Abandon attempt at alternative stratification

gyorilab · Mar 26, 2024 · e8a8679 · e8a8679
1 parent 9acc197
commit e8a8679
Showing 1 changed file with 52 additions and 17 deletions.
diff --git a/notebooks/evaluation_2024.03/scenario1/epi_eval_sc1_strains.ipynb b/notebooks/evaluation_2024.03/scenario1/epi_eval_sc1_strains.ipynb
@@ -283,7 +283,7 @@
    "id": "cc5147cc-9830-4b99-b144-0fa42eeaa61c",
    "metadata": {},
    "source": [
-    "## Alternative approach"
+    "## Alternative approach (currently abandoned)"
    ]
   },
   {
@@ -293,7 +293,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Do the recovery branches first\n",
+    "# # Do the recovery branches first\n",
+    "# # FixMe: this only doesn't cover the cross-recovery process e.g. \n",
+    "# #  I_alpha_delta -> R_alpha_delta is covered but I_delta_alpha -> R_alpha_delta isn't.\n",
     "# reinf_params = {}\n",
     "# recov_init = NaturalConversion(\n",
     "#     subject=infected,\n",
@@ -324,7 +326,35 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Couple the infection processes together\n",
+    "# # Couple the infectious states together with the susceptible states\n",
+    "# rec_concepts = recovery_model.get_concepts_name_map()\n",
+    "\n",
+    "# infected_alpha = rec_concepts['infected_population_alpha']\n",
+    "# recovered_alpha = rec_concepts['immune_population_alpha']\n",
+    "\n",
+    "#  = rec_concepts['infected_population_delta']\n",
+    "#  = rec_concepts['immune_population_delta']\n",
+    "\n",
+    "#  = rec_concepts['infected_population_omicron']\n",
+    "#  = rec_concepts['immune_population_omicron']\n",
+    "\n",
+    "#  = rec_concepts['infected_population_alpha_delta']\n",
+    "#  = rec_concepts['infected_population_delta_alpha']\n",
+    "#  = rec_concepts['immune_population_alpha_delta']\n",
+    "\n",
+    "#  = rec_concepts['infected_population_alpha_omicron']\n",
+    "#  = rec_concepts['infected_population_omicron_alpha']\n",
+    "#  = rec_concepts['immune_population_omicron_alpha']\n",
+    " \n",
+    "#  = rec_concepts['infected_population_delta_omicron']\n",
+    "#  = rec_concepts['infected_population_omicron_delta']\n",
+    "#  = rec_concepts['immune_population_delta_omicron']\n",
+    "\n",
+    "# infected_alpha_delta_omicron = rec_concepts['infected_population_alpha_delta_omicron']\n",
+    "# infected_alpha_omicron_delta = rec_concepts['infected_population_alpha_omicron_delta']\n",
+    "# infected_delta_omicron_alpha = rec_concepts['infected_population_delta_omicron_alpha']\n",
+    "#  = rec_concepts['immune_population_alpha_delta_omicron']\n",
+    "\n",
     "# alpha_infectors = [infected_alpha, infected_delta_alpha, infected_omicron_alpha, infected_delta_omicron_alpha]\n",
     "# alpha_susceptibles = [susceptible, recovered_delta, recovered_omicron, recovered_delta_omicron]\n",
     "\n",
@@ -335,15 +365,28 @@
     "# omicron_susceptibles = [susceptible, recovered_alpha, recovered_delta, recovered_alpha_delta]\n",
     "\n",
     "# infection_templates = []\n",
+    "# infection_parameters = {}\n",
+    "# inf_rate_name = \"beta_{ix}_{inf_name}\"\n",
     "# for strain, inf_agents, susceptibles in [\n",
     "#         ('alpha', alpha_infectors, alpha_susceptibles), \n",
     "#         ('delta', delta_infectors, delta_susceptibles),\n",
     "#         ('omicron', omicron_infectors, omicron_susceptibles)\n",
     "# ]:\n",
     "#     # For each each susceptible, create an infection process from all possible infection states\n",
-    "#     for subject in susceptibles:\n",
-    "#         for infected in inf_agents:\n",
-    "            "
+    "#     for subject, outcome in zip(susceptibles, inf_agents):\n",
+    "#         for ix, infected in enumerate(inf_agents):\n",
+    "#             cc = ControlledConversion(\n",
+    "#                 subject=subject,\n",
+    "#                 controller=infected,\n",
+    "#                 outcome=outcome\n",
+    "#             )\n",
+    "#             param_name = inf_rate_name.format(ix=ix, inf_name=strain)\n",
+    "#             cc.set_mass_action_rate_law(param_name)\n",
+    "#             infection_parameters[param_name] = Parameter(name=param_name, value=1)\n",
+    "#             infection_templates.append(cc)\n",
+    "\n",
+    "# infections_model = TemplateModel(templates=infection_templates, parameters=infection_parameters)\n",
+    "# infections_model.draw_jupyter('infections_model.png')"
    ]
   },
   {
@@ -353,18 +396,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Now do one stratification where the recovered from reinfection, R', get reinfected to \n",
-    "       \n",
-    "# strat1_model.draw_jupyter(\"sir_strat1.png\")"
+    "# # Now combine the infectiontion and recovery models\n",
+    "# alt_model = recovery_model.extend(template_model=infections_model, parameter_mapping=infections_model.parameters)\n",
+    "# alt_model.draw_jupyter(\"sir_3strain_alt.png\")"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "5fd7b879-18e9-4760-9b65-fa82d2505c34",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {