Merge branch 'master' of https://github.com/stan-dev/example-models

Author: mitzimorris

jupyter/covid-inf-rate/SantaClara_CmdStanPy.ipynb

@@ -6,7 +6,7 @@
       "name": "SantaClara_CmdStanPy.ipynb",
       "provenance": [],
       "collapsed_sections": [],
-      "authorship_tag": "ABX9TyMfi5qWhQilw+LVRY7NrH0W",
+      "authorship_tag": "ABX9TyNh1NuXuIIVzc5g9FQpoq1m",
       "include_colab_link": true
     },
     "kernelspec": {
@@ -382,7 +382,20 @@
       },
       "source": [
         "hier_model = CmdStanModel(stan_file='hier_sens_spec.stan')\n",
-        "hier_fit = hier_model.sample(data=hier_data)"
+        "hier_fit = hier_model.sample(data=hier_data, adapt_delta=0.98)"
+      ],
+      "execution_count": 0,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "qCOV7poz_nSM",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
+        "hier_fit.diagnose()"
       ],
       "execution_count": 0,
       "outputs": []
@@ -456,7 +469,20 @@
       },
       "source": [
         "hier_model_v2 = CmdStanModel(stan_file='hier_sens_spec_offset_mult.stan')\n",
-        "hier_fit_v2 = hier_model_v2.sample(data=hier_data)\n",
+        "hier_fit_v2 = hier_model_v2.sample(data=hier_data, adapt_delta=0.98)\n",
+        "hier_fit_v2.diagnose()"
+      ],
+      "execution_count": 0,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "metadata": {
+        "id": "K4pUuA7e_zpl",
+        "colab_type": "code",
+        "colab": {}
+      },
+      "source": [
         "hier_fit_v2.summary().loc[['p', 'mu_logit_spec', 'sigma_logit_spec', 'mu_logit_sens', 'sigma_logit_sens'],].round(decimals=3)"
       ],
       "execution_count": 0,