{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Logistic regression with scikit-learn: heart disease data set"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Read data "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>age</th>\n",
       "      <th>sex</th>\n",
       "      <th>cp</th>\n",
       "      <th>trestbps</th>\n",
       "      <th>chol</th>\n",
       "      <th>fbs</th>\n",
       "      <th>restecg</th>\n",
       "      <th>thalach</th>\n",
       "      <th>exang</th>\n",
       "      <th>oldpeak</th>\n",
       "      <th>slope</th>\n",
       "      <th>ca</th>\n",
       "      <th>thal</th>\n",
       "      <th>target</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>63</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>145</td>\n",
       "      <td>233</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>150</td>\n",
       "      <td>0</td>\n",
       "      <td>2.3</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>37</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>130</td>\n",
       "      <td>250</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>187</td>\n",
       "      <td>0</td>\n",
       "      <td>3.5</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>41</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>130</td>\n",
       "      <td>204</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>172</td>\n",
       "      <td>0</td>\n",
       "      <td>1.4</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>56</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>120</td>\n",
       "      <td>236</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>178</td>\n",
       "      <td>0</td>\n",
       "      <td>0.8</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>57</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>120</td>\n",
       "      <td>354</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>163</td>\n",
       "      <td>1</td>\n",
       "      <td>0.6</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>298</th>\n",
       "      <td>57</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>140</td>\n",
       "      <td>241</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>123</td>\n",
       "      <td>1</td>\n",
       "      <td>0.2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>299</th>\n",
       "      <td>45</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>110</td>\n",
       "      <td>264</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>132</td>\n",
       "      <td>0</td>\n",
       "      <td>1.2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>300</th>\n",
       "      <td>68</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>144</td>\n",
       "      <td>193</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>141</td>\n",
       "      <td>0</td>\n",
       "      <td>3.4</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>301</th>\n",
       "      <td>57</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>130</td>\n",
       "      <td>131</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>115</td>\n",
       "      <td>1</td>\n",
       "      <td>1.2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>302</th>\n",
       "      <td>57</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>130</td>\n",
       "      <td>236</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>174</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>303 rows × 14 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     age  sex  cp  trestbps  chol  fbs  restecg  thalach  exang  oldpeak  \\\n",
       "0     63    1   3       145   233    1        0      150      0      2.3   \n",
       "1     37    1   2       130   250    0        1      187      0      3.5   \n",
       "2     41    0   1       130   204    0        0      172      0      1.4   \n",
       "3     56    1   1       120   236    0        1      178      0      0.8   \n",
       "4     57    0   0       120   354    0        1      163      1      0.6   \n",
       "..   ...  ...  ..       ...   ...  ...      ...      ...    ...      ...   \n",
       "298   57    0   0       140   241    0        1      123      1      0.2   \n",
       "299   45    1   3       110   264    0        1      132      0      1.2   \n",
       "300   68    1   0       144   193    1        1      141      0      3.4   \n",
       "301   57    1   0       130   131    0        1      115      1      1.2   \n",
       "302   57    0   1       130   236    0        0      174      0      0.0   \n",
