Create kriged apportioned abundance documentation #216

brandynlucca · 2024-03-27T16:56:03Z

This includes a draft of the apportion_abundance document that covers how kriged biomass is reallocated into estimates of abundance, which is not to be confused with apportioning abundance estimates that were, themselves, kriged. A variety of images have been included that can be swapped out for equations.

leewujung · 2024-03-27T19:20:16Z

There's some weird missing ")" in the functions that is probably not used -- see https://github.com/OSOceanAcoustics/echopop/actions/runs/8455613434/job/23163503465?pr=216

I think it'll be good to resolve that before we merge this PR so that the main does not get broken.

leewujung · 2024-03-27T19:32:53Z

Ok, so I think you branched out after you did the code changes, so the 2 PRs are mingled. I fixed it by removing the 2 testing_* files and fixed the missing ")" just so that this PR is clean.

docs/theory/apportion_abundance.md

leewujung · 2024-10-09T18:11:15Z

See #218 for indexing!

leewujung

I did a PR to fix the indexing problems and simplified the text in brandynlucca#6.

I also created an issue #279 to reconcile repeated materials and notation differences between the 2 apportioning pages -- I'll take that on once this one is merged.

* fix indexing and simplify description * hyperlink and text tweak * small fixes * fix heading levels, fix indexing in first section * remove unused images * fix equation rendering * fix attention * change sequence of text and note * revert eq.4-7 to write out male and female expressions * tweak back calculation section * change page name * Apply suggestions from code review Co-authored-by: Brandyn Lucca <[email protected]> --------- Co-authored-by: Brandyn Lucca <[email protected]>

leewujung · 2024-10-18T17:48:41Z

Hey @brandynlucca - Why is sphinx.ext.autodoc from this? Seems out of the blue and results into a conflict?

leewujung

I think we can merge this now. I will submit a PR to add stratum $i$ to the Jolly-Hampton section, add the citation properly, make some symbol and terminology changes, and not the mapping of each variables to the original equations.

brandynlucca · 2024-10-18T17:56:08Z

Hey @brandynlucca - Why is sphinx.ext.autodoc from this? Seems out of the blue and results into a conflict?

To clarify: are you asking why it was added to _config.yml? If so, it was previously commented out in this PR and when trying to build the jupyter-book I ran into an error that informed me that the autodoc extension was missing. I think it may have been previously commented out to try and debug possible extension issues; however, I'm not sure why it is reporting a conflict here.

leewujung · 2024-10-18T18:26:18Z

Apparently I was missing a word in my comment, but I also misread the code, there was a "#" in front of the line, so there was no effect.

Could you pull in main and resolve the conflicts?

Also, on a second thought, could you remove the Jolly-Hampton stuff from this PR and submit it as a separate PR? I am likely not able to work on it until after next Wednesday because of a short-notice presentation that day, but I think we should release without that part of docs.

…ment_docs

brandynlucca · 2024-10-18T18:40:22Z

Also, on a second thought, could you remove the Jolly-Hampton stuff from this PR and submit it as a separate PR? I am likely not able to work on it until after next Wednesday because of a short-notice presentation that day, but I think we should release without that part of docs.

Done! This corresponds to #281 now.

leewujung · 2024-10-18T18:44:51Z

Remember to use "squash and merge" next time!