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Reorganize and streamline examples #656

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merged 23 commits into from
Mar 15, 2022
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@tsalo tsalo commented Mar 10, 2022

Closes None. I just thought I'd clean up the examples a bit.

Changes proposed in this pull request:

  • Generally improve documentation and examples.
  • Fix a bug in how the aggressive mask interacts with Correctors for IBMA Estimators. The NaNs from the aggressive mask were being included in the masked data, which resulted in the corrected p-values all being NaNs.
    • Based on the IBMA+MCC example, I don't think the generic correction methods are working as expected for two-sided tests. That said, I feel like that should be fixed in a separate PR. This one already sprawled more than is acceptable.
  • Fix the vfwe_only option in CBMAEstimator.correct_fwe_montecarlo.
    • I guess I had never actually tested that option before now.

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codecov bot commented Mar 10, 2022

Codecov Report

Merging #656 (3af7f35) into main (455afed) will increase coverage by 0.03%.
The diff coverage is 95.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##             main     #656      +/-   ##
==========================================
+ Coverage   85.25%   85.29%   +0.03%     
==========================================
  Files          40       40              
  Lines        4530     4542      +12     
==========================================
+ Hits         3862     3874      +12     
  Misses        668      668              
Impacted Files Coverage Δ
nimare/meta/utils.py 47.12% <80.00%> (+0.88%) ⬆️
nimare/correct.py 93.06% <100.00%> (+0.59%) ⬆️
nimare/meta/cbma/base.py 95.31% <100.00%> (+0.37%) ⬆️

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@tsalo tsalo added the documentation Improving documentation for the project label Mar 11, 2022
# -----------------------------------------------------------------------------
from nimare.meta.cbma.ale import ALESubtraction

meta = ALESubtraction(n_iters=10, n_cores=1)
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n_cores needs to be 1 because sphinx-gallery can't handle parallelization yet.

@tsalo tsalo merged commit bdc0363 into neurostuff:main Mar 15, 2022
@tsalo tsalo deleted the streamline-examples branch March 15, 2022 16:35
tsalo added a commit to tsalo/NiMARE that referenced this pull request Mar 21, 2022
tsalo added a commit to tsalo/NiMARE that referenced this pull request Mar 21, 2022
Also should have been part of neurostuff#656.
tsalo added a commit that referenced this pull request Mar 21, 2022
* Standardize example header lengths.

* Missed one.

* Replace manual conn definition with function.

* Convert _calculate_cluster_measures into a function.

* Improve spacing and docstring.

* Remove unused parameter definition.

* Update MKDAChi2 as well.

* Add a versionchanged directive for the vfwe_only fix.

This should have been part of #656.

* Test vfwe_only.

Also should have been part of #656.
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