R_in_Action-ch01.ipnb

R_in_Action-ch01

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 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Sage/text/R_in_Action (\u7af9\u672c\u6c0f\u306eblog ) <br> http://www.pwv.co.jp/~take/TakeWiki/index.php"
     ]
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "R in Action    Rob Kabacoff,  2014, Manning Publications"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "posted by Y.Sato on 30 Oct, 2014"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%load_ext sage"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import os\n",
      "DATA = os.getcwd() + '/' ; DATA"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 2,
       "text": [
        "'/home/satouy/Dropbox/work-Sage/sage-ipython/Take/R_in_Action/'"
       ]
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# Chrome\u3067\u306fPDF\u3092img\u30bf\u30b0\u3067\u8868\u793a\u3067\u304d\u306a\u3044\u306e\u3067\u3001png\u306b\u5909\u63db\u3059\u308b\u3088\u3046\u306b\u5909\u66f4 2012/06/27\n",
      "#\n",
      "# R\u306e\u30b0\u30e9\u30d5\u3092sage\u3067\u8868\u793a\u3059\u308b\u305f\u3081\u306e\u30e6\u30fc\u30c6\u30a3\u30ea\u30c6\u30a3\u95a2\u6570\n",
      "import time\n",
      "def preGraph(pdfFile):\n",
      "    filename = DATA+pdfFile\n",
      "    r.pdf(file='\"%s\"' %filename)\n",
      "    return pdfFile\n",
      "\n",
      "def offGraph():\n",
      "    r.dev_off()\n",
      "    \n",
      "def postGraph(pdfFile, fac=0.75):\n",
      "    r.dev_off()\n",
      "    width = int(640*fac)\n",
      "    # html('<img src=\"%s?%s\" width=\"%spx\">'%(pdfFile, time.time(), width))\n",
      "    pngFile = convertPdf2Png(pdfFile)\n",
      "    html('<img src=\"%s?%s\" width=\"%spx\">'%(pngFile, time.time(), width))\n",
      "\n",
      "def getGraph(pdfFile, fac=0.75):\n",
      "    width = int(640*fac)\n",
      "    # return '<img src=\"%s?%s\" width=\"%spx\">'%(pdfFile, time.time(), width)\n",
      "    pngFile = convertPdf2Png(pdfFile)\n",
      "    return '<img src=\"%s?%s\" width=\"%spx\">'%(pngFile, time.time(), width)\n",
      "    \n",
      "def convertPdf2Png(pdfFile):\n",
      "    pngFile = pdfFile.replace(\".pdf\", \".png\")\n",
      "    result = os.popen(\"cd %s; convert -density 600 -geometry 1000 %s %s\"%(DATA, pdfFile, pngFile)).read()\n",
      "    # print result\n",
      "    return pngFile "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from IPython.display import Image, display"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from IPython.display import display, Math\n",
      "def my_show(obj):\n",
      "    return display(Math(latex(obj)))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 5
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "Display List as Table in IPython Notebook <br>\n",
      "http://calebmadrigal.com/display-list-as-table-in-ipython-notebook/"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "class ListTable(list):\n",
      "    \"\"\" Overridden list class which takes a 2-dimensional list of \n",
      "        the form [[1,2,3],[4,5,6]], and renders an HTML Table in \n",
      "        IPython Notebook. \"\"\"\n",
      "    \n",
      "    def _repr_html_(self):\n",
      "        html = [\"<table>\"]\n",
      "        for row in self:\n",
      "            html.append(\"<tr>\")\n",
      "            \n",
      "            for col in row:\n",
      "                html.append(\"<td>{0}</td>\".format(col))\n",
      "            \n",
      "            html.append(\"</tr>\")\n",
      "        html.append(\"</table>\")\n",
      "        return ''.join(html)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# table = ListTable()\n",
      "# table.append([getGraph(fig_3_7a, fac=0.5), getGraph(fig_3_7b, fac=0.5)])\n",
      "# table"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 7
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "IPython's Rich Display System <br>\n",
      "http://nbviewer.ipython.org/github/ipython/ipython/blob/1.x/examples/notebooks/Part%205%20-%20Rich%20Display%20System.ipynb"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from IPython.display import HTML"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 8
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Begin of program"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# \u5909\u6570\u306e\u53d7\u3051\u6e21\u3057\n",
      "# Sage -> R\n",
      "# \u3059\u3079\u3066\u30ea\u30b9\u30c8\u306e\u5f62\u5f0f\u306b\u5909\u63db\u3055\u308c\u3066R\u306b\u6e21\u3055\u308c\u308b\n",
      "s_age = r([1,3,5,2,11,9,3,9,12,3]).name('age')\n",
      "# name\u95a2\u6570\u3067\u540d\u524d\u3092\u6307\u5b9a\u3059\u308b\u3053\u3068\u3067\u3001R\u306e\u5909\u6570\u3082\u5b9a\u7fa9\u3055\u308c\u308b\n",
      "print r('age')\n",
      "# R\u304b\u3089Sage\u3078\u306e\u5909\u63db\u306f\u3001sageobj\u95a2\u6570\u307e\u305f\u306f_sage_()\u30e1\u30bd\u30c3\u30c9\u3092\u4f7f\u7528\n",
      "print sageobj(r('age')) "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " [1]  1  3  5  2 11  9  3  9 12  3\n",
        "[1, 3, 5, 2, 11, 9, 3, 9, 12, 3]\n"
       ]
      }
     ],
     "prompt_number": 11
