cycquery.mimiciv.MIMICIVQuerier¶

class MIMICIVQuerier(dbms, user='', password='', host='', port=None, database='', schemas=None)[source]¶

Bases: DatasetQuerier

MIMICIV dataset querier.

Methods

`chartevents`	Query ICU chart events from the ICU module.
`diagnoses_icd`	Query MIMIC diagnosis data.
`get_table`	Get a table and possibly map columns to have standard names.
`labevents`	Query lab events from the hospital module.
`list_columns`	List columns in a table.
`list_custom_tables`	List custom tables methods provided by the dataset API.
`list_schemas`	List schemas in the database to query.
`list_tables`	List table methods that can be queried using the database.
`patients`	Query MIMIC patient data.
`procedures_icd`	Query MIMIC procedures data.

chartevents()[source]¶

Query ICU chart events from the ICU module.

Returns:: Constructed table, wrapped in an interface object.
Return type:: cycquery.interface.QueryInterface

diagnoses_icd()[source]¶

Query MIMIC diagnosis data.

Returns:: Constructed query, wrapped in an interface object.
Return type:: cycquery.interface.QueryInterface

get_table(schema_name, table_name, cast_timestamp_cols=True)¶

Get a table and possibly map columns to have standard names.

Standardizing column names allows for columns to be recognized in downstream processing.

Parameters:

schema_name (str) – Name of schema in the database.
table_name (str) – Name of table in the database.
cast_timestamp_cols (bool) – Whether to cast timestamp columns to datetime.

Returns:

Table with mapped columns.

Return type:

sqlalchemy.sql.selectable.Subquery

labevents()[source]¶

Query lab events from the hospital module.

Returns:: Constructed query, wrapped in an interface object.
Return type:: cycquery.interface.QueryInterface

list_columns(schema_name, table_name)¶

List columns in a table.

Parameters:

schema_name (str) – Name of schema in the database.
table_name (str) – Name of table in the database.

Returns:

List of column names.

Return type:

List[str]

list_custom_tables()¶

List custom tables methods provided by the dataset API.

Returns:: List of custom table names.
Return type:: List[str]

list_schemas()¶

List schemas in the database to query.

Returns:: List of schema names.
Return type:: List[str]

list_tables(schema_name=None)¶

List table methods that can be queried using the database.

Parameters:: schema_name (Optional[str]) – Name of schema in the database.
Returns:: List of table names.
Return type:: List[str]

patients()[source]¶

Query MIMIC patient data.

Returns:: Constructed query, wrapped in an interface object.
Return type:: cycquery.interface.QueryInterface

Notes

The function infers the approximate year a patient received care, using the anchor_year and anchor_year_group columns. The join and ops supplied are applied after the approximate year is inferred. dod is adjusted based on the inferred approximate year of care.

procedures_icd()[source]¶

Query MIMIC procedures data.

Returns:: Constructed query, wrapped in an interface object.
Return type:: cycquery.interface.QueryInterface