xquanl / biostats_ehr

EHR_Analysis

ehr-utils

The ehr-utils library provides some simple analytical capabilities for EHR data.

Modules

• ehr_analysis provides four simple analytical capabilities for EHR data and two class(Patient and Lab), including functions that are able to:

1. Read and parse the data files to store data into a SQLite database
2. Return the age in years of a given patient
3. Indicate a patient's situation based on a test result
4. Compute the age of a given patient when their earliest lab was recorded

Installation

Feel free to copy ehr_analysis.py.

Usage

The ehr_analysis contains two classes and one function.

1. Read and parse the data files

   This function takes both patient and lab file names, or the path to those files (string), inserts data in those files into a SQLite database, and produces two lists in a tuple format that contain patients' basic information(Patient class) and relevant lab data(Lab class), respectively.

   Example usage:

from ehr_analysis import parse_data

  def test_Patient_class() -> None:
  """Test the parse_data() Patient has the correct attributes."""
      with fake_files(temp_patient, temp_lab) as (patient, lab):
          patient, labs = parse_data(patient, lab)
      assert patient[0].id == "1"
      assert patient[0].gender == "F"
      assert patient[0].dob == "1947-01-01 00:00:00.000000"
      assert patient[0].race == "white"


  def test_Lab_class() -> None:
      """Test the parse_data() Lab has the correct attributes."""
      with fake_files(temp_patient, temp_lab) as (patient, lab):
          patient, labs = parse_data(patient, lab)
      assert labs[0].patient_id == "1"
      assert labs[0].lab_name == "HDL"
      assert labs[0].lab_value == "50"
      assert labs[0].lab_units == "mg/dL"
      assert labs[0].lab_date == "1980-01-01 00:00:00.000000"

2. Return the age in years of a given patient

   This is a property of the class Patient, which returns the age in years of the given patient.

   Example usage:

   from ehr_analysis import patient_age
   
   def test_patient_age() -> None:
   """test whether the Patient age property returns the correct age"""
   lab1 = Lab(
       patient_id="1",
   )
   patient1 = Patient(
       id="1",
   )
   assert patient1.age == 76
   

3. Indicate a patient's situation based on a test result

   This is a property of the class Patient, which takes a lab name (string), an operator (string), and a value of that lab result (float), returns a boolean indicating whether the patient has ever had a test with value above (">") or below ("<") the given level.

   Example usage:

   from ehr_analysis import patient_is_sick
   
   def test_is_sick() -> None:
   """Test whether the is_sick method returns the correct boolean value"""
   lab1 = Lab(
       patient_id="1",
   )
   patient1 = Patient(
       id="1",
   )
   assert patient1.is_sick("HDL", ">", 30) is True
   

4. Compute the age of a given patient when their earliest lab was recorded

   This is a method of the class Patient, which returns the age in years (int) of a given patient when their earliest lab was recorded.

   Example usage:

   from ehr_analysis import patient_is_sick
   
   def test_earliest_admission() -> None:
   """Test whether the earliest_admission property returns the correct age"""
   patient1 = Patient(
       id="1",
   )
   assert patient1.earliest_admission == 33
   

Development

We welcome contributions! Before opening a pull request, please confirm that existing regression tests pass:

python -m pytest tests/