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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"metadata": {},
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"%load_ext sql\n",
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"%sql mysql+mysqldb://root:cc3721b@127.0.0.1:3306/meta3_production\n",
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"\n",
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"import pandas as pd\n",
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"from dj_notebook import activate\n",
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"import numpy as np\n",
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"import matplotlib.pyplot as plt\n",
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"import seaborn as sns\n",
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"\n",
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"plus = activate(dotenv_file=\"/Users/erikvw/source/edc_source/meta-edc/.env\")"
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"metadata": {},
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"outputs": [],
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"source": [
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"from meta_screening.models import SubjectScreening\n",
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"from django_pandas.io import read_frame\n"
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"metadata": {},
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"outputs": [],
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"source": [
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"qs = SubjectScreening.objects.all()\n",
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"df = read_frame(qs)\n"
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"metadata": {},
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"outputs": [],
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"source": [
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"df[\"meta_phase_two\"] = df[\"meta_phase_two\"].apply(lambda x: \"No\" if not x else x)"
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"metadata": {},
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"outputs": [],
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"source": [
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"pd.crosstab(df['gender'], 'subjects')"
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"metadata": {},
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"outputs": [],
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"source": [
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"list(df.columns)"
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"metadata": {},
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"outputs": [],
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"source": [
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"gender = pd.crosstab(index=df['gender'], columns=[\"gender\"], margins=True)\n",
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"gender.columns = [\"gender\", 'rowtotal']\n",
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"gender.index = ['female', 'male', 'coltotal']\n",
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"gender"
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"outputs": [],
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"source": [
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"# counts by site - row, column\n",
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"gender_by_site = pd.crosstab(df['site'], df['gender'], margins=True)\n",
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"gender_by_site.columns = [\"female\", \"male\", \"rowtotal\"]\n",
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"gender_by_site.index = [\"amana\", \"hindu-mandal\", \"mnazi-moja\", \"mwananyamala\", \"temeke\", \"coltotal\"]\n",
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"gender_by_site"
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"source": [
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"# proportion of counts by row, column\n",
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"gender_by_site/gender_by_site.loc[\"coltotal\",\"rowtotal\"]"
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"source": [
