The {ospsuite.reportingengine}
package provides a framework in R to design and create reports evaluating PBPK models developed in the Open Systems Pharmacology ecosystem.
The {ospsuite.reportingengine}
package is compatible with version 4.x.x of R. Please follow the installation instructions below:
You can install the development version of {ospsuite.reportingengine}
from GitHub with:
# install.packages("remotes")
remotes::install_github("Open-Systems-Pharmacology/OSPSuite.ReportingEngine")
You can install the {ospsuite.reportingengine}
package by downloading and installing its zip or tar.gz bundle.
{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")
{ospsuite.reportingengine}
requires following packages to be installed:
|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 âš |
|{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 âš |
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)
Some of these packages may already be installed as dependencies of the Open Systems Pharmacology ecosystem
{dplyr}
{ggplot2}
>= 3.3.0 {jsonlite}
{R6}
{tidyr}
{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")
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
Install Pandoc (required for generation of reports in MS-Word format) by downloading one of the following files:
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)
A detailed account of existing functions and articles on how to use them can be found on the dedicated website.
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 code, please be familiar with the coding standards.
OSPSuite.ReportingEngine Library is released under the GPLv2 License.
All trademarks within this document belong to their legitimate owners.
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