Ensemble_Classifier.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "4c60161d",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/giulia/anaconda/lib/python3.6/site-packages/sklearn/utils/deprecation.py:143: FutureWarning: The sklearn.neighbors.base module is  deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.neighbors. Anything that cannot be imported from sklearn.neighbors is now part of the private API.\n",
      "  warnings.warn(message, FutureWarning)\n",
      "/Users/giulia/anaconda/lib/python3.6/site-packages/sklearn/utils/deprecation.py:143: FutureWarning: The sklearn.ensemble.bagging module is  deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.ensemble. Anything that cannot be imported from sklearn.ensemble is now part of the private API.\n",
      "  warnings.warn(message, FutureWarning)\n",
      "/Users/giulia/anaconda/lib/python3.6/site-packages/sklearn/utils/deprecation.py:143: FutureWarning: The sklearn.ensemble.base module is  deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.ensemble. Anything that cannot be imported from sklearn.ensemble is now part of the private API.\n",
      "  warnings.warn(message, FutureWarning)\n",
      "/Users/giulia/anaconda/lib/python3.6/site-packages/sklearn/utils/deprecation.py:143: FutureWarning: The sklearn.ensemble.forest module is  deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.ensemble. Anything that cannot be imported from sklearn.ensemble is now part of the private API.\n",
      "  warnings.warn(message, FutureWarning)\n",
      "/Users/giulia/anaconda/lib/python3.6/site-packages/sklearn/utils/deprecation.py:143: FutureWarning: The sklearn.utils.testing module is  deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.utils. Anything that cannot be imported from sklearn.utils is now part of the private API.\n",
      "  warnings.warn(message, FutureWarning)\n",
      "/Users/giulia/anaconda/lib/python3.6/site-packages/sklearn/utils/deprecation.py:143: FutureWarning: The sklearn.metrics.classification module is  deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.metrics. Anything that cannot be imported from sklearn.metrics is now part of the private API.\n",
      "  warnings.warn(message, FutureWarning)\n"
     ]
    }
   ],
   "source": [
    "import matplotlib\n",
    "import operator\n",
    "%matplotlib inline\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "import seaborn as sns\n",
    "import matplotlib.pyplot as plt\n",
    "from tqdm import tqdm\n",
    "import joblib\n",
    "\n",
    "# Set \n",
    "matplotlib.rcParams['font.serif'] = 'Times New Roman'\n",
    "matplotlib.rcParams['font.family'] = \"serif\"\n",
    "matplotlib.rcParams['font.size'] = 10\n",
    "\n",
    "# import custom functions\n",
    "from functions_statistical_performance import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "3a88df80",
   "metadata": {},
   "outputs": [],
   "source": [
    "# True to exactly reproduce the results presented in the paper (same classifiers)\n",
    "reproduceflag=True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "47743762",
   "metadata": {},
   "outputs": [],
   "source": [
    "# function to predict over a generic db when you already have the classifiers\n",
    "# it provides the average FPro \n",
    "def ClassifyDB(db, model_per_fold,nut_sel):\n",
    "    dbsel=db.loc[:,nut_sel]\n",
    "    Xnut=dbsel.values    \n",
    "    \n",
    "    indfold=0\n",
    "    for model in model_per_fold:\n",
    "        indfold+=1\n",
    "        y_pred = model.predict(Xnut)\n",
    "        y_probs= model.predict_proba(Xnut)\n",
    "        db['classf'+str(indfold)]=y_pred\n",
    "        db['p1f'+str(indfold)]=y_probs[:,0]\n",
    "        db['p2f'+str(indfold)]=y_probs[:,1]\n",
    "        db['p3f'+str(indfold)]=y_probs[:,2]\n",
    "        db['p4f'+str(indfold)]=y_probs[:,3]\n",
    "        db['FProf'+str(indfold)]=(1-db['p1f'+str(indfold)]+db['p4f'+str(indfold)])/2\n",
    "     \n",
    "    for p in range(1,5):\n",
    "        db['p'+str(p)]=db.loc[:, ['p'+str(p)+'f1', 'p'+str(p)+'f2', 'p'+str(p)+'f3','p'+str(p)+'f4', 'p'+str(p)+'f5' ]].mean(axis=1)\n",
    "        db['std_p'+str(p)]=db.loc[:, ['p'+str(p)+'f1', 'p'+str(p)+'f2', 'p'+str(p)+'f3','p'+str(p)+'f4', 'p'+str(p)+'f5' ]].std(axis=1)\n",
    "\n",
    "\n",
    "    db['FPro']=db.loc[:, ['FProf1', 'FProf2', 'FProf3','FProf4', 'FProf5' ]].mean(axis=1)\n",
    "    db['std_FPro']=db.loc[:, ['FProf1', 'FProf2', 'FProf3','FProf4', 'FProf5']].std(axis=1)\n",
    "    db['min_FPro']=db.loc[:, ['FProf1', 'FProf2', 'FProf3','FProf4', 'FProf5']].min(axis=1)\n",
    "\n",
    "\n",
    "    db['max_p']=db.loc[:, ['p1', 'p2', 'p3','p4' ]].idxmax(axis=1)\n",
    "    db['class']=[int(s[1])-1 for s in db.loc[:, ['p1', 'p2', 'p3','p4' ]].idxmax(axis=1)]\n",
    "    db['min_in_which_fold']=db.loc[:, ['FProf1', 'FProf2', 'FProf3','FProf4', 'FProf5']].idxmin(axis=1)\n",
    "    db['min_fold_id']=[int(s[-1]) for s in db.loc[:, ['FProf1', 'FProf2', 'FProf3','FProf4', 'FProf5']].idxmin(axis=1)]\n",
    "    db['min_class']=[db['classf'+str(db['min_fold_id'].iloc[n])].iloc[n] for n in range(db.shape[0])]\n",
    "    \n",
    "    for ind in range(1,5):\n",
    "        db['p'+str(ind)+'_minFPro']=[db['p'+str(ind)+'f'+str(db['min_fold_id'].iloc[n])].iloc[n] for n in range(db.shape[0])]\n",
    "    \n",
    "\n",
    "    return db"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ed381203",
   "metadata": {},
   "source": [
    "# Load 2009-2010 Data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "1565e0be",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
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       "      <th></th>\n",
       "      <th>Protein</th>\n",
       "      <th>Total Fat</th>\n",
       "      <th>Carbohydrate</th>\n",
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       "      <th>Calcium</th>\n",
       "      <th>...</th>\n",
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       "      <th>Total isoflavones</th>\n",
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       "      <th>Main_food_description</th>\n",
       "      <th>catnumb</th>\n",
       "      <th>catname</th>\n",
       "      <th>novaclass</th>\n",
       "      <th>macroclass</th>\n",
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       "      <td>-20.0</td>\n",
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       "      <td>-20.0</td>\n",
       "      <td>-2.128632</td>\n",
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       "      <td>-20.0</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>11100000</td>\n",
       "      <td>Milk, NFS</td>\n",
       "      <td>1004</td>\n",
       "      <td>Milk, reduced fat</td>\n",
       "      <td>1</td>\n",
       "      <td>Milk</td>\n",
       "      <td>0</td>\n",
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       "      <td>1002</td>\n",