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"# proportion of counts by column\n",
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"gender_by_site/gender_by_site.loc[\"coltotal\"]"
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"metadata": {},
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"outputs": [],
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"source": [
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"# proportion of counts by row\n",
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"prop = gender_by_site.div(gender_by_site[\"rowtotal\"], axis=0)\n",
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"prop"
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"metadata": {},
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"outputs": [],
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"source": [
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"# stats for female by site => mean=.718, well balanced\n",
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"prop['female'].describe()"
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"metadata": {},
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"outputs": [],
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"source": [
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"# part one variables\n",
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"\n",
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"# \"meta_phase_two\",\n",
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"# \"hiv_pos\",\n",
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"# \"art_six_months\",\n",
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"# \"on_rx_stable\",\n",
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"# \"vl_undetectable\",\n",
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"# \"lives_nearby\",\n",
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"# \"staying_nearby_12\",\n",
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"# \"pregnant\",\n"
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"metadata": {},
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"outputs": [],
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"source": [
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"meta_phase_two = pd.crosstab(index=df['meta_phase_two'], columns=[df[\"eligible\"],df[\"gender\"]], margins=True)\n",
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"# meta_phase_two.columns = [\"female\", \"male\", \"rowtotal\"]\n",
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"# meta_phase_two.index = [\"no\", \"yes\", \"coltotal\"]\n",
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"meta_phase_two"
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"metadata": {},
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"outputs": [],
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"source": [
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"on_rx_stable = pd.crosstab(index=df['on_rx_stable'], columns=df[\"gender\"], margins=True)\n",
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"on_rx_stable.columns = [\"female\", \"male\", \"rowtotal\"]\n",
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"on_rx_stable.index = [\"no\", \"n/a\", \"yes\", \"coltotal\"]\n",
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"on_rx_stable"
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"metadata": {},
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"outputs": [],
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"source": [
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"on_dm_medication = pd.crosstab(index=df['on_dm_medication'], columns=df[\"gender\"], margins=True)\n",
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"on_dm_medication.columns = [\"female\", \"male\", \"rowtotal\"]\n",
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"on_dm_medication.index = [\"no\", \"yes\", \"coltotal\"]\n",
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"on_dm_medication"
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"metadata": {},
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"outputs": [],
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"source": [
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"hiv_pos = pd.crosstab(index=df['hiv_pos'], columns=df[\"gender\"], margins=True)\n",
