional packages from CRAN
To install these packages, use the code below:
# Required packages
install.packages("data.table")
install.packages("checkmate")
install.packages("knitr")
install.packages("rmarkdown")
install.packages("ggplot2")
install.packages("tidyr")
install.packages("dplyr")
install.packages("openxlsx")
install.packages("jsonlite")
# Optional packages
install.packages("rstudioapi")
install.packages("cowplot")MS-Word reports
It is possible to convert markdown reports to MS-Word (.docx format) from the ospsuite.reportingframework package. This conversion requires the installation of an additional software: Pandoc.
Code of conduct
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.
Contribution
We encourage contribution to the Open Systems Pharmacology community. Before getting started please read the contribution guidelines. If you are contributing code, please be familiar with the coding standards.
License
OSPSuite.ReportingFramework Library is released under the GPLv2 License.
All trademarks within this document belong to their legitimate owners.