testing ipython notebook and magic.

ipython_test.ipynb

{
 "metadata": {
  "name": "footest"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# to get the R<->python magic"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%load_ext rmagic"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# now you can code in R:"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R\n",
      "library(survival)\n",
      "amod <- coxph(Surv(lung$time,lung$status) ~ lung$sex + lung$ph.karno)\n",
      "print(summary(amod))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "display_data",
       "text": [
        "Loading required package: splines\n",
        "Call:\n",
        "coxph(formula = Surv(lung$time, lung$status) ~ lung$sex + lung$ph.karno)\n",
        "\n",
        "  n= 227, number of events= 164 \n",
        "   (1 observation deleted due to missingness)\n",
        "\n",
        "                   coef exp(coef)  se(coef)      z Pr(>|z|)   \n",
        "lung$sex      -0.504210  0.603982  0.167723 -3.006  0.00265 **\n",
        "lung$ph.karno -0.015155  0.984959  0.005727 -2.646  0.00814 **\n",
        "---\n",
        "Signif. codes:  0 \u2018***\u2019 0.001 \u2018**\u2019 0.01 \u2018*\u2019 0.05 \u2018.\u2019 0.1 \u2018 \u2019 1 \n",
        "\n",
        "              exp(coef) exp(-coef) lower .95 upper .95\n",
        "lung$sex          0.604      1.656    0.4348    0.8391\n",
        "lung$ph.karno     0.985      1.015    0.9740    0.9961\n",
        "\n",
        "Concordance= 0.638  (se = 0.026 )\n",
        "Rsquare= 0.072   (max possible= 0.999 )\n",
        "Likelihood ratio test= 17.05  on 2 df,   p=0.0001981\n",
        "Wald test            = 17.18  on 2 df,   p=0.000186\n",
        "Score (logrank) test = 17.5  on 2 df,   p=0.0001583\n",
        "\n"
       ]
      }
     ],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# to get the octave<->python magic"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%load_ext octavemagic"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 5
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%octave -o y\n",
      "x = randn(100,20);\n",
      "y = sum(x,1);"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "display_data",
       "text": [
        "warning: mark_as_command is obsolete and will be removed from a future version of Octave\n",
        "********************************\n",
        "adding ~/lang/octave/m// to path\n",
        "********************************"
       ]
      }
     ],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "y"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 7,
       "text": [
        "array([[ -8.83067733,  -3.13032074,  -2.91806939,   1.14890723,\n",
        "          5.44526298,  10.23667501,  13.29263306,  -4.92289999,\n",
        "          2.36629103,   5.51218616,  17.05002896,   3.99914408,\n",
        "        -11.06913111,  -5.63449047,  -4.2435471 ,  -5.57522994,\n",
        "         -4.37502494, -10.54391426,  10.11748001,  -0.2811483 ]])"
       ]
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%octave -i y -o z\n",
      "z = sum(y);"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "z"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 9,
       "text": [
        "7.6441549485344096"
       ]
      }
     ],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}