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"hiv_pos.columns = [\"female\", \"male\", \"rowtotal\"]\n",
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"hiv_pos.index = [\"no\", \"yes\", \"coltotal\"]\n",
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"hiv_pos"
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"metadata": {},
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"outputs": [],
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"source": [
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"art_six_months = pd.crosstab(index=df['art_six_months'], columns=df[\"gender\"], margins=True)\n",
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"art_six_months.columns = [\"female\", \"male\", \"rowtotal\"]\n",
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"art_six_months.index = [\"no\", \"n/a\", \"yes\", \"coltotal\"]\n",
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"art_six_months"
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"metadata": {},
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"outputs": [],
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"source": [
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"vl_undetectable = pd.crosstab(index=df['vl_undetectable'], columns=df[\"gender\"], margins=True)\n",
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"vl_undetectable.columns = [\"female\", \"male\", \"rowtotal\"]\n",
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"vl_undetectable.index = [\"no\", \"n/a\", \"yes\", \"coltotal\"]\n",
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"metadata": {},
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"outputs": [],
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"source": [
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"lives_nearby = pd.crosstab(index=df['lives_nearby'], columns=df[\"gender\"], margins=True)\n",
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"lives_nearby.columns = [\"female\", \"male\", \"rowtotal\"]\n",
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"lives_nearby.index = [\"no\", \"yes\", \"coltotal\"]\n",
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"metadata": {},
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"outputs": [],
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"source": [
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"staying_nearby_12 = pd.crosstab(index=df['staying_nearby_12'], columns=df[\"gender\"], margins=True)\n",
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"staying_nearby_12.columns = [\"female\", \"male\", \"rowtotal\"]\n",
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"staying_nearby_12.index = [\"no\", \"yes\", \"coltotal\"]\n",
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"metadata": {},
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"outputs": [],
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"source": [
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"pregnant = pd.crosstab(index=df['pregnant'], columns=df[\"gender\"], margins=True)\n",
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293
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+
"pregnant.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
294
|
+
"pregnant.index = [\"no\", \"n/a\", \"yes\", \"coltotal\"]\n",
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|
+
"pregnant"
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+
]
|
297
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},
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{
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+
"cell_type": "code",
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300
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+
"execution_count": null,
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301
|
+
"id": "24",
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302
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+
"metadata": {},
|
303
|
+
"outputs": [],
|
304
|
+
"source": [
|
305
|
+
"eligible_part_one = pd.crosstab(index=df['eligible_part_one'], columns=df[\"gender\"], margins=True)\n",
|
306
|
+
"eligible_part_one.columns = [\"female\", \"male\", \"rowtotal\"]\n",
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307
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+
"eligible_part_one.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
308
|
+
