01_Numpy and Pandas Intro.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Why python for data analysis, machine learning?\n",
    "There are lots of reasons that we want to use python for doing data science. It is certainly one of the younger programming languages used in the data science ecosystem (compared to say R and SAS) but it is used just as frequently for analysis as SAS and R. Having a good foundation in python, R, and SAS should be a *must* for **every data scientist** and machine learning enthusiast. \n",
    "\n",
    "In this course, python allows for an open source method of performing machine learning that runs from just about any machine. So let's start with looking at Numpy and Pandas pachages for analyzing data. \n",
    "\n",
    "With that in mind, let's go over the following:\n",
    "- Numpy matrices\n",
    "- Simple operations on arrays and matrices\n",
    "- Indexing with numpy\n",
    "- Pandas for tabular data\n",
    "- Representing categorical data (discussion point)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "3.5.4 |Continuum Analytics, Inc.| (default, Aug 14 2017, 12:43:10) \n",
      "[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)]\n",
      "1.13.1\n"
     ]
    }
   ],
   "source": [
    "import sys\n",
    "import numpy as np\n",
    "\n",
    "print(sys.version)\n",
    "print(np.__version__)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[ 0.71123289,  0.02519477,  0.97639939],\n",
       "       [ 0.71015964,  0.54387223,  0.54625691],\n",
       "       [ 0.83366462,  0.38765327,  0.28341864],\n",
       "       [ 0.1430888 ,  0.49790126,  0.22830317],\n",
       "       [ 0.38527387,  0.50612705,  0.65231672]])"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x = np.random.rand(5,3)\n",
    "x"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(5, 3)"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "dtype('float64')"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x.dtype"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "ValueError",
     "evalue": "operands could not be broadcast together with shapes (5,3) (3,4) ",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-6-46ef1a6f18aa>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0my\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrandom\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrand\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m3\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m4\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mz\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0my\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      3\u001b[0m \u001b[0mz\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mValueError\u001b[0m: operands could not be broadcast together with shapes (5,3) (3,4) "
     ]
    }
   ],
   "source": [
    "y = np.random.rand(3,4)\n",
    "z = x*y\n",
    "z"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[ 1.08966006,  0.98434136,  0.53632961,  1.17053715],\n",
       "       [ 0.91356761,  1.12450633,  0.6075623 ,  1.0364879 ],\n",
       "       [ 0.90606393,  0.82077882,  0.58884151,  0.73276967],\n",
       "       [ 0.2483236 ,  0.6673954 ,  0.24593795,  0.53561538],\n",
       "       [ 0.6599712 ,  1.07203995,  0.4429758 ,  1.02276153]])"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "z = np.dot(x,y)\n",
    "z"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[ 1.08966006,  0.98434136,  0.53632961,  1.17053715],\n",
       "       [ 0.91356761,  1.12450633,  0.6075623 ,  1.0364879 ],\n",
       "       [ 0.90606393,  0.82077882,  0.58884151,  0.73276967],\n",
       "       [ 0.2483236 ,  0.6673954 ,  0.24593795,  0.53561538],\n",
       "       [ 0.6599712 ,  1.07203995,  0.4429758 ,  1.02276153]])"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "z = x @ y\n",
    "z"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Indexing"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[1, 2, 3],\n",
       "       [4, 5, 6],\n",
       "       [7, 8, 9]])"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x1 = np.array([[1,2,3],\n",
    "               [4,5,6],\n",
    "               [7,8,9]])\n",
    "x1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2\n",
      "5\n",
      "8\n"
     ]
    }
   ],
   "source": [
    "for row in range(x1.shape[0]):\n",
    "    print(x1[row,1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([2, 5, 8])"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x1[:,1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([False,  True,  True], dtype=bool)"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x1[:,1]>3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[4, 5, 6],\n",
       "       [7, 8, 9]])"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x1[ x1[:,1]>3 ]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x2 = np.array(range(10))\n",
    "x2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(10,)"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x2.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([False, False, False, False, False, False,  True,  True,  True,  True], dtype=bool)"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "idx = x2>5\n",
    "idx"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([6, 7, 8, 9])"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x2[idx]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([6, 7, 8, 9])"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x2[x2>5]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Named columns\n",
    "So what if we have a matrix of data where each row is some observation of features and the feature values are represented in each column?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[  64, 2100,    1],\n",
       "       [  50, 2200,    1],\n",
       "       [  48, 2300,    1],\n",
       "       [  34,    0,    2],\n",
       "       [  30,  100,    5]])"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "col_names = ['temperature','time','day']\n",
    "data = np.array([[64,2100,1],\n",
    "                 [50,2200,1],\n",
    "                 [48,2300,1],\n",
    "                 [34,0,   2],\n",
