Idaho Wild Fish Community Manuscript Quarto Draft

[LorenStearmanNOAA]

This is a manuscript we are currently working on out of the Pasco field station. We are exploring community and ecological dynamics of a long-term bycatch dataset to look for important lessons for our focal species.

What we've learned so far:

• Quarto - the basics of how to use it
• We have working figures, tables, in-line statistical text, and citations
• Using Quarto with input csv files and R scripts

What we are still working on

• Formatting - can we match what journals require?
• Accommodating different tech (MS Word, etc)
• Integrating Google Slides or another presentation app

[jules32]

When the time comes - journal formats!
https://quarto.org/docs/journals/formats.html

[stefaniebutland]

Some Quarto manuscripts from @alex-koiter

• https://github.com/alex-koiter/riparian-grazing-manuscript
• https://github.com/alex-koiter/spatial-variability-soil-manuscript
• https://github.com/alex-koiter/sampling-design-manuscript

[Kourtney-Burger]

Regarding your comment to integrate slides, you can use quarto docs to make presentation with a few different output formats. The revealjs option has some really cool ways to integrate code and outputs into your presentation

[alex-koiter]

I will be curious to follow your progress on this. In particular, I found formatting to match journal requirements to be tricky. Lots of journals have some pretty specific requirements for what gets submitted. I ended up doing some manual minor editing of the .doc to match the required formatting so I am curious if you find a good solution. The other issue I ran into is that many journals want a track changes version when submitting a revised version. I am not sure how to do that with Quarto, so my solution was to make changes in both the .doc and Quarto versions simultaneously, which is time consuming.

[stefaniebutland]

many journals want a track changes version when submitting a revised version. I am not sure how to do that with Quarto, so my solution was to make changes in both the .doc and Quarto versions simultaneously, which is time consuming.

@noamross & @jmlondon I know you've dealt with this kind of thing. Any tips? See Alex's comment above.

[LorenStearmanNOAA]

I just found something that might be worth a look for all of us - the trackdown package (https://claudiozandonella.github.io/trackdown/). It looks like it might be a means to have some tracking of document development, as well as possibly a way to collaboratively code. This might be what I dig into exploring over the next few days.

[stefaniebutland]

tagging @shannonrankin for 👀

[LorenStearmanNOAA]

tagging @shannonrankin for 👀

Update on this: we currently have some issues with permission uploading to Google Drive. We get a 403 forbidden error due to insufficient permissions. I'll keep exploring if we can get around this but for the time being trackdown might not be a viable method of collaborative editing for us.

[shannonrankin]

Here is another example of a research compendium w/ journal formatting for Elsevier: Beaked whale banter. I agree with @alex-koiter that it was not as straightforward to adopt the journal formatting as the instructions appear (and I have blocked those from my memory, just the scars remain).

I have had a few nightmares related to exporting quarto to Word and I would be extremely cautious on that front and test with formatting prior to committing (if that is the ultimate output needed).

If you have success with the trackdown package- please share with the mentor community-- I would be very interested!

[jmlondon]

many journals want a track changes version when submitting a revised version. I am not sure how to do that with Quarto, so my solution was to make changes in both the .doc and Quarto versions simultaneously, which is time consuming.

@noamross & @jmlondon I know you've dealt with this kind of thing. Any tips? See Alex's comment above.

I've handled this by creating a PDF from the submitted version/release and a PDF from the revised version/release then relying on Adobe Acrobat's Compare tool to create a 'track changes' version.

There's also a tool latexdiff that could be used to create a comparison/diff file from two tex files. I'd imagine there might soon (if not already) be something similar for Typst. If the journal requires a docx track changes then I'm not sure there's any solution -- other than manual.

Worth having a convo with the Assoc Editor assigned to the manuscript whether the track changes file is needed or if a git diff (e.g., comparing between releases) would be sufficient

[jmlondon]

tagging @shannonrankin for 👀

Update on this: we currently have some issues with permission uploading to Google Drive. We get a 403 forbidden error due to insufficient permissions. I'll keep exploring if we can get around this but for the time being trackdown might not be a viable method of collaborative editing for us.

There are some known limitations/issues with trackdown and the Google API for authentication and interacting with Google Drive. See https://claudiozandonella.github.io/trackdown/articles/oauth-client-configuration.html which is a possible solution IF you aren't working under our NOAA GCP umbrella.

I've worked with our AFSC IT folks to spool up a solution and the initial test worked. But, I haven't had time to revisit, test, and document.