Unit1-module2-R/R.intro.1.ipynb

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 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# R intro\n",
    "Huitian Diao\n",
    "* Reference: \n",
    "* Quick-R by DataCamp\n",
    "* R for Beginners by emmanuel Paradis"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## R syntax"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 1. Value assignment and function"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "my.string <- \"Hello, world!\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"Hello, world!\"\n"
     ]
    }
   ],
   "source": [
    "print(my.string)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "* Exercise: make R print your name"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 2. Comments"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"Hello Apple!\"\n"
     ]
    }
   ],
   "source": [
    "print(\"Hello Apple!\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "#print(\"Hello Banana?\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"Hello Cranberry!\"\n"
     ]
    }
   ],
   "source": [
    "print (\"Hello Cranberry!\") #Cranberry is delicious"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 3. Working directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
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   "source": [
    "getwd()"
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   "execution_count": 7,
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   "source": [
    "setwd('/Users/yolandatiao/Documents/0_Bioinformatics2017/2018_Bioinformatics/Applied-Bioinformatics-Course')\n",
    "getwd()"
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   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
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    "list.files()"
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       "[1] \"2016\"\n",
       "\n",
       "$month\n",
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       "$day\n",
       "[1] \"31\"\n",
       "\n",
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       "[1] \"R\"\n",
       "\n",
       "$version.string\n",
       "[1] \"R version 3.3.2 (2016-10-31)\"\n",
       "\n",
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       "[1] \"Sincere Pumpkin Patch\"\n"
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   ],
   "source": [
    "R.Version()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "help(\"print\") # And also google..."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Data in R"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 1. Objects: name, content and attribute"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "my.string <- \"foo\"\n",
    "my.number <- 888\n",
    "my.logic <- TRUE\n",
    "my.vector <- c(1, 2, 3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "'character'"
      ],
      "text/latex": [
       "'character'"
      ],
      "text/markdown": [
       "'character'"
      ],
      "text/plain": [
       "[1] \"character\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
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       "'numeric'"
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       "'numeric'"
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       "[1] \"numeric\""
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     "metadata": {},
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       "'logical'"
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       "'logical'"
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       "'logical'"
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       "[1] \"logical\""
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     "metadata": {},
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       "[1] \"numeric\""
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     },
     "metadata": {},
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   ],
   "source": [
    "mode(my.string)\n",
    "mode(my.number)\n",
    "mode(my.logic)\n",
    "mode(my.vector)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 2. Data types"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 2.1 Vectors: a sequence of data elements of the same basic type. Members in a vector are called components."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "my.numbers <- c(1,2,3)\n",
    "my.fruits <- c(\"Apple\",\"Banana\",\"Cranberry\")\n",
    "my.logic <- c(TRUE,FALSE,TRUE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "'numeric'"
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       "'numeric'"
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       "'numeric'"
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       "'character'"
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       "'character'"
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       "[1] \"character\""
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       "'logical'"
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       "[1] \"logical\""
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   ],
   "source": [
    "mode(my.numbers)\n",
    "mode(my.fruits)\n",
    "mode(my.logic)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "'character'"
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      "text/latex": [
       "'character'"
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       "'character'"
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     "metadata": {},
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   ],
   "source": [
    "my.vector <- c(1,2,\"a\",FALSE)\n",
    "mode(my.vector) # All the elements are considered to be characters, to keep the consistency of data typein the vector"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "TRUE"
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      "text/latex": [
       "TRUE"
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       "TRUE"
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       "[1] TRUE"
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       "<ol class=list-inline>\n",
       "\t<li>'Apple'</li>\n",
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       "\\begin{enumerate*}\n",
       "\\item 'Apple'\n",
       "\\item 'Cranberry'\n",
       "\\end{enumerate*}\n"
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       "1. 'Apple'\n",
       "2. 'Cranberry'\n",
       "\n",