"eligible_part_one"
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+
]
|
310
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+
},
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|
+
{
|
312
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+
"cell_type": "code",
|
313
|
+
"execution_count": null,
|
314
|
+
"id": "25",
|
315
|
+
"metadata": {},
|
316
|
+
"outputs": [],
|
317
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+
"source": [
|
318
|
+
"# df_part_one eligible\n",
|
319
|
+
"# \"meta_phase_two\",\n",
|
320
|
+
"# \"hiv_pos\",\n",
|
321
|
+
"# \"art_six_months\",\n",
|
322
|
+
"# \"on_rx_stable\",\n",
|
323
|
+
"# \"vl_undetectable\",\n",
|
324
|
+
"# \"lives_nearby\",\n",
|
325
|
+
"# \"staying_nearby_12\",\n",
|
326
|
+
"# \"pregnant\",\n",
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327
|
+
"\n",
|
328
|
+
"df_part_one = df[(df[\"meta_phase_two\"]==\"No\") & (df[\"hiv_pos\"]==\"Yes\") & (df[\"art_six_months\"]==\"Yes\") & (df[\"on_rx_stable\"]==\"Yes\") & (df[\"vl_undetectable\"]==\"Yes\") & (df[\"lives_nearby\"]==\"Yes\") & (df[\"staying_nearby_12\"]==\"Yes\") & (df[\"pregnant\"]!=\"Yes\")]\n",
|
329
|
+
"len(df_part_one)\n"
|
330
|
+
]
|
331
|
+
},
|
332
|
+
{
|
333
|
+
"cell_type": "code",
|
334
|
+
"execution_count": null,
|
335
|
+
"id": "26",
|
336
|
+
"metadata": {},
|
337
|
+
"outputs": [],
|
338
|
+
"source": [
|
339
|
+
"df_p1_eligible = df[df[\"meta_phase_two\"]!=\"Yes\"]['meta_phase_two']"
|
340
|
+
]
|
341
|
+
},
|
342
|
+
{
|
343
|
+
"cell_type": "code",
|
344
|
+
"execution_count": null,
|
345
|
+
"id": "27",
|
346
|
+
"metadata": {},
|
347
|
+
"outputs": [],
|
348
|
+
"source": [
|
349
|
+
"# PART TWO\n",
|
350
|
+
"# \"congestive_heart_failure\",\n",
|
351
|
+
"# \"liver_disease\",\n",
|
352
|
+
"# \"alcoholism\",\n",
|
353
|
+
"# \"acute_metabolic_acidosis\",\n",
|
354
|
+
"# \"renal_function_condition\",\n",
|
355
|
+
"# \"tissue_hypoxia_condition\",\n",
|
356
|
+
"# \"acute_condition\",\n",
|
357
|
+
"# \"metformin_sensitivity\",\n",
|
358
|
+
"# \"has_dm\",\n",
|
359
|
+
"# \"on_dm_medication\","
|
360
|
+
]
|
361
|
+
},
|
362
|
+
{
|
363
|
+
"cell_type": "code",
|
364
|
+
"execution_count": null,
|
365
|
+
"id": "28",
|
366
|
+
"metadata": {},
|
367
|
+
"outputs": [],
|
368
|
+
"source": [
|
369
|
+
"\n",
|
370
|
+
"congestive_heart_failure = pd.crosstab(index=df['congestive_heart_failure'], columns=df[\"gender\"], margins=True)\n",
|
371
|
+
"congestive_heart_failure.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
372
|
+
"congestive_heart_failure.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
373
|
+
"congestive_heart_failure"
|
374
|
+
]
|
375
|
+
},
|
376
|
+
{
|
377
|
+
"cell_type": "code",
|
378
|
+
"execution_count": null,
|
379
|
+
"id": "29",
|
380
|
+
"metadata": {},
|
381
|
+
"outputs": [],
|
382
|
+
"source": [
|
383
|
+
"liver_disease = pd.crosstab(index=df['liver_disease'], columns=df[\"gender\"], margins=True)\n",
|
384
|
+
"liver_disease.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
385
|
+
"liver_disease.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
386
|
+
"liver_disease"
|
387
|
+
]
|
388
|
+
},
|
389
|
+
{
|
390
|
+
"cell_type": "code",
|
391
|
+
"execution_count": null,
|
392
|
+
"id": "30",
|
393
|
+
"metadata": {},
|
394
|
+
"outputs": [],
|
395
|
+
"source": [
|
396
|
+
"alcoholism = pd.crosstab(index=df['alcoholism'], columns=df[\"gender\"], margins=True)\n",
|
397
|
+
"alcoholism.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
398
|
+
"alcoholism.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
399
|
+
"alcoholism"
|
400
|
+
]
|
401
|
+
},
|
402
|
+
{
|
403
|
+
"cell_type": "code",
|
404
|
+
"execution_count": null,
|
405
|
+
"id": "31",
|
406
|
+
"metadata": {},
|
407
|
+
"outputs": [],
|
408
|
+
"source": [
|
409
|
+
"\n",
|
410
|
+
"acute_metabolic_acidosis = pd.crosstab(index=df['acute_metabolic_acidosis'], columns=df[\"gender\"], margins=True)\n",
|
411
|
+
"acute_metabolic_acidosis.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
412
|
+
"acute_metabolic_acidosis.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
413
|
+
"acute_metabolic_acidosis"
|
414
|
+
]
|
415
|
+
},
|
416
|
+
{
|
417
|
+
"cell_type": "code",
|
418
|
+
"execution_count": null,
|
419
|
+
"id": "32",
|
420
|
+
"metadata": {},
|
421
|
+
"outputs": [],
|
422
|
+
"source": [
|
423
|
+
"\n",
|
424
