eds-scikit
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aphp
eds-scikit is a Python library providing tools to process and analyse OMOP data
## Feature type A new method for Phenotype Class: ```python def add_inclusion_criteria(self, inclusion_criteria: pd.DataFrame, level="patient", threshold=1): ``` ## Description In order to improve the Phenotype class and make it more...
## Feature type New pipeline ## Description I would be super interested to port the biology report introduced in [`plot_concepts_set`] (https://github.com/aphp/eds-scikit/blob/main/eds_scikit/biology/viz/plot.py) to other type of concepts such as billing codes...
## Description Problems when using `eds_scikit` on Windows. We might want to add testing on Windows in the CI. For instance `time.tzset()` (used in `__init__.py`) does not exist on Windows
## Description Currently, adding concept sets is quite hacky: ```python from eds_scikit.biology import ConceptsSet protein_blood = ConceptsSet("Protein_Blood_Quantitative") protein_urine = ConceptsSet("Protein_Urine_Quantitative") protein = ConceptsSet( name="Protein_Quantitative", concept_codes=protein_blood.concept_codes + protein_urine.concept_codes, ) ``` It...
## Feature type Functionality to plot patient trajectory based on various events. More generaly, it can handle any sequence of events. ## Description For the moment, the entry data will...
## Description - Fix undeterministic merge_visits due to `sort_values(...).groupby(...).first()` being undeterministic in Koalas. - Force user to provide `open_stay_end_datetime` to prevent from unexpected undeterministic results. ## Checklist - [ ]...
## Description ## Checklist - [ ] If this PR is a bug fix, the bug is documented in the test suite. - [ ] Changes were documented in the...
r" URG| SAU | UHCDb | ZHTCD" using the regex suggested on the documentation on care_site_names, I got a lot of False positives for tagging Emergency Units (ex : Chirurgie,...
## Description prepare_measurement_table returns error ``` MissingConceptError: The DataFrame is missing some columns, namely: - measurement_date ``` there is often issues with "date columns" in spark + Pandas. We should...
