Created using Colaboratory

Author: mitzimorris

jupyter/covid-inf-rate/SantaClara_CmdStanR.ipynb

@@ -350,6 +350,16 @@
       "execution_count": 0,
       "outputs": []
     },
+    {
+      "cell_type": "markdown",
+      "metadata": {
+        "id": "yWNEf0sdC1Kk",
+        "colab_type": "text"
+      },
+      "source": [
+        "In order to avoid divergent iterations, which result in biased estimates, we set the parameter `adapt_delta` to 0.98."
+      ]
+    },
     {
       "cell_type": "code",
       "metadata": {
@@ -359,7 +369,7 @@
       },
       "source": [
         "hier_model <- cmdstan_model(stan_file='hier_sens_spec.stan')\n",
-        "hier_fit <- hier_model$sample(data='santa_clara_all.data.json')\n"
+        "hier_fit <- hier_model$sample(data='santa_clara_all.data.json', adapt_delta=0.98)\n"
       ],
       "execution_count": 0,
       "outputs": []
@@ -421,7 +431,7 @@
       },
       "source": [
         "hier_model_v2 <- cmdstan_model(stan_file='hier_sens_spec_offset_mult.stan')\n",
-        "hier_fit_v2 <- hier_model_v2$sample(data='santa_clara_all.data.json')"
+        "hier_fit_v2 <- hier_model_v2$sample(data='santa_clara_all.data.json', adapt_delta=0.98)"
       ],
       "execution_count": 0,
       "outputs": []