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       "      <td>1</td>\n",
       "      <td>Milk</td>\n",
       "      <td>0</td>\n",
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       "      <td>7802</td>\n",
       "      <td>Flavored or carbonated water</td>\n",
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       "      <td>Propel Water</td>\n",
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       "      <td>Enhanced or fortified water</td>\n",
       "      <td>4</td>\n",
       "      <td>Other</td>\n",
       "      <td>3</td>\n",
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       "</table>\n",
       "<p>7254 rows × 106 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        Protein  Total Fat  Carbohydrate  Alcohol     Water  Caffeine  \\\n",
       "0    -20.000000 -20.000000    -20.000000    -20.0 -1.609438     -20.0   \n",
       "1      0.029559   1.477049      1.930071    -20.0  4.471639     -20.0   \n",
       "2      1.187843   0.647103      1.578979    -20.0  4.491441     -20.0   \n",
       "3      1.147402   1.178655      1.568616    -20.0  4.478813     -20.0   \n",
       "4      1.131402   1.241269      1.495149    -20.0  4.479607     -20.0   \n",
       "...         ...        ...           ...      ...       ...       ...   \n",
       "7249 -20.000000 -20.000000     -1.897120    -20.0  4.603669     -20.0   \n",
       "7250 -20.000000 -20.000000      1.504077    -20.0  4.547965     -20.0   \n",
       "7251 -20.000000 -20.000000      0.198851    -20.0  4.592895     -20.0   \n",
       "7252 -20.000000 -20.000000      1.702928    -20.0  4.547965     -20.0   \n",
       "7253 -20.000000 -20.000000    -20.000000    -20.0  4.604970     -20.0   \n",
       "\n",
       "      Theobromine  Sugars, total  Fiber, total dietary   Calcium  ...  \\\n",
       "0           -20.0     -20.000000                 -20.0 -3.729701  ...   \n",
       "1           -20.0       1.930071                 -20.0 -3.442019  ...   \n",
       "2           -20.0       1.625311                 -20.0 -2.128632  ...   \n",
       "3           -20.0       1.619388                 -20.0 -2.180367  ...   \n",
       "4           -20.0       1.495149                 -20.0 -2.292635  ...   \n",
       "...           ...            ...                   ...       ...  ...   \n",
       "7249        -20.0     -20.000000                 -20.0 -6.907755  ...   \n",
       "7250        -20.0       1.504077                 -20.0 -4.074542  ...   \n",
       "7251        -20.0       0.198851                 -20.0 -6.907755  ...   \n",
       "7252        -20.0       1.702928                 -20.0 -4.074542  ...   \n",
       "7253        -20.0     -20.000000                 -20.0 -4.605170  ...   \n",
       "\n",
       "      Total flavones  Total flavonols  Total isoflavones  Food_code  \\\n",
       "0              -20.0            -20.0              -20.0       2047   \n",
       "1              -20.0            -20.0              -20.0   11000000   \n",
       "2              -20.0            -20.0              -20.0   11100000   \n",
       "3              -20.0            -20.0              -20.0   11111000   \n",
       "4              -20.0            -20.0              -20.0   11111100   \n",
       "...              ...              ...                ...        ...   \n",
       "7249           -20.0            -20.0              -20.0   94100200   \n",
       "7250           -20.0            -20.0              -20.0   94100300   \n",
       "7251           -20.0            -20.0              -20.0   94210100   \n",
       "7252           -20.0            -20.0              -20.0   94210200   \n",
       "7253           -20.0            -20.0              -20.0   94300100   \n",
       "\n",
       "                                  Main_food_description  catnumb  \\\n",
       "0                                           Salt, table        0   \n",
       "1                                           Milk, human     9602   \n",
       "2                                             Milk, NFS     1004   \n",
       "3                             Milk, cow's, fluid, whole     1002   \n",
       "4                 Milk, cow's, fluid, whole, low-sodium     1002   \n",
       "...                                                 ...      ...   \n",
       "7249  Water, bottled, sweetened, with low or no calo...     7802   \n",
       "7250  Water, fruit flavored, sweetened, with high fr...     7802   \n",
       "7251                                       Propel Water     7804   \n",
       "7252                                      Glaceau Water     7804   \n",
       "7253                  Water, baby, bottled, unsweetened     9204   \n",
       "\n",
       "                           catname  novaclass  macroclass  pythonlabel  \n",
       "0                     addition1516          2       Other            1  \n",
       "1                       Human milk          1        Milk            0  \n",
       "2                Milk, reduced fat          1        Milk            0  \n",
       "3                      Milk, whole          1        Milk            0  \n",
       "4                      Milk, whole          1        Milk            0  \n",
       "...                            ...        ...         ...          ...  \n",
       "7249  Flavored or carbonated water          4       Other            3  \n",
       "7250  Flavored or carbonated water          4       Other            3  \n",
       "7251   Enhanced or fortified water          4       Other            3  \n",
       "7252   Enhanced or fortified water          4       Other            3  \n",
       "7253                    Baby water          1       Other            0  \n",
       "\n",
       "[7254 rows x 106 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# log-transformed nutrient content per 100 grams\n",
    "RFFNDDS=pd.read_csv('./input_data/FNDDS_2009-10_Training_Data.csv')\n",
    "RFFNDDS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "e122eb9e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "99"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# total nutrient list\n",
    "nl=list(RFFNDDS.columns)\n",
    "nl=nl[0:-7]\n",
    "len(nl)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0cd01618",
   "metadata": {},
   "source": [
    "# Whole Nutrient Panel Analysis"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "bd16beea",
   "metadata": {},
   "outputs": [],
   "source": [
    "if reproduceflag:\n",
    "    model_per_foldWNP=joblib.load(\"./paper_classifiers_outcomes/FNDDS0910_99Nutrients_5folds_SMOTE.pkl\")\n",
    "else:\n",
    "    data2train=RFFNDDS[RFFNDDS.pythonlabel!=-1]\n",
    "    X=data2train.loc[:, 'Protein': 'Total isoflavones']\n",
    "    y=data2train['pythonlabel']\n",
    "    smoteflag=True\n",