|
+
"renal_function_condition = pd.crosstab(index=df['renal_function_condition'], columns=df[\"gender\"], margins=True)\n",
|
425
|
+
"renal_function_condition.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
426
|
+
"renal_function_condition.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
427
|
+
"renal_function_condition"
|
428
|
+
]
|
429
|
+
},
|
430
|
+
{
|
431
|
+
"cell_type": "code",
|
432
|
+
"execution_count": null,
|
433
|
+
"id": "33",
|
434
|
+
"metadata": {},
|
435
|
+
"outputs": [],
|
436
|
+
"source": [
|
437
|
+
"\n",
|
438
|
+
"tissue_hypoxia_condition = pd.crosstab(index=df['tissue_hypoxia_condition'], columns=df[\"gender\"], margins=True)\n",
|
439
|
+
"tissue_hypoxia_condition.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
440
|
+
"tissue_hypoxia_condition.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
441
|
+
"tissue_hypoxia_condition"
|
442
|
+
]
|
443
|
+
},
|
444
|
+
{
|
445
|
+
"cell_type": "code",
|
446
|
+
"execution_count": null,
|
447
|
+
"id": "34",
|
448
|
+
"metadata": {},
|
449
|
+
"outputs": [],
|
450
|
+
"source": [
|
451
|
+
"\n",
|
452
|
+
"metformin_sensitivity = pd.crosstab(index=df['metformin_sensitivity'], columns=df[\"gender\"], margins=True)\n",
|
453
|
+
"metformin_sensitivity.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
454
|
+
"metformin_sensitivity.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
455
|
+
"metformin_sensitivity"
|
456
|
+
]
|
457
|
+
},
|
458
|
+
{
|
459
|
+
"cell_type": "code",
|
460
|
+
"execution_count": null,
|
461
|
+
"id": "35",
|
462
|
+
"metadata": {},
|
463
|
+
"outputs": [],
|
464
|
+
"source": [
|
465
|
+
"\n",
|
466
|
+
"acute_condition = pd.crosstab(index=df['acute_condition'], columns=df[\"gender\"], margins=True)\n",
|
467
|
+
"acute_condition.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
468
|
+
"acute_condition.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
469
|
+
"acute_condition"
|
470
|
+
]
|
471
|
+
},
|
472
|
+
{
|
473
|
+
"cell_type": "code",
|
474
|
+
"execution_count": null,
|
475
|
+
"id": "36",
|
476
|
+
"metadata": {},
|
477
|
+
"outputs": [],
|
478
|
+
"source": [
|
479
|
+
"# has_dm by gender (if not eligible_part_one)\n",
|
480
|
+
"has_dm = pd.crosstab(index=df[df[\"eligible_part_one\"]==\"Yes\"]['has_dm'], columns=df[\"gender\"], margins=True)\n",
|
481
|
+
"has_dm.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
482
|
+
"has_dm.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
483
|
+
"has_dm"
|
484
|
+
]
|
485
|
+
},
|
486
|
+
{
|
487
|
+
"cell_type": "code",
|
488
|
+
"execution_count": null,
|
489
|
+
"id": "37",
|
490
|
+
"metadata": {},
|
491
|
+
"outputs": [],
|
492
|
+
"source": [
|
493
|
+
"# has_dm by gender, eligible_part_one\n",
|
494
|
+
"has_dm = pd.crosstab(index=df['has_dm'], columns=[df[\"gender\"],df[\"eligible_part_one\"]], margins=True)\n",
|
495
|
+
"# has_dm.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
496
|
+
"# has_dm.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
497
|
+
"has_dm"
|
498
|
+
]
|
499
|
+
},
|
500
|
+
{
|
501
|
+
"cell_type": "code",
|
502
|
+
"execution_count": null,
|
503
|
+
"id": "38",
|
504
|
+
"metadata": {},
|
505
|
+
"outputs": [],
|
506
|
+
"source": [
|
507
|
+
"# has_dm by gender\n",
|
508
|
+
"has_dm = pd.crosstab(index=df['has_dm'], columns=df[\"gender\"], margins=True)\n",
|
509
|
+
"has_dm.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
510
|
+
"has_dm.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
511
|
+
"has_dm"
|
512
|
+
]
|
513
|
+
},
|
514
|
+
{
|
515
|
+
"cell_type": "code",
|
516
|
+
"execution_count": null,
|
517
|
+
"id": "39",
|
518
|
+
"metadata": {},
|
519
|
+
"outputs": [],
|
520
|
+
"source": [
|
521
|
+
"has_dm.div(has_dm[\"rowtotal\"], axis=0)"
|
522
|
+
]
|
523
|
+
},
|
524
|
+
{
|
525
|
+
"cell_type": "code",
|
526
|
+
"execution_count": null,
|
527
|
+
"id": "40",
|
528
|
+
"metadata": {},
|
529
|
+
"outputs": [],
|
530
|
+
"source": [
|
531
|
+
"has_dm / len(df)"
|
532
|
+
]
|
533
|
+
},
|
534
|
+
{
|
535
|
+
"cell_type": "code",
|
536
|
+
"execution_count": null,
|
537
|
+
"id": "41",
|
538
|
+
"metadata": {},
|
539
|
+
"outputs": [],
|
540
|
+
"source": [
|
541
|
+
"df[\"eligible_part_one\"].value_counts()"
|
542
|
+
]
|
543
|
+
},
|
544
|
+
{
|
545
|
+
"cell_type": "code",
|
546
|
+
"execution_count": null,
|
547
|
+
"id": "42",
|
548
|
