Update hospitalisation_prediction_uti.ipynb

opensafely · Mar 22, 2024 · 0ba8b79 · 0ba8b79
1 parent c33ed0a
commit 0ba8b79
Showing 1 changed file with 88 additions and 0 deletions.
diff --git a/analysis/hospitalisation_prediction_uti.ipynb b/analysis/hospitalisation_prediction_uti.ipynb
@@ -2175,6 +2175,30 @@
     "\n"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from lifelines import CoxPHFitter\n",
+    "\n",
+    "# Assuming you have already fitted your Cox model (cph_lrti_no_abs_incdt)\n",
+    "# Make sure you have imported necessary libraries and packages for CoxPHFitter\n",
+    "\n",
+    "# Assuming data_uti_no_abs_incdt_test contains the test dataset\n",
+    "\n",
+    "# Fit the Cox model on the test dataset\n",
+    "cph_uti_no_abs_incdt.fit(data_uti_no_abs_incdt_test, duration_col='duration_uti_admitted', event_col='event_uti_admitted')\n",
+    "\n",
+    "# Predict the survival probabilities at day 30\n",
+    "time_to_predict = 30  # in days\n",
+    "survival_probability_at_30_days = cph_uti_no_abs_incdt.predict_survival_function(pd.Series([time_to_predict]))\n",
+    "\n",
+    "# Print or use the predicted survival probability\n",
+    "print(\"Survival probability at day 30:\", survival_probability_at_30_days.iloc[0, 0])"
+   ]
+  },
   {
    "attachments": {},
    "cell_type": "markdown",
@@ -3069,6 +3093,30 @@
     "    print(\"\\nerror_4: an error occurred in calculating c-stats of validation dataset and/or printing outputs.\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from lifelines import CoxPHFitter\n",
+    "\n",
+    "# Assuming you have already fitted your Cox model (cph_lrti_abs_incdt)\n",
+    "# Make sure you have imported necessary libraries and packages for CoxPHFitter\n",
+    "\n",
+    "# Assuming data_uti_no_abs_incdt_test contains the test dataset\n",
+    "\n",
+    "# Fit the Cox model on the test dataset\n",
+    "cph_uti_abs_incdt.fit(data_uti_no_abs_incdt_test, duration_col='duration_uti_admitted', event_col='event_uti_admitted')\n",
+    "\n",
+    "# Predict the survival probabilities at day 30\n",
+    "time_to_predict = 30  # in days\n",
+    "survival_probability_at_30_days = cph_uti_abs_incdt.predict_survival_function(pd.Series([time_to_predict]))\n",
+    "\n",
+    "# Print or use the predicted survival probability\n",
+    "print(\"Survival probability at day 30:\", survival_probability_at_30_days.iloc[0, 0])"
+   ]
+  },
   {
    "attachments": {},
    "cell_type": "markdown",
@@ -3963,6 +4011,26 @@
     "    print(\"\\nerror_4: an error occurred in calculating c-stats of validation dataset and/or printing outputs.\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from lifelines import CoxPHFitter\n",
+    "\n",
+    "\n",
+    "# Fit the Cox model on the test dataset\n",
+    "cph_uti_no_abs_prevl.fit(data_uti_no_abs_incdt_test, duration_col='duration_uti_admitted', event_col='event_uti_admitted')\n",
+    "\n",
+    "# Predict the survival probabilities at day 30\n",
+    "time_to_predict = 30  # in days\n",
+    "survival_probability_at_30_days = cph_uti_no_abs_prevl.predict_survival_function(pd.Series([time_to_predict]))\n",
+    "\n",
+    "# Print or use the predicted survival probability\n",
+    "print(\"Survival probability at day 30:\", survival_probability_at_30_days.iloc[0, 0])"
+   ]
+  },
   {
    "attachments": {},
    "cell_type": "markdown",
@@ -4858,6 +4926,26 @@
     "    print(\"\\nerror_4: an error occurred in calculating c-stats of validation dataset and/or printing outputs.\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from lifelines import CoxPHFitter\n",
+    "\n",
+    "\n",
+    "# Fit the Cox model on the test dataset\n",
+    "cph_uti_abs_prevl.fit(data_uti_no_abs_incdt_test, duration_col='duration_uti_admitted', event_col='event_uti_admitted')\n",
+    "\n",
+    "# Predict the survival probabilities at day 30\n",
+    "time_to_predict = 30  # in days\n",
+    "survival_probability_at_30_days = cph_uti_abs_prevl.predict_survival_function(pd.Series([time_to_predict]))\n",
+    "\n",
+    "# Print or use the predicted survival probability\n",
+    "print(\"Survival probability at day 30:\", survival_probability_at_30_days.iloc[0, 0])"
+   ]
+  },
   {
    "attachments": {},
    "cell_type": "markdown",