       "\n"
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      "text/plain": [
       "[1] \"Apple\"     \"Cranberry\""
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     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
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       "\\begin{enumerate*}\n",
       "\\item 1\n",
       "\\item 2\n",
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       "1. 1\n",
       "2. 2\n",
       "\n",
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       "[1] 1 2"
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   "source": [
    "my.logic[1] # Retrive one element\n",
    "my.fruits[c(1,3)] # Retrive multiple element\n",
    "my.numbers[c(1,2)] # Keep in mind that in R the number of elements start with 1, not 0!!!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>'1'</li>\n",
       "\t<li>'2'</li>\n",
       "\t<li>'3'</li>\n",
       "\t<li>'Apple'</li>\n",
       "\t<li>'Banana'</li>\n",
       "\t<li>'Cranberry'</li>\n",
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       "\\begin{enumerate*}\n",
       "\\item '1'\n",
       "\\item '2'\n",
       "\\item '3'\n",
       "\\item 'Apple'\n",
       "\\item 'Banana'\n",
       "\\item 'Cranberry'\n",
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       "1. '1'\n",
       "2. '2'\n",
       "3. '3'\n",
       "4. 'Apple'\n",
       "5. 'Banana'\n",
       "6. 'Cranberry'\n",
       "\n",
       "\n"
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       "[1] \"1\"         \"2\"         \"3\"         \"Apple\"     \"Banana\"    \"Cranberry\""
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   ],
   "source": [
    "new.vector <- c(my.numbers, my.fruits) # Combining vectors\n",
    "new.vector # Again, all the elements became characters"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 2.2 Matrix: elements arranged in a two-dimensional rectangular layout. Elements in matrix are the same type."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
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       "\n",
       "| 1  |  6 | 11 | 16 | \n",
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       "[5,] 5    10   15   20  "
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   "source": [
    "my.matrix <- matrix(1:20, nrow=5, ncol=4) # Simple initialization of a numeric matrix\n",
    "my.matrix"
   ]
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  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
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       "\n",
       "| <!--/--> | ColA | ColB | \n",
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       "| Row1 | Apple     | Bananna   | \n",
       "| Row2 | Cranberry | Durian    | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "     ColA      ColB   \n",
       "Row1 Apple     Bananna\n",
       "Row2 Cranberry Durian "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "my.fruits <- c(\"Apple\",\"Bananna\",\"Cranberry\",\"Durian\")\n",
    "row.names <- c(\"Row1\", \"Row2\")\n",
    "column.names <- c(\"ColA\", \"ColB\")\n",
    "# Create a matrix from a vector, and add names for the dimensions\n",
    "my.fruits.matrix <- matrix(my.fruits, nrow=2, ncol=2, byrow=TRUE, dimnames=list(row.names, column.names)) \n",
    "my.fruits.matrix"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 2.3 Array: like matrices but can store more than 2 dimensions."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ", , theMatrix\n",
      "\n",
      "     ColA ColB ColC\n",
      "Row1    0    3    6\n",
      "Row2    1    4    7\n",
      "Row3    2    5    8\n",
      "\n",
      ", , theMatrixReloaded\n",
      "\n",
      "     ColA ColB ColC\n",
      "Row1    9   12   15\n",
      "Row2   10   13   16\n",
      "Row3   11   14   17\n",
      "\n",
      ", , theMatrixRevolutions\n",
      "\n",
      "     ColA ColB ColC\n",
      "Row1   18   21   24\n",
      "Row2   19   22   25\n",
      "Row3   20   23   26\n",
      "\n"
     ]
    }
   ],
   "source": [
    "vector.1 <- seq(0,26,by=1) # Create a vector of numbers from 0 to 26.\n",
    "column.names <- c(\"ColA\",\"ColB\",\"ColC\") # A vector for the column names\n",
    "row.names <- c(\"Row1\",\"Row2\",\"Row3\") # A vector for row names\n",
    "matrix.names <- c(\"theMatrix\",\"theMatrixReloaded\",\"theMatrixRevolutions\") # A vector for matrix names (third dimension)\n",
    "# Create an array from vector\n",
    "array.1 <- array(vector.1, dim=c(3,3,3), dimnames=list(row.names,column.names,matrix.names))\n",
    "print(array.1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 2.4 Data Frames: like matrices, but different columns can have different modes."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>fruits.type</th><th scope=col>fruits.numbers</th><th scope=col>fruits.price</th><th scope=col>fruits.smell</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>Apple    </td><td> 10      </td><td> 5       </td><td>FALSE    </td></tr>\n",
       "\t<tr><td>Bananna  </td><td> 20      </td><td>10       </td><td>FALSE    </td></tr>\n",
       "\t<tr><td>Cranberry</td><td>100      </td><td>15       </td><td>FALSE    </td></tr>\n",
       "\t<tr><td>Durian   </td><td>  4      </td><td>20       </td><td> TRUE    </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llll}\n",
       " fruits.type & fruits.numbers & fruits.price & fruits.smell\\\\\n",
       "\\hline\n",
       "\t Apple     &  10       &  5        & FALSE    \\\\\n",
       "\t Bananna   &  20       & 10        & FALSE    \\\\\n",
       "\t Cranberry & 100       & 15        & FALSE    \\\\\n",
       "\t Durian    &   4       & 20        &  TRUE    \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "fruits.type | fruits.numbers | fruits.price | fruits.smell | \n",
       "|---|---|---|---|\n",
       "| Apple     |  10       |  5        | FALSE     | \n",
       "| Bananna   |  20       | 10        | FALSE     | \n",
       "| Cranberry | 100       | 15        | FALSE     | \n",
       "| Durian    |   4       | 20        |  TRUE     | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "  fruits.type fruits.numbers fruits.price fruits.smell\n",
       "1 Apple        10             5           FALSE       \n",
       "2 Bananna      20            10           FALSE       \n",
       "3 Cranberry   100            15           FALSE       \n",