+
"metadata": {},
|
549
|
+
"outputs": [],
|
550
|
+
"source": [
|
551
|
+
"df[\"eligible_part_two\"].value_counts()"
|
552
|
+
]
|
553
|
+
},
|
554
|
+
{
|
555
|
+
"cell_type": "code",
|
556
|
+
"execution_count": null,
|
557
|
+
"id": "43",
|
558
|
+
"metadata": {},
|
559
|
+
"outputs": [],
|
560
|
+
"source": [
|
561
|
+
"df[\"eligible_part_three\"].value_counts()"
|
562
|
+
]
|
563
|
+
},
|
564
|
+
{
|
565
|
+
"cell_type": "code",
|
566
|
+
"execution_count": null,
|
567
|
+
"id": "44",
|
568
|
+
"metadata": {},
|
569
|
+
"outputs": [],
|
570
|
+
"source": [
|
571
|
+
"df[\"eligible\"].value_counts()"
|
572
|
+
]
|
573
|
+
},
|
574
|
+
{
|
575
|
+
"cell_type": "code",
|
576
|
+
"execution_count": null,
|
577
|
+
"id": "45",
|
578
|
+
"metadata": {},
|
579
|
+
"outputs": [],
|
580
|
+
"source": [
|
581
|
+
"df[\"consented\"].value_counts()"
|
582
|
+
]
|
583
|
+
},
|
584
|
+
{
|
585
|
+
"cell_type": "code",
|
586
|
+
"execution_count": null,
|
587
|
+
"id": "46",
|
588
|
+
"metadata": {},
|
589
|
+
"outputs": [],
|
590
|
+
"source": [
|
591
|
+
"df[\"eligible\"].value_counts()\n"
|
592
|
+
]
|
593
|
+
},
|
594
|
+
{
|
595
|
+
"cell_type": "code",
|
596
|
+
"execution_count": null,
|
597
|
+
"id": "47",
|
598
|
+
"metadata": {},
|
599
|
+
"outputs": [],
|
600
|
+
"source": [
|
601
|
+
"pd.crosstab(index=df['eligible'], columns=df[\"gender\"], margins=True)"
|
602
|
+
]
|
603
|
+
},
|
604
|
+
{
|
605
|
+
"cell_type": "code",
|
606
|
+
"execution_count": null,
|
607
|
+
"id": "48",
|
608
|
+
"metadata": {},
|
609
|
+
"outputs": [],
|
610
|
+
"source": [
|
611
|
+
"# let's start here for the consort chart"
|
612
|
+
]
|
613
|
+
},
|
614
|
+
{
|
615
|
+
"cell_type": "code",
|
616
|
+
"execution_count": null,
|
617
|
+
"id": "49",
|
618
|
+
"metadata": {},
|
619
|
+
"outputs": [],
|
620
|
+
"source": [
|
621
|
+
"dm1 = df[df[\"meta_phase_two\"]==\"No\"]\n",
|
622
|
+
"dm1 = pd.crosstab(index=dm1['eligible'], columns=df[\"gender\"], margins=True, dropna=False)\n",
|
623
|
+
"dm1.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
624
|
+
"dm1.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
625
|
+
"dm1"
|
626
|
+
]
|
627
|
+
},
|
628
|
+
{
|
629
|
+
"cell_type": "code",
|
630
|
+
"execution_count": null,
|
631
|
+
"id": "50",
|
632
|
+
"metadata": {},
|
633
|
+
"outputs": [],
|
634
|
+
"source": [
|
635
|
+
"df1 = df[(df[\"meta_phase_two\"]==\"No\")]"
|
636
|
+
]
|
637
|
+
},
|
638
|
+
{
|
639
|
+
"cell_type": "code",
|
640
|
+
"execution_count": null,
|
641
|
+
"id": "51",
|
642
|
+
"metadata": {},
|
643
|
+
"outputs": [],
|
644
|
+
"source": [
|
645
|
+
"hiv_pos = pd.crosstab(index=df1['hiv_pos'], columns=df1[\"gender\"], margins=True)\n",
|
646
|
+
"hiv_pos.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
647
|
+
"hiv_pos.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
648
|
+
"hiv_pos"
|
649
|
+
]
|
650
|
+
},
|
651
|
+
{
|
652
|
+
"cell_type": "code",
|
653
|
+
"execution_count": null,
|
654
|
+
"id": "52",
|
655
|
+
"metadata": {},
|
656
|
+
"outputs": [],
|
657
|
+
"source": [
|
658
|
+
"art_six_months = pd.crosstab(index=df1['art_six_months'], columns=df1[\"gender\"], margins=True)\n",
|
659
|
+
"art_six_months.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
660
|
+
"art_six_months.index = [\"no\", \"na\", \"yes\", \"coltotal\"]\n",
|
661
|
+
"art_six_months"
|
662
|
+
]
|
663
|
+
},
|
664
|
+
{
|
665
|
+
"cell_type": "code",
|
666
|
+
"execution_count": null,
|
667
|
+
"id": "53",
|
668
|
+
"metadata": {},
|
669
|
+
"outputs": [],
|
670
|
+
"source": [
|
671
|
+
"on_rx_stable = pd.crosstab(index=df1['on_rx_stable'], columns=df1[\"gender\"], margins=True)\n",
|
672
|
+
"on_rx_stable.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
673
|
+
"on_rx_stable.index = [\"no\", \"na\", \"yes\", \"coltotal\"]\n",
|
674
|
+
"on_rx_stable"
|
675
|
+
]
|
676
|
+
},
|
677
|
+
{
|
678
|
+
"cell_type": "code",
|
679
|
+
"execution_count": null,
|
680
|
+
"id": "54",
|
681
|
+
"metadata": {},
|
682
|
+
"outputs": [],
|
683
|
+
"source": [
|
684
|
+
"vl_undetectable = pd.crosstab(index=df1['vl_undetectable'], columns=df1[\"gender\"], margins=True)\n",
|
685
|
+
"vl_undetectable.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
686
|
+
"vl_undetectable.index = [\"no\", \"na\", \"yes\", \"coltotal\"]\n",
|
687
|
+
"vl_undetectable"
|
688
|
+
]
|
689
|
+
},
|
690
|
+
{
|
691
|
+
