Version control for scientific workflows workshop at Division of Insurance Medicine, Karolinska Institutet

This repository is licensed under the Creative Commons Attribution 4.0 International license. Please see the license file.

This project makes use of the rproj-template Github template created by Daniel Morillo and licensed under the Creative Commons Attribution 4.0 International license.

Dataset nwtco from the R survival package v3.5-5, originally from:

Adapted from the nwtco help page of the R survival package v3.5-5.

Origin of all the image files attributed in the corresponding slides in output/slide-deck.qmd.

• Install R version 4.3.0: In Windows, using the binary installer is recommended.

• Rstudio Desktop: Although not strictly necessary, it is recommended to install the Rstudio IDE; for strict reproducibility, use build 2023.03.1+446 for Windows 10/11.

• Quarto publishing system: An additional component used by Rstudio to generate and publish literate computing outputs. For strict reproducibility please use build 1.3.353; On Windows, use the 64-bit installer.

• Git client: Install the Git client in order to be able to clone locally the project repository. On Windows, use the 64-bit Windows installer.

This project is hosted as a GitHub repository. It can be cloned as a local Git repository following these instructions (steps 2 through 7). Note that this will create a local copy of (‘clone’) the GitHub repository as an Rstudio project in the folder specified. The URL that must be entered into the Repository URL text box is:

https://github.com/DaniMori/vc-workshop.git

After cloning the repository, the Rstudio project will open automatically in the Rstudio IDE. If it doesn’t, or you want to return later to the project in Rstudio, you can do so by double clicking on the file rstudio_project.Rproj that has been created in the project folder when cloning the repository.

NOTE: It is common practice to avoid using and versioning .Rprofile files. However, this project uses package renv to create a reproducible environment, which needs the .Rprofile file that lives in the root directory of the project. Please DO NOT delete or edit this file; it will install and activate the renv package and make it ready for restoring the environment.

The reproducible environment created by renv must be restored to install all the packages this project needs to be built properly. In order to this, you will need to install package renv first:

install.packages("renv")

Once it is successfully installed, use the “renv” -> “Restore library…” button in Rstudio’s “Packages” tab to restore the environment. Alternatively, you can type in the console:

renv::restore()

The file structure of this repository is as follows:

vc-workshop
|
|--- dat          (To store input datasets; must NEVER be checked-in to Github)
|
|--- doc          (To store important documentation of the project)
|    |
|    |--- minutes (To store meeting minutes)
|
|--- notebooks    (Notebooks to explore data and test processes live here)
|
|--- output       (Processing outputs; files must be individually "checked-in"
|                 when necessary)
|
|--- R            (R functions created for this project live here)
|
|--- renv         (System library necesssary for `renv` to work. DON'T TOUCH)
|
|--- src          (Source scripts that implement the main processes)
|
|--- www          (Project assets, e.g., images, bibliography files, etc.)

Use the folders as indicated to store the different files and generate the outputs of the processes.