       "4 Durian        4            20            TRUE       "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "fruits.type <- c(\"Apple\",\"Bananna\",\"Cranberry\",\"Durian\")\n",
    "fruits.numbers <- c(10,20,100,4)\n",
    "fruits.price <- c(5,10,15,20)\n",
    "fruits.smell <- c(FALSE, FALSE, FALSE, TRUE)\n",
    "# Create a data frame from vectors\n",
    "df.fruits <- data.frame(fruits.type, fruits.numbers, fruits.price, fruits.smell)\n",
    "df.fruits"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>Type</th><th scope=col>Number</th><th scope=col>Price</th><th scope=col>Smell</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>Apple    </td><td> 10      </td><td> 5       </td><td>FALSE    </td></tr>\n",
       "\t<tr><td>Bananna  </td><td> 20      </td><td>10       </td><td>FALSE    </td></tr>\n",
       "\t<tr><td>Cranberry</td><td>100      </td><td>15       </td><td>FALSE    </td></tr>\n",
       "\t<tr><td>Durian   </td><td>  4      </td><td>20       </td><td> TRUE    </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llll}\n",
       " Type & Number & Price & Smell\\\\\n",
       "\\hline\n",
       "\t Apple     &  10       &  5        & FALSE    \\\\\n",
       "\t Bananna   &  20       & 10        & FALSE    \\\\\n",
       "\t Cranberry & 100       & 15        & FALSE    \\\\\n",
       "\t Durian    &   4       & 20        &  TRUE    \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "Type | Number | Price | Smell | \n",
       "|---|---|---|---|\n",
       "| Apple     |  10       |  5        | FALSE     | \n",
       "| Bananna   |  20       | 10        | FALSE     | \n",
       "| Cranberry | 100       | 15        | FALSE     | \n",
       "| Durian    |   4       | 20        |  TRUE     | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "  Type      Number Price Smell\n",
       "1 Apple      10     5    FALSE\n",
       "2 Bananna    20    10    FALSE\n",
       "3 Cranberry 100    15    FALSE\n",
       "4 Durian      4    20     TRUE"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "names(df.fruits) <- c(\"Type\",\"Number\",\"Price\",\"Smell\") # Rename columns\n",
    "df.fruits"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th></th><th scope=col>Type</th><th scope=col>Number</th><th scope=col>Price</th><th scope=col>Smell</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>row1</th><td>Apple    </td><td> 10      </td><td> 5       </td><td>FALSE    </td></tr>\n",
       "\t<tr><th scope=row>row2</th><td>Bananna  </td><td> 20      </td><td>10       </td><td>FALSE    </td></tr>\n",
       "\t<tr><th scope=row>row3</th><td>Cranberry</td><td>100      </td><td>15       </td><td>FALSE    </td></tr>\n",
       "\t<tr><th scope=row>row4</th><td>Durian   </td><td>  4      </td><td>20       </td><td> TRUE    </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llll}\n",
       "  & Type & Number & Price & Smell\\\\\n",
       "\\hline\n",
       "\trow1 & Apple     &  10       &  5        & FALSE    \\\\\n",
       "\trow2 & Bananna   &  20       & 10        & FALSE    \\\\\n",
       "\trow3 & Cranberry & 100       & 15        & FALSE    \\\\\n",
       "\trow4 & Durian    &   4       & 20        &  TRUE    \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "| <!--/--> | Type | Number | Price | Smell | \n",
       "|---|---|---|---|\n",
       "| row1 | Apple     |  10       |  5        | FALSE     | \n",
       "| row2 | Bananna   |  20       | 10        | FALSE     | \n",
       "| row3 | Cranberry | 100       | 15        | FALSE     | \n",
       "| row4 | Durian    |   4       | 20        |  TRUE     | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "     Type      Number Price Smell\n",
       "row1 Apple      10     5    FALSE\n",
       "row2 Bananna    20    10    FALSE\n",
       "row3 Cranberry 100    15    FALSE\n",
       "row4 Durian      4    20     TRUE"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "row.names(df.fruits) <- c(\"row1\", \"row2\", \"row3\", \"row4\") # Rename rows\n",
    "df.fruits"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th></th><th scope=col>Type</th><th scope=col>Price</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>row1</th><td>Apple    </td><td> 5       </td></tr>\n",
       "\t<tr><th scope=row>row2</th><td>Bananna  </td><td>10       </td></tr>\n",
       "\t<tr><th scope=row>row3</th><td>Cranberry</td><td>15       </td></tr>\n",
       "\t<tr><th scope=row>row4</th><td>Durian   </td><td>20       </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|ll}\n",
       "  & Type & Price\\\\\n",
       "\\hline\n",
       "\trow1 & Apple     &  5       \\\\\n",
       "\trow2 & Bananna   & 10       \\\\\n",
       "\trow3 & Cranberry & 15       \\\\\n",
       "\trow4 & Durian    & 20       \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "| <!--/--> | Type | Price | \n",
       "|---|---|---|---|\n",
       "| row1 | Apple     |  5        | \n",
       "| row2 | Bananna   | 10        | \n",
       "| row3 | Cranberry | 15        | \n",
       "| row4 | Durian    | 20        | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "     Type      Price\n",
       "row1 Apple      5   \n",
       "row2 Bananna   10   \n",
       "row3 Cranberry 15   \n",
       "row4 Durian    20   "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "df.fruits[c(\"Type\",\"Price\")] # Extract columns with IDs \"Type\" and \"Price\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th></th><th scope=col>Type</th><th scope=col>Number</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>row1</th><td>Apple    </td><td> 10      </td></tr>\n",
       "\t<tr><th scope=row>row2</th><td>Bananna  </td><td> 20      </td></tr>\n",
       "\t<tr><th scope=row>row3</th><td>Cranberry</td><td>100      </td></tr>\n",
       "\t<tr><th scope=row>row4</th><td>Durian   </td><td>  4      </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|ll}\n",
       "  & Type & Number\\\\\n",
       "\\hline\n",
       "\trow1 & Apple     &  10      \\\\\n",
       "\trow2 & Bananna   &  20      \\\\\n",
       "\trow3 & Cranberry & 100      \\\\\n",
       "\trow4 & Durian    &   4      \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "| <!--/--> | Type | Number | \n",
       "|---|---|---|---|\n",
       "| row1 | Apple     |  10       | \n",
       "| row2 | Bananna   |  20       | \n",
       "| row3 | Cranberry | 100       | \n",
       "| row4 | Durian    |   4       | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "     Type      Number\n",
