survival_demo.ipynb

{
 "metadata": {
  "name": "survival_demo"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "# Survival Analysis in iPython via R\n",
      "\n",
      "The R code is cribbed from the [UCLA course](http://www.ats.ucla.edu/stat/r/examples/asa/default.htm), based on Hosmer & Lemeshow.\n",
      "\n",
      "First, which version of iPython are you using?"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import IPython\n",
      "print 'ipython version is %s'% IPython.release.version\n",
      "print 'rmagic is >= 0.13, I believe'"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "ipython version is 0.14.dev\n",
        "rmagic is >= 0.13, I believe\n"
       ]
      }
     ],
     "prompt_number": 1
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "now load the R module:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%load_ext rmagic"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R\n",
      "# you are now dropped down in R;\n",
      "# which version of R am I using, BTW?\n",
      "print(R.version)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "display_data",
       "text": [
        "               _                            \n",
        "platform       x86_64-pc-linux-gnu          \n",
        "arch           x86_64                       \n",
        "os             linux-gnu                    \n",
        "system         x86_64, linux-gnu            \n",
        "status                                      \n",
        "major          2                            \n",
        "minor          15.2                         \n",
        "year           2012                         \n",
        "month          10                           \n",
        "day            26                           \n",
        "svn rev        61015                        \n",
        "language       R                            \n",
        "version.string R version 2.15.2 (2012-10-26)\n",
        "nickname       Trick or Treat               \n"
       ]
      }
     ],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R\n",
      "# my notebook is wider than the default 80 chars, so set it here:\n",
      "options(width=300)\n",
      "# get the survival package if you do not have it:\n",
      "if (! length(which(.packages(all.available=TRUE) %in% \"survival\"))) {\n",
      "    install.packages(\"survival\",repos=\"http://cran.cnr.berkeley.edu/\")\n",
      "}\n",
      "library(survival)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "display_data",
       "text": [
        "Loading required package: splines\n"
       ]
      }
     ],
     "prompt_number": 4
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Start using R as you would normally, although echoing has to be performed explicitly."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R\n",
      "hmohiv<-read.table(\"http://www.ats.ucla.edu/stat/r/examples/asa/hmohiv.csv\", sep=\",\", header = TRUE)\n",
      "attach(hmohiv)\n",
      "print(head(hmohiv))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "display_data",
       "text": [
        "  ID time age drug censor    entdate     enddate\n",
        "1  1    5  46    0      1 5/15/1990  10/14/1990 \n",
        "2  2    6  35    1      0 9/19/1989   3/20/1990 \n",
        "3  3    8  30    1      1 4/21/1991  12/20/1991 \n",
        "4  4    3  30    1      1  1/3/1991    4/4/1991 \n",
        "5  5   22  36    0      1 9/18/1989   7/19/1991 \n",
        "6  6    1  32    1      0 3/18/1991   4/17/1991 \n"
       ]
      }
     ],
     "prompt_number": 5
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R -w 800 -h 600\n",