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# \u6587\u5b57\u5217\u914d\u5217\u306e\u53d7\u3051\u6e21\u3057\u304c\u3067\u304d\u306a\u3044\u3053\u3068\u304c\u5206\u304b\u308a\u307e\u3057\u305f\u3002\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u7121\u7406\u77e2\u7406\u30bb\u30c3\u30c8\u3057\u3066\u304f\u3060\u3055\u3044\u3002\n",
      "ary = [\"a\", \"b\"]\n",
      "ss = str(ary)[1:-1]; print ss # \u30ea\u30b9\u30c8\u3092\u6587\u5b57\u5217\u306b\u5909\u63db\u3057\u3066[\u3068]\u3092\u53d6\u308a\u9664\u304f\n",
      "rary = r('c(%s)'%ss).name('rary')\n",
      "print rary # R\u306b\u5909\u63db\u3057\u305f\u914d\u5217\n",
      "sary = sageobj(rary)\n",
      "print sary # sage\u306b\u623b\u3057\u305f\u914d\u5217 "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "'a', 'b'\n",
        "[1] \"a\" \"b\"\n",
        "['a', 'b']\n"
       ]
      }
     ],
     "prompt_number": 12
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# \u30de\u30c8\u30ea\u30c3\u30af\u30b9\u306e\u751f\u6210\u3082\u540c\u69d8\u306b\u751f\u6210\u5f8c\u306b\u540d\u524d\u3092\u3064\u3051\u3066\u4ee3\u5165\u3059\u308c\u3070\u3088\u3044\n",
      "m = r.matrix([1, 2, 3, 4], 2, 2, byrow=True).name('m'); m "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 13,
       "text": [
        "     [,1] [,2]\n",
        "[1,]    1    2\n",
        "[2,]    3    4"
       ]
      }
     ],
     "prompt_number": 13
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# r\u3067\u3082\u540c\u3058\u5909\u6570\u540d\u304c\u5b9a\u7fa9\u3055\u308c\u308b\n",
      "r('m') "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 14,
       "text": [
        "     [,1] [,2]\n",
        "[1,]    1    2\n",
        "[2,]    3    4"
       ]
      }
     ],
     "prompt_number": 14
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# from IPython.display import display, Math\n",
      "# def my_show(obj): return display(Math(latex(obj)))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 15
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# R\u306e\u30de\u30c8\u30ea\u30c3\u30af\u30b9\u5909\u6570\u3092sage\u306e\u5909\u6570\u306b\u5909\u63db\u3059\u308b\n",
      "print type(m)\n",
      "sm = sageobj(m)\n",
      "my_show(sm)\n",
      "print type(sm) "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "<class 'sage.interfaces.r.RElement'>\n"
       ]
      },
      {
       "latex": [
        "$$\\left(\\begin{array}{rr}\n",
        "1 & 2 \\\\\n",
        "3 & 4\n",
        "\\end{array}\\right)$$"
       ],
       "metadata": {},
       "output_type": "display_data",
       "text": [
        "<IPython.core.display.Math at 0x7ff3a2965e50>"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "<type 'sage.matrix.matrix_integer_dense.Matrix_integer_dense'>\n"
       ]
      }
     ],
     "prompt_number": 16
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "\u30b0\u30e9\u30d5\u8868\u793a"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "Chapter 1  Introduction to R"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# fig1.4\n",
      "age = r([1,3,5,2,11,9,3,9,12,3]).name('age')\n",
      "weight = r([4.4,5.3,7.2,5.2,8.5,7.3,6.0,10.4,10.2,6.1]).name('weight')\n",
      "print r.mean(weight)\n",
      "print r.sd(weight)\n",
      "print r.cor(age, weight) "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[1] 7.06\n",
        "[1] 2.077498\n",
        "[1] 0.9075655\n"
       ]
      }
     ],
     "prompt_number": 17
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# \u30b0\u30e9\u30d5\u8868\u793a\n",
      "graph = preGraph(\"fig1.4.pdf\")\n",
      "r.plot(age, weight)\n",
      "postGraph(graph, fac=0.5) "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "<html><font color='black'><img src=\"fig1.4.png?1414657856.97\" width=\"320px\"></font></html>\n"
       ]
      }
     ],
     "prompt_number": 18
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# ImageMagick \u306e convert \u3092\u4f7f\u3063\u3066\u3044\u308b\n",
      "os.system(\"convert -resize 400x fig1.4.png fig1.4b.png\")\n",
      "display(Image('fig1.4b.png'))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "display_data",
       "png": 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       "text": [
        "<IPython.core.display.Image at 0x7ff3a004dc90>"
       ]
      }
     ],
     "prompt_number": 19
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# \u30bf\u30a4\u30c8\u30eb\u3092\u8ffd\u52a0\u3059\u308b\u5834\u5408\u306b\u306f\u3001r.plot\u3067\u306f\u306a\u304f\u3001r\u95a2\u6570\u3092\u4f7f\u7528\u3059\u308b\n",
      "graph = preGraph(\"fig1.4withTitle.pdf\")\n",
      "r(\"plot(age, weight, main='Title')\")\n",
      "postGraph(graph, fac=0.5) "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "<html><font color='black'><img src=\"fig1.4withTitle.png?1414657859.12\" width=\"320px\"></font></html>\n"
       ]
      }
     ],
     "prompt_number": 20
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "os.system(\"convert -resize 400x fig1.4withTitle.png fig1.4withTitleb.png\")\n",
      "display(Image('fig1.4withTitleb.png'))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "display_data",
       "png": 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       "text": [
        "<IPython.core.display.Image at 0x7ff3a004df90>"
       ]
      }
     ],
     "prompt_number": 21
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "Chapter 3   Getting started with graphics"
     ]
    }
   ],
   "metadata": {}
  }
 ]
}