       "row1 Apple      10   \n",
       "row2 Bananna    20   \n",
       "row3 Cranberry 100   \n",
       "row4 Durian      4   "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "df.fruits[1:2] # Extract columns 1-2 of data frame"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>Apple</li>\n",
       "\t<li>Bananna</li>\n",
       "\t<li>Cranberry</li>\n",
       "\t<li>Durian</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item Apple\n",
       "\\item Bananna\n",
       "\\item Cranberry\n",
       "\\item Durian\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. Apple\n",
       "2. Bananna\n",
       "3. Cranberry\n",
       "4. Durian\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] Apple     Bananna   Cranberry Durian   \n",
       "Levels: Apple Bananna Cranberry Durian"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "df.fruits$Type # Extract \"Type\" from data frame"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>X1</th><th scope=col>X2</th><th scope=col>X3</th><th scope=col>X4</th><th scope=col>X5</th><th scope=col>X6</th><th scope=col>X7</th><th scope=col>X8</th><th scope=col>X9</th><th scope=col>X10</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr>\n",
       "\t<tr><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr>\n",
       "\t<tr><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr>\n",
       "\t<tr><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr>\n",
       "\t<tr><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llllllllll}\n",
       " X1 & X2 & X3 & X4 & X5 & X6 & X7 & X8 & X9 & X10\\\\\n",
       "\\hline\n",
       "\t NA & NA & NA & NA & NA & NA & NA & NA & NA & NA\\\\\n",
       "\t NA & NA & NA & NA & NA & NA & NA & NA & NA & NA\\\\\n",
       "\t NA & NA & NA & NA & NA & NA & NA & NA & NA & NA\\\\\n",
       "\t NA & NA & NA & NA & NA & NA & NA & NA & NA & NA\\\\\n",
       "\t NA & NA & NA & NA & NA & NA & NA & NA & NA & NA\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "X1 | X2 | X3 | X4 | X5 | X6 | X7 | X8 | X9 | X10 | \n",
       "|---|---|---|---|---|\n",
       "| NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | \n",
       "| NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | \n",
       "| NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | \n",
       "| NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | \n",
       "| NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "  X1 X2 X3 X4 X5 X6 X7 X8 X9 X10\n",
       "1 NA NA NA NA NA NA NA NA NA NA \n",
       "2 NA NA NA NA NA NA NA NA NA NA \n",
       "3 NA NA NA NA NA NA NA NA NA NA \n",
       "4 NA NA NA NA NA NA NA NA NA NA \n",
       "5 NA NA NA NA NA NA NA NA NA NA "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "df.emp <- data.frame(matrix(ncol = 10, nrow = 5)) # Initializing an empty dataframe with matrix\n",
    "df.emp"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 2.5 List: an ordered collection of objects. A list allows you to gather a variety of objects."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<dl>\n",
       "\t<dt>$my.name</dt>\n",
       "\t\t<dd>'Nutella'</dd>\n",
       "\t<dt>$my.species</dt>\n",
       "\t\t<dd>'Mus.Musculus'</dd>\n",
       "\t<dt>$my.age</dt>\n",
       "\t\t<dd>0.2</dd>\n",
       "\t<dt>$my.color</dt>\n",
       "\t\t<dd>'Brown'</dd>\n",
       "\t<dt>$my.favorite</dt>\n",
       "\t\t<dd><ol class=list-inline>\n",
       "\t<li>'chocolate'</li>\n",
       "\t<li>'peanut'</li>\n",
       "\t<li>'cheese'</li>\n",
       "</ol>\n",
       "</dd>\n",
       "\t<dt>$my.matrix</dt>\n",
       "\t\t<dd><table>\n",
       "<tbody>\n",
       "\t<tr><td>1 </td><td> 6</td><td>11</td><td>16</td></tr>\n",
       "\t<tr><td>2 </td><td> 7</td><td>12</td><td>17</td></tr>\n",
       "\t<tr><td>3 </td><td> 8</td><td>13</td><td>18</td></tr>\n",
       "\t<tr><td>4 </td><td> 9</td><td>14</td><td>19</td></tr>\n",
       "\t<tr><td>5 </td><td>10</td><td>15</td><td>20</td></tr>\n",
       "</tbody>\n",
       "</table>\n",
       "</dd>\n",
       "</dl>\n"
      ],
      "text/latex": [
       "\\begin{description}\n",
       "\\item[\\$my.name] 'Nutella'\n",
       "\\item[\\$my.species] 'Mus.Musculus'\n",
       "\\item[\\$my.age] 0.2\n",
       "\\item[\\$my.color] 'Brown'\n",
       "\\item[\\$my.favorite] \\begin{enumerate*}\n",
       "\\item 'chocolate'\n",
       "\\item 'peanut'\n",
       "\\item 'cheese'\n",
       "\\end{enumerate*}\n",
       "\n",
       "\\item[\\$my.matrix] \\begin{tabular}{llll}\n",
       "\t 1  &  6 & 11 & 16\\\\\n",
       "\t 2  &  7 & 12 & 17\\\\\n",
       "\t 3  &  8 & 13 & 18\\\\\n",
       "\t 4  &  9 & 14 & 19\\\\\n",
       "\t 5  & 10 & 15 & 20\\\\\n",
       "\\end{tabular}\n",
       "\n",
       "\\end{description}\n"
      ],
      "text/markdown": [
       "$my.name\n",
       ":   'Nutella'\n",
       "$my.species\n",
       ":   'Mus.Musculus'\n",
       "$my.age\n",
       ":   0.2\n",
       "$my.color\n",
       ":   'Brown'\n",
       "$my.favorite\n",
       ":   1. 'chocolate'\n",
       "2. 'peanut'\n",
       "3. 'cheese'\n",
       "\n",
       "\n",
       "\n",
       "$my.matrix\n",
       ":   \n",
       "| 1  |  6 | 11 | 16 | \n",
       "| 2  |  7 | 12 | 17 | \n",
       "| 3  |  8 | 13 | 18 | \n",
       "| 4  |  9 | 14 | 19 | \n",
       "| 5  | 10 | 15 | 20 | \n",
       "\n",
       "\n",
       "\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "$my.name\n",
       "[1] \"Nutella\"\n",
       "\n",
       "$my.species\n",
       "[1] \"Mus.Musculus\"\n",
       "\n",
       "$my.age\n",
       "[1] 0.2\n",
       "\n",
       "$my.color\n",
       "[1] \"Brown\"\n",
       "\n",
       "$my.favorite\n",
       "[1] \"chocolate\" \"peanut\"    \"cheese\"   \n",
       "\n",
       "$my.matrix\n",
       "     [,1] [,2] [,3] [,4]\n",
       "[1,]    1    6   11   16\n",
       "[2,]    2    7   12   17\n",
       "[3,]    3    8   13   18\n",
       "[4,]    4    9   14   19\n",
       "[5,]    5   10   15   20\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "nutella.favorite <- c(\"chocolate\", \"peanut\", \"cheese\")\n",
    "nutella.matrix <- matrix(1:20, nrow=5, ncol=4)\n",
    "# Create list with different types of data\n",
    "nutella.info <- list(my.name=\"Nutella\", my.species=\"Mus.Musculus\", my.age=0.2, my.color=\"Brown\", \n",
    "                my.favorite=nutella.favorite, my.matrix=nutella.matrix)\n",
