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Revamp survival analysis interface (#842)
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* cox_ph add all arguments

* updated test to use keywords

* weibull_aft arguments update

* log_logistic update

* updated log logistic example

* store summary df in adata.uns

* try moving np

* omit inplace keyword

* added explanation, as to where the results are stored

* corrected spelling

* updated tests to check for .uns ( should be removed later, when the univariates are updated )

* fix argument order, doc fixes

* slightly simpler wording

* fiexed spelling

Co-authored-by: Lukas Heumos <[email protected]>

* Update ehrapy/tools/_sa.py

Co-authored-by: Lukas Heumos <[email protected]>

* Update ehrapy/tools/_sa.py

Co-authored-by: Lukas Heumos <[email protected]>

* Update ehrapy/tools/_sa.py

Co-authored-by: Lukas Heumos <[email protected]>

* Update ehrapy/tools/_sa.py

Co-authored-by: Lukas Heumos <[email protected]>

* Update ehrapy/tools/_sa.py

Co-authored-by: Lukas Heumos <[email protected]>

* Update ehrapy/tools/_sa.py

Co-authored-by: Lukas Heumos <[email protected]>

* Update ehrapy/tools/_sa.py

Co-authored-by: Lukas Heumos <[email protected]>

* renamed function to be clearer

* Add uns_key parameter to Kaplan-Meier, Nelson-Aalen, and Weibull functions for customizable storage in AnnData object

* Update test assertions in TestSA for event_table handling and pass adata to assertion method

* uns to  in doc

---------

Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: eroell <[email protected]>
Co-authored-by: Eljas Roellin <[email protected]>
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4 people authored Jan 10, 2025
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