edc-egfr 0.1.0

Classes and utils to handle eGFR collection and reporting for clinicedc/edc projects

edc-egfr

Classes and utils to handle eGFR collection and reporting

Includes calculators for CKD-EPI Creatinine equation (2009) and Cockcroft-Gault.

Calculate value, grade, percent drop, percent drop grade

The calculators use edc_reportable to reference DAIDS tox tables.

egfr1 = EgfrCkdEpi(
        gender=MALE,
        ethnicity=BLACK,
        creatinine_value=53.0,
        age_in_years=30,
        creatinine_units=MICROMOLES_PER_LITER,
    )
self.assertEqual(round(egfr1.value, 2), 156.43)

and the eGFR grade

self.assertEqual(egfr1.egfr_grade, 0)

Percent drop from baseline

In a trial, we are interested in the eGFR percent from baseline. Any reference value can be passed as the baseline value.

If the baseline value is not provided, the percent drop = 0:

# see edc-reportable for `reference_range_collection_name`
opts = dict(
    gender=MALE,
    age_in_years=25,
    ethnicity=BLACK,
    creatinine_value=10.15,
    creatinine_units=MILLIGRAMS_PER_DECILITER,
    report_datetime=get_utcnow(),
    reference_range_collection_name="my_reference_list",
    calculator_name="ckd-epi",
)
egfr = Egfr(**opts)
self.assertEqual(egfr.egfr_drop_value, 0.0)

If a baseline value is provided, the percent drop is calculated:

egfr = Egfr(baseline_egfr_value=23.0, **opts)
self.assertEqual(round(egfr.egfr_value, 2), 7.33)
self.assertEqual(egfr.egfr_grade, 4)
self.assertEqual(round(egfr.egfr_drop_value, 2), 68.15)
self.assertEqual(egfr.egfr_drop_grade, 4)

Notify on percent drop

We can notify when the drop is more than a given percent. eGFR uses a custom model to be updated.

A edc lab result CRF is filled in, calling_crf, that has the creatinine value and units. The calling_crf has a subject_visit, report_datetime, assay_datetime, creatinine_value, and creatinine_units.

egfr = Egfr(
    baseline_egfr_value=220.1,
    notify_on_percent_drop=20,
    calling_crf=crf,
    **opts,
)
self.assertEqual(round(egfr.egfr_drop_value, 2), 28.93)
self.assertTrue(
    EgfrDropNotification.objects.filter(subject_visit=subject_visit).exists()
)

Connecting a custom drop notification model with edc-action-item

from edc_crf.crf_with_action_model_mixin import CrfWithActionModelMixin
from edc_egfr.constants import EGFR_DROP_NOTIFICATION_ACTION
from edc_egfr.model_mixins import EgfrDropNotificationModelMixin
from edc_model import models as edc_models


class EgfrDropNotification(
    EgfrDropNotificationModelMixin,
    CrfWithActionModelMixin,
    edc_models.BaseUuidModel,
):

    action_name = EGFR_DROP_NOTIFICATION_ACTION

    tracking_identifier_prefix = "EG"

    class Meta(edc_models.BaseUuidModel.Meta):
        verbose_name = "eGFR Drop Notification"
        verbose_name_plural = "eGFR Drop Notifications"

Adding to an EDC model.save()

For example, from the BloodResultRft model in meta-edc

class BloodResultsRft(
    CrfModelMixin,
    CreatinineModelMixin,
    EgfrModelMixin,
    EgfrDropModelMixin,
    CrfWithRequisitionModelMixin,
    BloodResultsModelMixin,
    edc_models.BaseUuidModel,
):
    lab_panel = rft_panel
    egfr_formula_name = "ckd-epi"

    class Meta(CrfWithActionModelMixin.Meta, edc_models.BaseUuidModel.Meta):
        verbose_name = "Blood Result: RFT"
        verbose_name_plural = "Blood Results: RFT"