OSPSuite.ReportingEngine

The ospsuite.reportingengine package provides a framework in R to design and create reports evaluating PBPK models developed in the Open Systems Pharmacology ecosystem.

Installation

The ospsuite.reportingengine package is compatible with version 4.x.x of R. Please follow the installation instructions below:

From Github

You can install the development version of ospsuite.reportingengine from GitHub with:

# install.packages("remotes")
remotes::install_github("Open-Systems-Pharmacology/OSPSuite.ReportingEngine")

Using the package bundle 📦

You can install the ospsuite.reportingengine package by downloading and installing its zip or tar.gz bundle.

• The package bundle for the release version is available here 📦.
• The package bundle for the development version is available here 📦.
• The package bundles for specific versions of ospsuite.reportingengine are available here 📦.

Then, to install manually, replace the path/to/ospsuite.reportingengine.zip by your actual local path to the .zip or tar.gz file in the code below:

install.packages(path/to/ospsuite.reportingengine.zip, repos = NULL)

To install the package along with its tests, the .tar.gz bundle is required. Then, use the install-tests option as illustrated below.

install.packages(path/to/ospsuite.reportingengine.tar.gz, repos = NULL, INSTALL_opts = "--install-tests")

Required packages

ospsuite.reportingengine requires following packages to be installed:

• From the Open Systems Pharmacology ecosystem:

Package	Version	Installation Instructions
{ospsuite.utils}	$\geq$ 1.5	Download and install package bundle here 📦
{tlf}	$\geq$ 1.5	Download and install package bundle here 📦 ⚠ Visit {tlf} Documentation to install its dependencies ⚠
{rSharp}	$\geq$ 1.0	Instructions are available here 📖
{ospsuite}	$\geq$ 12.1	Download and install package bundle here 📦 Instructions are available here 📖 ⚠ Visit {ospsuite} Documentation to install its dependencies ⚠

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.utils.zip"), repos = NULL)
install.packages(file.path(bundlePath,"tlf.zip"), repos = NULL)
install.packages(file.path(bundlePath,"rSharp.zip"), repos = NULL)
install.packages(file.path(bundlePath,"ospsuite.zip"), repos = NULL)

• Required packages from CRAN: > Some of these packages may already be installed as dependencies of the Open Systems Pharmacology ecosystem
  • {dplyr}
  • {ggplot2} >= 3.3.0
  • {jsonlite}
  • {R6}
  • {tidyr}
• Optional packages from CRAN
  • {crayon}
  • {knitr}
  • {parallel}
  • {readxl}
  • {Rmpi}
  • {styler}

To install these packages, use the code below:

# Required packages
install.packages("dplyr")
install.packages("ggplot2")
install.packages("jsonlite")
install.packages("R6")
install.packages("tidyr")
# Optional packages
install.packages("crayon")
install.packages("knitr")
install.packages("parallel")
install.packages("readxl")
install.packages("Rmpi")
install.packages("styler")

MS-Word reports

It is possible to convert markdown reports to MS-Word (.docx format) from the ospsuite.reportingengine package. This conversion requires the installation of an additional software: Pandoc.

A dedicated article details how to create MS-Word reports using the ospsuite.reportingengine package: here

[OPTIONAL] Pandoc Installation

Install Pandoc (required for generation of reports in MS-Word format) by downloading one of the following files:

• Pandoc Installer (Windows)

• Pandoc Installer (Linux)

[OPTIONAL] Use SVG figures

In order to use SVG figures in MS-Word report, you need to install rsvg-convert (required by Pandoc for conversion of images in SVG format)

• Installer (Windows)
  • ⚠ The installation folder must be added to the system path. ⚠
• For Linux, librsvg package must be installed (package name depends on distribution, e.g. librsvg2-bin for Ubuntu).

Documentation 📖

A detailed account of existing functions and articles on how to use them can be found on the dedicated website.

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.ReportingEngine Library is released under the GPLv2 License.

All trademarks within this document belong to their legitimate owners.