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.
Files changed (63) hide show
  1. meta_ae/action_items.py +10 -2
  2. meta_ae/baker_recipes.py +1 -2
  3. meta_ae/tests/tests/test_actions.py +1 -2
  4. meta_analytics/README.rst +1 -2
  5. meta_analytics/notebooks/anu.ipynb +95 -0
  6. meta_analytics/notebooks/appointment_planning.ipynb +329 -0
  7. meta_analytics/notebooks/arvs.ipynb +103 -0
  8. meta_analytics/notebooks/cleaning/consent_v1_ext.ipynb +227 -0
  9. meta_analytics/notebooks/cleaning/offschedule_eos.ipynb +353 -0
  10. meta_analytics/notebooks/dsmc/renal_dysfunction.ipynb +435 -0
  11. meta_analytics/notebooks/endpoints/meta_endpoints_by_date.ipynb +664 -0
  12. meta_analytics/notebooks/followup_examination.ipynb +141 -0
  13. meta_analytics/notebooks/hba1c.ipynb +136 -0
  14. meta_analytics/notebooks/hiv_regimens.ipynb +122 -118
  15. meta_analytics/notebooks/incidence.ipynb +232 -0
  16. meta_analytics/notebooks/liver.ipynb +389 -0
  17. meta_analytics/notebooks/magreth.ipynb +645 -0
  18. meta_analytics/notebooks/monitoring_report.ipynb +721 -448
  19. meta_analytics/notebooks/pharmacy.ipynb +405 -306
  20. meta_analytics/notebooks/pharmacy_stock_202410.ipynb +306 -0
  21. meta_analytics/notebooks/steering.ipynb +61 -0
  22. meta_analytics/notebooks/undiagnosed/meta3_screening_consort_chart.ipynb +1176 -0
  23. meta_analytics/notebooks/undiagnosed/meta3_screening_undiagnosed.ipynb +519 -0
  24. meta_analytics/notebooks/undiagnosed/meta_screening_table2.ipynb +964 -0
  25. meta_analytics/notebooks/undiagnosed/screen_undiagnosed_or.ipynb +296 -0
  26. meta_analytics/notebooks/undiagnosed/screening.ipynb +273 -0
  27. meta_analytics/notebooks/undiagnosed/screening2.ipynb +958 -0
  28. meta_analytics/notebooks/undiagnosed/screening_undiagnosed_20241002.ipynb +958 -0
  29. meta_analytics/notebooks/ven.ipynb +191 -0
  30. meta_analytics/notebooks/vitals.ipynb +263 -0
  31. meta_edc/settings/debug.py +3 -2
  32. meta_edc/urls.py +1 -0
  33. {meta_edc-1.0.7.dist-info → meta_edc-1.1.1.dist-info}/METADATA +3 -3
  34. {meta_edc-1.0.7.dist-info → meta_edc-1.1.1.dist-info}/RECORD +62 -35
  35. {meta_edc-1.0.7.dist-info → meta_edc-1.1.1.dist-info}/WHEEL +1 -1
  36. meta_labs/reportables.py +14 -11
  37. meta_labs/tests/test_reportables.py +33 -12
  38. meta_pharmacy/notebooks/pharmacy.ipynb +41 -0
  39. meta_prn/admin/offschedule_pregnancy_admin.py +3 -3
  40. meta_prn/admin/onschedule_dm_referral_admin.py +5 -5
  41. meta_prn/form_validators/end_of_study.py +2 -2
  42. meta_prn/migrations/0063_historicaloffstudymedication_singleton_field_and_more.py +37 -0
  43. meta_prn/migrations/0064_auto_20250602_2143.py +18 -0
  44. meta_prn/models/end_of_study.py +2 -0
  45. meta_prn/models/off_study_medication.py +2 -0
  46. meta_reports/admin/last_imp_refill_admin.py +3 -2
