meta-edc 1.0.7__py3-none-any.whl → 1.1.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- meta_ae/action_items.py +10 -2
- meta_ae/baker_recipes.py +1 -2
- meta_ae/tests/tests/test_actions.py +1 -2
- meta_analytics/README.rst +1 -2
- meta_analytics/notebooks/anu.ipynb +95 -0
- meta_analytics/notebooks/appointment_planning.ipynb +329 -0
- meta_analytics/notebooks/arvs.ipynb +103 -0
- meta_analytics/notebooks/cleaning/consent_v1_ext.ipynb +227 -0
- meta_analytics/notebooks/cleaning/offschedule_eos.ipynb +353 -0
- meta_analytics/notebooks/dsmc/renal_dysfunction.ipynb +435 -0
- meta_analytics/notebooks/endpoints/meta_endpoints_by_date.ipynb +664 -0
- meta_analytics/notebooks/followup_examination.ipynb +141 -0
- meta_analytics/notebooks/hba1c.ipynb +136 -0
- meta_analytics/notebooks/hiv_regimens.ipynb +122 -118
- meta_analytics/notebooks/incidence.ipynb +232 -0
- meta_analytics/notebooks/liver.ipynb +389 -0
- meta_analytics/notebooks/magreth.ipynb +645 -0
- meta_analytics/notebooks/monitoring_report.ipynb +721 -448
- meta_analytics/notebooks/pharmacy.ipynb +405 -306
- meta_analytics/notebooks/pharmacy_stock_202410.ipynb +306 -0
- meta_analytics/notebooks/steering.ipynb +61 -0
- meta_analytics/notebooks/undiagnosed/meta3_screening_consort_chart.ipynb +1176 -0
- meta_analytics/notebooks/undiagnosed/meta3_screening_undiagnosed.ipynb +519 -0
- meta_analytics/notebooks/undiagnosed/meta_screening_table2.ipynb +964 -0
- meta_analytics/notebooks/undiagnosed/screen_undiagnosed_or.ipynb +296 -0
- meta_analytics/notebooks/undiagnosed/screening.ipynb +273 -0
- meta_analytics/notebooks/undiagnosed/screening2.ipynb +958 -0
- meta_analytics/notebooks/undiagnosed/screening_undiagnosed_20241002.ipynb +958 -0
- meta_analytics/notebooks/ven.ipynb +191 -0
- meta_analytics/notebooks/vitals.ipynb +263 -0
- meta_edc/settings/debug.py +3 -2
- meta_edc/urls.py +1 -0
- {meta_edc-1.0.7.dist-info → meta_edc-1.1.1.dist-info}/METADATA +3 -3
- {meta_edc-1.0.7.dist-info → meta_edc-1.1.1.dist-info}/RECORD +62 -35
- {meta_edc-1.0.7.dist-info → meta_edc-1.1.1.dist-info}/WHEEL +1 -1
- meta_labs/reportables.py +14 -11
- meta_labs/tests/test_reportables.py +33 -12
- meta_pharmacy/notebooks/pharmacy.ipynb +41 -0
- meta_prn/admin/offschedule_pregnancy_admin.py +3 -3
- meta_prn/admin/onschedule_dm_referral_admin.py +5 -5
- meta_prn/form_validators/end_of_study.py +2 -2
- meta_prn/migrations/0063_historicaloffstudymedication_singleton_field_and_more.py +37 -0
- meta_prn/migrations/0064_auto_20250602_2143.py +18 -0
- meta_prn/models/end_of_study.py +2 -0
- meta_prn/models/off_study_medication.py +2 -0
- meta_reports/admin/last_imp_refill_admin.py +3 -2
- meta_screening/eligibility/eligibility_part_three/base_eligibility_part_three.py +59 -47
- meta_screening/form_validators/screening_part_three.py +6 -1
- meta_screening/tests/meta_test_case_mixin.py +3 -0
- meta_screening/tests/tests/test_forms.py +9 -2
- meta_screening/tests/tests/test_screening_part_three.py +11 -14
- meta_subject/action_items.py +2 -3
- meta_subject/choices.py +2 -1
- meta_subject/form_validators/delivery_form_validator.py +1 -0
- meta_subject/forms/blood_results/blood_results_rft_form.py +60 -3
- meta_subject/forms/delivery_form.py +2 -0
- meta_subject/migrations/0223_bloodresultsfbc_errors_bloodresultsgludummy_errors_and_more.py +83 -0
- meta_subject/migrations/0224_bloodresultsfbc_abnormal_summary_and_more.py +153 -0
- meta_subject/tests/tests/test_egfr.py +5 -5
- meta_analytics/dataframes/enrolled/__init__.py +0 -0
- {meta_edc-1.0.7.dist-info → meta_edc-1.1.1.dist-info}/licenses/AUTHORS.rst +0 -0
- {meta_edc-1.0.7.dist-info → meta_edc-1.1.1.dist-info}/licenses/LICENSE +0 -0
- {meta_edc-1.0.7.dist-info → meta_edc-1.1.1.dist-info}/top_level.txt +0 -0
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"%%capture\n",
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"import os\n",
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"pharmacy_folder = Path(os.environ[\"META_PHARMACY_FOLDER\"])\n",
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"plus = activate(dotenv_file=env_file)\n",
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"from edc_pdutils.dataframes import get_crf, get_subject_visit\n",
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"from edc_constants.constants import YES\n",
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"cutoff_datetime = datetime(2026,3,1)\n",
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"df_patienthistory = get_crf(\"meta_subject.patienthistory\", subject_visit_model=\"meta_subject.subjectvisit\")\n",
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"df_followup_examination = get_crf(\"meta_subject.FollowupExamination\", subject_visit_model=\"meta_subject.subjectvisit\")"
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"df_patienthistory['regimen'] = df_patienthistory[\"current_arv_regimen\"]\n",
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"df_followup_examination.loc[(df_followup_examination[\"art_change\"]==YES) & (df_followup_examination.art_new_regimen_other.notna()), \"regimen\"] = df_followup_examination[\"art_new_regimen_other\"]\n",
