Look into developing a research compendium

[MarylouStaman-NOAA]

• rrtools: Tools for Writing Reproducible Research in R (https://github.com/benmarwick/rrtools)
• https://frbcesab.github.io/rcompendium/

[stefaniebutland]

@MarylouStaman-NOAA any chance you and @chomweaverNOAA are doing this together or already connected about it? There's a thread in Champions GSpace where she asked about this. (you could search "compendium" there to find it). rrtools was top on the list and @benmarwick (author) is very a awesome human.

[chomweaverNOAA]

@stefaniebutland @MarylouStaman-NOAA , SWFSC is in the process of developing our own template. We were recently having issues with rendering but I believe we should have it sorted now. Once the template is ready to share, I will pass it along. Should be later this week

[MarylouStaman-NOAA]

Hey yes thank you @stefaniebutland, that's actually where I first heard about compendiums! And copied that link from there. I see I missed one of the linked resources in that thread though so I've added that now, and I would LOVE to see what SW has been cooking @chomweaverNOAA. Thanks both very much! -ML

[chomweaverNOAA]

Hi @MarylouStaman-NOAA , we have updated our quarto.yml and it now appears that everything on this template is working. Here is the link

In this website, you will see how to set it up on GitHub. You will also need to go into the quarto.yml once you have cloned the template and change the website URL and repo to your own. Please let me know if you end up having questions when you get to this part.

The output for this template is a website using gh-pages

[MarylouStaman-NOAA]

@chomweaverNOAA WOW this is amazing! I think this is exactly what I had in mind for my 'data management -> products' improvement project. After reading through the folder structure on the website, I think I still have questions but I'm going to poke around a little more first to get oriented.

I have a question that is probably due to me being new to all this... if I have two products that I need to (re)produce from the same data sources and that will use similar figures ('small report A' and 'big report B'), would you create two compendium repositories? I was imagining them being described on the same GitHub website (the website being a landing page for the project in general). Maybe this is better described over the phone, but I'd so appreciate any tips you have about this. Mahalo!!

[chomweaverNOAA]

Hi @MarylouStaman-NOAA , so I think a little more detail here would help. I'm also tagging @shannonrankin as she worked on compiling a very large report for a multi year project (ADRIFT) and ultimately had two repos but I think it really depends on what your projects look like and how much overlap you have. Do you need both to be websites? If so then yes two repos would be a good idea. If you're just producing reports then I believe you should be able to work from just the one repo.

I too am fairly new at all of this and am still learning a lot.

[shannonrankin]

Hi-- This compendium is intended to be simple yet flexible-- my primary concern was to get our PAM colleagues creating research compendiums and using a consistent approach. So, it is really simple (the approach is largely based off Max's approach). Other details:

• My original Adrift compendium was based on one of Eli's great templates, but I f--d it up so badly that I had to start again from scratch-- so, for a bit I did have 2 compendiums, but the old one has now been deleted.
• Eli has some great repo templates, including some that accommodate >1 output types. This is what I originally started with, but had too many problems, especially related to formatting. In the end-- I used the repo for the html and to store the manuscripts, which were done in Word. Annoying, but sometimes you just have to get the work done.

Two tools that would appear great, but I was too busy to dig into:

• In addition to rrtools: Tools for Writing Reproducible Research in R (https://github.com/benmarwick/rrtools)
• There is also NMFS Reports

Eventually I hope to look into those more-- but for now, just created a simple compendium template with a relatively low barrier to entry for our PAM folks. Guaranteed we will improve it over time (and thanks to @chomweaverNOAA for fixing the broken bit!

If you find anything else worth adopting, let us know! we have so much to learn!
shannon

[Kourtney-Burger]

This is a great conversation! Just wanted to add another example of a research compendium website. This one is a bit older, but its still a great example.

Here's Max's repo that Shannon mentioned above (https://github.com/mbjoseph/intro-research-compendia). There is also a link to the talk he gave on this topic.