    "    (performancesAUCWNP, performancesAUPWNP, splitsWNP, model_per_foldWNP)=AUCAUPkfold(X,y,smoteflag)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "632585ac",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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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>Protein</th>\n",
       "      <th>Total Fat</th>\n",
       "      <th>Carbohydrate</th>\n",
       "      <th>Alcohol</th>\n",
       "      <th>Water</th>\n",
       "      <th>Caffeine</th>\n",
       "      <th>Theobromine</th>\n",
       "      <th>Sugars, total</th>\n",
       "      <th>Fiber, total dietary</th>\n",
       "      <th>Calcium</th>\n",
       "      <th>...</th>\n",
       "      <th>min_FPro</th>\n",
       "      <th>max_p</th>\n",
       "      <th>class</th>\n",
       "      <th>min_in_which_fold</th>\n",
       "      <th>min_fold_id</th>\n",
       "      <th>min_class</th>\n",
       "      <th>p1_minFPro</th>\n",
       "      <th>p2_minFPro</th>\n",
       "      <th>p3_minFPro</th>\n",
       "      <th>p4_minFPro</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-1.609438</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-3.729701</td>\n",
       "      <td>...</td>\n",
       "      <td>0.524444</td>\n",
       "      <td>p2</td>\n",
       "      <td>1</td>\n",
       "      <td>FProf2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0.021667</td>\n",
       "      <td>0.906111</td>\n",
       "      <td>0.001667</td>\n",
       "      <td>0.070556</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0.029559</td>\n",
       "      <td>1.477049</td>\n",
       "      <td>1.930071</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>4.471639</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>1.930071</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-3.442019</td>\n",
       "      <td>...</td>\n",
       "      <td>0.055833</td>\n",
       "      <td>p1</td>\n",
       "      <td>0</td>\n",
       "      <td>FProf2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0.936111</td>\n",
       "      <td>0.001667</td>\n",
       "      <td>0.014444</td>\n",
       "      <td>0.047778</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1.187843</td>\n",
       "      <td>0.647103</td>\n",
       "      <td>1.578979</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>4.491441</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>1.625311</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-2.128632</td>\n",
       "      <td>...</td>\n",
       "      <td>0.002222</td>\n",
       "      <td>p1</td>\n",
       "      <td>0</td>\n",
       "      <td>FProf2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0.997222</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.001111</td>\n",
       "      <td>0.001667</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1.147402</td>\n",
       "      <td>1.178655</td>\n",
       "      <td>1.568616</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>4.478813</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>1.619388</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-2.180367</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>p1</td>\n",
       "      <td>0</td>\n",
       "      <td>FProf2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1.131402</td>\n",
       "      <td>1.241269</td>\n",
       "      <td>1.495149</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>4.479607</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>1.495149</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-2.292635</td>\n",
       "      <td>...</td>\n",
       "      <td>0.023472</td>\n",
       "      <td>p1</td>\n",
       "      <td>0</td>\n",
       "      <td>FProf1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0.971528</td>\n",
       "      <td>0.007222</td>\n",
       "      <td>0.002778</td>\n",
       "      <td>0.018472</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",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>7249</th>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-1.897120</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>4.603669</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-6.907755</td>\n",
       "      <td>...</td>\n",
       "      <td>0.600660</td>\n",
       "      <td>p4</td>\n",
       "      <td>3</td>\n",
       "      <td>FProf4</td>\n",
       "      <td>4</td>\n",
       "      <td>3</td>\n",
       "      <td>0.303333</td>\n",
       "      <td>0.189236</td>\n",
       "      <td>0.002778</td>\n",
       "      <td>0.504653</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7250</th>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>1.504077</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>4.547965</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>1.504077</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-4.074542</td>\n",
       "      <td>...</td>\n",
       "      <td>0.933611</td>\n",
       "      <td>p4</td>\n",
       "      <td>3</td>\n",
       "      <td>FProf2</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>0.039444</td>\n",
       "      <td>0.032778</td>\n",
       "      <td>0.021111</td>\n",
       "      <td>0.906667</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7251</th>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>0.198851</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>4.592895</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>0.198851</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-6.907755</td>\n",
       "      <td>...</td>\n",
       "      <td>0.950833</td>\n",
       "      <td>p4</td>\n",
       "      <td>3</td>\n",
       "      <td>FProf3</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>0.023889</td>\n",
       "      <td>0.031667</td>\n",
       "      <td>0.018889</td>\n",
       "      <td>0.925556</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7252</th>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>1.702928</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>4.547965</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>1.702928</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-4.074542</td>\n",
       "      <td>...</td>\n",
       "      <td>0.889097</td>\n",
       "      <td>p4</td>\n",
       "      <td>3</td>\n",
       "      <td>FProf3</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>0.070833</td>\n",
       "      <td>0.040139</td>\n",
       "      <td>0.040000</td>\n",
       "      <td>0.849028</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7253</th>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>4.604970</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-4.605170</td>\n",
       "      <td>...</td>\n",
       "      <td>0.006944</td>\n",
       "      <td>p1</td>\n",
       "      <td>0</td>\n",
       "      <td>FProf4</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0.992222</td>\n",
