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Add SDM-PSI Estimator #591

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Add SDM-PSI Estimator #591

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@tsalo tsalo commented Oct 27, 2021

Closes #183, but is nowhere near usable. Like so, so far from merging, and I don't have time to work on it right now.

To do:

  • Create and save correlation templates
    • I threw together templates using the nilearn VBM dataset, but we'll want something better for the real deal. I also don't even know if I got the different directions right in the ones I made. See this notebook for how I did it.
  • Function to create the lower and upper bound MA maps
  • Function to estimate most likely coefficients and tau2 from lower and upper bound MA maps with MLE
  • Function to impute study-level maps from lower and upper bound MA maps
  • Perform meta-analysis
  • Permutation procedure
  • Combine results across permutations with Rubin's rules

@tsalo tsalo added the enhancement New feature or request label Nov 6, 2021
@tsalo tsalo added the help wanted Extra attention is needed label Nov 17, 2021
@tsalo tsalo changed the title [ENH] Add SDM Estimator [ENH] Add SDM-PSI Estimator Dec 19, 2021
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codecov bot commented Jan 16, 2022

Codecov Report

Merging #591 (a24104f) into main (1957869) will decrease coverage by 6.81%.
The diff coverage is 36.49%.

❗ Current head a24104f differs from pull request most recent head ee28f73. Consider uploading reports for the commit ee28f73 to get more accurate results

@@            Coverage Diff             @@
##             main     #591      +/-   ##
==========================================
- Coverage   88.56%   81.74%   -6.82%     
==========================================
  Files          38       42       +4     
  Lines        4371     4886     +515     
==========================================
+ Hits         3871     3994     +123     
- Misses        500      892     +392     
Impacted Files Coverage Δ
nimare/transforms.py 72.01% <12.50%> (-3.35%) ⬇️
nimare/meta/cbma/sdm.py 27.70% <27.70%> (ø)
nimare/meta/__init__.py 100.00% <100.00%> (ø)
nimare/meta/cbma/__init__.py 100.00% <100.00%> (ø)
nimare/meta/cbma/tests/test_sdm.py 100.00% <100.00%> (ø)
nimare/meta/utils.py 52.80% <0.00%> (-42.96%) ⬇️
nimare/meta/kernel.py 80.44% <0.00%> (-6.96%) ⬇️
nimare/extract/extract.py 42.97% <0.00%> (-4.90%) ⬇️
nimare/stats.py 94.23% <0.00%> (-4.75%) ⬇️
nimare/meta/cbma/ale.py 94.14% <0.00%> (-2.48%) ⬇️
... and 27 more

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@jdkent jdkent mentioned this pull request Jan 26, 2023
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Implement SDM meta-analysis techniques
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