       "\n",
       "     slope  ca  thal  target  \n",
       "0        0   0     1       1  \n",
       "1        0   0     2       1  \n",
       "2        2   0     2       1  \n",
       "3        2   0     2       1  \n",
       "4        2   0     2       1  \n",
       "..     ...  ..   ...     ...  \n",
       "298      1   0     3       0  \n",
       "299      1   0     3       0  \n",
       "300      1   2     3       0  \n",
       "301      1   1     3       0  \n",
       "302      1   1     2       0  \n",
       "\n",
       "[303 rows x 14 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# filename = \"heart.csv\"\n",
    "filename = \"https://www.physi.uni-heidelberg.de/~reygers/lectures/2021/ml/data/heart.csv\"\n",
    "df = pd.read_csv(filename)\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "y = df['target'].values\n",
    "X = df[[col for col in df.columns if col!=\"target\"]]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "from sklearn.model_selection import train_test_split\n",
    "X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.5, shuffle=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Fit the model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/local/home/marks/anaconda3/envs/myML/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:1173: FutureWarning: `penalty='none'`has been deprecated in 1.2 and will be removed in 1.4. To keep the past behaviour, set `penalty=None`.\n",
      "  warnings.warn(\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<style>#sk-container-id-1 {color: black;background-color: white;}#sk-container-id-1 pre{padding: 0;}#sk-container-id-1 div.sk-toggleable {background-color: white;}#sk-container-id-1 label.sk-toggleable__label {cursor: pointer;display: block;width: 100%;margin-bottom: 0;padding: 0.3em;box-sizing: border-box;text-align: center;}#sk-container-id-1 label.sk-toggleable__label-arrow:before {content: \"▸\";float: left;margin-right: 0.25em;color: #696969;}#sk-container-id-1 label.sk-toggleable__label-arrow:hover:before {color: black;}#sk-container-id-1 div.sk-estimator:hover label.sk-toggleable__label-arrow:before {color: black;}#sk-container-id-1 div.sk-toggleable__content {max-height: 0;max-width: 0;overflow: hidden;text-align: left;background-color: #f0f8ff;}#sk-container-id-1 div.sk-toggleable__content pre {margin: 0.2em;color: black;border-radius: 0.25em;background-color: #f0f8ff;}#sk-container-id-1 input.sk-toggleable__control:checked~div.sk-toggleable__content {max-height: 200px;max-width: 100%;overflow: auto;}#sk-container-id-1 input.sk-toggleable__control:checked~label.sk-toggleable__label-arrow:before {content: \"▾\";}#sk-container-id-1 div.sk-estimator input.sk-toggleable__control:checked~label.sk-toggleable__label {background-color: #d4ebff;}#sk-container-id-1 div.sk-label input.sk-toggleable__control:checked~label.sk-toggleable__label {background-color: #d4ebff;}#sk-container-id-1 input.sk-hidden--visually {border: 0;clip: rect(1px 1px 1px 1px);clip: rect(1px, 1px, 1px, 1px);height: 1px;margin: -1px;overflow: hidden;padding: 0;position: absolute;width: 1px;}#sk-container-id-1 div.sk-estimator {font-family: monospace;background-color: #f0f8ff;border: 1px dotted black;border-radius: 0.25em;box-sizing: border-box;margin-bottom: 0.5em;}#sk-container-id-1 div.sk-estimator:hover {background-color: #d4ebff;}#sk-container-id-1 div.sk-parallel-item::after {content: \"\";width: 100%;border-bottom: 1px solid gray;flex-grow: 1;}#sk-container-id-1 div.sk-label:hover label.sk-toggleable__label {background-color: #d4ebff;}#sk-container-id-1 div.sk-serial::before {content: \"\";position: absolute;border-left: 1px solid gray;box-sizing: border-box;top: 0;bottom: 0;left: 50%;z-index: 0;}#sk-container-id-1 div.sk-serial {display: flex;flex-direction: column;align-items: center;background-color: white;padding-right: 0.2em;padding-left: 0.2em;position: relative;}#sk-container-id-1 div.sk-item {position: relative;z-index: 1;}#sk-container-id-1 div.sk-parallel {display: flex;align-items: stretch;justify-content: center;background-color: white;position: relative;}#sk-container-id-1 div.sk-item::before, #sk-container-id-1 div.sk-parallel-item::before {content: \"\";position: absolute;border-left: 1px solid gray;box-sizing: border-box;top: 0;bottom: 0;left: 50%;z-index: -1;}#sk-container-id-1 div.sk-parallel-item {display: flex;flex-direction: column;z-index: 1;position: relative;background-color: white;}#sk-container-id-1 div.sk-parallel-item:first-child::after {align-self: