pyhealth.data.Visit#

Another basic data structure in the package. A Visit is a single encounter in hospital. It is a container a sequence of Event for each information aspect, such as diagnosis or medications. It also contains other necessary attributes for supporting healthcare tasks, such as the date of the visit.

class pyhealth.data.Visit(visit_id, patient_id, encounter_time=None, discharge_time=None, discharge_status=None, **attr)[source]#

Bases: object

Contains information about a single visit.

A visit is a period of time in which a patient is admitted to a hospital or a specific department. Each visit is associated with a patient and contains a list of different events.

Parameters:

visit_id (str) – unique identifier of the visit.
patient_id (str) – unique identifier of the patient.
encounter_time (Optional[datetime]) – timestamp of visit’s encounter. Default is None.
discharge_time (Optional[datetime]) – timestamp of visit’s discharge. Default is None.
discharge_status – patient’s status upon discharge. Default is None.
**attr – optional attributes to add to the visit as key=value pairs.

attr_dict#: Dict, dictionary of visit attributes. Each key is an attribute name and each value is the attribute’s value.

event_list_dict#: Dict[str, List[Event]], dictionary of event lists. Each key is a table name and each value is a list of events from that table ordered by timestamp.

Examples

>>> from pyhealth.data import Event, Visit
>>> event = Event(
...     code="00069153041",
...     table="PRESCRIPTIONS",
...     vocabulary="NDC",
...     visit_id="v001",
...     patient_id="p001",
...     dosage="250mg",
... )
>>> visit = Visit(
...     visit_id="v001",
...     patient_id="p001",
... )
>>> visit.add_event(event)
>>> visit
Visit v001 from patient p001 with 1 events from tables ['PRESCRIPTIONS']
>>> visit.available_tables
['PRESCRIPTIONS']
>>> visit.num_events
1
>>> visit.get_event_list('PRESCRIPTIONS')
[Event with NDC code 00069153041 from table PRESCRIPTIONS]
>>> visit.get_code_list('PRESCRIPTIONS')
['00069153041']
>>> patient.available_tables
['PRESCRIPTIONS']
>>> patient.get_visit_by_index(0)
Visit v001 from patient p001 with 1 events from tables ['PRESCRIPTIONS']
>>> patient.get_visit_by_index(0).get_code_list(table="PRESCRIPTIONS")
['00069153041']

add_event(event)[source]#

Adds an event to the visit.

If the event’s table is not in the visit’s event list dictionary, it is added as a new key. The event is then added to the list of events of that table.

Parameters:: event (Event) – event to add.

Note

As for now, there is no check on the order of the events. The new event: is simply appended to end of the list.

Return type:: None

get_event_list(table)[source]#

Returns a list of events from a specific table.

If the table is not in the visit’s event list dictionary, an empty list is returned.

Parameters:: table (str) – name of the table.
Return type:: List[Event]
Returns:: List of events from the specified table.

Note

As for now, there is no check on the order of the events. The list of: events is simply returned as is.

get_code_list(table, remove_duplicate=True)[source]#

Returns a list of codes from a specific table.

If the table is not in the visit’s event list dictionary, an empty list is returned.

Parameters:

table (str) – name of the table.
remove_duplicate (Optional[bool]) – whether to remove duplicate codes (but keep the relative order). Default is True.

Return type:

List[str]

Returns:

List of codes from the specified table.

Note

As for now, there is no check on the order of the codes. The list of: codes is simply returned as is.

set_event_list(table, event_list)[source]#

Sets the list of events from a specific table.

This function will overwrite any existing list of events from the specified table.

Parameters:

table (str) – name of the table.
event_list (List[Event]) – list of events to set.

Note

As for now, there is no check on the order of the events. The list of: events is simply set as is.

Return type:: None

property available_tables: List[str]#

Returns a list of available tables for the visit.

Return type:: List[str]
Returns:: List of available tables.

property num_events: int#

Returns the total number of events in the visit.

Return type:: int
Returns:: Total number of events.