    "nutella.info"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 2.6 Factors: a nominal variable"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "   Length     Class      Mode \n",
       "       50 character character "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "gender <- c(rep(\"male\",20), rep(\"female\", 30)) \n",
    "summary(gender)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<dl class=dl-horizontal>\n",
       "\t<dt>female</dt>\n",
       "\t\t<dd>30</dd>\n",
       "\t<dt>male</dt>\n",
       "\t\t<dd>20</dd>\n",
       "</dl>\n"
      ],
      "text/latex": [
       "\\begin{description*}\n",
       "\\item[female] 30\n",
       "\\item[male] 20\n",
       "\\end{description*}\n"
      ],
      "text/markdown": [
       "female\n",
       ":   30male\n",
       ":   20\n",
       "\n"
      ],
      "text/plain": [
       "female   male \n",
       "    30     20 "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "gender <- factor(gender) # Convert the vector's data type to factor, and then summary()\n",
    "summary(gender)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 2.7 Data type conversion"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "'character'"
      ],
      "text/latex": [
       "'character'"
      ],
      "text/markdown": [
       "'character'"
      ],
      "text/plain": [
       "[1] \"character\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "'numeric'"
      ],
      "text/latex": [
       "'numeric'"
      ],
      "text/markdown": [
       "'numeric'"
      ],
      "text/plain": [
       "[1] \"numeric\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "my.numbers <- c(\"1\",\"2\",\"3\",\"4\")\n",
    "class(my.numbers)\n",
    "my.numbers <- as.numeric(my.numbers)\n",
    "class(my.numbers)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "'logical'"
      ],
      "text/latex": [
       "'logical'"
      ],
      "text/markdown": [
       "'logical'"
      ],
      "text/plain": [
       "[1] \"logical\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "'character'"
      ],
      "text/latex": [
       "'character'"
      ],
      "text/markdown": [
       "'character'"
      ],
      "text/plain": [
       "[1] \"character\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "my.logic <- c(TRUE, TRUE, FALSE)\n",
    "class(my.logic)\n",
    "my.logic <- as.character(my.logic)\n",
    "class(my.logic)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 3. Basic functions for objects"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "'list'"
      ],
      "text/latex": [
       "'list'"
      ],
      "text/markdown": [
       "'list'"
      ],
      "text/plain": [
       "[1] \"list\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "class(nutella.info) # Type of object"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>'my.name'</li>\n",
       "\t<li>'my.species'</li>\n",
       "\t<li>'my.age'</li>\n",
       "\t<li>'my.color'</li>\n",
       "\t<li>'my.favorite'</li>\n",
       "\t<li>'my.matrix'</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 'my.name'\n",
       "\\item 'my.species'\n",
       "\\item 'my.age'\n",
       "\\item 'my.color'\n",
       "\\item 'my.favorite'\n",
       "\\item 'my.matrix'\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 'my.name'\n",
       "2. 'my.species'\n",
       "3. 'my.age'\n",
       "4. 'my.color'\n",
       "5. 'my.favorite'\n",
       "6. 'my.matrix'\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] \"my.name\"     \"my.species\"  \"my.age\"      \"my.color\"    \"my.favorite\"\n",
       "[6] \"my.matrix\"  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "names(nutella.info) # Names"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "List of 6\n",
      " $ my.name    : chr \"Nutella\"\n",
      " $ my.species : chr \"Mus.Musculus\"\n",
      " $ my.age     : num 0.2\n",
      " $ my.color   : chr \"Brown\"\n",
      " $ my.favorite: chr [1:3] \"chocolate\" \"peanut\" \"cheese\"\n",
      " $ my.matrix  : int [1:5, 1:4] 1 2 3 4 5 6 7 8 9 10 ...\n"
     ]
    }
   ],
   "source": [
    "str(nutella.info) # Structure of an object"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "6"
      ],
      "text/latex": [
       "6"
      ],
      "text/markdown": [
       "6"
      ],
      "text/plain": [
       "[1] 6"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "length(nutella.info) # Number of elements"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>'array.1'</li>\n",
       "\t<li>'column.names'</li>\n",
       "\t<li>'df.emp'</li>\n",
       "\t<li>'df.fruits'</li>\n",
       "\t<li>'fruits.numbers'</li>\n",
       "\t<li>'fruits.price'</li>\n",
       "\t<li>'fruits.smell'</li>\n",
       "\t<li>'fruits.type'</li>\n",
       "\t<li>'gender'</li>\n",
       "\t<li>'matrix.names'</li>\n",
       "\t<li>'my.fruits'</li>\n",
       "\t<li>'my.fruits.matrix'</li>\n",
       "\t<li>'my.logic'</li>\n",
       "\t<li>'my.matrix'</li>\n",
       "\t<li>'my.number'</li>\n",
       "\t<li>'my.numbers'</li>\n",
       "\t<li>'my.string'</li>\n",
       "\t<li>'my.vector'</li>\n",
       "\t<li>'new.vector'</li>\n",
       "\t<li>'nutella.favorite'</li>\n",
       "\t<li>'nutella.info'</li>\n",
       "\t<li>'nutella.matrix'</li>\n",
       "\t<li>'row.names'</li>\n",
       "\t<li>'vector.1'</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 'array.1'\n",
       "\\item 'column.names'\n",
       "\\item 'df.emp'\n",
       "\\item 'df.fruits'\n",
       "\\item 'fruits.numbers'\n",
       "\\item 'fruits.price'\n",
       "\\item 'fruits.smell'\n",
       "\\item 'fruits.type'\n",
       "\\item 'gender'\n",
       "\\item 'matrix.names'\n",
       "\\item 'my.fruits'\n",
       "\\item 'my.fruits.matrix'\n",
       "\\item 'my.logic'\n",
       "\\item 'my.matrix'\n",
       "\\item 'my.number'\n",
       "\\item 'my.numbers'\n",
       "\\item 'my.string'\n",
       "\\item 'my.vector'\n",
       "\\item 'new.vector'\n",
       "\\item 'nutella.favorite'\n",
       "\\item 'nutella.info'\n",
       "\\item 'nutella.matrix'\n",
       "\\item 'row.names'\n",
       "\\item 'vector.1'\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 'array.1'\n",
       "2. 'column.names'\n",
       "3. 'df.emp'\n",
       "4. 'df.fruits'\n",
       "5. 'fruits.numbers'\n",
       "6. 'fruits.price'\n",
       "7. 'fruits.smell'\n",