      "# figures work fine, but you may want to set the height and width with the -w and -h flags as above\n",
      "psymbol<-censor+1\n",
      "table(psymbol)\n",
      "plot(age, time, pch=(psymbol))\n",
      "legend(40, 60, c(\"Censor=1\", \"Censor=0\"), pch=(psymbol))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "display_data",
       "png": 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JUpKaK4YtjXOj3b4V08Jvj7LO8VaF4rr1oWW3rxDzsmxsM5IrB4rXLggtyukq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\nWwAAAABJRU5ErkJggg==\n"
      }
     ],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%R\n",
      "# this is all still cribbed from the UCLA page\n",
      "test <- survreg( Surv(time, censor) ~ age, dist=\"exponential\")\n",
      "# note again, you have to explicitly echo\n",
      "print(summary(test))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "display_data",
       "text": [
        "\n",
        "Call:\n",
        "survreg(formula = Surv(time, censor) ~ age, dist = \"exponential\")\n",
        "              Value Std. Error     z        p\n",
        "(Intercept)  5.8590     0.5853 10.01 1.37e-23\n",
        "age         -0.0939     0.0158 -5.96 2.59e-09\n",
        "\n",
        "Scale fixed at 1 \n",
        "\n",
        "Exponential distribution\n",
        "Loglik(model)= -275   Loglik(intercept only)= -292.3\n",
        "\tChisq= 34.5 on 1 degrees of freedom, p= 4.3e-09 \n",
        "Number of Newton-Raphson Iterations: 4 \n",
        "n= 100 \n",
        "\n"
       ]
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "You can pass data back and forth, but I am not an expert on this aspect; Access the ipython help for ```Rpush``` and ```Rpull``` for more details."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%Rpull hmohiv"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# for a raw pull, the column information is lost?\n",
      "hmohiv"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 9,
       "text": [
        "array([[  1,   2,   3,   4,   5,   6,   7,   8,   9,  10,  11,  12,  13,\n",
        "         14,  15,  16,  17,  18,  19,  20,  21,  22,  23,  24,  25,  26,\n",
        "         27,  28,  29,  30,  31,  32,  33,  34,  35,  36,  37,  38,  39,\n",
        "         40,  41,  42,  43,  44,  45,  46,  47,  48,  49,  50,  51,  52,\n",
        "         53,  54,  55,  56,  57,  58,  59,  60,  61,  62,  63,  64,  65,\n",
        "         66,  67,  68,  69,  70,  71,  72,  73,  74,  75,  76,  77,  78,\n",
        "         79,  80,  81,  82,  83,  84,  85,  86,  87,  88,  89,  90,  91,\n",
        "         92,  93,  94,  95,  96,  97,  98,  99, 100],\n",
        "       [  5,   6,   8,   3,  22,   1,   7,   9,   3,  12,   2,  12,   1,\n",
        "         15,  34,   1,   4,  19,   3,   2,   2,   6,  60,  11,   2,   5,\n",
        "          4,   1,  13,   3,   2,   1,  30,   7,   4,   8,   5,  10,   2,\n",
        "          9,  36,   3,   9,   3,  35,   8,  11,  56,   2,   3,  15,   1,\n",
        "         10,   1,   7,   3,   3,   2,  32,   3,  10,  11,   3,   7,   5,\n",
        "         31,   5,  58,   1,   3,  43,   1,   6,  53,  14,   4,  54,   1,\n",
        "          1,   8,   5,   1,   1,   2,   7,   1,  10,  24,   7,  12,   4,\n",
        "         57,   1,  12,   7,   1,   5,  60,   2,   1],\n",
        "       [ 46,  35,  30,  30,  36,  32,  36,  31,  48,  47,  28,  34,  44,\n",
        "         32,  36,  36,  54,  35,  44,  38,  40,  34,  25,  32,  42,  47,\n",
        "         30,  47,  41,  40,  43,  41,  30,  37,  42,  31,  39,  32,  51,\n",
        "         36,  43,  39,  33,  45,  33,  28,  31,  20,  44,  39,  33,  31,\n",
        "         33,  50,  36,  30,  42,  32,  34,  38,  33,  39,  39,  33,  34,\n",
