|pypi| |actions| |codecov| |downloads|
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.
.. code-block:: python
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
.. code-block:: python
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:
.. code-block:: python
# 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:
.. code-block:: python
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``.
.. code-block:: python
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
================================================================
.. code-block:: python
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`_
.. code-block:: python
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"
.. |pypi| image:: https://img.shields.io/pypi/v/edc-egfr.svg
:target: https://pypi.python.org/pypi/edc-egfr
.. |actions| image:: https://github.com/clinicedc/edc-egfr/actions/workflows/build.yml/badge.svg
:target: https://github.com/clinicedc/edc-egfr/actions/workflows/build.yml
.. |codecov| image:: https://codecov.io/gh/clinicedc/edc-egfr/branch/develop/graph/badge.svg
:target: https://codecov.io/gh/clinicedc/edc-egfr
.. |downloads| image:: https://pepy.tech/badge/edc-egfr
:target: https://pepy.tech/project/edc-egfr
.. _meta-edc: https://github.com/meta-trial/meta-edc/blob/develop/meta_subject/models/blood_results/blood_results_rft.py
Raw data
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"description": "|pypi| |actions| |codecov| |downloads|\n\nedc-egfr\n--------\nClasses and utils to handle eGFR collection and reporting\n\nIncludes calculators for `CKD-EPI Creatinine equation (2009)`\nand `Cockcroft-Gault`.\n\nCalculate value, grade, percent drop, percent drop grade\n========================================================\n\nThe calculators use ``edc_reportable`` to reference DAIDS tox tables.\n\n.. code-block:: python\n\n egfr1 = EgfrCkdEpi(\n gender=MALE,\n ethnicity=BLACK,\n creatinine_value=53.0,\n age_in_years=30,\n creatinine_units=MICROMOLES_PER_LITER,\n )\n self.assertEqual(round(egfr1.value, 2), 156.43)\n\nand the eGFR grade\n\n.. code-block:: python\n\n self.assertEqual(egfr1.egfr_grade, 0)\n\n\nPercent drop from baseline\n==========================\nIn a trial, we are interested in the eGFR percent from baseline. Any reference value can be passed as the\nbaseline value.\n\nIf the baseline value is not provided, the percent drop = 0:\n\n.. code-block:: python\n\n # see edc-reportable for `reference_range_collection_name`\n opts = dict(\n gender=MALE,\n age_in_years=25,\n ethnicity=BLACK,\n creatinine_value=10.15,\n creatinine_units=MILLIGRAMS_PER_DECILITER,\n report_datetime=get_utcnow(),\n reference_range_collection_name=\"my_reference_list\",\n calculator_name=\"ckd-epi\",\n )\n egfr = Egfr(**opts)\n self.assertEqual(egfr.egfr_drop_value, 0.0)\n\nIf a baseline value is provided, the percent drop is calculated:\n\n.. code-block:: python\n\n egfr = Egfr(baseline_egfr_value=23.0, **opts)\n self.assertEqual(round(egfr.egfr_value, 2), 7.33)\n self.assertEqual(egfr.egfr_grade, 4)\n self.assertEqual(round(egfr.egfr_drop_value, 2), 68.15)\n self.assertEqual(egfr.egfr_drop_grade, 4)\n\nNotify on percent drop\n======================\n\nWe can notify when the drop is more than a given percent. ``eGFR`` uses a custom\nmodel to be updated.\n\nA `edc` lab result CRF is filled in, ``calling_crf``, that has the creatinine value and units.\nThe ``calling_crf`` has a ``subject_visit``, ``report_datetime``, ``assay_datetime``, ``creatinine_value``, and ``creatinine_units``.\n\n.. code-block:: python\n\n egfr = Egfr(\n baseline_egfr_value=220.1,\n notify_on_percent_drop=20,\n calling_crf=crf,\n **opts,\n )\n self.assertEqual(round(egfr.egfr_drop_value, 2), 28.93)\n self.assertTrue(\n EgfrDropNotification.objects.filter(subject_visit=subject_visit).exists()\n )\n\nConnecting a custom drop notification model with edc-action-item\n================================================================\n\n.. code-block:: python\n\n from edc_crf.crf_with_action_model_mixin import CrfWithActionModelMixin\n from edc_egfr.constants import EGFR_DROP_NOTIFICATION_ACTION\n from edc_egfr.model_mixins import EgfrDropNotificationModelMixin\n from edc_model import models as edc_models\n\n\n class EgfrDropNotification(\n EgfrDropNotificationModelMixin,\n CrfWithActionModelMixin,\n edc_models.BaseUuidModel,\n ):\n\n action_name = EGFR_DROP_NOTIFICATION_ACTION\n\n tracking_identifier_prefix = \"EG\"\n\n class Meta(edc_models.BaseUuidModel.Meta):\n verbose_name = \"eGFR Drop Notification\"\n verbose_name_plural = \"eGFR Drop Notifications\"\n\n\nAdding to an EDC model.save()\n=============================\n\nFor example, from the BloodResultRft model in `meta-edc`_\n\n.. code-block:: python\n\n class BloodResultsRft(\n CrfModelMixin,\n CreatinineModelMixin,\n EgfrModelMixin,\n EgfrDropModelMixin,\n CrfWithRequisitionModelMixin,\n BloodResultsModelMixin,\n edc_models.BaseUuidModel,\n ):\n lab_panel = rft_panel\n egfr_formula_name = \"ckd-epi\"\n\n class Meta(CrfWithActionModelMixin.Meta, edc_models.BaseUuidModel.Meta):\n verbose_name = \"Blood Result: RFT\"\n verbose_name_plural = \"Blood Results: RFT\"\n\n\n\n\n\n.. |pypi| image:: https://img.shields.io/pypi/v/edc-egfr.svg\n :target: https://pypi.python.org/pypi/edc-egfr\n\n.. |actions| image:: https://github.com/clinicedc/edc-egfr/actions/workflows/build.yml/badge.svg\n :target: https://github.com/clinicedc/edc-egfr/actions/workflows/build.yml\n\n.. |codecov| image:: https://codecov.io/gh/clinicedc/edc-egfr/branch/develop/graph/badge.svg\n :target: https://codecov.io/gh/clinicedc/edc-egfr\n\n.. |downloads| image:: https://pepy.tech/badge/edc-egfr\n :target: https://pepy.tech/project/edc-egfr\n\n.. _meta-edc: https://github.com/meta-trial/meta-edc/blob/develop/meta_subject/models/blood_results/blood_results_rft.py\n",
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