       "8. 'fruits.type'\n",
       "9. 'gender'\n",
       "10. 'matrix.names'\n",
       "11. 'my.fruits'\n",
       "12. 'my.fruits.matrix'\n",
       "13. 'my.logic'\n",
       "14. 'my.matrix'\n",
       "15. 'my.number'\n",
       "16. 'my.numbers'\n",
       "17. 'my.string'\n",
       "18. 'my.vector'\n",
       "19. 'new.vector'\n",
       "20. 'nutella.favorite'\n",
       "21. 'nutella.info'\n",
       "22. 'nutella.matrix'\n",
       "23. 'row.names'\n",
       "24. 'vector.1'\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       " [1] \"array.1\"          \"column.names\"     \"df.emp\"           \"df.fruits\"       \n",
       " [5] \"fruits.numbers\"   \"fruits.price\"     \"fruits.smell\"     \"fruits.type\"     \n",
       " [9] \"gender\"           \"matrix.names\"     \"my.fruits\"        \"my.fruits.matrix\"\n",
       "[13] \"my.logic\"         \"my.matrix\"        \"my.number\"        \"my.numbers\"      \n",
       "[17] \"my.string\"        \"my.vector\"        \"new.vector\"       \"nutella.favorite\"\n",
       "[21] \"nutella.info\"     \"nutella.matrix\"   \"row.names\"        \"vector.1\"        "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "ls() # List current objects"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>'array.1'</li>\n",
       "\t<li>'column.names'</li>\n",
       "\t<li>'df.emp'</li>\n",
       "\t<li>'df.fruits'</li>\n",
       "\t<li>'fruits.numbers'</li>\n",
       "\t<li>'fruits.price'</li>\n",
       "\t<li>'fruits.smell'</li>\n",
       "\t<li>'fruits.type'</li>\n",
       "\t<li>'gender'</li>\n",
       "\t<li>'matrix.names'</li>\n",
       "\t<li>'my.fruits'</li>\n",
       "\t<li>'my.fruits.matrix'</li>\n",
       "\t<li>'my.logic'</li>\n",
       "\t<li>'my.matrix'</li>\n",
       "\t<li>'my.number'</li>\n",
       "\t<li>'my.numbers'</li>\n",
       "\t<li>'my.string'</li>\n",
       "\t<li>'my.vector'</li>\n",
       "\t<li>'new.vector'</li>\n",
       "\t<li>'nutella.favorite'</li>\n",
       "\t<li>'nutella.matrix'</li>\n",
       "\t<li>'row.names'</li>\n",
       "\t<li>'vector.1'</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 'array.1'\n",
       "\\item 'column.names'\n",
       "\\item 'df.emp'\n",
       "\\item 'df.fruits'\n",
       "\\item 'fruits.numbers'\n",
       "\\item 'fruits.price'\n",
       "\\item 'fruits.smell'\n",
       "\\item 'fruits.type'\n",
       "\\item 'gender'\n",
       "\\item 'matrix.names'\n",
       "\\item 'my.fruits'\n",
       "\\item 'my.fruits.matrix'\n",
       "\\item 'my.logic'\n",
       "\\item 'my.matrix'\n",
       "\\item 'my.number'\n",
       "\\item 'my.numbers'\n",
       "\\item 'my.string'\n",
       "\\item 'my.vector'\n",
       "\\item 'new.vector'\n",
       "\\item 'nutella.favorite'\n",
       "\\item 'nutella.matrix'\n",
       "\\item 'row.names'\n",
       "\\item 'vector.1'\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 'array.1'\n",
       "2. 'column.names'\n",
       "3. 'df.emp'\n",
       "4. 'df.fruits'\n",
       "5. 'fruits.numbers'\n",
       "6. 'fruits.price'\n",
       "7. 'fruits.smell'\n",
       "8. 'fruits.type'\n",
       "9. 'gender'\n",
       "10. 'matrix.names'\n",
       "11. 'my.fruits'\n",
       "12. 'my.fruits.matrix'\n",
       "13. 'my.logic'\n",
       "14. 'my.matrix'\n",
       "15. 'my.number'\n",
       "16. 'my.numbers'\n",
       "17. 'my.string'\n",
       "18. 'my.vector'\n",
       "19. 'new.vector'\n",
       "20. 'nutella.favorite'\n",
       "21. 'nutella.matrix'\n",
       "22. 'row.names'\n",
       "23. 'vector.1'\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       " [1] \"array.1\"          \"column.names\"     \"df.emp\"           \"df.fruits\"       \n",
       " [5] \"fruits.numbers\"   \"fruits.price\"     \"fruits.smell\"     \"fruits.type\"     \n",
       " [9] \"gender\"           \"matrix.names\"     \"my.fruits\"        \"my.fruits.matrix\"\n",
       "[13] \"my.logic\"         \"my.matrix\"        \"my.number\"        \"my.numbers\"      \n",
       "[17] \"my.string\"        \"my.vector\"        \"new.vector\"       \"nutella.favorite\"\n",
       "[21] \"nutella.matrix\"   \"row.names\"        \"vector.1\"        "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "rm(nutella.info) # Delete a object\n",
    "ls()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "## Basic data operations"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 1. Operators"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 1.1 Arithemetic operators"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "5"
      ],
      "text/latex": [
       "5"
      ],
      "text/markdown": [
       "5"
      ],
      "text/plain": [
       "[1] 5"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "-1"
      ],
      "text/latex": [
       "-1"
      ],
      "text/markdown": [
       "-1"
      ],
      "text/plain": [
       "[1] -1"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "6"
      ],
      "text/latex": [
       "6"
      ],
      "text/markdown": [
       "6"
      ],
      "text/plain": [
       "[1] 6"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "0.666666666666667"
      ],
      "text/latex": [
       "0.666666666666667"
      ],
      "text/markdown": [
       "0.666666666666667"
      ],
      "text/plain": [
       "[1] 0.6666667"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "8"
      ],
      "text/latex": [
       "8"
      ],
      "text/markdown": [
       "8"
      ],
      "text/plain": [
       "[1] 8"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "2"
      ],
      "text/latex": [
       "2"
      ],
      "text/markdown": [
       "2"
      ],
      "text/plain": [
       "[1] 2"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "0"
      ],
      "text/latex": [
       "0"
      ],
      "text/markdown": [
       "0"
      ],
      "text/plain": [
       "[1] 0"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "x <- 2\n",
    "y <- 3\n",
    "x+y\n",
    "x-y\n",
    "x*y\n",
    "x/y\n",
    "x**y # exponentiation\n",
    "x%%y # modulus\n",
    "x%/%y # integer division"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 1.2 Logical operators"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "TRUE"
      ],
      "text/latex": [
       "TRUE"
      ],
      "text/markdown": [
       "TRUE"
      ],
      "text/plain": [
       "[1] TRUE"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "FALSE"