    "                 [30,100, 5]])\n",
    "data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[  64, 2100,    1],\n",
       "       [  50, 2200,    1],\n",
       "       [  48, 2300,    1]])"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data2 = data[data[:,1]>1500]\n",
    "data2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style>\n",
       "    .dataframe thead tr:only-child th {\n",
       "        text-align: right;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>temperature</th>\n",
       "      <th>time</th>\n",
       "      <th>day</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>64</td>\n",
       "      <td>2100</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>50</td>\n",
       "      <td>2200</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>48</td>\n",
       "      <td>2300</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>34</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>30</td>\n",
       "      <td>100</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   temperature  time  day\n",
       "0           64  2100    1\n",
       "1           50  2200    1\n",
       "2           48  2300    1\n",
       "3           34     0    2\n",
       "4           30   100    5"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# pandas to the rescue\n",
    "import pandas as pd\n",
    "\n",
    "df = pd.DataFrame(data,columns=col_names)\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>temperature</th>\n",
       "      <th>time</th>\n",
       "      <th>day</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>64</td>\n",
       "      <td>2100</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>50</td>\n",
       "      <td>2200</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>48</td>\n",
       "      <td>2300</td>\n",
       "      <td>1</td>\n",
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       "  </tbody>\n",
       "</table>\n",
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      ],
      "text/plain": [
       "   temperature  time  day\n",
       "0           64  2100    1\n",
       "1           50  2200    1\n",
       "2           48  2300    1"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df[df.time>1500]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "RangeIndex: 5 entries, 0 to 4\n",
      "Data columns (total 3 columns):\n",
      "temperature    5 non-null int64\n",
      "time           5 non-null int64\n",
      "day            5 non-null int64\n",
      "dtypes: int64(3)\n",
      "memory usage: 200.0 bytes\n"
     ]
    }
   ],
   "source": [
    "# lets get a description of the data\n",
    "df.info()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>temperature</th>\n",
       "      <th>time</th>\n",
       "      <th>day</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>64</td>\n",
       "      <td>2100</td>\n",
       "      <td>Mon</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>50</td>\n",
       "      <td>2200</td>\n",
       "      <td>Mon</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>48</td>\n",
       "      <td>2300</td>\n",
       "      <td>Mon</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>34</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>30</td>\n",
       "      <td>100</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   temperature  time  day\n",
       "0           64  2100  Mon\n",
       "1           50  2200  Mon\n",
       "2           48  2300  Mon\n",
       "3           34     0    2\n",
       "4           30   100    5"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.day[df.day==1] = 'Mon'\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>temperature</th>\n",
       "      <th>time</th>\n",
       "      <th>day</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>64</td>\n",
       "      <td>2100</td>\n",
       "      <td>Mon</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>50</td>\n",
       "      <td>2200</td>\n",
       "      <td>Mon</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>48</td>\n",
       "      <td>2300</td>\n",
       "      <td>Mon</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>34</td>\n",
       "      <td>0</td>\n",
       "      <td>Tues</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>30</td>\n",
       "      <td>100</td>\n",
       "      <td>Fri</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   temperature  time   day\n",
       "0           64  2100   Mon\n",
       "1           50  2200   Mon\n",
       "2           48  2300   Mon\n",
       "3           34     0  Tues\n",
       "4           30   100   Fri"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# there is almost always a more efficient built in pandas function\n",
    "df.day.replace(to_replace=range(7),\n",
    "               value=['Su','Mon','Tues','Wed','Th','Fri','Sat'],\n",
    "               inplace=True)\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "RangeIndex: 5 entries, 0 to 4\n",
      "Data columns (total 3 columns):\n",
      "temperature    5 non-null int64\n",
      "time           5 non-null int64\n",
      "day            5 non-null object\n",
      "dtypes: int64(2), object(1)\n",
      "memory usage: 200.0+ bytes\n"
     ]
    }
   ],
   "source": [
    "# notice how the type of the column has changed to an object \"categorical\"\n",
    "df.info()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style>\n",
       "    .dataframe thead tr:only-child th {\n",
       "        text-align: right;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: left;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Fri</th>\n",
       "      <th>Mon</th>\n",
       "      <th>Tues</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   Fri  Mon  Tues\n",
       "0    0    1     0\n",
       "1    0    1     0\n",
       "2    0    1     0\n",
       "3    0    0     1\n",
       "4    1    0     0"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# one hot encoding example\n",
    "pd.get_dummies(df.day)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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