  47. meta_screening/eligibility/eligibility_part_three/base_eligibility_part_three.py +59 -47
  48. meta_screening/form_validators/screening_part_three.py +6 -1
  49. meta_screening/tests/meta_test_case_mixin.py +3 -0
  50. meta_screening/tests/tests/test_forms.py +9 -2
  51. meta_screening/tests/tests/test_screening_part_three.py +11 -14
  52. meta_subject/action_items.py +2 -3
  53. meta_subject/choices.py +2 -1
  54. meta_subject/form_validators/delivery_form_validator.py +1 -0
  55. meta_subject/forms/blood_results/blood_results_rft_form.py +60 -3
  56. meta_subject/forms/delivery_form.py +2 -0
  57. meta_subject/migrations/0223_bloodresultsfbc_errors_bloodresultsgludummy_errors_and_more.py +83 -0
  58. meta_subject/migrations/0224_bloodresultsfbc_abnormal_summary_and_more.py +153 -0
  59. meta_subject/tests/tests/test_egfr.py +5 -5
  60. meta_analytics/dataframes/enrolled/__init__.py +0 -0
  61. {meta_edc-1.0.7.dist-info → meta_edc-1.1.1.dist-info}/licenses/AUTHORS.rst +0 -0
  62. {meta_edc-1.0.7.dist-info → meta_edc-1.1.1.dist-info}/licenses/LICENSE +0 -0
  63. {meta_edc-1.0.7.dist-info → meta_edc-1.1.1.dist-info}/top_level.txt +0 -0
meta_analytics/notebooks/followup_examination.ipynb ADDED
@@ -0,0 +1,141 @@
1
+ {
2
+ "cells": [
3
+ {
4
+ "cell_type": "code",
5
+ "execution_count": null,
6
+ "id": "0",
7
+ "metadata": {},
8
+ "outputs": [],
9
+ "source": [
10
+ "%%capture\n",
11
+ "import os\n",
12
+ "from pathlib import Path\n",
13
+ "import pandas as pd\n",
14
+ "from dj_notebook import activate\n",
15
+ "\n",
16
+ "env_file = os.environ[\"META_ENV\"]\n",
17
+ "reports_folder = Path(os.environ[\"META_REPORTS_FOLDER\"])\n",
18
+ "analysis_folder = Path(os.environ[\"META_ANALYSIS_FOLDER\"])\n",
19
+ "pharmacy_folder = Path(os.environ[\"META_PHARMACY_FOLDER\"])\n",
20
+ "plus = activate(dotenv_file=env_file)"
21
+ ]
22
+ },
23
+ {
24
+ "cell_type": "code",
25
+ "execution_count": null,
26
+ "id": "1",
27
+ "metadata": {},
28
+ "outputs": [],
29
+ "source": [
30
+ "from edc_pdutils.dataframes.get_subject_visit import convert_visit_code_to_float\n",
31
+ "from edc_pdutils.dataframes import get_crf\n",
32
+ "from edc_model_to_dataframe import read_frame_edc\n",
33
+ "from meta_subject.models import FollowupExamination\n"
34
+ ]
35
+ },
36
+ {
37
+ "cell_type": "code",
38
+ "execution_count": null,
39
+ "id": "2",
40
+ "metadata": {},
41
+ "outputs": [],
42
+ "source": [
43
+ "\n",
44
+ "df = read_frame_edc(FollowupExamination.objects.all(), drop_sys_columns=True, drop_action_item_columns=True)\n",
45
+ "df = df.replace(\"none\", pd.NA)\n",
46
+ "df = df.replace(\"none\", pd.NA)\n",
47
+ "df = df.fillna(pd.NA)\n",
48
+ "convert_visit_code_to_float(df)"
49
+ ]
50
+ },
51
+ {
52
+ "cell_type": "code",
53
+ "execution_count": null,
54
+ "id": "3",
55
+ "metadata": {},
56
+ "outputs": [],
57
+ "source": [
58