       "      <td>0.001667</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.006111</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7254 rows × 156 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        Protein  Total Fat  Carbohydrate  Alcohol     Water  Caffeine  \\\n",
       "0    -20.000000 -20.000000    -20.000000    -20.0 -1.609438     -20.0   \n",
       "1      0.029559   1.477049      1.930071    -20.0  4.471639     -20.0   \n",
       "2      1.187843   0.647103      1.578979    -20.0  4.491441     -20.0   \n",
       "3      1.147402   1.178655      1.568616    -20.0  4.478813     -20.0   \n",
       "4      1.131402   1.241269      1.495149    -20.0  4.479607     -20.0   \n",
       "...         ...        ...           ...      ...       ...       ...   \n",
       "7249 -20.000000 -20.000000     -1.897120    -20.0  4.603669     -20.0   \n",
       "7250 -20.000000 -20.000000      1.504077    -20.0  4.547965     -20.0   \n",
       "7251 -20.000000 -20.000000      0.198851    -20.0  4.592895     -20.0   \n",
       "7252 -20.000000 -20.000000      1.702928    -20.0  4.547965     -20.0   \n",
       "7253 -20.000000 -20.000000    -20.000000    -20.0  4.604970     -20.0   \n",
       "\n",
       "      Theobromine  Sugars, total  Fiber, total dietary   Calcium  ...  \\\n",
       "0           -20.0     -20.000000                 -20.0 -3.729701  ...   \n",
       "1           -20.0       1.930071                 -20.0 -3.442019  ...   \n",
       "2           -20.0       1.625311                 -20.0 -2.128632  ...   \n",
       "3           -20.0       1.619388                 -20.0 -2.180367  ...   \n",
       "4           -20.0       1.495149                 -20.0 -2.292635  ...   \n",
       "...           ...            ...                   ...       ...  ...   \n",
       "7249        -20.0     -20.000000                 -20.0 -6.907755  ...   \n",
       "7250        -20.0       1.504077                 -20.0 -4.074542  ...   \n",
       "7251        -20.0       0.198851                 -20.0 -6.907755  ...   \n",
       "7252        -20.0       1.702928                 -20.0 -4.074542  ...   \n",
       "7253        -20.0     -20.000000                 -20.0 -4.605170  ...   \n",
       "\n",
       "      min_FPro  max_p  class  min_in_which_fold  min_fold_id  min_class  \\\n",
       "0     0.524444     p2      1             FProf2            2          1   \n",
       "1     0.055833     p1      0             FProf2            2          0   \n",
       "2     0.002222     p1      0             FProf2            2          0   \n",
       "3     0.000000     p1      0             FProf2            2          0   \n",
       "4     0.023472     p1      0             FProf1            1          0   \n",
       "...        ...    ...    ...                ...          ...        ...   \n",
       "7249  0.600660     p4      3             FProf4            4          3   \n",
       "7250  0.933611     p4      3             FProf2            2          3   \n",
       "7251  0.950833     p4      3             FProf3            3          3   \n",
       "7252  0.889097     p4      3             FProf3            3          3   \n",
       "7253  0.006944     p1      0             FProf4            4          0   \n",
       "\n",
       "      p1_minFPro  p2_minFPro  p3_minFPro  p4_minFPro  \n",
       "0       0.021667    0.906111    0.001667    0.070556  \n",
       "1       0.936111    0.001667    0.014444    0.047778  \n",
       "2       0.997222    0.000000    0.001111    0.001667  \n",
       "3       1.000000    0.000000    0.000000    0.000000  \n",
       "4       0.971528    0.007222    0.002778    0.018472  \n",
       "...          ...         ...         ...         ...  \n",
       "7249    0.303333    0.189236    0.002778    0.504653  \n",
       "7250    0.039444    0.032778    0.021111    0.906667  \n",
       "7251    0.023889    0.031667    0.018889    0.925556  \n",
       "7252    0.070833    0.040139    0.040000    0.849028  \n",
       "7253    0.992222    0.001667    0.000000    0.006111  \n",
       "\n",
       "[7254 rows x 156 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# summary database\n",
    "df=RFFNDDS.copy()\n",
    "df=ClassifyDB(df,model_per_foldWNP, nl)\n",
    "df.to_csv('./output_data/FNDDS_2009-10_99_Nutrients_ensemble_5folds.csv')\n",
    "df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c4ac8c79",
   "metadata": {},
   "source": [
    "# Standard Release FNDDS (for releases without flavonoids)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "67310a91",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of Nutrients in the Standard Nutrient Panel\n",
      "62\n"
     ]
    }
   ],
   "source": [
    "RFFNDDSSR=RFFNDDS.loc[:, 'Protein': 'Fatty acids, total polyunsaturated']\n",
    "StandardNutPanel=list(RFFNDDSSR.columns)\n",
    "RFFNDDSSR['pythonlabel']=RFFNDDS['pythonlabel'].copy()\n",
    "print('Number of Nutrients in the Standard Nutrient Panel')\n",
    "print(len(StandardNutPanel))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "c7ac49b3",
   "metadata": {},
   "outputs": [],
   "source": [
    "if reproduceflag:\n",
    "    model_per_fold62nut=joblib.load(\"./paper_classifiers_outcomes/FNDDS0910_62Nutrients_5folds_SMOTE.pkl\")\n",
    "else:\n",
    "    data2train=RFFNDDSSR[RFFNDDSSR.pythonlabel!=-1]\n",
    "    X=data2train.loc[:, 'Protein': 'Fatty acids, total polyunsaturated']\n",
    "    y=data2train['pythonlabel']\n",
    "    smoteflag=True\n",
    "    (performancesAUC62nut, performancesAUP62nut, splits62nut, model_per_fold62nut)=AUCAUPkfold(X,y,smoteflag)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "b0b51bb5",
   "metadata": {},
   "outputs": [
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       "        Protein  Total Fat  Carbohydrate  Alcohol     Water  Caffeine  \\\n",
       "0    -20.000000 -20.000000    -20.000000    -20.0 -1.609438     -20.0   \n",
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       "2      1.187843   0.647103      1.578979    -20.0  4.491441     -20.0   \n",
       "3      1.147402   1.178655      1.568616    -20.0  4.478813     -20.0   \n",
       "4      1.131402   1.241269      1.495149    -20.0  4.479607     -20.0   \n",
       "...         ...        ...           ...      ...       ...       ...   \n",
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       "7253 -20.000000 -20.000000    -20.000000    -20.0  4.604970     -20.0   \n",
       "\n",
       "      Theobromine  Sugars, total  Fiber, total dietary   Calcium  ...  \\\n",
       "0           -20.0     -20.000000                 -20.0 -3.729701  ...   \n",
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       "7253        -20.0     -20.000000                 -20.0 -4.605170  ...   \n",
       "\n",
       "      min_FPro  max_p  class  min_in_which_fold  min_fold_id  min_class  \\\n",
