research-it-swiss-tph / stphtoolbox

Swiss TPH R toolbox for reproducible research

stphtoolbox

The Swiss TPH Toolbox (stphtoolbox) is an R package designed to facilitate reproducible research by providing custom document templates and graphic representations.

Features

• 📄 Document templates: streamline your research workflows with custom Swiss TPH templates (Word, Powerpoint).
• 📊 Graphic representation: leverage the capabilities of ggplot2 and create visually appealing graphics in accordance with the Swiss TPH branding guidelines.

About

This package was developed on a Windows 10 x64 (build 19045) operating system, with R version 4.3.2 (2023-10-31 ucrt), RStudio version 2023.09.1 Build 494 and Rtools43. For Windows users, it is recommended to install Rtools first, followed by R and RStudio in that order for a smoother experience.

Installation from GitHub

To install the stphtoolbox package on your workstation, you have two options:

Download and build locally

Download the master branch as a ZIP file and build the package locally.

Install the latest released version (preferred option)

Install the package directly from the GitHub repository using the following code:

library(devtools)
devtools::install_github("Research-IT-Swiss-TPH/stphtoolbox")

Documentation

An index of available documentation for the stphtoolbox is displayed using the help() function

help(package="stphtoolbox")

Usage example

Generate a Word report using the generate_word_report function:

# Load the stphtoolbox package
library(stphtoolbox)
# Generate a Word report
stphtoolbox::generate_word_report(qmd_filename  = "my_content_input.qmd",
                                  docx_filename = "my_word_report")

This will create a Word document by processing the content of your specified Quarto document "my_content_input.qmd" and save the resulting Word report as "my_word_report.docx" in your current working directory.

Package development

Bug reports and suggestions

If you encounter bugs or have suggestions for improvements, please open an issue. Your feedback is valuable and helps improving the package.

Contributing

Pull requests are welcome on the development branch. For major changes, please open an issue first to discuss what you would like to change.

stphtoolbox's Issues

Leverage Quarto (dynamic reporting) for reproducible research

Software installation and configuration

• Check up to which RStudio version Quarto is back compatible
• Check what RStudio version is available on the software centre => future update scheduled in Q1 2024
• Test Rtools / R / Rstudio installation on test server for IT before packaging for availability in the software centre

R package

Develop a R package that contains data visualisations aligned with Swiss TPH's graphical chart.
For instance, see HTML visualisation below

• Create R package on GitHub
  Package available at the following link
• Create initial DOCX template inspired from the Swiss TPH graphical chart link
• Create R function to apply the Swiss TPH template to any Quarto document link
• Create minimal example in README file
• Create simple visualisation functions (based on ggplot2)
• Add a minimal example retrieving and displaying data from ODK and from REDCap
• Explore adding templates from journals (supported journals are listed here)