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v0.9.0 #143

Merged
merged 62 commits into from
Dec 30, 2020
Merged

v0.9.0 #143

merged 62 commits into from
Dec 30, 2020

Commits on Jul 2, 2020

  1. adding functionality for DAG

    @pzivich
    pzivich committed Jul 2, 2020
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Commits on Jul 5, 2020

  1. adding direct input from networkx object

    @pzivich
    pzivich committed Jul 5, 2020
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  2. adding functionality to load and optional networkx dependency

    @pzivich
    pzivich committed Jul 5, 2020
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  3. adding tests for causal graphs

    @pzivich
    pzivich committed Jul 5, 2020
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  4. adding better error handling

    @pzivich
    pzivich committed Jul 5, 2020
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  5. adding documentation for DirectedAcyclicGraph

    @pzivich
    pzivich committed Jul 5, 2020
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  6. travis updates

    @pzivich
    pzivich committed Jul 5, 2020
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  7. versioning numpy on travis for python 3.5

    @pzivich
    pzivich committed Jul 5, 2020
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Commits on Jul 12, 2020

  1. init 0.9.0 and new travis setup

    @pzivich
    pzivich committed Jul 12, 2020
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  2. optional import in init

    @pzivich
    pzivich committed Jul 12, 2020
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  3. Merge branch 'dag' into v0.9.0

    @pzivich
    pzivich committed Jul 12, 2020
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Commits on Jul 19, 2020

  1. Cross-fit AIPTW implementations

    @pzivich
    pzivich committed Jul 19, 2020
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  2. adding tests for causal graphs

    @pzivich
    pzivich committed Jul 19, 2020
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  3. aipw_calculator as function in utils

    @pzivich
    pzivich committed Jul 19, 2020
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Commits on Aug 3, 2020

  1. fixing returning IDs via #126

    @pzivich
    pzivich committed Aug 3, 2020
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  2. a working zipper plot implementation

    @pzivich
    pzivich committed Aug 3, 2020
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Commits on Dec 12, 2020

  1. Adoption of SuperLearner into zEpid. Adds EmpiricalMeanSL and Stepwis… 

    …eSL as estimation functions following the sklearn syntax for use with SuperLearner
    @pzivich
    pzivich committed Dec 12, 2020
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  2. Finished both forward and backward step-wise selection for the models

    @pzivich
    pzivich committed Dec 12, 2020
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Commits on Dec 13, 2020

  1. SuperLearner implementation added. Still need to compare to R, write … 

    …tests, and add docs to website
    @pzivich
    pzivich committed Dec 13, 2020
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  2. Added examples of use to documentation

    @pzivich
    pzivich committed Dec 13, 2020
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  3. Adding test to SuperLearner and the candidate estimators

    @pzivich
    pzivich committed Dec 13, 2020
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Commits on Dec 14, 2020

  1. Finished tests

    @pzivich
    pzivich committed Dec 14, 2020
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  2. Having SuperLearner return self so it works with the current setup … 

    …of machine learning with TMLE and CrossFit
    @pzivich
    pzivich committed Dec 14, 2020
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Commits on Dec 15, 2020

  1. adding custom_model to AIPW

    @pzivich
    pzivich committed Dec 15, 2020
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  2. replacing bounding in TMLE with new format

    @pzivich
    pzivich committed Dec 15, 2020
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  3. further tweaks to superlearner

    @pzivich
    pzivich committed Dec 15, 2020
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  4. adding better tests for TMLE with custom_model

    @pzivich
    pzivich committed Dec 15, 2020
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  5. finishing replacement of _bounding_ with zepid.calc.utils.probability… 

    …_bounds
    @pzivich
    pzivich committed Dec 15, 2020
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Commits on Dec 16, 2020

  1. updating readthedocs to have Super Learner documentation

    @pzivich
    pzivich committed Dec 16, 2020
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  2. Adding risk-ratio support for AIPTW and CrossfitAIPTW

    @pzivich
    pzivich committed Dec 16, 2020
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  3. Adding seeds for partitioning procedure for reproducibility

    @pzivich
    pzivich committed Dec 16, 2020
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  4. Adding example data set for the crossfit estimators

