pyhealth.data.Patient

Another basic data structure in the package. A Patient is a collection of Visit for the current patients. It contains all necessary attributes of a patient, such as ethnicity, mortality status, gender, etc. It can support various healthcare tasks.

class pyhealth.data.Patient(patient_id, birth_datetime=None, death_datetime=None, gender=None, ethnicity=None, **attr)

Bases: object

Contains information about a single patient.

A patient is a person who is admitted at least once to a hospital or a specific department. Each patient is associated with a list of visits.

Parameters:

• patient_id (str) – unique identifier of the patient.

• birth_datetime (Optional[datetime]) – timestamp of patient’s birth. Default is None.

• death_datetime (Optional[datetime]) – timestamp of patient’s death. Default is None.

• gender – gender of the patient. Default is None.

• ethnicity – ethnicity of the patient. Default is None.

• **attr – optional attributes to add to the patient as key=value pairs.

attr_dict

Dict, dictionary of patient attributes. Each key is an attribute name and each value is the attribute’s value.

visits

OrderedDict[str, Visit], an ordered dictionary of visits. Each key is a visit_id and each value is a visit.

index_to_visit_id

Dict[int, str], dictionary that maps the index of a visit in the visits list to the corresponding visit_id.

Examples

>>> from pyhealth.data import Event, Visit, Patient
>>> 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)
>>> patient = Patient(
...     patient_id="p001",
... )
>>> patient.add_visit(visit)
>>> patient
Patient p001 with 1 visits

add_visit(visit)

Adds a visit to the patient.

If the visit’s visit_id is already in the patient’s visits dictionary, it will be overwritten by the new visit.

Parameters:

visit (Visit) – visit to add.

Note

As for now, there is no check on the order of the visits. The new visit

is simply added to the end of the ordered dictionary of visits.

Return type:

None

add_event(event)

Adds an event to the patient.

If the event’s visit_id is not in the patient’s visits dictionary, this function will raise KeyError.

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 the end of the list of events of the corresponding visit.

Return type:

None

get_visit_by_id(visit_id)

Returns a visit by visit_id.

Parameters:

visit_id (str) – unique identifier of the visit.

Return type:

Visit

Returns:

Visit with the given visit_id.

get_visit_by_index(index)

Returns a visit by its index.

Parameters:

index (int) – int, index of the visit to return.

Return type:

Visit

Returns:

Visit with the given index.

property available_tables: List[str]

Returns a list of available tables for the patient.

Return type:

List[str]

Returns:

List of available tables.