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       "7253  0.000000     p1      0             FProf1            1          0   \n",
       "\n",
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       "...          ...         ...         ...         ...  \n",
       "7249    0.386667    0.138935    0.002222    0.472176  \n",
       "7250    0.061111    0.023519    0.022222    0.893148  \n",
       "7251    0.041111    0.031667    0.023333    0.903889  \n",
       "7252    0.083889    0.039444    0.047222    0.829444  \n",
       "7253    1.000000    0.000000    0.000000    0.000000  \n",
       "\n",
       "[7254 rows x 113 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# summary database\n",
    "df=RFFNDDSSR.copy()\n",
    "df=ClassifyDB(df,model_per_fold62nut,StandardNutPanel)\n",
    "df.to_csv('./output_data/FNDDS_2009-10_62Nutrients_ensemble_5folds.csv')\n",
    "df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2d31c1c4",
   "metadata": {},
   "source": [
    "# Classify FNDDS 2015-2016 with 62 Nutrients"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "502df4ce",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/giulia/anaconda/lib/python3.6/site-packages/IPython/core/interactiveshell.py:3072: DtypeWarning: Columns (7) have mixed types.Specify dtype option on import or set low_memory=False.\n",
      "  interactivity=interactivity, compiler=compiler, result=result)\n"
     ]
    },
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       "      <th></th>\n",
       "      <th>Food code</th>\n",
       "      <th>Main food description</th>\n",
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       "      <th>cat_digit_2</th>\n",
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       "      <th>cat_digit_5</th>\n",
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       "      <th>1</th>\n",
       "      <td>11100000</td>\n",
       "      <td>Milk, NFS</td>\n",
       "      <td>2015</td>\n",
       "      <td>Milk and Milk Products</td>\n",
       "      <td>Milks and milk drinks</td>\n",
       "      <td>Milk, fluid (regular; filled; buttermilk; and ...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1004</td>\n",
       "      <td>Milk, reduced fat</td>\n",
       "      <td>...</td>\n",
       "      <td>0.005278</td>\n",
       "      <td>p1</td>\n",
       "      <td>0</td>\n",
       "      <td>FProf3</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0.993333</td>\n",
       "      <td>0.002778</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.003889</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>11111000</td>\n",
       "      <td>Milk, whole</td>\n",
       "      <td>2015</td>\n",
       "      <td>Milk and Milk Products</td>\n",
       "      <td>Milks and milk drinks</td>\n",
       "      <td>Milk, fluid (regular; filled; buttermilk; and ...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1002</td>\n",
       "      <td>Milk, whole</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>p1</td>\n",
       "      <td>0</td>\n",
       "      <td>FProf1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>11111100</td>\n",
       "      <td>Milk, low sodium, whole</td>\n",
       "      <td>2015</td>\n",
       "      <td>Milk and Milk Products</td>\n",
       "      <td>Milks and milk drinks</td>\n",
       "      <td>Milk, fluid (regular; filled; buttermilk; and ...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1002</td>\n",
       "      <td>Milk, whole</td>\n",
       "      <td>...</td>\n",
       "      <td>0.051667</td>\n",
       "      <td>p1</td>\n",
       "      <td>0</td>\n",
       "      <td>FProf3</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0.937778</td>\n",
       "      <td>0.015000</td>\n",
       "      <td>0.006111</td>\n",
       "      <td>0.041111</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>11111150</td>\n",
       "      <td>Milk, calcium fortified, whole</td>\n",
       "      <td>2015</td>\n",
       "      <td>Milk and Milk Products</td>\n",
       "      <td>Milks and milk drinks</td>\n",
       "      <td>Milk, fluid (regular; filled; buttermilk; and ...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1002</td>\n",
       "      <td>Milk, whole</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>p1</td>\n",
       "      <td>0</td>\n",
       "      <td>FProf1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</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",
       "      <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>8685</th>\n",
       "      <td>99991400</td>\n",
       "      <td>Cheese as ingredient in sandwiches</td>\n",
       "      <td>2015</td>\n",
       "      <td>Sugars, Sweets, and Beverages</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>9999</td>\n",
       "      <td>Not included in a food category</td>\n",
       "      <td>...</td>\n",
       "      <td>0.563333</td>\n",
       "      <td>p3</td>\n",
       "      <td>2</td>\n",
       "      <td>FProf3</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>0.016667</td>\n",
       "      <td>0.001667</td>\n",
       "      <td>0.838333</td>\n",
       "      <td>0.143333</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8686</th>\n",
       "      <td>99995000</td>\n",
       "      <td>Breading or batter as ingredient in food</td>\n",
       "      <td>2015</td>\n",
       "      <td>Sugars, Sweets, and Beverages</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>9999</td>\n",
       "      <td>Not included in a food category</td>\n",
       "      <td>...</td>\n",
       "      <td>0.985278</td>\n",
       "      <td>p4</td>\n",
       "      <td>3</td>\n",
       "      <td>FProf2</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>0.007778</td>\n",
       "      <td>0.000556</td>\n",
       "      <td>0.013333</td>\n",
       "      <td>0.978333</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8687</th>\n",
       "      <td>99995130</td>\n",
       "      <td>Wheat bread as ingredient in sandwiches</td>\n",
       "      <td>2015</td>\n",
       "      <td>Sugars, Sweets, and Beverages</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>9999</td>\n",
       "      <td>Not included in a food category</td>\n",
       "      <td>...</td>\n",
       "      <td>0.996389</td>\n",
       "      <td>p4</td>\n",
       "      <td>3</td>\n",
       "      <td>FProf4</td>\n",
       "      <td>4</td>\n",
       "      <td>3</td>\n",
       "      <td>0.002778</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.001667</td>\n",
       "      <td>0.995556</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8688</th>\n",
       "      <td>99998130</td>\n",
       "      <td>Sauce as ingredient in hamburgers</td>\n",
       "      <td>2015</td>\n",
       "      <td>Sugars, Sweets, and Beverages</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>9999</td>\n",
