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Incorporate Estimator and Corrector descriptions into MetaResult objects #724

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merged 50 commits into from Mar 14, 2023

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@tsalo tsalo commented Jun 20, 2022

Closes #690.

Changes proposed in this pull request:

  • Add a description parameter and description_ attribute to the MetaResult class.
  • Draft descriptions for ALE, ALESubtraction, SCALE, MKDADensity, KDA, MKDAChi2, Fishers, Stouffers, DerSimonianLaird, Hedges, SampleSizeBasedLikelihood, VarianceBasedLikelihood, and WeightedLeastSquares Estimators, as well as FWECorrector and FDRCorrector Correctors.
    • If we do move forward with this, I would love to get input on the descriptions.
  • Draft descriptions for kernel transformers as well.
  • Add a bibtex_ attribute to the MetaResult class with the references from the description only.

To do/open questions:

  • Review new descriptions.
    • I would love input from anyone with expertise in any of the methods on the best way to describe each (especially the IBMA estimators).
  • Replace workflow boilerplates with the new Estimator/Corrector descriptions.
  • Do we want to create Dataset descriptions? Do we want to describe the Datasets within the Estimator descriptions?
    • I think we might want to do the latter, since Datasets' relevant elements depend on the analyses being done. However, the drawback is that there are often elements we might want to report outside of the analysis parameters (e.g., total sample sizes in MKDA Estimators, where sample size is not directly used).

@tsalo tsalo added enhancement New feature or request ibma Issues/PRs pertaining to image-based meta-analysis cbma Issues/PRs pertaining to coordinate-based meta-analysis correct Issues related to the correct module labels Jun 20, 2022
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tsalo commented Jun 21, 2022

I'm not sure how to extract relevant BibTeX references from the appropriate bib file, but I'd love to incorporate that into the MetaResults.

UPDATE: It's working now!

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codecov bot commented Jun 21, 2022

Codecov Report

Patch coverage: 91.02% and project coverage change: +0.19 🎉

Comparison is base (c30add5) 88.85% compared to head (780cab3) 89.05%.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #724      +/-   ##
==========================================
+ Coverage   88.85%   89.05%   +0.19%     
==========================================
  Files          39       39              
  Lines        4405     4603     +198     
==========================================
+ Hits         3914     4099     +185     
- Misses        491      504      +13     
Impacted Files Coverage Δ
nimare/base.py 84.52% <ø> (ø)
nimare/dataset.py 89.57% <ø> (ø)
nimare/workflows/macm.py 21.95% <0.00%> (-3.05%) ⬇️
nimare/estimator.py 84.84% <80.00%> (-1.82%) ⬇️
nimare/meta/kernel.py 94.49% <85.71%> (-1.30%) ⬇️
nimare/meta/cbma/ale.py 95.79% <90.90%> (-0.83%) ⬇️
nimare/utils.py 95.53% <95.52%> (-0.01%) ⬇️
nimare/correct.py 94.59% <100.00%> (+0.20%) ⬆️
nimare/meta/cbma/base.py 96.10% <100.00%> (+0.09%) ⬆️
nimare/meta/cbma/mkda.py 98.83% <100.00%> (+0.07%) ⬆️
... and 3 more

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@tsalo tsalo marked this pull request as draft June 21, 2022 15:12
@tsalo tsalo requested a review from angielaird October 27, 2022 17:23
@jdkent jdkent self-requested a review December 1, 2022 21:12
@tsalo tsalo added this to the 0.0.14 milestone Jan 17, 2023
@jdkent jdkent self-assigned this Jan 26, 2023
nimare/meta/cbma/ale.py Outdated Show resolved Hide resolved
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just a couple small details from me for readability, but otherwise looks good to me!

@jdkent jdkent marked this pull request as ready for review January 26, 2023 22:05
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tsalo commented Feb 2, 2023

I've made the requested changes. I realized it might take a bit of effort to append the copyright waiver to the boilerplate in the workflow functions, so I'd rather not add that in this PR.

@jdkent jdkent self-requested a review February 6, 2023 19:02
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structurally looks good, just went and fixed the conflicts and added some print statements to the example notebooks

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tsalo commented Mar 14, 2023

Thanks!

@tsalo tsalo merged commit caa5ab8 into neurostuff:main Mar 14, 2023
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jdkent commented Mar 14, 2023

great work @tsalo!

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Enhance/refactor workflow-generated boilerplates
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