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"df_followup_examination.loc[(df_followup_examination[\"art_change\"]==YES) & (df_followup_examination.art_new_regimen_other.isna()), \"regimen\"] = \"CHANGE_NOT_REPORTED\""
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"df_regimen = pd.concat([df_patienthistory[[\"subject_identifier\", \"visit_datetime\", \"regimen\"]], df_followup_examination[[\"subject_identifier\", \"visit_datetime\", \"regimen\"]]])\n",
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"df_regimen[\"regimen\"] = df_regimen[\"regimen\"].replace({\"Other second line\": \"CHANGE_NOT_REPORTED\"})\n",
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"df_regimen[\"regimen\"] = pd.Categorical(df_regimen[\"regimen\"], categories=list(df_regimen.query(\"regimen.notna()\").regimen.unique()), ordered=False)\n",
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"df_regimen = df_regimen.sort_values([\"subject_identifier\", \"visit_datetime\"])\n",
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"df_pivot = df_regimen.pivot_table(values=\"visit_datetime\", columns=\"regimen\", index=\"subject_identifier\", observed=True)\n",
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"def get_df_main(df_visit:pd.DataFrame, lower_days:float|None=None, upper_days:float|None=None):\n",
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" lower_days = -1\n",
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" cutoff_datetime = df_visit.query(\"@lower_days<followup_days<=@upper_days\").visit_datetime.max()\n",
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" # exclude subjects for this reason\n",
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" offstudy_reasons = ['Patient fulfilled late exclusion criteria (due to abnormal blood values or raised blood pressure at enrolment']\n",
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"\n",
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" df_eos = get_eos_df()\n",
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" df_eos\n",
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" .query(\"followup_days<@lower_days and followup_days<=@upper_days and offstudy_reason.isin(@offstudy_reasons)\")\n",
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" )\n",
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" df_visit.query(\"@lower_days<followup_days<=@upper_days and reason!='missed'\")\n",
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" .merge(df_eos_excluded[[\"subject_identifier\"]], on=\"subject_identifier\", how=\"left\", suffixes=(\"\", \"_y\"), indicator=True)\n",
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" .query(\"_merge=='left_only'\")\n",
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" )\n",
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" df_visit_final\n",
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" .groupby(by=[\"subject_identifier\"])[[\"baseline_datetime\", \"visit_datetime\", \"followup_days\"]]\n",
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" )\n",
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"\n",
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" .merge(\n",
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" df_endpoint.query(\"days_to_endpoint>@lower_days\")[[\"subject_identifier\", \"endpoint_label\", \"endpoint_type\", \"days_to_endpoint\"]],\n",
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" how=\"left\",\n",
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" on=[\"subject_identifier\"])\n",
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" .reset_index(drop=True)\n",
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" )\n",
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" if lower_days>=365.25:\n",
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" df_main[\"followup_days\"] = df_main[\"followup_days\"] - lower_days\n",
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" df_main[\"followup_years\"] = df_main[\"followup_days\"]/365.25\n",
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" return df_main, len(df_main), len(df_main.query(\"@lower_days<days_to_endpoint<=@upper_days and endpoint_label.notna()\"))\n",
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"\n",
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"def get_rate_and_ci(events, person_years_total):\n",
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" lower_ci = (chi2.ppf(0.025, 2 * events) / (2 * person_years_total)) * 1000\n",
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" upper_ci = (chi2.ppf(0.975, 2 * (events + 1)) / (2 * person_years_total)) * 1000\n",
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" return events/person_years_total*1000, lower_ci, upper_ci\n",
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"\n",
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"def get_incidence_data(term:str, lower_days:float, upper_days:float):\n",
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" data = {}\n",
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" df_main, subjects, events = get_df_main(df_visit, lower_days=lower_days, upper_days=upper_days)\n",
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" person_years_total = df_main.followup_years.sum()\n",
