pat2vec.pat2vec_get_methods.get_method_vte_status

Functions

`calculate_vte_features`(features_data, ...[, ...])	Generates numeric summary features from VTE observations.
`get_vte_status`(current_pat_client_id_code, ...)	Retrieves CORE_VTE_STATUS features for a patient within a date range.
`prepare_vte_data`(raw_data)	Filters for valid CORE_VTE_STATUS records and drops NAs.
`search_vte`([...])	Searches for CORE_VTE_STATUS observations.

pat2vec.pat2vec_get_methods.get_method_vte_status.search_vte(cohort_searcher_with_terms_and_search=None, client_id_codes=None, observations_time_field='observationdocument_recordeddtm', 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')[source]

Searches for CORE_VTE_STATUS 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 ‘observationdocument_recordeddtm’.
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”.

Returns:

A DataFrame containing the raw VTE status 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_vte_status.prepare_vte_data(raw_data)[source]

Filters for valid CORE_VTE_STATUS records and drops NAs.

Parameters:: raw_data (pd.DataFrame) – The raw observation data.
Returns:: A cleaned DataFrame containing only valid VTE status records.
Return type:: pd.DataFrame

pat2vec.pat2vec_get_methods.get_method_vte_status.calculate_vte_features(features_data, current_pat_client_id_code, negate_biochem=False)[source]

Generates numeric summary features from VTE observations.

Maps VTE status strings to binary values and calculates summary statistics (mean, median, std, etc.).

Parameters:

features_data (pd.DataFrame) – The prepared VTE status data.
current_pat_client_id_code (str) – The patient’s client ID.
negate_biochem (bool) – If True, returns features with NaN values when no data is available. Defaults to False.

Returns:

A single-row DataFrame with summary statistics for VTE status.

Return type:

pd.DataFrame

pat2vec.pat2vec_get_methods.get_method_vte_status.get_vte_status(current_pat_client_id_code, target_date_range, pat_batch, config_obj=None, cohort_searcher_with_terms_and_search=None)[source]

Retrieves CORE_VTE_STATUS features for a patient within a date range.

This function fetches VTE status observation data, either from a pre-loaded batch or by searching. It then maps the statuses to numeric values and calculates summary statistics.

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 with settings like batch_mode and negate_biochem. Defaults to None.
cohort_searcher_with_terms_and_search (Optional[Callable]) – The function for cohort searching. Defaults to None.

Returns:

A DataFrame containing VTE status features for the patient.

Return type:

pd.DataFrame

Raises:

ValueError – If config_obj is None.