       "      <td>Not included in a food category</td>\n",
       "      <td>...</td>\n",
       "      <td>0.925833</td>\n",
       "      <td>p4</td>\n",
       "      <td>3</td>\n",
       "      <td>FProf2</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>0.011111</td>\n",
       "      <td>0.000556</td>\n",
       "      <td>0.125556</td>\n",
       "      <td>0.862778</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8689</th>\n",
       "      <td>99998210</td>\n",
       "      <td>Industrial oil as ingredient in food</td>\n",
       "      <td>2015</td>\n",
       "      <td>Sugars, Sweets, and Beverages</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>9999</td>\n",
       "      <td>Not included in a food category</td>\n",
       "      <td>...</td>\n",
       "      <td>0.511389</td>\n",
       "      <td>p2</td>\n",
       "      <td>1</td>\n",
       "      <td>FProf1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.977222</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.022778</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>8690 rows × 123 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      Food code                     Main food description  year  \\\n",
       "0      11000000                               Milk, human  2015   \n",
       "1      11100000                                 Milk, NFS  2015   \n",
       "2      11111000                               Milk, whole  2015   \n",
       "3      11111100                   Milk, low sodium, whole  2015   \n",
       "4      11111150            Milk, calcium fortified, whole  2015   \n",
       "...         ...                                       ...   ...   \n",
       "8685   99991400        Cheese as ingredient in sandwiches  2015   \n",
       "8686   99995000  Breading or batter as ingredient in food  2015   \n",
       "8687   99995130   Wheat bread as ingredient in sandwiches  2015   \n",
       "8688   99998130         Sauce as ingredient in hamburgers  2015   \n",
       "8689   99998210      Industrial oil as ingredient in food  2015   \n",
       "\n",
       "                        cat_digit_1            cat_digit_2  \\\n",
       "0            Milk and Milk Products  Milks and milk drinks   \n",
       "1            Milk and Milk Products  Milks and milk drinks   \n",
       "2            Milk and Milk Products  Milks and milk drinks   \n",
       "3            Milk and Milk Products  Milks and milk drinks   \n",
       "4            Milk and Milk Products  Milks and milk drinks   \n",
       "...                             ...                    ...   \n",
       "8685  Sugars, Sweets, and Beverages                    NaN   \n",
       "8686  Sugars, Sweets, and Beverages                    NaN   \n",
       "8687  Sugars, Sweets, and Beverages                    NaN   \n",
       "8688  Sugars, Sweets, and Beverages                    NaN   \n",
       "8689  Sugars, Sweets, and Beverages                    NaN   \n",
       "\n",
       "                                            cat_digit_3 cat_digit_4  \\\n",
       "0                                           Milk, human         NaN   \n",
       "1     Milk, fluid (regular; filled; buttermilk; and ...         NaN   \n",
       "2     Milk, fluid (regular; filled; buttermilk; and ...         NaN   \n",
       "3     Milk, fluid (regular; filled; buttermilk; and ...         NaN   \n",
       "4     Milk, fluid (regular; filled; buttermilk; and ...         NaN   \n",
       "...                                                 ...         ...   \n",
       "8685                                                NaN         NaN   \n",
       "8686                                                NaN         NaN   \n",
       "8687                                                NaN         NaN   \n",
       "8688                                                NaN         NaN   \n",
       "8689                                                NaN         NaN   \n",
       "\n",
       "     cat_digit_5  WWEIA Category number       WWEIA Category description  ...  \\\n",
       "0            NaN                   9602                       Human milk  ...   \n",
       "1            NaN                   1004                Milk, reduced fat  ...   \n",
       "2            NaN                   1002                      Milk, whole  ...   \n",
       "3            NaN                   1002                      Milk, whole  ...   \n",
       "4            NaN                   1002                      Milk, whole  ...   \n",
       "...          ...                    ...                              ...  ...   \n",
       "8685         NaN                   9999  Not included in a food category  ...   \n",
       "8686         NaN                   9999  Not included in a food category  ...   \n",
       "8687         NaN                   9999  Not included in a food category  ...   \n",
       "8688         NaN                   9999  Not included in a food category  ...   \n",
       "8689         NaN                   9999  Not included in a food category  ...   \n",
       "\n",
       "      min_FPro  max_p  class  min_in_which_fold  min_fold_id  min_class  \\\n",
       "0     0.058287     p1      0             FProf1            1          0   \n",
       "1     0.005278     p1      0             FProf3            3          0   \n",
       "2     0.000000     p1      0             FProf1            1          0   \n",
       "3     0.051667     p1      0             FProf3            3          0   \n",
       "4     0.000000     p1      0             FProf1            1          0   \n",
       "...        ...    ...    ...                ...          ...        ...   \n",
       "8685  0.563333     p3      2             FProf3            3          2   \n",
       "8686  0.985278     p4      3             FProf2            2          3   \n",
       "8687  0.996389     p4      3             FProf4            4          3   \n",
       "8688  0.925833     p4      3             FProf2            2          3   \n",
       "8689  0.511389     p2      1             FProf1            1          1   \n",
       "\n",
       "      p1_minFPro  p2_minFPro  p3_minFPro  p4_minFPro  \n",
       "0       0.931435    0.005000    0.015556    0.048009  \n",
       "1       0.993333    0.002778    0.000000    0.003889  \n",
       "2       1.000000    0.000000    0.000000    0.000000  \n",
       "3       0.937778    0.015000    0.006111    0.041111  \n",
       "4       1.000000    0.000000    0.000000    0.000000  \n",
       "...          ...         ...         ...         ...  \n",
       "8685    0.016667    0.001667    0.838333    0.143333  \n",
       "8686    0.007778    0.000556    0.013333    0.978333  \n",
       "8687    0.002778    0.000000    0.001667    0.995556  \n",
       "8688    0.011111    0.000556    0.125556    0.862778  \n",
