### Workshop on:
### **Reproducible workflows using Git/GitHub and RStudio**
This Wiki contains all the necessary information for this workshop. We will follow the step-by-step guide originally created by Mike Croucher, and then adapted by Malika Ihle. This guide is available at:
https://malikaihle.github.io/Introduction-RStudio-Git-GitHub/
Please, strickly follow the steps described in that wonderful guide.
For a simple example on how to organize and prepare repository, check out the repository that we have created for this workshop [here](https://github.com/ASanchez-Tojar/open_science_course).
If you finish the first tutorial above, feel free to play around with the following tutorial on how to collaborate using GitHub: https://malikaihle.github.io/Collaborative-RStudio-GitHub/
### Solving issues
If you encounter issues installing *homebrew* and *Git* on Mac, this two videos should help ([video 1](https://www.youtube.com/watch?v=c-1tOojFDFM), [video 2](https://www.youtube.com/watch?v=hMEyBtsuAJE&t=199s)).
Beawere that RStudio is currently messing up the home directory of the SSH key so there might be an error during your first push, including the warning:
*Warning for Windows OS with RStudio > 2022.12.0 If you get an error saying you do not have a SSH key in the appropriate location, this is due to a known bug in the RStudio / Git bash interaction which we expect to be eventually resolved with updates. A temporary solution is to open the Windows Power Shell instead of Git Bash as terminal within RStudio: for this, go to RStudio -> Tools -> Global Options -> Terminal -> New terminals open with -> choose Windows Power Shell -> Click Apply -> close the panel -> Complete the steps above (i.e. paste or type the commands presented by your new GitHub repo) -> change back the default terminal within RStudio to Git Bash.*
If you encounter **additional issues**, please check [Malika's cheet sheet](https://osf.io/5drzc) and see if the solution to your problem is there.
### Acknowledgements
Last, but not least, as a little thank you to Malika for creating all this material and sharing it with us, **go to Malika's repository and give it a STAR**: https://github.com/MalikaIhle/Introduction-RStudio-Git-GitHub (click on the start located in the upper-right hand-side of that page).
### Additional resources
1. Article: [Low availability of code in ecology: A call for urgent action](https://doi.org/10.1371/journal.pbio.3000763)
2. Article: [Implementing code review in the scientific workflow: Insights from ecology and evolutionary biology](https://doi.org/10.1111/jeb.14230)
3. Book chapter: [Computational Reproduciblity]( https://lakens.github.io/statistical_inferences/14-computationalreproducibility.html)
4. For information on how to choose a license visit: https://choosealicense.com/
5. https://happygitwithr.com/
6. https://help.github.com/
7. To provide a DOI to your GitHub repository, something you would normally do as the last stage before publication, simply do a Google search for: *conecting github repositories with zenodo*. There are plenty of guides out there. Make sure to add a DOI to your repository rather than sharing the GitHub link to the repository because the repository is fluid and can change over time (e.g. if you find and fix errors after publication), whereas the version provided with a DOI (via Zenodo) is a time-stamped version.
