Python Measure.Measure Beispiele

Beispiel #1

            "category": {
                "ratios": {
                    "STP1": 0.5,
                    "STP2": 0.5
                }
            },
        },
    ),
    first_dose=patients.with_these_clinical_events(
        first_dose_code,
        returning="binary_flag",
        between=["index_date", "index_date + 1 month"],
        return_expectations={"incidence": 0.4}),
    second_dose=patients.with_these_clinical_events(
        second_dose_code,
        returning="binary_flag",
        between=["index_date", "index_date + 1 month"],
        return_expectations={"incidence": 0.4}),
)

measures = [
    Measure(id="first_dose_stp",
            numerator="first_dose",
            denominator="population",
            group_by=["stp", "age_group", "sex"]),
    Measure(id="second_dose_stp",
            numerator="second_dose",
            denominator="population",
            group_by=["stp", "age_group", "sex"]),
]

Beispiel #2

Datei: study_definition_pregnant.py Projekt: YatishRam/OpenSafely-covid-vaccine-uptake-ethnicity

            "category": {
                "ratios": {
                    "STP1": 0.5,
                    "STP2": 0.5
                }
            },
        },
    ),
    first_dose=patients.with_these_clinical_events(
        first_dose_code,
        returning="binary_flag",
        between=["index_date", "index_date + 1 month"],
        return_expectations={"incidence": 0.4}),
    second_dose=patients.with_these_clinical_events(
        second_dose_code,
        returning="binary_flag",
        between=["index_date", "index_date + 1 month"],
        return_expectations={"incidence": 0.4}),
)

measures = [
    Measure(id="first_dose_stp",
            numerator="first_dose",
            denominator="population",
            group_by=["stp", "clinical_riskgroup"]),
    Measure(id="second_dose_stp",
            numerator="second_dose",
            denominator="population",
            group_by=["stp", "clinical_riskgroup"]),
]

Beispiel #3

Datei: study_definition.py Projekt: ralmond-nhs-e-i/sro-template-CVD

        codelist=codelist,
        between=["index_date", "last_day_of_month(index_date)"],
        returning="code",
        return_expectations={
            "category": {
                "ratios": {
                    codelist_expectation_codes: 1
                }
            },
        }),
)

# Create default measures
measures = [
    Measure(id="total",
            numerator="event",
            denominator="population",
            group_by=["age_band"]),
    Measure(id="event_code",
            numerator="event",
            denominator="population",
            group_by=["age_band", "event_code"]),
    Measure(id="practice",
            numerator="event",
            denominator="population",
            group_by=["age_band", "practice"]),
]

#Add demographics measures

for d in demographics:

Beispiel #4

import numpy as np
import pandas as pd
from cohortextractor import Measure

measures = [
    Measure(
        id="cvd_total_rate",
        numerator="cvd_emergency_elective",
        denominator="population",
        group_by=["AgeGroup"],
    ),
    Measure(
        id="cvd_emergency_rate",
        numerator="cvd_emergency",
        denominator="population",
        group_by=["AgeGroup"],
    ),
    Measure(
        id="cvd_elective_rate",
        numerator="cvd_elective",
        denominator="population",
        group_by=["AgeGroup"],
    ),
    Measure(
        id="respiratory_disease_total_rate",
        numerator="respiratory_disease_emergency_elective",
        denominator="population",
        group_by=["AgeGroup"],
    ),
    Measure(
        id="respiratory_disease_emergency_rate",

Beispiel #5

Datei: study_definition.py Projekt: machrisaa/opensafely-cohort-extractor

    ),
    recent_salbutamol_count=patients.with_these_medications(
        salbutamol_codes,
        between=["index_date - 2 years", "index_date"],
        returning="number_of_matches_in_period",
        return_expectations={
            "incidence": 0.6,
            "int": {"distribution": "normal", "mean": 8, "stddev": 2},
        },
    ),
)

measures = [
    Measure(
        id="liver_disease",
        numerator="has_chronic_liver_disease",
        denominator="population",
    ),
    Measure(
        id="liver_disease_one_group",
        numerator="has_chronic_liver_disease",
        denominator="population",
        group_by="population",
    ),
    Measure(
        id="liver_disease_by_stp",
        numerator="has_chronic_liver_disease",
        denominator="population",
        group_by="stp",
    ),
    Measure(

Beispiel #6

        },
    ),
    recent_salbutamol_count=patients.with_these_medications(
        salbutamol_codes,
        between=["index_date - 2 years", "index_date"],
        returning="number_of_matches_in_period",
        return_expectations={
            "incidence": 0.6,
            "int": {
                "distribution": "normal",
                "mean": 8,
                "stddev": 2
            },
        },
    ),
)

measures = [
    Measure(
        id="liver_disease",
        numerator="has_chronic_liver_disease",
        denominator="population",
    ),
    Measure(
        id="liver_disease_by_stp",
        numerator="has_chronic_liver_disease",
        denominator="population",
        group_by="stp",
    ),
]