       "8689    0.000000    0.977222    0.000000    0.022778  \n",
       "\n",
       "[8690 rows x 123 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# log-transformed nutrient content per 100 grams\n",
    "RFFNDDS20152016=pd.read_csv('./input_data/FNDDS_2015-16.csv')\n",
    "df=ClassifyDB(RFFNDDS20152016,model_per_fold62nut,StandardNutPanel)\n",
    "df.to_csv(\"./output_data/FNDDS_2015-16_62Nutrients_ensemble_5folds.csv\")\n",
    "df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "63bdfda4",
   "metadata": {},
   "source": [
    "# Nutrition Facts Analysis"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "d5653567",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of Nutrients in the Nutrition Facts Panel\n",
      "12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/giulia/anaconda/lib/python3.6/site-packages/ipykernel_launcher.py:5: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
      "Try using .loc[row_indexer,col_indexer] = value instead\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  \"\"\"\n"
     ]
    }
   ],
   "source": [
    "nutrition_facts=['Protein','Total Fat','Carbohydrate','Sugars, total','Fiber, total dietary','Calcium','Iron', 'Sodium','Retinol','Carotene, beta',\n",
    " 'Carotene, alpha','Cryptoxanthin, beta','Vitamin C','Cholesterol', 'Fatty acids, total saturated'];\n",
    "VitaminA=['Retinol','Carotene, beta','Carotene, alpha','Cryptoxanthin, beta']\n",
    "RFFNDDSNF=RFFNDDS[nutrition_facts]\n",
    "RFFNDDSNF['Total Vitamin A']=RFFNDDS[VitaminA].apply(np.exp).sum(axis=1).apply(np.log)\n",
    "RFFNDDSNF=RFFNDDSNF.drop(VitaminA, axis=1)\n",
    "nutrition_facts=list(RFFNDDSNF.columns)\n",
    "print('Number of Nutrients in the Nutrition Facts Panel')\n",
    "print(len(nutrition_facts))\n",
    "RFFNDDSNF['pythonlabel']=RFFNDDS['pythonlabel'].copy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "bd2b5d29",
   "metadata": {},
   "outputs": [],
   "source": [
    "if reproduceflag:\n",
    "    model_per_fold12nut=joblib.load(\"./paper_classifiers_outcomes/FNDDS0910_12Nutrients_5folds_SMOTE.pkl\")\n",
    "else:\n",
    "    data2train=RFFNDDSNF[RFFNDDSNF.pythonlabel!=-1]\n",
    "    X=data2train.loc[:, 'Protein': 'Total Vitamin A']\n",
    "    y=data2train['pythonlabel']\n",
    "    smoteflag=True\n",
    "    (performancesAUC12nut, performancesAUP12nut, splits12nut, model_per_fold12nut)=AUCAUPkfold(X,y,smoteflag)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "8a7b87c1",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Protein</th>\n",
       "      <th>Total Fat</th>\n",
       "      <th>Carbohydrate</th>\n",
       "      <th>Sugars, total</th>\n",
       "      <th>Fiber, total dietary</th>\n",
       "      <th>Calcium</th>\n",
       "      <th>Iron</th>\n",
       "      <th>Sodium</th>\n",
       "      <th>Vitamin C</th>\n",
       "      <th>Cholesterol</th>\n",
       "      <th>...</th>\n",
       "      <th>min_FPro</th>\n",
       "      <th>max_p</th>\n",
       "      <th>class</th>\n",
       "      <th>min_in_which_fold</th>\n",
       "      <th>min_fold_id</th>\n",
       "      <th>min_class</th>\n",
       "      <th>p1_minFPro</th>\n",
       "      <th>p2_minFPro</th>\n",
       "      <th>p3_minFPro</th>\n",
       "      <th>p4_minFPro</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-3.729701</td>\n",
       "      <td>-8.016418</td>\n",
       "      <td>3.657337</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.502778</td>\n",
       "      <td>p2</td>\n",
       "      <td>1</td>\n",
       "      <td>FProf2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0.017778</td>\n",
       "      <td>0.956667</td>\n",
       "      <td>0.002222</td>\n",
       "      <td>0.023333</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0.029559</td>\n",
       "      <td>1.477049</td>\n",
       "      <td>1.930071</td>\n",
       "      <td>1.930071</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-3.442019</td>\n",
       "      <td>-10.414313</td>\n",
       "      <td>-4.074542</td>\n",
       "      <td>-5.298317</td>\n",
       "      <td>-4.268698</td>\n",
       "      <td>...</td>\n",
       "      <td>0.183333</td>\n",
       "      <td>p1</td>\n",
       "      <td>0</td>\n",
       "      <td>FProf3</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0.806667</td>\n",
       "      <td>0.007222</td>\n",
       "      <td>0.012778</td>\n",
       "      <td>0.173333</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1.187843</td>\n",
       "      <td>0.647103</td>\n",
       "      <td>1.578979</td>\n",
       "      <td>1.625311</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-2.128632</td>\n",
       "      <td>-10.414313</td>\n",
       "      <td>-3.123566</td>\n",
       "      <td>-9.210340</td>\n",
       "      <td>-4.961845</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>p1</td>\n",
       "      <td>0</td>\n",
       "      <td>FProf1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1.147402</td>\n",
       "      <td>1.178655</td>\n",
       "      <td>1.568616</td>\n",
       "      <td>1.619388</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-2.180367</td>\n",
       "      <td>-10.414313</td>\n",
       "      <td>-3.146555</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-4.605170</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>p1</td>\n",
       "      <td>0</td>\n",
       "      <td>FProf1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1.131402</td>\n",
       "      <td>1.241269</td>\n",
       "      <td>1.495149</td>\n",
       "      <td>1.495149</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-2.292635</td>\n",
       "      <td>-9.903488</td>\n",
       "      <td>-5.809143</td>\n",
       "      <td>-7.013116</td>\n",
       "      <td>-4.268698</td>\n",
       "      <td>...</td>\n",
       "      <td>0.048222</td>\n",
       "      <td>p1</td>\n",
       "      <td>0</td>\n",
       "      <td>FProf1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0.946500</td>\n",
       "      <td>0.008333</td>\n",
       "      <td>0.002222</td>\n",
       "      <td>0.042944</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",
       "      <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>7249</th>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-1.897120</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-6.907755</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-5.809143</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.330509</td>\n",
       "      <td>p4</td>\n",
       "      <td>3</td>\n",
       "      <td>FProf5</td>\n",
       "      <td>5</td>\n",
       "      <td>0</td>\n",
       "      <td>0.611667</td>\n",
       "      <td>0.109537</td>\n",
       "      <td>0.006111</td>\n",
       "      <td>0.272685</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7250</th>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>1.504077</td>\n",
