ReportGelaDURT

This project builds a bookdown HTML document that contains the figures for the paper Gela (2022) - Effects of BCG vaccination on donor unrestricted T cells in two prospective cohort studies.

It relies on data processed in DataTidyGelaDURT.

Reproducing analyses

Using VS Code and Docker

Using Linux (WSL or "bare"), with git, Docker and VS Code with the Remote Extensions Pack installed and set up, do the following:

1. Clone this repository using git clone /~https://github.com/ReportGelaDURT.

2. Create the environment variable DirProjectGelaDURT, and set this equal to the directory to which you would save all non-code materials related to this project. If you are only running this part of the analysis (i.e. not also running DataTidyGelaDURT), then all this does is set where the figures are saved to.

To make this permanent, you could add this to the ~/.bashrc file as follows: export DirProjectGelaDURT=<path_to_project.

For example: export DirProjectGelaDURT=~/projects/ProjectGelaDRT.

• Notes:
  • The base name of the path (e.g. ProjectGelaDURT in ~/projects/ProjectGelaDURT) does not need to be ProjectGelaDURT but can be anything (e.g. "xyz").
  • This directory need not exist before starting the container.

3. Open the directory ReportGelaDURT as a workspace in VS Code.

4. Click Control Panel >> Remote-Containers: Rebuild and reopen in container. Wait for container to build.

Note that the devcontainer.json file assumes that the logged-in user has user ID 1000.

5. Start R and run renv::restore(). Restart R.

6. Run bookdown::render_book().

The book will be built to ./_book, and the figures will be saved to $ProjectGelaDURT/Output/figures/manuscript.

Without Docker

Ensure that you have R version 4.1.3 installed.

1. Clone this repository using git clone /~https://github.com/ReportGelaDURT.

2. Open R (version 4.1.3) and run renv::restore(). Restart R.

Note that if you are using RStudio and have installed R version 4.1.3, you can open R4.1.3 in RStudio by clicking Tools >> Global Options >> General >> Change... (where Change... is next to a path underneath R version:), choosing an option ending in R-4.1.3, clicking OK, clicking OK again and restarting RStudio (not just R!).

3. Run bookdown::render_book().

The book will be built to ./_book.