        "         34,  46,  22,  44,  37,  25,  38,  32,  34,  29,  36,  21,  26,\n",
        "         32,  42,  40,  37,  47,  32,  41,  46,  26,  30,  32,  31,  35,\n",
        "         36,  41,  36,  35,  34,  28,  29,  35,  34],\n",
        "       [  0,   1,   1,   1,   0,   1,   1,   1,   0,   0,   1,   0,   1,\n",
        "          1,   0,   0,   0,   0,   1,   0,   0,   1,   0,   0,   1,   0,\n",
        "          0,   1,   0,   1,   0,   0,   0,   0,   1,   1,   1,   0,   0,\n",
        "          0,   0,   0,   0,   1,   0,   0,   0,   1,   0,   1,   0,   0,\n",
        "          0,   1,   1,   1,   1,   1,   0,   1,   0,   1,   1,   1,   1,\n",
        "          0,   1,   0,   1,   0,   0,   0,   0,   0,   0,   1,   0,   1,\n",
        "          1,   0,   1,   1,   0,   1,   1,   1,   1,   0,   1,   1,   0,\n",
        "          0,   1,   1,   1,   1,   0,   0,   1,   1],\n",
        "       [  1,   0,   1,   1,   1,   0,   1,   1,   1,   1,   0,   1,   1,\n",
        "          1,   1,   1,   1,   0,   0,   1,   0,   1,   0,   1,   0,   1,\n",
        "          0,   1,   1,   1,   1,   1,   1,   1,   1,   1,   1,   1,   1,\n",
        "          1,   1,   1,   1,   1,   1,   1,   1,   0,   0,   1,   1,   1,\n",
        "          1,   1,   1,   1,   1,   1,   1,   1,   0,   1,   1,   1,   1,\n",
        "          1,   1,   1,   1,   0,   1,   1,   1,   1,   1,   1,   1,   1,\n",
        "          1,   1,   1,   1,   1,   1,   0,   0,   1,   0,   1,   0,   1,\n",
        "          1,   1,   0,   1,   1,   1,   0,   0,   1],\n",
        "       [ 57,  94,  45,  27,  93,  34,   6,  10,  29,  78,  43,  53,  12,\n",
        "         31,  51,  41,  85,  66,  68,  28,  83,  63,   8,  65,  88,  19,\n",
        "         64,  54,  38,  73,  92,  70,  48,  58,  33,  32,  86,  77,  20,\n",
        "         47,  23,  49,  76,  22,  18,  71,  43,  61,   7,  13,   6,   3,\n",
        "         36,  75,  72,   5,  40,  37,  89,  90,  50,  44,  26,  91,  25,\n",
        "         39,  44,  69,   3,  30,  56,  87,  17,  81,  14,  82,  59,  35,\n",
        "          4,  60,  67,  84,  21,  95,   9,  74,   2,   1,  24,  96,  42,\n",
        "         15,  16,  11,  80,  79,  62,  46,  55,  52],\n",
        "       [  3,  46,  28,  57,  78,  53,  72,  85,  63,  83,  71,  60,  38,\n",
        "         64,  42,  59,  29,  35,  88,  48,   8,  15,  12,  59,  21,  66,\n",
        "         91,  67,  56,   4,  13,  79,   7,  27,  75,   5,  34,  71,  40,\n",
        "         32,  31,  80,  58,  49,  14,  39,  44,  23,  10,  55,  36,   9,\n",
        "         20,  86,  37,  43,  77,  62,  61,  26,  41,  46,  65,  51,  69,\n",
        "          2,  90,  52,   9,  68,  24,  93,  73,  25,  45,  30,  11,  54,\n",
        "         19,  22,  21,  92,  33,  16,  74,  84,  82,   1,  81,  93,  87,\n",
        "         94,  18,  17,  47,  89,   6,  50,  76,  70]], dtype=int32)"
       ]
      }
     ],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%Rpull -d hmohiv"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 10
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# now it is pulled as something else, but what I am not sure\n",
      "hmohiv"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 11,
       "text": [
        "array([(1, 5, 46, 0, 1, 57, 3), (2, 6, 35, 1, 0, 94, 46),\n",
        "       (3, 8, 30, 1, 1, 45, 28), (4, 3, 30, 1, 1, 27, 57),\n",
        "       (5, 22, 36, 0, 1, 93, 78), (6, 1, 32, 1, 0, 34, 53),\n",
        "       (7, 7, 36, 1, 1, 6, 72), (8, 9, 31, 1, 1, 10, 85),\n",
        "       (9, 3, 48, 0, 1, 29, 63), (10, 12, 47, 0, 1, 78, 83),\n",
        "       (11, 2, 28, 1, 0, 43, 71), (12, 12, 34, 0, 1, 53, 60),\n",