Beispiel #7

Datei: rate_calculation_demographics.py Projekt: opensafely/hospital-disruption-research

import numpy as np
import pandas as pd
from cohortextractor import Measure

measures = [
   
    Measure(
        id="cvd_rate_total_sex",
        numerator="cvd_emergency_elective",
        denominator="population",
        group_by=["AgeGroup", "sex"],
    ),

    Measure(
        id="cvd_rate_total_ethnicity",
        numerator="cvd_emergency_elective",
        denominator="population",
        group_by=["AgeGroup", "ethnicity"],
    ),
    Measure(
        id="cvd_rate_total_imd",
        numerator="cvd_emergency_elective",
        denominator="population",
        group_by=["AgeGroup", "imd"],
    ),
    
    Measure(
        id="cvd_rate_emergency_sex",
        numerator="cvd_emergency",
        denominator="population",
        group_by=["AgeGroup", "sex"],

Beispiel #8

            "incidence": 1.0,
            "date": {
                "earliest": "1950-01-01",
                "latest": "index_date"
            },
        },
    ),
    stp=patients.registered_practice_as_of(
        "index_date",
        returning="stp_code",
        return_expectations={
            "rate": "universal",
            "category": {
                "ratios": {
                    "STP1": 1.0
                }
            },
        },
    ),
)

measures = [
    Measure(
        id="liver_disease_by_stp",
        numerator="has_chronic_liver_disease",
        denominator="population",
        group_by="stp",
        small_number_suppression=True,
    ),
]

Beispiel #9

Datei: study_definition_measures.py Projekt: opensafely/population-outcomes-burden-research

        ketoacidosis_ons=patients.with_these_codes_on_death_certificate(
            ketoacidosis_codes,
            between=["index_date", "last_day_of_month(index_date)"],
            return_expectations={"incidence": 0.05},
        ),
    ),
    died=patients.died_from_any_cause(
        between=["index_date", "last_day_of_month(index_date)"],
        return_expectations={"incidence": 0.1},
    ),
)

measures = [
    Measure(
        id="died_rate",
        numerator="died",
        denominator="population",
        group_by=["covid_hospitalisation"],
    ),
    Measure(
        id="DVT_rate",
        numerator="DVT",
        denominator="population",
        group_by=["covid_hospitalisation"],
    ),
    Measure(
        id="PE_rate",
        numerator="PE",
        denominator="population",
        group_by=["covid_hospitalisation"],
    ),
    Measure(

Beispiel #10

        return_expectations={"incidence": 0.4}),
    vl_first_dose=patients.with_these_clinical_events(
        vl_first_dose_code,
        returning="binary_flag",
        between=["index_date", "index_date + 1 month"],
        return_expectations={"incidence": 0.4}),
    vl_second_dose=patients.with_these_clinical_events(
        vl_second_dose_code,
        returning="binary_flag",
        between=["index_date", "index_date + 1 month"],
        return_expectations={"incidence": 0.4}),
)

measures = [
    Measure(id="first_dose_stp",
            numerator="first_dose",
            denominator="population",
            group_by=["stp", "age_group"]),
    Measure(id="second_dose_stp",
            numerator="second_dose",
            denominator="population",
            group_by=["stp", "age_group"]),
    Measure(id="vl_second_dose_stp",
            numerator="vl_second_dose",
            denominator="population",
            group_by=["stp", "age_group"]),
    Measure(id="vl_first_dose_stp",
            numerator="vl_first_dose",
            denominator="population",
            group_by=["stp", "age_group"]),
    Measure(id="pf_second_dose_stp",
            numerator="pf_second_dose",

Beispiel #11

Datei: study_definition_3_activity.py Projekt: dkdryan/opensafely-hf-research

        codes_inr,
        returning="number_of_episodes",
        between=["index_date", "index_date + 1 month"],
        return_expectations={
            "int": {
                "distribution": "normal",
                "mean": 3,
                "stddev": 0.5
            }
        },
    ),
)

measures = [
    Measure(id="cholesterol_practice",
            numerator="cholesterol",
            denominator="population",
            group_by="practice"),
    Measure(id="cholesterol_stp",
            numerator="cholesterol",
            denominator="population",
            group_by="stp"),
    Measure(id="inr_practice",
            numerator="inr",
            denominator="population",
            group_by="practice"),
    Measure(id="inr_stp",
            numerator="inr",
            denominator="population",
            group_by="stp"),
]