meta-edc 1.1.8__py3-none-any.whl → 1.1.12__py3-none-any.whl

meta_analytics/notebooks/followup_examination.ipynb

@@ -1,141 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "0",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%%capture\n",
-    "import os\n",
-    "from pathlib import Path\n",
-    "import pandas as pd\n",
-    "from dj_notebook import activate\n",
-    "\n",
-    "env_file = os.environ[\"META_ENV\"]\n",
-    "reports_folder = Path(os.environ[\"META_REPORTS_FOLDER\"])\n",
-    "analysis_folder = Path(os.environ[\"META_ANALYSIS_FOLDER\"])\n",
-    "pharmacy_folder = Path(os.environ[\"META_PHARMACY_FOLDER\"])\n",
-    "plus = activate(dotenv_file=env_file)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from edc_pdutils.dataframes.get_subject_visit import convert_visit_code_to_float\n",
-    "from edc_pdutils.dataframes import get_crf\n",
-    "from edc_model_to_dataframe import read_frame_edc\n",
-    "from meta_subject.models import FollowupExamination\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "2",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "\n",
-    "df = read_frame_edc(FollowupExamination.objects.all(), drop_sys_columns=True, drop_action_item_columns=True)\n",
-    "df = df.replace(\"none\", pd.NA)\n",
-    "df = df.replace(\"none\", pd.NA)\n",
-    "df = df.fillna(pd.NA)\n",
-    "convert_visit_code_to_float(df)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "3",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from edc_analytics.stata import get_stata_labels_from_model\n",
-    "\n",
-    "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",
-    "\n",
-    "df = df.astype(\n",
-    "    {col: \"Float64\" for col in df.select_dtypes(include=[\"float\", \"float64\"]).columns}\n",
-    ")\n",
-    "df_meds = df.astype(\n",
-    "    {col: \"Int64\" for col in df.select_dtypes(include=[\"int\", \"int64\"]).columns}\n",
-    ")\n",
-    "df = df.astype(\n",
-    "    {\n",
-    "        col: \"datetime64[ns]\"\n",
-    "        for col in df.select_dtypes(include=[\"datetime\", \"datetime64\"]).columns\n",
-    "    }\n",
-    ")\n",
-    "df = df.astype(\n",
-    "    {\n",
-    "        col: str\n",
-    "        for col in df.select_dtypes(include=[\"object\"]).columns\n",
-    "    }\n",
-    ")\n",
-    "df = df.fillna(pd.NA)\n",
-    "\n",
-    "variable_labels = {}\n",
-    "variable_labels.update(**get_stata_labels_from_model(df, model=\"meta_subject.followupexamination\", suffix=None))\n",
-    "\n",
-    "df.to_stata(\n",
-    "    path=analysis_folder / \"followupexamination.dta\",\n",
-    "    variable_labels=variable_labels,\n",
-    "    version=118,\n",
-    "    write_index=False,\n",
-    ")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "4",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# with get_crf\n",
-    "df2 = get_crf(model=\"meta_subject.followupexamination\", subject_visit_model=\"meta_subject.subjectvisit\")\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "5",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df2.to_stata(\n",
-    "    path=analysis_folder / \"followupexamination.dta\",\n",
-    "    variable_labels=variable_labels,\n",
-    "    version=118,\n",
-    "    write_index=False,\n",
-    ")"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 2
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.6"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

meta_analytics/notebooks/hba1c.ipynb

@@ -1,136 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "0",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%%capture\n",
-    "import os\n",
-    "import pandas as pd\n",
-    "import numpy as np\n",
-    "from dj_notebook import activate\n",
-    "from django_pandas.io import read_frame\n",
-    "from pathlib import Path\n",
-    "\n",
-    "env_file = os.environ[\"META_ENV\"]\n",
-    "documents_folder = os.environ[\"META_DOCUMENTS_FOLDER\"]\n",
-    "plus = activate(dotenv_file=env_file)\n",
-    "report_folder = Path(documents_folder)\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from meta_screening.models import SubjectScreening\n",
-    "\n",
-    "df = read_frame(SubjectScreening.objects.values(\"screening_identifier\", \"hba1c_performed\", \"hba1c_datetime\", \"hba1c_value\").all())"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "2",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df.hba1c_value.describe()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "3",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df[\"hba1c_value\"] = df.hba1c_value.astype(float)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "4",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df.hba1c_value.describe()\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "5",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df[df.hba1c_value<=6.4][\"hba1c_value\"].describe()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df[df.hba1c_value<6.5][\"hba1c_value\"].describe()\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df[df.hba1c_value>=6.5][\"hba1c_value\"].describe()\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "8",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df.to_csv(report_folder / \"hba1c.csv\")\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "9",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 2
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.6"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}