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Connectivity guide update #53

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merged 15 commits into from
Jun 21, 2022

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Gauravu2
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Code for Granger Causality (Pairwise), Power and cross power spectral density, and welch coherence are added

Gauravu2 added 2 commits June 16, 2022 14:39
The code can generate plots for pairwise granger causality, PSD, CPSD, and coherence
@Gauravu2 Gauravu2 added this to the Version 0.2 milestone Jun 16, 2022
@Gauravu2 Gauravu2 self-assigned this Jun 16, 2022
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codecov-commenter commented Jun 16, 2022

Codecov Report

Merging #53 (96fe93a) into update-0.1.1 (c1e4b06) will decrease coverage by 1.68%.
The diff coverage is 25.00%.

@@               Coverage Diff                @@
##           update-0.1.1      #53      +/-   ##
================================================
- Coverage         41.98%   40.30%   -1.69%     
================================================
  Files                24       26       +2     
  Lines               724      794      +70     
  Branches             84       87       +3     
================================================
+ Hits                304      320      +16     
- Misses              418      472      +54     
  Partials              2        2              
Flag Coverage Δ
unittests 40.30% <25.00%> (-1.69%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
miv/visualization/fft_domain.py 18.75% <10.71%> (-17.62%) ⬇️
miv/visualization/causality.py 28.57% <28.57%> (ø)
miv/statistics/pairwise_causality.py 35.71% <35.71%> (ø)
miv/statistics/__init__.py 100.00% <100.00%> (ø)
miv/visualization/__init__.py 100.00% <100.00%> (ø)

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@skim0119 skim0119 added the documentation Improvements or additions to documentation label Jun 16, 2022
@skim0119 skim0119 changed the base branch from main to doc_patch June 16, 2022 21:33
@skim0119 skim0119 changed the title Issue #51 [WIP] Connectivity documentation update Jun 17, 2022
@skim0119 skim0119 changed the title [WIP] Connectivity documentation update [WIP] Connectivity guide update Jun 17, 2022
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  1. I updated how to setup the workspace here. Please have it setup. You'll also need extra installation for documentation.
  2. Take a look at this one as well, especially second point in key things to remember.
  3. Add some descriptions and references inside the documentation as well. (example)
  4. Rename the file: granger_causality_psd_cpsd_coherence. (no capital)
  5. Plotting function can be moved to miv/visualization/connectivity.py (or you name it). Take a look at other files in the same folder for examples.

@skim0119 skim0119 removed the request for review from armantekinalp June 17, 2022 11:52
@skim0119 skim0119 linked an issue Jun 17, 2022 that may be closed by this pull request
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Added functions for causality, causality plots and spectral plots. Updated the init files in statistics and visualization. The documentation is added to docs/guide

@skim0119 skim0119 changed the base branch from doc_patch to update-0.1.1 June 21, 2022 06:01
@skim0119 skim0119 changed the title [WIP] Connectivity guide update WIP Connectivity guide update Jun 21, 2022
@skim0119 skim0119 changed the title WIP Connectivity guide update Connectivity guide update Jun 21, 2022
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LGTM. @Gauravu2 I made some changes in the documentation. Please take a look.

@Gauravu2 Gauravu2 merged commit e8ab3b8 into GazzolaLab:update-0.1.1 Jun 21, 2022
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Connectivity: granger causality and cross-entropy
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