    @pzivich
    pzivich committed Dec 16, 2020
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  5. AIPTW cross-fitting fit tests. Just check that current operationaliza… 

    …tion is not broken by any future changes (do not have an outside or ground-truth comparison due to how randomness factors in)
    @pzivich
    pzivich committed Dec 16, 2020
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Commits on Dec 17, 2020

  1. adding CrossfitTMLE to cross-fitting estimators

    @pzivich
    pzivich committed Dec 17, 2020
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Commits on Dec 27, 2020

  1. fixing random_state flow

    @pzivich
    pzivich committed Dec 27, 2020
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  2. adding AIPTW OOB detector

    @pzivich
    pzivich committed Dec 27, 2020
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  3. adding additional superlearner probability bound check for predict_proba

    @pzivich
    pzivich committed Dec 27, 2020
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  4. adding diagnostics to cross-fit estimators

    @pzivich
    pzivich committed Dec 27, 2020
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  5. updating setup.py to drop python 3.5 support

    @pzivich
    pzivich committed Dec 27, 2020
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  6. fixing AIPW warning to avoid misdetection for continuous outcomes

    @pzivich
    pzivich committed Dec 27, 2020
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  7. adding more tests for the cross-fit estimators

    @pzivich
    pzivich committed Dec 27, 2020
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  8. some test fixes. I think it will still fail due to seeds though

    @pzivich
    pzivich committed Dec 27, 2020
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Commits on Dec 28, 2020

  1. should fix travisci issue...

    @pzivich
    pzivich committed Dec 28, 2020
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  2. Alternative way to specify RandomState for travisci compat?

    @pzivich
    pzivich committed Dec 28, 2020
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  3. checking if on numpy or pandas side for differences

    @pzivich
    pzivich committed Dec 28, 2020
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  4. well it isn't numpy, so maybe it is pandas...

    @pzivich
    pzivich committed Dec 28, 2020
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  5. the issue is reproducibility is not a function of the sample splittin… 

    …g by numpy/pandas, nor a result of version differences between numpy, pandas, scikit-learn
    @pzivich
    pzivich committed Dec 28, 2020
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  6. fix travis-requirements typo...

    @pzivich
    pzivich committed Dec 28, 2020
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  7. adding GLM SuperLearner functionality (since sci-kit learn has extra … 

    …stuff and doesn't always match statsmodels)
    @pzivich
    pzivich committed Dec 28, 2020
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  8. Updating crossfit and other DR estimators to use GLMSL rather than sk… 

    …learn
    @pzivich
    pzivich committed Dec 28, 2020
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  9. fixing equal to all_close in GMLSL tests

    @pzivich
    pzivich committed Dec 28, 2020
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Commits on Dec 29, 2020

  1. adding function to load formatted data (and checked it with IPTW)

    @pzivich
    pzivich committed Dec 29, 2020
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  2. added binary exposure check to check_input_data as this is in GEstima… 

    …tionSNM
    @pzivich
    pzivich committed Dec 29, 2020
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  3. Replaced check_input_data in most estimators! (generalize will eventu… 

    …ally need their own custom option)
    @pzivich
    pzivich committed Dec 29, 2020
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  4. Better looking print_results returned

    @pzivich
    pzivich committed Dec 29, 2020
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  5. adding variance warning to IPTW confidence intervals for the ATT and … 

    …the ATU
    @pzivich
    pzivich committed Dec 29, 2020
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  6. adding manual test for zipper_plot

    @pzivich
    pzivich committed Dec 29, 2020
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  7. adding zipper_plot to ReadTheDocs

    @pzivich
    pzivich committed Dec 29, 2020
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  8. Adding GLMSL docs to ReadTheDocs

    @pzivich
    pzivich committed Dec 29, 2020
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Commits on Dec 30, 2020

  1. Updating ReadTheDocs (and making it easier to manage going forward)

    @pzivich
    pzivich committed Dec 30, 2020
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  2. Update DAG ReadTheDocs

    @pzivich
    pzivich committed Dec 30, 2020
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  3. Updating Change-log for all v0.9.0 additions

    @pzivich
    pzivich committed Dec 30, 2020
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