Tx compare refactor #54
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I've just realised that this breaks SampCompDB.save_report(). I'm fixing it. |
a-slide
approved these changes
Mar 26, 2019
| @@ -155,12 +163,43 @@ def gmm_test_anova(data, log_dwell=True, verbose=False): | |||
| # Generate an array of sample labels | |||
| Y = [ k for k,v in data[condition_labels[0]].items() for _ in v['intensity'] ] + [ k for k,v in data[condition_labels[1]].items() for _ in v['intensity'] ] | |||
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| # Loop over multiple cv_types and n_components and for each fit a GMM | |||
| gmm_fit = fit_best_gmm(X, max_components=2, cv_types=['spherical', 'tied', 'diag', 'full']) | |||
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Do you try all of the possible fits ? Isn't it enough to use "full" only ?
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This is a good point, not sure here... the model that is kept in the end is not always the 'full'.. sometimes the lowest bic has different convariance types. However, using only full would save a lot of time...
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I think I would be acceptable to use only full. The others are special cases of full anyway aren't they ?
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I've added unit tests (using pytest) and refactored TxCompare. Now the GMM option can do (and report) both the anova and logit while doing the GMM fitting only once. I've also added the relevant options in the CLI.