Few more changes to tidy up notebook 06

monash-emu · Feb 8, 2024 · d6ecd96 · d6ecd96
1 parent da7f87b
commit d6ecd96
Showing 1 changed file with 8 additions and 35 deletions.
diff --git a/renew/06-calibration.ipynb b/renew/06-calibration.ipynb
@@ -86,7 +86,7 @@
     "priors.append(esp.UniformPrior(proc_req['name'], (proc_req['lower'], proc_req['upper']), size=n_process_periods))\n",
     "renewal_model = RenewalModel(calib_kwargs['pop'], n_times, run_in, n_process_periods)\n",
     "obj_func = get_obj_func(renewal_model)\n",
-    "n_draws = 100\n",
+    "n_draws = 100  # This is obviously far too short - demonstration code only\n",
     "\n",
     "with pm.Model() as pmm:\n",
     "    variables = use_model(priors, obj_func)\n",
@@ -103,33 +103,16 @@
     "az.summary(idata)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "8e294388",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "mean_posterior_params = mpp = np.array(az.summary(idata)[\"mean\"])"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "85898c36",
    "metadata": {},
    "outputs": [],
    "source": [
-    "incidence = renewal_model.func(mpp[0], mpp[1], mpp[4:], np.log(mpp[3])).incidence * mpp[2]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "5f77ea75-5a92-45ec-bafc-2e417d7457c2",
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "# Pull out a parameter set to look at a single run\n",
+    "mpp = np.array(az.summary(idata)[\"mean\"])\n",
+    "incidence = renewal_model.func(mpp[0], mpp[1], mpp[4:], np.log(mpp[3])).incidence * mpp[2]\n",
     "inc = pd.DataFrame(incidence)\n",
     "inc[\"targets\"] = mys_data\n",
     "inc.plot()"
@@ -159,9 +142,10 @@
     "spaghetti = pd.DataFrame()\n",
     "for i, p in enumerate(sample_params):\n",
     "    incidence = renewal_model.func(p['gen_mean'], p['gen_sd'], p['random_process'], np.log(p['seed'])).incidence\n",
-    "    cdr = p['cdr']\n",
-    "    spaghetti[i] = incidence * cdr\n",
-    "spaghetti.columns = sample_params.index.to_flat_index().map(str)"
+    "    spaghetti[i] = incidence * p['cdr']\n",
+    "spaghetti.columns = sample_params.index.to_flat_index().map(str)\n",
+    "spaghetti['targets'] = calib_kwargs['targets']\n",
+    "spaghetti.plot()"
    ]
   },
   {
@@ -177,17 +161,6 @@
     "params_table = params_table.rename_axis(None)\n",
     "params_table = params_table.rename(columns={'init': 'Starting value', 'lower': 'Lower limit', 'upper': 'Upper limit'})"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "70ab40ed-8da4-4464-bb7b-64058bf063f1",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "spaghetti['targets'] = calib_kwargs['targets']\n",
-    "spaghetti.plot()"
-   ]
   }
  ],
  "metadata": {