      ],
      "text/latex": [
       "FALSE"
      ],
      "text/markdown": [
       "FALSE"
      ],
      "text/plain": [
       "[1] FALSE"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "TRUE"
      ],
      "text/latex": [
       "TRUE"
      ],
      "text/markdown": [
       "TRUE"
      ],
      "text/plain": [
       "[1] TRUE"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "FALSE"
      ],
      "text/latex": [
       "FALSE"
      ],
      "text/markdown": [
       "FALSE"
      ],
      "text/plain": [
       "[1] FALSE"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "FALSE"
      ],
      "text/latex": [
       "FALSE"
      ],
      "text/markdown": [
       "FALSE"
      ],
      "text/plain": [
       "[1] FALSE"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "TRUE"
      ],
      "text/latex": [
       "TRUE"
      ],
      "text/markdown": [
       "TRUE"
      ],
      "text/plain": [
       "[1] TRUE"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "x <- 5\n",
    "y <- 11\n",
    "x < y\n",
    "x > y\n",
    "x <= y\n",
    "x >= y\n",
    "x == y\n",
    "x != y"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "FALSE"
      ],
      "text/latex": [
       "FALSE"
      ],
      "text/markdown": [
       "FALSE"
      ],
      "text/plain": [
       "[1] FALSE"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "TRUE"
      ],
      "text/latex": [
       "TRUE"
      ],
      "text/markdown": [
       "TRUE"
      ],
      "text/plain": [
       "[1] TRUE"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "FALSE"
      ],
      "text/latex": [
       "FALSE"
      ],
      "text/markdown": [
       "FALSE"
      ],
      "text/plain": [
       "[1] FALSE"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "FALSE"
      ],
      "text/latex": [
       "FALSE"
      ],
      "text/markdown": [
       "FALSE"
      ],
      "text/plain": [
       "[1] FALSE"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "like.chocolate <- TRUE\n",
    "like.spam <- FALSE\n",
    "!like.chocolate\n",
    "like.chocolate | like.spam\n",
    "like.chocolate & like.spam\n",
    "isTRUE(like.spam)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 1.3 Built-in functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "16"
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      "text/latex": [
       "16"
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      "text/markdown": [
       "16"
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      "text/plain": [
       "[1] 16"
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     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "4"
      ],
      "text/latex": [
       "4"
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      "text/markdown": [
       "4"
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      "text/plain": [
       "[1] 4"
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     },
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     "output_type": "display_data"
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    {
     "data": {
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       "2"
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      "text/latex": [
       "2"
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      "text/markdown": [
       "2"
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      "text/plain": [
       "[1] 2"
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     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "-3"
      ],
      "text/latex": [
       "-3"
      ],
      "text/markdown": [
       "-3"
      ],
      "text/plain": [
       "[1] -3"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "-2"
      ],
      "text/latex": [
       "-2"
      ],
      "text/markdown": [
       "-2"
      ],
      "text/plain": [
       "[1] -2"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "1.24"
      ],
      "text/latex": [
       "1.24"
      ],
      "text/markdown": [
       "1.24"
      ],
      "text/plain": [
       "[1] 1.24"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "1.2"
      ],
      "text/latex": [
       "1.2"
      ],
      "text/markdown": [
       "1.2"
      ],
      "text/plain": [
       "[1] 1.2"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "-0.957659480323385"
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      "text/latex": [
       "-0.957659480323385"
      ],
      "text/markdown": [
       "-0.957659480323385"
      ],
      "text/plain": [
       "[1] -0.9576595"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "0.287903316665065"
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      "text/latex": [
       "0.287903316665065"
      ],
      "text/markdown": [
       "0.287903316665065"
      ],
      "text/plain": [
       "[1] 0.2879033"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "-0.300632242023903"
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      "text/latex": [
       "-0.300632242023903"
      ],
      "text/markdown": [
       "-0.300632242023903"
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      "text/plain": [
       "[1] -0.3006322"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "0.214304602647005"
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      "text/latex": [
       "0.214304602647005"
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      "text/markdown": [
       "0.214304602647005"
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      "text/plain": [
       "[1] 0.2143046"
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     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "0.0930713063760635"
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      "text/latex": [
       "0.0930713063760635"
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      "text/markdown": [
       "0.0930713063760635"
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      "text/plain": [
       "[1] 0.09307131"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "1.12535174719259e-07"
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      "text/latex": [
       "1.12535174719259e-07"
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      "text/markdown": [
       "1.12535174719259e-07"
      ],
      "text/plain": [
       "[1] 1.125352e-07"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "x <- -16\n",
    "y <- 1.239\n",
