umop.v1.omop.cohort package

Submodules

umop.v1.omop.cohort.complete_cohort module

OMOP Complete Cohort Documentation.

umop.v1.omop.cohort.complete_cohort.get_cohort(engine, include_icd10s=[], exclude_icd10s=[], start_date=None, end_date=None, age_cutoff=None)

This method returns the cohort based on inclusion and exclusion ICD10s. In addition, start_date, end_date and age_cutoff optional arguments can be provided to further limit the cohort.

>>> from umop.v1.omop.cohort.complete_cohort import get_cohort
  Arguments:
  ==========
  include_icd10s  = ['U07.1', 'U07.0']  # For example, Strong COVID ICD10s
  exclude_icd10s  = ['O70.0']           # For example, Perineum in Pregnancy ICD10
  start_date      = "2020-01-01"        # Date Format "YYYY-MM-DD"
  end_date        = "2020-05-31"        # Date Format "YYYY-MM-DD"
  age_cutoff      = 18                  # Limits cohort to 18 years of age or more
  Returns:
  ========
  "PERSON_ID", "ICD10", "VISIT_OCCURRENCE_ID", "CONDITION_CONCEPT_ID", "PRIMARY_DIAGNOSIS_YN",
  "VISIT_TYPE", "VISIT_START_DATE", "VISIT_END_DATE", "PROVIDER_ID"

umop.v1.omop.cohort.demographics module

OMOP Cohort’s Demographics Documentation.

Given a list of patients ids, returns demographics information for those patients.

umop.v1.omop.cohort.demographics.get_demographics(engine, pat_list=[])

Example:

This method can be used as follows:

>>> from umop.v1.omop.cohort.demographics import get_demographics

Given a list of patient ids, it will return
PERSON_ID, DOB (random date-shifted), SEX, RACE, ETHNICITY, CITY, STATE, and ZIP.

Module contents