pat2vec.pat2vec_get_methods.get_method_covid

Functions

calculate_covid_features(features_data, ...)

Generates a binary feature for COVID-19 test results.

get_covid(current_pat_client_id_code, ...[, ...])

Retrieves COVID-19 test features for a patient within a date range.

search_covid([...])

Searches for COVID-19 test observations.
pat2vec.pat2vec_get_methods.get_method_covid.search_covid(cohort_searcher_with_terms_and_search=None, client_id_codes=None, observations_time_field='basicobs_entered', fields_override=None, start_year='1995', start_month='01', start_day='01', end_year='2025', end_month='12', end_day='12', additional_custom_search_string=None, client_idcode_term_name='client_idcode.keyword', index_name='basic_observations', output_filename='covid_search_results.csv', overwrite=False, config_obj=None)[source]

Searches for COVID-19 test observations.

Parameters:

  • cohort_searcher_with_terms_and_search (Optional[Callable]) – The function for cohort searching. Defaults to None.

  • client_id_codes (Optional[Union[str, List[str]]]) – The client ID code(s) of the patient(s). Defaults to None.

  • observations_time_field (str) – The timestamp field for filtering observations. Defaults to ‘basicobs_entered’.

  • fields_override (Optional[List[str]]) – A list of fields to override the default COVID_FIELDS. Defaults to None.

  • start_year (str) – Start year for the search. Defaults to ‘1995’.

  • start_month (str) – Start month for the search. Defaults to ‘01’.

  • start_day (str) – Start day for the search. Defaults to ‘01’.

  • end_year (str) – End year for the search. Defaults to ‘2025’.

  • end_month (str) – End month for the search. Defaults to ‘12’.

  • end_day (str) – End day for the search. Defaults to ‘12’.

  • additional_custom_search_string (Optional[str]) – An additional string to append to the search query. Defaults to None.

  • client_idcode_term_name (str) – The name of the client ID code field in the index. Defaults to “client_idcode.keyword”.

  • index_name (str) – The name of the Elasticsearch index to search. Defaults to “basic_observations”.

  • output_filename (Optional[str]) – The filename or path to a CSV file to load from or save to. Defaults to “covid_search_results.csv”.

  • overwrite (bool) – If True, perform the search even if output_filename exists. Defaults to False.

  • config_obj (Optional[object]) – Configuration object containing root_path. Defaults to None.

Returns:

A DataFrame containing the raw COVID-19 test observation data.

Return type:

pd.DataFrame

Raises:

ValueError – If cohort_searcher_with_terms_and_search or client_id_codes is None.

pat2vec.pat2vec_get_methods.get_method_covid.calculate_covid_features(features_data, current_pat_client_id_code, negate_biochem=False)[source]

Generates a binary feature for COVID-19 test results.

Creates a binary flag covid_positive which is 1 if any ‘positive’ result is found, 0 if only ‘negative’ results are found, and NaN if no results are found (or 0 if negate_biochem is True).

Parameters:

  • features_data (pd.DataFrame) – The prepared COVID-19 test data.

  • current_pat_client_id_code (str) – The patient’s client ID.

  • negate_biochem (bool) – If True, returns 0 when no data is available. Defaults to False.

Returns:

A single-row DataFrame with the covid_positive feature.

Return type:

pd.DataFrame

pat2vec.pat2vec_get_methods.get_method_covid.get_covid(current_pat_client_id_code, target_date_range, pat_batch, config_obj=None, cohort_searcher_with_terms_and_search=None)[source]

Retrieves COVID-19 test features for a patient within a date range.

Parameters:

  • current_pat_client_id_code (str) – The client ID code of the patient.

  • target_date_range (Tuple) – A tuple representing the target date range.

  • pat_batch (pd.DataFrame) – The DataFrame containing patient data for batch mode.

  • config_obj (Optional[object]) – Configuration object. Defaults to None.

  • cohort_searcher_with_terms_and_search (Optional[Callable]) – The function for cohort searching. Defaults to None.

Returns:

A DataFrame containing the COVID-19 test feature for the patient.

Return type:

pd.DataFrame