        "       (13, 1, 44, 1, 1, 12, 38), (14, 15, 32, 1, 1, 31, 64),\n",
        "       (15, 34, 36, 0, 1, 51, 42), (16, 1, 36, 0, 1, 41, 59),\n",
        "       (17, 4, 54, 0, 1, 85, 29), (18, 19, 35, 0, 0, 66, 35),\n",
        "       (19, 3, 44, 1, 0, 68, 88), (20, 2, 38, 0, 1, 28, 48),\n",
        "       (21, 2, 40, 0, 0, 83, 8), (22, 6, 34, 1, 1, 63, 15),\n",
        "       (23, 60, 25, 0, 0, 8, 12), (24, 11, 32, 0, 1, 65, 59),\n",
        "       (25, 2, 42, 1, 0, 88, 21), (26, 5, 47, 0, 1, 19, 66),\n",
        "       (27, 4, 30, 0, 0, 64, 91), (28, 1, 47, 1, 1, 54, 67),\n",
        "       (29, 13, 41, 0, 1, 38, 56), (30, 3, 40, 1, 1, 73, 4),\n",
        "       (31, 2, 43, 0, 1, 92, 13), (32, 1, 41, 0, 1, 70, 79),\n",
        "       (33, 30, 30, 0, 1, 48, 7), (34, 7, 37, 0, 1, 58, 27),\n",
        "       (35, 4, 42, 1, 1, 33, 75), (36, 8, 31, 1, 1, 32, 5),\n",
        "       (37, 5, 39, 1, 1, 86, 34), (38, 10, 32, 0, 1, 77, 71),\n",
        "       (39, 2, 51, 0, 1, 20, 40), (40, 9, 36, 0, 1, 47, 32),\n",
        "       (41, 36, 43, 0, 1, 23, 31), (42, 3, 39, 0, 1, 49, 80),\n",
        "       (43, 9, 33, 0, 1, 76, 58), (44, 3, 45, 1, 1, 22, 49),\n",
        "       (45, 35, 33, 0, 1, 18, 14), (46, 8, 28, 0, 1, 71, 39),\n",
        "       (47, 11, 31, 0, 1, 43, 44), (48, 56, 20, 1, 0, 61, 23),\n",
        "       (49, 2, 44, 0, 0, 7, 10), (50, 3, 39, 1, 1, 13, 55),\n",
        "       (51, 15, 33, 0, 1, 6, 36), (52, 1, 31, 0, 1, 3, 9),\n",
        "       (53, 10, 33, 0, 1, 36, 20), (54, 1, 50, 1, 1, 75, 86),\n",
        "       (55, 7, 36, 1, 1, 72, 37), (56, 3, 30, 1, 1, 5, 43),\n",
        "       (57, 3, 42, 1, 1, 40, 77), (58, 2, 32, 1, 1, 37, 62),\n",
        "       (59, 32, 34, 0, 1, 89, 61), (60, 3, 38, 1, 1, 90, 26),\n",
        "       (61, 10, 33, 0, 0, 50, 41), (62, 11, 39, 1, 1, 44, 46),\n",
        "       (63, 3, 39, 1, 1, 26, 65), (64, 7, 33, 1, 1, 91, 51),\n",
        "       (65, 5, 34, 1, 1, 25, 69), (66, 31, 34, 0, 1, 39, 2),\n",
        "       (67, 5, 46, 1, 1, 44, 90), (68, 58, 22, 0, 1, 69, 52),\n",
        "       (69, 1, 44, 1, 1, 3, 9), (70, 3, 37, 0, 0, 30, 68),\n",
        "       (71, 43, 25, 0, 1, 56, 24), (72, 1, 38, 0, 1, 87, 93),\n",
        "       (73, 6, 32, 0, 1, 17, 73), (74, 53, 34, 0, 1, 81, 25),\n",
        "       (75, 14, 29, 0, 1, 14, 45), (76, 4, 36, 1, 1, 82, 30),\n",
        "       (77, 54, 21, 0, 1, 59, 11), (78, 1, 26, 1, 1, 35, 54),\n",
        "       (79, 1, 32, 1, 1, 4, 19), (80, 8, 42, 0, 1, 60, 22),\n",
        "       (81, 5, 40, 1, 1, 67, 21), (82, 1, 37, 1, 1, 84, 92),\n",
        "       (83, 1, 47, 0, 1, 21, 33), (84, 2, 32, 1, 1, 95, 16),\n",
        "       (85, 7, 41, 1, 0, 9, 74), (86, 1, 46, 1, 0, 74, 84),\n",
        "       (87, 10, 26, 1, 1, 2, 82), (88, 24, 30, 0, 0, 1, 1),\n",
        "       (89, 7, 32, 1, 1, 24, 81), (90, 12, 31, 1, 0, 96, 93),\n",
        "       (91, 4, 35, 0, 1, 42, 87), (92, 57, 36, 0, 1, 15, 94),\n",
        "       (93, 1, 41, 1, 1, 16, 18), (94, 12, 36, 1, 0, 11, 17),\n",
        "       (95, 7, 35, 1, 1, 80, 47), (96, 1, 34, 1, 1, 79, 89),\n",
        "       (97, 5, 28, 0, 1, 62, 6), (98, 60, 29, 0, 0, 46, 50),\n",
        "       (99, 2, 35, 1, 0, 55, 76), (100, 1, 34, 1, 1, 52, 70)], \n",
        "      dtype=[('ID', '<i4'), ('time', '<i4'), ('age', '<i4'), ('drug', '<i4'), ('censor', '<i4'), ('entdate', '<i4'), ('enddate', '<i4')])"
       ]
      }
     ],
     "prompt_number": 11
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "?Rpull"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 12
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 12
    }
   ],
   "metadata": {}
  }
 ]
}