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" data.update({term:[person_years_total, subjects, events, *get_rate_and_ci(events, person_years_total)]})\n",
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"incidence_data = {}\n",
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"incidence_data.update(get_incidence_data(\"total\", lower_days=0, upper_days=10000))\n",
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"incidence_data.update(get_incidence_data(\"0-1 years\", lower_days=0, upper_days=365.25))\n",
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"incidence_data.update(get_incidence_data(\"1-2 years\", lower_days=365.25, upper_days=2*365.25))\n",
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"incidence_data.update(get_incidence_data(\"2-3 years\", lower_days=2*365.25, upper_days=3*365.25))\n",
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"incidence_data.update(get_incidence_data(\"3+ years\", lower_days=3*365.25, upper_days=10*365.25))"
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"metadata": {},
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"outputs": [],
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"source": [
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"data = dict(label=[], person_years=[], failures=[], rate=[], lower_ci=[], upper_ci=[])\n",
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+
"for k in incidence_data:\n",
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" data[\"label\"].append(k)\n",
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"\n",
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+
"for v in incidence_data.values():\n",
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" data[\"person_years\"].append(v[0])\n",
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" data[\"failures\"].append(v[2])\n",
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" data[\"rate\"].append(v[3])\n",
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" data[\"lower_ci\"].append(v[4])\n",
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+
" data[\"upper_ci\"].append(v[5])\n",
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"\n",
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"df = pd.DataFrame(data=data)"
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]
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"metadata": {},
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"outputs": [],
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"source": [
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"gt = df_as_great_table(\n",
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" df,\n",
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+
" title=\"Table 9: Incident Rate per 1000 person years\",\n",
|
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|
+
" subtitle=md(\"using randomisation to diabetes/last seen\"),\n",
|
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|
+
")\n",
|
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|
+
"gt = gt.fmt_number(columns=[\"person_years\", \"failures\", \"rate\", \"lower_ci\", \"upper_ci\"], decimals=2)\n",
|
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|
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"gt = (gt\n",
|
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|
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" .cols_label({\"label\": \"Label\", \"person_years\": \"Person years\", \"failures\": \"Failures\", \"rate\": \"Rate\", \"lower_ci\": \"Lower\", \"upper_ci\": \"Upper\"})\n",
|
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|
+
" .cols_align(align=\"left\", columns=[\"label\"])\n",
|
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+
" .cols_align(align=\"center\", columns=[\"person_years\", \"failures\", \"rate\", \"lower_ci\", \"upper_ci\"])\n",
|
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" .tab_spanner(\n",
|
190
|
+
" label=\"95%CI\",\n",
|
191
|
+
" columns=[\"lower_ci\", \"upper_ci\"],\n",
|
192
|
+
" )\n",
|
193
|
+
")\n",
|
194
|
+
"gt.show()\n",
|
195
|
+
"html_data.append(gt.as_raw_html())\n"
|
196
|
+
]
|
197
|
+
},
|
198
|
+
{
|
199
|
+
"cell_type": "code",
|
200
|
+
"execution_count": null,
|
201
|
+
"id": "9",
|
202
|
+
"metadata": {},
|
203
|
+
"outputs": [],
|
204
|
+
"source": [
|
205
|
+
"raw_html = \"</BR>\".join(html_data)\n",
|
206
|
+
"raw_html = '<!DOCTYPE html>\\n<html lang=\"en\">\\n<head>\\n<meta charset=\"utf-8\"/>\\n</head>\\n<body>\\n' + raw_html + '\\n</body>\\n</html>\\n'\n",
|
207
|
+
"pdfkit.from_string(raw_html, str(analysis_folder / \"incident_rate.pdf\"))\n"
|
208
|
+
]
|
209
|
+
}
|
210
|
+
],
|
211
|
+
"metadata": {
|
212
|
+
"kernelspec": {
|
213
|
+
"display_name": "Python 3 (ipykernel)",
|
214
|
+
"language": "python",
|
215
|
+
"name": "python3"
|
216
|
+
},
|
217
|
+
"language_info": {
|
218
|
+
"codemirror_mode": {
|
219
|
+
"name": "ipython",
|
220
|
+
"version": 3
|
221
|
+
},
|
222
|
+
"file_extension": ".py",
|
223
|
+
"mimetype": "text/x-python",
|
224
|
+
"name": "python",
|
225
|
+
"nbconvert_exporter": "python",
|
226
|
+
"pygments_lexer": "ipython3",
|
227
|
+
"version": "3.12.4"
|
228
|
+
}
|
229
|
+
},
|
230
|
+
"nbformat": 4,
|
231
|
+
"nbformat_minor": 5
|
232
|
+
}
|