    "z <- -2.251\n",
    "abs(x)\n",
    "sqrt(-x)\n",
    "ceiling(y)\n",
    "floor(z)\n",
    "trunc(z)\n",
    "round(y, digits=2)\n",
    "signif(y, digits=2)\n",
    "cos(x)\n",
    "sin(x)\n",
    "tan(x)\n",
    "log(y)\n",
    "log10(y)\n",
    "exp(x)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [],
   "source": [
    "my.name <- \"Nutella\"\n",
    "my.fav <- c(\"chocolate\", \"peanut\", \"cheese\")\n",
    "my.motto <- \"I love chocolate. --Nutella\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "'Nutel'"
      ],
      "text/latex": [
       "'Nutel'"
      ],
      "text/markdown": [
       "'Nutel'"
      ],
      "text/plain": [
       "[1] \"Nutel\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "substr(my.name, start=1, stop=5) # Extract part of the string"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "3"
      ],
      "text/latex": [
       "3"
      ],
      "text/markdown": [
       "3"
      ],
      "text/plain": [
       "[1] 3"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "grep(\"cheese\", my.fav) # Search for pattern (It is different from Bash Grep!!!!!!)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "'I love cheese. --Nutella'"
      ],
      "text/latex": [
       "'I love cheese. --Nutella'"
      ],
      "text/markdown": [
       "'I love cheese. --Nutella'"
      ],
      "text/plain": [
       "[1] \"I love cheese. --Nutella\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "sub( \"chocolate\",\"cheese\", my.motto) # Replace pattern"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol>\n",
       "\t<li><ol class=list-inline>\n",
       "\t<li>'I'</li>\n",
       "\t<li>'love'</li>\n",
       "\t<li>'chocolate.'</li>\n",
       "\t<li>'--Nutella'</li>\n",
       "</ol>\n",
       "</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate}\n",
       "\\item \\begin{enumerate*}\n",
       "\\item 'I'\n",
       "\\item 'love'\n",
       "\\item 'chocolate.'\n",
       "\\item '--Nutella'\n",
       "\\end{enumerate*}\n",
       "\n",
       "\\end{enumerate}\n"
      ],
      "text/markdown": [
       "1. 1. 'I'\n",
       "2. 'love'\n",
       "3. 'chocolate.'\n",
       "4. '--Nutella'\n",
       "\n",
       "\n",
       "\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[[1]]\n",
       "[1] \"I\"          \"love\"       \"chocolate.\" \"--Nutella\" \n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "strsplit(my.motto, \" \") # Split elements"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>'1: chocolate'</li>\n",
       "\t<li>'2: peanut'</li>\n",
       "\t<li>'3: cheese'</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item '1: chocolate'\n",
       "\\item '2: peanut'\n",
       "\\item '3: cheese'\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. '1: chocolate'\n",
       "2. '2: peanut'\n",
       "3. '3: cheese'\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] \"1: chocolate\" \"2: peanut\"    \"3: cheese\"   "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "paste(1:3, my.fav, sep=\": \") # Concatenate strings"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "'I LOVE CHOCOLATE. --NUTELLA'"
      ],
      "text/latex": [
       "'I LOVE CHOCOLATE. --NUTELLA'"
      ],
      "text/markdown": [
       "'I LOVE CHOCOLATE. --NUTELLA'"
      ],
      "text/plain": [
       "[1] \"I LOVE CHOCOLATE. --NUTELLA\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "toupper(my.motto)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "'i love chocolate. --nutella'"
      ],
      "text/latex": [
       "'i love chocolate. --nutella'"
      ],
      "text/markdown": [
       "'i love chocolate. --nutella'"
      ],
      "text/plain": [
       "[1] \"i love chocolate. --nutella\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "tolower(my.motto)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 2. Control structures"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 2.1 if-else"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"I like peanuts!\"\n"
     ]
    }
   ],
   "source": [
    "like.peanut <- TRUE\n",
    "if (like.peanut){\n",
    "    print(\"I like peanuts!\")\n",
    "} else {\n",
    "    print(\"What do I like?\")\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"I like to build my nest with cotton!\"\n"
     ]
    }
   ],
   "source": [
    "like.hay <- FALSE\n",
    "like.cotton <- TRUE\n",
    "if (like.hay){\n",
    "    print(\"I like to build my nest with hay!\")\n",
    "} else if (like.cotton){\n",
    "    print(\"I like to build my nest with cotton!\")\n",
    "} else {\n",
    "    print(\"Ummm.... what should I use...?\")\n",
    "}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 2.2 for"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n"
     ]
    }
   ],
   "source": [
    "for (i in c(1:10)) {\n",
    "    print(\"More chocolate please!\")\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"More chocolate please!\"\n",
      "[1] \"More peanut please!\"\n",
      "[1] \"More cheese please!\"\n"
     ]
    }
   ],
   "source": [
    "my.fav <- c(\"chocolate\", \"peanut\", \"cheese\")\n",
    "for (i in my.fav) {\n",
    "    out.put <- paste(\"More\", i, \"please!\") # Paste 3 elements into a single string\n",
    "    print(out.put)\n",
    "}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### 2.3 while"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n",
      "[1] \"More chocolate please!\"\n"
     ]
    }
   ],
   "source": [
    "i <- 0\n",
    "while (i < 10) {\n",
    "    print(\"More chocolate please!\")\n",
    "    i <- i+1 # Super important! Or your while loop will never end...\n",
    "}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Homework"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1. Hello world everyday!\n",
    "### 1.1 Make a vector containing days of the week, from Monday to Sunday.\n",
    "### 1.2 Use a for loop to pring \"Hello world XXXday!\" for each day of the week."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2. The Pie\n",
    "### 2.1 In the first 100 digits of pie, count how many numbers are even. \n",
    "### 2.2 Convert the first 200 digits of pie into a 20x10 matrix"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 3. Install Swirl,  do \"R programming\" and \"Data analysis\"\n",
    "https://swirlstats.com/students.html Do it as you like!"
   ]
  }
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