       "      <td>1.504077</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-4.074542</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-4.828314</td>\n",
       "      <td>-4.366153</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.941111</td>\n",
       "      <td>p4</td>\n",
       "      <td>3</td>\n",
       "      <td>FProf4</td>\n",
       "      <td>4</td>\n",
       "      <td>3</td>\n",
       "      <td>0.041667</td>\n",
       "      <td>0.022778</td>\n",
       "      <td>0.011667</td>\n",
       "      <td>0.923889</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7251</th>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>0.198851</td>\n",
       "      <td>0.198851</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-6.907755</td>\n",
       "      <td>-10.414313</td>\n",
       "      <td>-4.342806</td>\n",
       "      <td>-4.733004</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.890833</td>\n",
       "      <td>p4</td>\n",
       "      <td>3</td>\n",
       "      <td>FProf1</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>0.008889</td>\n",
       "      <td>0.191667</td>\n",
       "      <td>0.008889</td>\n",
       "      <td>0.790556</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7252</th>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>1.702928</td>\n",
       "      <td>1.702928</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-4.074542</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-4.366153</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.791771</td>\n",
       "      <td>p4</td>\n",
       "      <td>3</td>\n",
       "      <td>FProf5</td>\n",
       "      <td>5</td>\n",
       "      <td>3</td>\n",
       "      <td>0.085556</td>\n",
       "      <td>0.104792</td>\n",
       "      <td>0.140556</td>\n",
       "      <td>0.669097</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7253</th>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.0</td>\n",
       "      <td>-4.605170</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-6.214608</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>-20.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.004444</td>\n",
       "      <td>p1</td>\n",
       "      <td>0</td>\n",
       "      <td>FProf2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0.994444</td>\n",
       "      <td>0.002222</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.003333</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7254 rows × 63 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        Protein  Total Fat  Carbohydrate  Sugars, total  Fiber, total dietary  \\\n",
       "0    -20.000000 -20.000000    -20.000000     -20.000000                 -20.0   \n",
       "1      0.029559   1.477049      1.930071       1.930071                 -20.0   \n",
       "2      1.187843   0.647103      1.578979       1.625311                 -20.0   \n",
       "3      1.147402   1.178655      1.568616       1.619388                 -20.0   \n",
       "4      1.131402   1.241269      1.495149       1.495149                 -20.0   \n",
       "...         ...        ...           ...            ...                   ...   \n",
       "7249 -20.000000 -20.000000     -1.897120     -20.000000                 -20.0   \n",
       "7250 -20.000000 -20.000000      1.504077       1.504077                 -20.0   \n",
       "7251 -20.000000 -20.000000      0.198851       0.198851                 -20.0   \n",
       "7252 -20.000000 -20.000000      1.702928       1.702928                 -20.0   \n",
       "7253 -20.000000 -20.000000    -20.000000     -20.000000                 -20.0   \n",
       "\n",
       "       Calcium       Iron     Sodium  Vitamin C  Cholesterol  ...  min_FPro  \\\n",
       "0    -3.729701  -8.016418   3.657337 -20.000000   -20.000000  ...  0.502778   \n",
       "1    -3.442019 -10.414313  -4.074542  -5.298317    -4.268698  ...  0.183333   \n",
       "2    -2.128632 -10.414313  -3.123566  -9.210340    -4.961845  ...  0.000000   \n",
       "3    -2.180367 -10.414313  -3.146555 -20.000000    -4.605170  ...  0.000000   \n",
       "4    -2.292635  -9.903488  -5.809143  -7.013116    -4.268698  ...  0.048222   \n",
       "...        ...        ...        ...        ...          ...  ...       ...   \n",
       "7249 -6.907755 -20.000000  -5.809143 -20.000000   -20.000000  ...  0.330509   \n",
       "7250 -4.074542 -20.000000  -4.828314  -4.366153   -20.000000  ...  0.941111   \n",
       "7251 -6.907755 -10.414313  -4.342806  -4.733004   -20.000000  ...  0.890833   \n",
       "7252 -4.074542 -20.000000 -20.000000  -4.366153   -20.000000  ...  0.791771   \n",
       "7253 -4.605170 -20.000000  -6.214608 -20.000000   -20.000000  ...  0.004444   \n",
       "\n",
       "      max_p  class  min_in_which_fold  min_fold_id  min_class  p1_minFPro  \\\n",
       "0        p2      1             FProf2            2          1    0.017778   \n",
       "1        p1      0             FProf3            3          0    0.806667   \n",
       "2        p1      0             FProf1            1          0    1.000000   \n",
       "3        p1      0             FProf1            1          0    1.000000   \n",
       "4        p1      0             FProf1            1          0    0.946500   \n",
       "...     ...    ...                ...          ...        ...         ...   \n",
       "7249     p4      3             FProf5            5          0    0.611667   \n",
       "7250     p4      3             FProf4            4          3    0.041667   \n",
       "7251     p4      3             FProf1            1          3    0.008889   \n",
       "7252     p4      3             FProf5            5          3    0.085556   \n",
       "7253     p1      0             FProf2            2          0    0.994444   \n",
       "\n",
       "      p2_minFPro  p3_minFPro  p4_minFPro  \n",
       "0       0.956667    0.002222    0.023333  \n",
       "1       0.007222    0.012778    0.173333  \n",
       "2       0.000000    0.000000    0.000000  \n",
       "3       0.000000    0.000000    0.000000  \n",
       "4       0.008333    0.002222    0.042944  \n",
       "...          ...         ...         ...  \n",
       "7249    0.109537    0.006111    0.272685  \n",
       "7250    0.022778    0.011667    0.923889  \n",
       "7251    0.191667    0.008889    0.790556  \n",
       "7252    0.104792    0.140556    0.669097  \n",
       "7253    0.002222    0.000000    0.003333  \n",
       "\n",
       "[7254 rows x 63 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# summary database\n",
    "df=RFFNDDSNF.copy()\n",
    "df=ClassifyDB(df,model_per_fold12nut,nutrition_facts)\n",
    "df.to_csv('./output_data/FNDDS_2009-10_12Nutrients_ensemble_5folds.csv')\n",
    "df"
   ]
  }
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