flex-end;width: 50%;}#sk-container-id-1 div.sk-parallel-item:last-child::after {align-self: flex-start;width: 50%;}#sk-container-id-1 div.sk-parallel-item:only-child::after {width: 0;}#sk-container-id-1 div.sk-dashed-wrapped {border: 1px dashed gray;margin: 0 0.4em 0.5em 0.4em;box-sizing: border-box;padding-bottom: 0.4em;background-color: white;}#sk-container-id-1 div.sk-label label {font-family: monospace;font-weight: bold;display: inline-block;line-height: 1.2em;}#sk-container-id-1 div.sk-label-container {text-align: center;}#sk-container-id-1 div.sk-container {/* jupyter's `normalize.less` sets `[hidden] { display: none; }` but bootstrap.min.css set `[hidden] { display: none !important; }` so we also need the `!important` here to be able to override the default hidden behavior on the sphinx rendered scikit-learn.org. See: https://github.com/scikit-learn/scikit-learn/issues/21755 */display: inline-block !important;position: relative;}#sk-container-id-1 div.sk-text-repr-fallback {display: none;}</style><div id=\"sk-container-id-1\" class=\"sk-top-container\"><div class=\"sk-text-repr-fallback\"><pre>LogisticRegression(max_iter=5000, penalty=&#x27;none&#x27;, tol=1e-05)</pre><b>In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook. <br />On GitHub, the HTML representation is unable to render, please try loading this page with nbviewer.org.</b></div><div class=\"sk-container\" hidden><div class=\"sk-item\"><div class=\"sk-estimator sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"sk-estimator-id-1\" type=\"checkbox\" checked><label for=\"sk-estimator-id-1\" class=\"sk-toggleable__label sk-toggleable__label-arrow\">LogisticRegression</label><div class=\"sk-toggleable__content\"><pre>LogisticRegression(max_iter=5000, penalty=&#x27;none&#x27;, tol=1e-05)</pre></div></div></div></div></div>"
      ],
      "text/plain": [
       "LogisticRegression(max_iter=5000, penalty='none', tol=1e-05)"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from sklearn.linear_model import LogisticRegression\n",
    "lr = LogisticRegression(penalty='none', fit_intercept=True, max_iter=5000, tol=1E-5)\n",
    "lr.fit(X_train, y_train)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Test predictions on test data set"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "              precision    recall  f1-score   support\n",
      "\n",
      "           0       0.82      0.76      0.79        76\n",
      "           1       0.78      0.83      0.80        76\n",
      "\n",
      "    accuracy                           0.80       152\n",
      "   macro avg       0.80      0.80      0.80       152\n",
      "weighted avg       0.80      0.80      0.80       152\n",
      "\n"
     ]
    }
   ],
   "source": [
    "from sklearn.metrics import classification_report\n",
    "y_pred_lr = lr.predict(X_test)\n",
    "print(classification_report(y_test, y_pred_lr))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Compare two classifiers using the ROC curve"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "from sklearn.ensemble import RandomForestClassifier\n",
    "rf = RandomForestClassifier(max_depth=3)\n",
    "rf.fit(X_train, y_train)\n",
    "y_pred_rf = rf.predict(X_test)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "[encoded data, 27456 characters]",
      "text/plain": [
       "<Figure size 640x480 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from sklearn.metrics import roc_curve\n",
    "\n",
    "y_pred_prob_lr = lr.predict_proba(X_test) # predicted probabilities\n",
    "fpr_lr, tpr_lr, _ = roc_curve(y_test, y_pred_prob_lr[:,1])\n",
    "\n",
    "y_pred_prob_rf = rf.predict_proba(X_test) # predicted probabilities\n",
    "fpr_rf, tpr_rf, _ = roc_curve(y_test, y_pred_prob_rf[:,1])\n",
    "\n",
    "plt.plot(tpr_lr, 1-fpr_lr, label=\"log. regression\")\n",
    "plt.plot(tpr_rf, 1-fpr_rf, label=\"random forest\")\n",
    "\n",
    "plt.xlabel('Recall', fontsize=18)\n",
    "plt.ylabel('Precision', fontsize=18);\n",
    "plt.legend(fontsize=15)\n",
    "\n",
    "plt.savefig(\"03_ml_basics_log_regr_heart_disease.pdf\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Area under Curve (AUC) scores: 0.80, 0.80\n"
     ]
    }
   ],
   "source": [
    "from sklearn.metrics import roc_auc_score\n",
    "auc_lr = roc_auc_score(y_test,y_pred_lr)\n",
    "auc_rf = roc_auc_score(y_test,y_pred_rf)\n",
    "print(f\"Area under Curve (AUC) scores: {auc_lr:.2f}, {auc_rf:.2f}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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