"cell_type": "code",
|
692
|
+
"execution_count": null,
|
693
|
+
"id": "55",
|
694
|
+
"metadata": {},
|
695
|
+
"outputs": [],
|
696
|
+
"source": [
|
697
|
+
"len(df1)"
|
698
|
+
]
|
699
|
+
},
|
700
|
+
{
|
701
|
+
"cell_type": "code",
|
702
|
+
"execution_count": null,
|
703
|
+
"id": "56",
|
704
|
+
"metadata": {},
|
705
|
+
"outputs": [],
|
706
|
+
"source": [
|
707
|
+
"\n",
|
708
|
+
"df2 = df1[(df1[\"hiv_pos\"]==\"Yes\") & (df1[\"art_six_months\"]!=\"No\") & (df1[\"on_rx_stable\"]!=\"No\") & (df1[\"vl_undetectable\"]!=\"No\")]\n",
|
709
|
+
"len(df2)\n"
|
710
|
+
]
|
711
|
+
},
|
712
|
+
{
|
713
|
+
"cell_type": "code",
|
714
|
+
"execution_count": null,
|
715
|
+
"id": "57",
|
716
|
+
"metadata": {},
|
717
|
+
"outputs": [],
|
718
|
+
"source": [
|
719
|
+
"dftmp = pd.crosstab(index=df2['eligible'], columns=df2[\"gender\"], margins=True, dropna=False)\n",
|
720
|
+
"dftmp.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
721
|
+
"dftmp.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
722
|
+
"dftmp"
|
723
|
+
]
|
724
|
+
},
|
725
|
+
{
|
726
|
+
"cell_type": "code",
|
727
|
+
"execution_count": null,
|
728
|
+
"id": "58",
|
729
|
+
"metadata": {},
|
730
|
+
"outputs": [],
|
731
|
+
"source": [
|
732
|
+
"# \"lives_nearby\",\n",
|
733
|
+
"# \"staying_nearby_12\",\n",
|
734
|
+
"# \"pregnant\",\n",
|
735
|
+
"\n",
|
736
|
+
"df3 = df2[(df2[\"lives_nearby\"]==\"Yes\") & (df2[\"staying_nearby_12\"]==\"Yes\")]\n",
|
737
|
+
"len(df3)\n"
|
738
|
+
]
|
739
|
+
},
|
740
|
+
{
|
741
|
+
"cell_type": "code",
|
742
|
+
"execution_count": null,
|
743
|
+
"id": "59",
|
744
|
+
"metadata": {},
|
745
|
+
"outputs": [],
|
746
|
+
"source": [
|
747
|
+
"dftmp = pd.crosstab(index=df3['eligible'], columns=df3[\"gender\"], margins=True, dropna=False)\n",
|
748
|
+
"dftmp.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
749
|
+
"dftmp.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
750
|
+
"dftmp"
|
751
|
+
]
|
752
|
+
},
|
753
|
+
{
|
754
|
+
"cell_type": "code",
|
755
|
+
"execution_count": null,
|
756
|
+
"id": "60",
|
757
|
+
"metadata": {},
|
758
|
+
"outputs": [],
|
759
|
+
"source": [
|
760
|
+
"lives_nearby = pd.crosstab(index=df2['lives_nearby'], columns=df2[\"gender\"], margins=True, dropna=False)\n",
|
761
|
+
"lives_nearby.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
762
|
+
"lives_nearby.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
763
|
+
"lives_nearby"
|
764
|
+
]
|
765
|
+
},
|
766
|
+
{
|
767
|
+
"cell_type": "code",
|
768
|
+
"execution_count": null,
|
769
|
+
"id": "61",
|
770
|
+
"metadata": {},
|
771
|
+
"outputs": [],
|
772
|
+
"source": [
|
773
|
+
"tmp = df2[df2['lives_nearby']==\"Yes\"]\n",
|
774
|
+
"staying_nearby_12 = pd.crosstab(index=tmp['staying_nearby_12'], columns=tmp[\"gender\"], margins=True, dropna=False)\n",
|
775
|
+
"staying_nearby_12.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
776
|
+
"staying_nearby_12.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
777
|
+
"staying_nearby_12"
|
778
|
+
]
|
779
|
+
},
|
780
|
+
{
|
781
|
+
"cell_type": "code",
|
782
|
+
"execution_count": null,
|
783
|
+
"id": "62",
|
784
|
+
"metadata": {},
|
785
|
+
"outputs": [],
|
786
|
+
"source": [
|
787
|
+
"df4 = df3[(df3[\"pregnant\"]!=\"Yes\")]\n",
|
788
|
+
"len(df4)\n"
|
789
|
+
]
|
790
|
+
},
|
791
|
+
{
|
792
|
+
"cell_type": "code",
|
793
|
+
"execution_count": null,
|
794
|
+
"id": "63",
|
795
|
+
"metadata": {},
|
796
|
+
"outputs": [],
|
797
|
+
"source": [
|
798
|
+
"dftmp = pd.crosstab(index=df4['eligible'], columns=df4[\"gender\"], margins=True, dropna=False)\n",
|
799
|
+
"dftmp.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
800
|
+
"dftmp.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
801
|
+
"dftmp"
|
802
|
+
]
|
803
|
+
},
|
804
|
+
{
|
805
|
+
"cell_type": "code",
|
806
|
+
"execution_count": null,
|
807
|
+
"id": "64",
|
808
|
+
"metadata": {},
|
809
|
+
"outputs": [],
|
810
|
+
"source": [
|
811
|
+
"dftmp = pd.crosstab(index=df4['eligible_part_two'], columns=df4[\"gender\"], margins=True, dropna=True)\n",
|
812
|
+
"# dftmp.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
813
|
+
"# dftmp.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
814
|
+
"dftmp"
|
815
|
+
]
|
816
|
+
},
|
817
|
+
{
|
818
|
+
"cell_type": "code",
|
819
|
+
"execution_count": null,
|
820
|
+
"id": "65",
|
821
|
+
"metadata": {},