+ "from edc_analytics.stata import get_stata_labels_from_model\n",
59
+ "\n",
60
+ "df = df[[\"subject_identifier\", \"subject_visit_id\", \"report_datetime\", \"visit_code\", \"site_id\", \"site_name\", \"visit_reason\", \"symptoms\",\"symptoms_detail\", \"symptoms_sought_care\", \"symptoms_g3\", \"symptoms_g4\", \"comment\"]].copy().reset_index(drop=True)\n",
61
+ "\n",
62
+ "df = df.astype(\n",
63
+ " {col: \"Float64\" for col in df.select_dtypes(include=[\"float\", \"float64\"]).columns}\n",
64
+ ")\n",
65
+ "df_meds = df.astype(\n",
66
+ " {col: \"Int64\" for col in df.select_dtypes(include=[\"int\", \"int64\"]).columns}\n",
67
+ ")\n",
68
+ "df = df.astype(\n",
69
+ " {\n",
70
+ " col: \"datetime64[ns]\"\n",
71
+ " for col in df.select_dtypes(include=[\"datetime\", \"datetime64\"]).columns\n",
72
+ " }\n",
73
+ ")\n",
74
+ "df = df.astype(\n",
75
+ " {\n",
76
+ " col: str\n",
77
+ " for col in df.select_dtypes(include=[\"object\"]).columns\n",
78
+ " }\n",
79
+ ")\n",
80
+ "df = df.fillna(pd.NA)\n",
81
+ "\n",
82
+ "variable_labels = {}\n",
83
+ "variable_labels.update(**get_stata_labels_from_model(df, model=\"meta_subject.followupexamination\", suffix=None))\n",
84
+ "\n",
85
+ "df.to_stata(\n",
86
+ " path=analysis_folder / \"followupexamination.dta\",\n",
87
+ " variable_labels=variable_labels,\n",
88
+ " version=118,\n",
89
+ " write_index=False,\n",
90
+ ")"
91
+ ]
92
+ },
93
+ {
94
+ "cell_type": "code",
95
+ "execution_count": null,
96
+ "id": "4",
97
+ "metadata": {},
98
+ "outputs": [],
99
+ "source": [
100
+ "# with get_crf\n",
101
+ "df2 = get_crf(model=\"meta_subject.followupexamination\", subject_visit_model=\"meta_subject.subjectvisit\")\n"
102
+ ]
103
+ },
104
+ {
105
+ "cell_type": "code",
106
+ "execution_count": null,
107
+ "id": "5",
108
+ "metadata": {},
109
+ "outputs": [],
110
+ "source": [
111
+ "df2.to_stata(\n",
112
+ " path=analysis_folder / \"followupexamination.dta\",\n",
113
+ " variable_labels=variable_labels,\n",
114
+ " version=118,\n",
115
+ " write_index=False,\n",
116
+ ")"
117
+ ]
118
+ }
119
+ ],
120
+ "metadata": {
121
+ "kernelspec": {
122
+ "display_name": "Python 3",
123
+ "language": "python",
124
+ "name": "python3"
125
+ },
126
+ "language_info": {
127
+ "codemirror_mode": {
128
+ "name": "ipython",
129
+ "version": 2
130
+ },
131
+ "file_extension": ".py",
132
+ "mimetype": "text/x-python",
133
+ "name": "python",
134
+ "nbconvert_exporter": "python",
135
+ "pygments_lexer": "ipython2",
136
+ "version": "2.7.6"
137
+ }
138
+ },
139
+ "nbformat": 4,
140
+ "nbformat_minor": 5
141
+ }
meta_analytics/notebooks/hba1c.ipynb ADDED
@@ -0,0 +1,136 @@
1
+ {
2
+ "cells": [
3
+ {
4
+ "cell_type": "code",
5
+ "execution_count": null,
6
+ "id": "0",
7
+ "metadata": {},
8
+ "outputs": [],
9
+ "source": [
10
+ "%%capture\n",
11
+ "import os\n",
12
+ "import pandas as pd\n",
13
