Implement age-specific param table

docs/tex/tex_descriptions/models/sm_covid/model_description.tex

@@ -114,6 +114,9 @@ \subsubsection{Model parameters}
 \renewcommand{\arraystretch}{1.3}
 \input{../../tex_descriptions/projects/sm_covid/param_table.tex} 
 
+\renewcommand{\arraystretch}{1.3}
+\input{../../tex_descriptions/projects/sm_covid/agespec_table.tex} 
+
 % ____________________________________________________
 % Now, let's talk about the convolution processes
 %______________________________________________________

docs/tex/tex_descriptions/projects/sm_covid/agespec_table.tex

@@ -0,0 +1,28 @@
+\begin{table}
+\centering
+\caption{Age-specific parameters for wild-type COVID-19}
+\label{agespec_table}
+\begin{tabular}{p{2cm} p{3cm} p{3cm} p{3cm} p{3cm}}
+\toprule
+   Age group & Rel. suscepitbility to infection (ref. 15-69 y.o.)\cite{zhang-2020-a} & Proportion symptomatic\cite{sah-2021} & Proportion of symptomatic patients hospitalised [CURRENTLY USING Dutch GGD report from 4th August 2020, Table 3] & Infection fatality rate\cite{odriscoll-2021} \\
+\midrule
+0-4 & 0.36 & 0.533 & 0.0777 & 0.00003 \\
+5-9 & 0.36 & 0.533 & 0.0069 & 0.00001 \\
+10-14 & 0.36 & 0.533 & 0.0034 & 0.00001 \\
+15-19 & 1.00 & 0.533 & 0.0051 & 0.00003 \\
+20-24 & 1.00 & 0.679 & 0.0068 & 0.00006 \\
+25-29 & 1.00 & 0.679 & 0.0080 & 0.00013 \\
+30-34 & 1.00 & 0.679 & 0.0124 & 0.00024 \\
+35-39 & 1.00 & 0.679 & 0.0129 & 0.00040 \\
+40-44 & 1.00 & 0.679 & 0.0190 & 0.00075 \\
+45-49 & 1.00 & 0.679 & 0.0331 & 0.00121 \\
+50-54 & 1.00 & 0.679 & 0.0383 & 0.00207 \\
+55-59 & 1.00 & 0.679 & 0.0579 & 0.00323 \\
+60-64 & 1.00 & 0.803 & 0.0617 & 0.00456 \\
+65-69 & 1.00 & 0.803 & 0.1030 & 0.01075 \\
+70-74 & 1.41 & 0.803 & 0.1072 & 0.01674 \\
+75-79 & 1.41 & 0.803 & 0.0703 & 0.03203 \\
+80 and above & 1.41 & 0.803 & 0.0703 & 0.08292 \\
+\bottomrule
+\end{tabular}
+\end{table}

notebooks/user/rragonnet/project_specific/School_Closure/agespec_param_table.ipynb

@@ -0,0 +1,148 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from autumn.projects.sm_covid2.common_school.project_maker import get_school_project_parameter_set\n",
+    "import pandas as pd\n",
+    "from copy import copy\n",
+    "from pathlib import Path"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model_params = get_school_project_parameter_set(\n",
+    "    iso3 = \"FRA\",\n",
+    "    first_date_with_death = 0,\n",
+    "    sero_age_min = 0,\n",
+    "    sero_age_max = 100,\n",
+    "    analysis='main'\n",
+    ").baseline\n",
+    "age_params = model_params['age_stratification']"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df = pd.DataFrame()\n",
+    "df['ifr'] = pd.Series(age_params['ifr']['values'])\n",
+    "df['susceptibility'] = pd.Series(age_params['susceptibility'])\n",
+    "df['prop_symptomatic'] = pd.Series(age_params['prop_symptomatic'])\n",
+    "df['prop_hospital'] = pd.Series(age_params['prop_hospital']['values'])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# fill missing values for 80+ category\n",
+    "for column in (\"susceptibility\", \"prop_symptomatic\", \"prop_hospital\"):\n",
+    "    df[column].loc[80] = df[column].loc[75]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# new column for age group\n",
+    "def get_agegroup_str(idx):\n",
+    "    if idx < 80:\n",
+    "        return f\"{idx}-{idx + 4}\"\n",
+    "    else:\n",
+    "        return \"80 and above\"\n",
+    "\n",
+    "df['agegroup'] = [get_agegroup_str(idx) for idx in df.index]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pd.set_option('display.max_colwidth', 2)\n",
+    "tex_table = df.to_latex(\n",
+    "    columns=['agegroup', 'susceptibility', 'prop_symptomatic', 'prop_hospital', 'ifr'],\n",
+    "    header=['Age group', \"Rel. suscepitbility to infection (ref. 15-69 y.o.)\\cite{zhang-2020-a}\", \"Proportion symptomatic\\cite{sah-2021}\", \"Proportion of symptomatic patients hospitalised [CURRENTLY USING Dutch GGD report from 4th August 2020, Table 3]\", \"Infection fatality rate\\cite{odriscoll-2021}\"],\n",
+    "    index=False,\n",
+    "    label=\"agespec_table\",\n",
+    "    caption=\"Age-specific parameters for wild-type COVID-19\"\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tex_table = tex_table.replace(\"{lrrrr}\", \"{p{2cm} p{3cm} p{3cm} p{3cm} p{3cm}}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Handle citations\n",
+    "tex_table = tex_table.replace(\"\\\\textbackslash cite\\\\\", r\"\\cite\").replace(\"\\\\}\", \"}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "out_path = Path.home() / \"Models\"/ \"AuTuMN_new\" / \"docs\" / \"tex\" / \"tex_descriptions\" / \"projects\" / \"sm_covid\" / \"agespec_table.tex\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with out_path.open(\"w\") as f:\n",
+    "    f.write(tex_table)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "summer2",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.11"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}