|
822
|
+
"outputs": [],
|
823
|
+
"source": [
|
824
|
+
"# \"congestive_heart_failure\",\n",
|
825
|
+
"# \"liver_disease\",\n",
|
826
|
+
"# \"alcoholism\",\n",
|
827
|
+
"# \"acute_metabolic_acidosis\",\n",
|
828
|
+
"# \"renal_function_condition\",\n",
|
829
|
+
"# \"tissue_hypoxia_condition\",\n",
|
830
|
+
"# \"acute_condition\",\n",
|
831
|
+
"# \"metformin_sensitivity\",\n",
|
832
|
+
"# \"has_dm\",\n",
|
833
|
+
"# \"on_dm_medication\","
|
834
|
+
]
|
835
|
+
},
|
836
|
+
{
|
837
|
+
"cell_type": "code",
|
838
|
+
"execution_count": null,
|
839
|
+
"id": "66",
|
840
|
+
"metadata": {},
|
841
|
+
"outputs": [],
|
842
|
+
"source": [
|
843
|
+
"tmp1 = pd.crosstab(index=df4['acute_condition'], columns=tmp[\"gender\"], margins=True, dropna=False)\n",
|
844
|
+
"tmp1.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
845
|
+
"# tmp1.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
846
|
+
"tmp1"
|
847
|
+
]
|
848
|
+
},
|
849
|
+
{
|
850
|
+
"cell_type": "code",
|
851
|
+
"execution_count": null,
|
852
|
+
"id": "67",
|
853
|
+
"metadata": {},
|
854
|
+
"outputs": [],
|
855
|
+
"source": [
|
856
|
+
"\n",
|
857
|
+
"df5 = df4[(df4[\"congestive_heart_failure\"]!=\"Yes\") & (df4[\"liver_disease\"]!=\"Yes\") & (df4[\"alcoholism\"]!=\"Yes\") & (df4[\"acute_metabolic_acidosis\"]!=\"Yes\") & (df4[\"renal_function_condition\"]!=\"Yes\") & (df4[\"tissue_hypoxia_condition\"]!=\"Yes\") & (df4[\"acute_condition\"]!=\"Yes\")]\n",
|
858
|
+
"len(df5)"
|
859
|
+
]
|
860
|
+
},
|
861
|
+
{
|
862
|
+
"cell_type": "code",
|
863
|
+
"execution_count": null,
|
864
|
+
"id": "68",
|
865
|
+
"metadata": {},
|
866
|
+
"outputs": [],
|
867
|
+
"source": [
|
868
|
+
"dftmp = pd.crosstab(index=df5['eligible_part_two'], columns=df5[\"gender\"], margins=True, dropna=True)\n",
|
869
|
+
"dftmp"
|
870
|
+
]
|
871
|
+
},
|
872
|
+
{
|
873
|
+
"cell_type": "code",
|
874
|
+
"execution_count": null,
|
875
|
+
"id": "69",
|
876
|
+
"metadata": {},
|
877
|
+
"outputs": [],
|
878
|
+
"source": [
|
879
|
+
"tmp1 = pd.crosstab(index=df5['on_dm_medication'], columns=tmp[\"gender\"], margins=True, dropna=False)\n",
|
880
|
+
"tmp1.columns = [\"female\", \"male\", \"rowtotal\"]\n",
|
881
|
+
"# tmp1.index = [\"no\", \"yes\", \"coltotal\"]\n",
|
882
|
+
"tmp1"
|
883
|
+
]
|
884
|
+
},
|
885
|
+
{
|
886
|
+
"cell_type": "code",
|
887
|
+
"execution_count": null,
|
888
|
+
"id": "70",
|
889
|
+
"metadata": {},
|
890
|
+
"outputs": [],
|
891
|
+
"source": [
|
892
|
+
"df6 = df5[(df5[\"has_dm\"]==\"No\") & (df5[\"on_dm_medication\"]==\"No\") & (df5[\"metformin_sensitivity\"]==\"No\")]\n",
|
893
|
+
"len(df6)"
|
894
|
+
]
|
895
|
+
},
|
896
|
+
{
|
897
|
+
"cell_type": "code",
|
898
|
+
"execution_count": null,
|
899
|
+
"id": "71",
|
900
|
+
"metadata": {},
|
901
|
+
"outputs": [],
|
902
|
+
"source": [
|
903
|
+
"dftmp = pd.crosstab(index=df6['eligible_part_two'], columns=df6[\"gender\"], margins=True, dropna=True)\n",
|
904
|
+
"dftmp"
|
905
|
+
]
|
906
|
+
},
|
907
|
+
{
|
908
|
+
"cell_type": "code",
|
909
|
+
"execution_count": null,
|
910
|
+
"id": "72",
|
911
|
+
"metadata": {},
|
912
|
+
"outputs": [],
|
913
|
+
"source": [
|
914
|
+
"dftmp = pd.crosstab(index=df['eligible_part_two'], columns=df[\"gender\"], margins=True, dropna=True)\n",
|
915
|
+
"dftmp"
|
916
|
+
]
|
917
|
+
},
|
918
|
+
{
|
919
|
+
"cell_type": "code",
|
920
|
+
"execution_count": null,
|
921
|
+
"id": "73",
|
922
|
+
"metadata": {},
|
923
|
+
"outputs": [],
|
924
|
+
"source": [
|
925
|
+
"df['eligible_part_two'].values_count()"
|
926
|
+
]
|
927
|
+
},
|
928
|
+
{
|
929
|
+
"cell_type": "code",
|
930
|
+
"execution_count": null,
|
931
|
+
"id": "74",
|
932
|
+
"metadata": {},
|
933
|
+
"outputs": [],
|
934
|
+
"source": []
|
935
|
+
}
|
936
|
+
],
|
937
|
+
"metadata": {
|
938
|
+
"kernelspec": {
|
939
|
+
"display_name": "Python 3 (ipykernel)",
|
940
|
+
"language": "python",
|
941
|
+
"name": "python3"
|
942
|
+
},
|
943
|
+
"language_info": {
|
944
|
+
"codemirror_mode": {
|
945
|
+
"name": "ipython",
|
946
|
+
"version": 3
|
947
|
+
},
|
948
|
+
"file_extension": ".py",
|
949
|
+
"mimetype": "text/x-python",
|
950
|
+
"name": "python",
|
951
|
+
"nbconvert_exporter": "python",
|
952
|
+
"pygments_lexer": "ipython3",
|
953
|
+
"version": "3.12.2"
|
954
|
+
}
|
955
|
+
},
|
956
|
+
"nbformat": 4,
|
957
|
+
"nbformat_minor": 5
|
958
|
+
}
|