+ "import numpy as np\n",
14
+ "from dj_notebook import activate\n",
15
+ "from django_pandas.io import read_frame\n",
16
+ "from pathlib import Path\n",
17
+ "\n",
18
+ "env_file = os.environ[\"META_ENV\"]\n",
19
+ "documents_folder = os.environ[\"META_DOCUMENTS_FOLDER\"]\n",
20
+ "plus = activate(dotenv_file=env_file)\n",
21
+ "report_folder = Path(documents_folder)\n"
22
+ ]
23
+ },
24
+ {
25
+ "cell_type": "code",
26
+ "execution_count": null,
27
+ "id": "1",
28
+ "metadata": {},
29
+ "outputs": [],
30
+ "source": [
31
+ "from meta_screening.models import SubjectScreening\n",
32
+ "\n",
33
+ "df = read_frame(SubjectScreening.objects.values(\"screening_identifier\", \"hba1c_performed\", \"hba1c_datetime\", \"hba1c_value\").all())"
34
+ ]
35
+ },
36
+ {
37
+ "cell_type": "code",
38
+ "execution_count": null,
39
+ "id": "2",
40
+ "metadata": {},
41
+ "outputs": [],
42
+ "source": [
43
+ "df.hba1c_value.describe()"
44
+ ]
45
+ },
46
+ {
47
+ "cell_type": "code",
48
+ "execution_count": null,
49
+ "id": "3",
50
+ "metadata": {},
51
+ "outputs": [],
52
+ "source": [
53
+ "df[\"hba1c_value\"] = df.hba1c_value.astype(float)"
54
+ ]
55
+ },
56
+ {
57
+ "cell_type": "code",
58
+ "execution_count": null,
59
+ "id": "4",
60
+ "metadata": {},
61
+ "outputs": [],
62
+ "source": [
63
+ "df.hba1c_value.describe()\n"
64
+ ]
65
+ },
66
+ {
67
+ "cell_type": "code",
68
+ "execution_count": null,
69
+ "id": "5",
70
+ "metadata": {},
71
+ "outputs": [],
72
+ "source": [
73
+ "df[df.hba1c_value<=6.4][\"hba1c_value\"].describe()"
74
+ ]
75
+ },
76
+ {
77
+ "cell_type": "code",
78
+ "execution_count": null,
79
+ "id": "6",
80
+ "metadata": {},
81
+ "outputs": [],
82
+ "source": [
83
+ "df[df.hba1c_value<6.5][\"hba1c_value\"].describe()\n"
84
+ ]
85
+ },
86
+ {
87
+ "cell_type": "code",
88
+ "execution_count": null,
89
+ "id": "7",
90
+ "metadata": {},
91
+ "outputs": [],
92
+ "source": [
93
+ "df[df.hba1c_value>=6.5][\"hba1c_value\"].describe()\n"
94
+ ]
95
+ },
96
+ {
97
+ "cell_type": "code",
98
+ "execution_count": null,
99
+ "id": "8",
100
+ "metadata": {},
101
+ "outputs": [],
102
+ "source": [
103
+ "df.to_csv(report_folder / \"hba1c.csv\")\n"
104
+ ]
105
+ },
106
+ {
107
+ "cell_type": "code",
108
+ "execution_count": null,
109
+ "id": "9",
110
+ "metadata": {},
111
+ "outputs": [],
112
+ "source": []
113
+ }
114
+ ],
115
+ "metadata": {
116
+ "kernelspec": {
117
+ "display_name": "Python 3",
118
+ "language": "python",
119
+ "name": "python3"
120
+ },
121
+ "language_info": {
122
+ "codemirror_mode": {
123
+ "name": "ipython",
124
+ "version": 2
125
+ },
126
+ "file_extension": ".py",
127
+ "mimetype": "text/x-python",
128
+ "name": "python",
129
+ "nbconvert_exporter": "python",
130
+ "pygments_lexer": "ipython2",
131
+ "version": "2.7.6"
132
+ }
133
+ },
134
+ "nbformat": 4,
135
+ "nbformat_minor": 5
136
+ }