Use tidyverse packages in R exercise files

[NeuroShepherd]

We teach the use of tidyverse packages, and we probably want to reinforce that more in the Exercises for this tutorial. As such, we should update the functions used in the exercises to follow this.

See also #22 for a related discussion.

[darakhshannehal]

@NeuroShepherd Hi, I'd like to work on this issue (and related one in #22). Planning to submit a PR in the next few days.

[MalikaIhle]

@darakhshannehal thanks for your interest in contributing to our training material! Note that

1. we are currently working on contribution guidelines and putting in place processes to review contributions and provide appropriate recognition for them - we are not ready for that at this stage, and everyone is currently working at full capacity so that may take a while...

2. this tutorial is one of my oldest one (maybe even my first?) so the format is very much outdated. I'm not sure what exactly you aim on doing, but basically if we were to upgtrade this tutorial (which I wish to be done but can't find the time) we would follow this tutorial template: https://github.com/lmu-osc/tutorial-template and these guidelines: https://lmu-osc.github.io/manual/authoring_tutorials/introduction.html, that is, add code and putput in the website as code to copy and output to open from a call out box, provide hints in different collapsable boxes ect.

Feel free to submit a PR, and if interested in supporting with the above points, we could have a call!

[darakhshannehal]

@MalikaIhle I agree, the template looks great and I’d love to help!

Just a suggestion: perhaps we could begin with two foundational steps:

• Converting the .R script to .qmd
• Replacing base R with efficient tidyverse alternatives

Since .qmd already supports code chunks, it’ll be easy to layer in features like copy buttons, callouts, and collapsible hints later. Starting with these two steps would give us a clean base to build on. What do you think?

[MalikaIhle]

Hi @darakhshannehal

But if the exercices scripts (.R) are converted to qmd but we don't change the website, I'm not sure we can keep this as a public version. I think the R code chuncks needs to be integrate to the qmd pages of the website as code and output in collapsible boxes that we expect people to copy and paste in the Rstudio environment to complete the exercices. Otherwise, if they still download the whole repo (because at this stage they don't know Git) and open qmd files instead of R files (tough at this stage they don't know quarto) I'm not sure it is better than the current stage from the user's perspective. Besides, our repo will make webpages our of these new qmd files which shouldn't be stand alone webpages in fact.

Also currently the R scripts with exercices contains code for the figures that are displayed on the website, the students don't need to see those really, so if the exercices are integrated in the website they wouldn't see it, or at least only optionally. This is maybe the largest pieces of code that are using base R for plotting instead of ggplot. For the rest I'm not sure whether there would be much changes if converting to tidyverse? I would perhaps need to see it done.

Feel free to submit a PR so I have an idea of what you wanted to do or feel free to email me to schedule a call so we can have a look and decide together on what needs to be done and how to proceed.

[NeuroShepherd]

Hi @darakhshannehal, thanks for your interest in helping out! How about just a PR for transitioning to {tidyverse} packages?

In general, we're converting as many of our tutorials to the use of Quarto as possible so good instinct on trying to switch files over to .qmd, but I think this tutorial will probably have to continue to use .R files as it generally appears in our curriculum before we teach Quarto to students.

Looking forward to your contribution!