1 | // $Id: score_test.cc 747 2007-02-11 13:26:41Z peter $ |
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2 | |
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3 | /* |
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4 | Copyright (C) The authors contributing to this file. |
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5 | |
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6 | This file is part of the yat library, http://lev.thep.lu.se/trac/yat |
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7 | |
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8 | The yat library is free software; you can redistribute it and/or |
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9 | modify it under the terms of the GNU General Public License as |
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10 | published by the Free Software Foundation; either version 2 of the |
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11 | License, or (at your option) any later version. |
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12 | |
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13 | The yat library is distributed in the hope that it will be useful, |
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14 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
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15 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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16 | General Public License for more details. |
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17 | |
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18 | You should have received a copy of the GNU General Public License |
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19 | along with this program; if not, write to the Free Software |
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20 | Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA |
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21 | 02111-1307, USA. |
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22 | */ |
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23 | |
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24 | #include "yat/classifier/Target.h" |
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25 | #include "yat/statistics/FoldChange.h" |
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26 | #include "yat/statistics/Pearson.h" |
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27 | #include "yat/statistics/ROC.h" |
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28 | #include "yat/statistics/SAM.h" |
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29 | #include "yat/statistics/tScore.h" |
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30 | #include "yat/statistics/WilcoxonFoldChange.h" |
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31 | #include "yat/utility/matrix.h" |
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32 | #include "yat/utility/vector.h" |
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33 | |
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34 | #include <cmath> |
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35 | #include <fstream> |
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36 | #include <iostream> |
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37 | |
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38 | |
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39 | using namespace theplu::yat; |
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40 | |
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41 | int main(const int argc,const char* argv[]) |
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42 | { |
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43 | std::ostream* error; |
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44 | if (argc>1 && argv[1]==std::string("-v")) |
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45 | error = &std::cerr; |
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46 | else { |
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47 | error = new std::ofstream("/dev/null"); |
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48 | if (argc>1) |
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49 | std::cout << "score_test -v : for printing extra information\n"; |
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50 | } |
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51 | *error << "testing score classes" << std::endl; |
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52 | bool ok = true; |
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53 | |
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54 | *error << "testing ROC" << std::endl; |
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55 | utility::vector value(31); |
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56 | std::vector<std::string> label(31,"negative"); |
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57 | for (size_t i=0; i<16; i++) |
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58 | label[i] = "positive"; |
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59 | classifier::Target target(label); |
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60 | for (size_t i=0; i<value.size(); i++) |
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61 | value(i)=i; |
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62 | statistics::ROC roc; |
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63 | double area = roc.score(target, value); |
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64 | if (area!=1.0){ |
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65 | *error << "test_roc: area is " << area << " should be 1.0" |
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66 | << std::endl; |
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67 | ok = false; |
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68 | } |
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69 | target.set_binary(0,false); |
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70 | target.set_binary(1,true); |
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71 | area = roc.score(target, value); |
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72 | if (area!=1.0){ |
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73 | *error << "test_roc: area is " << area << " should be 1.0" |
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74 | << std::endl; |
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75 | ok = false; |
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76 | } |
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77 | |
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78 | double p = roc.p_value(); |
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79 | double p_matlab = 0.00000115; |
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80 | if (p/p_matlab > 1.01 | p/p_matlab < 0.99){ |
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81 | *error << "get_p_approx: p-value not correct" << std::endl; |
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82 | ok = false; |
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83 | } |
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84 | roc.minimum_size() = 20; |
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85 | p = roc.p_value(); |
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86 | if (p > pow(10, -8.0) | p < pow(10, -9.0)){ |
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87 | *error << "get_p_exact: p-value not correct" << std::endl; |
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88 | ok = false; |
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89 | } |
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90 | |
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91 | std::ifstream is("data/rank_data.txt"); |
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92 | utility::matrix data(is); |
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93 | is.close(); |
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94 | |
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95 | is.open("data/rank_target.txt"); |
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96 | classifier::Target target2(is); |
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97 | is.close(); |
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98 | |
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99 | utility::vector correct_area(3); |
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100 | correct_area(0)=8.0/9.0; |
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101 | correct_area(1)=6.0/9.0; |
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102 | correct_area(2)=1.0; |
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103 | |
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104 | const double tol = 0.001; |
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105 | for (size_t i=0; i<data.rows(); i++){ |
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106 | utility::vector vec(data,i); |
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107 | if (vec.size()!=target2.size()){ |
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108 | *error << "vec.size() is " << vec.size() << " and target2.size() is " |
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109 | << target2.size() << ". Should be equal." << std::endl; |
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110 | ok=false; |
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111 | } |
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112 | area = roc.score(target2,vec); |
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113 | if (area<correct_area(i)-tol || area>correct_area(i)+tol){ |
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114 | *error << "test_roc: area is " << area << " should be " |
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115 | << correct_area(i) << std::endl; |
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116 | ok=false; |
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117 | } |
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118 | } |
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119 | |
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120 | utility::vector weight(target2.size(),1); |
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121 | for (size_t i=0; i<data.rows(); i++){ |
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122 | utility::vector vec(data,i); |
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123 | area = roc.score(target2, vec, weight); |
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124 | if (area<correct_area(i)-tol || area>correct_area(i)+tol){ |
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125 | *error << "test_roc: weighted area is " << area << " should be " |
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126 | << correct_area(i) << std::endl; |
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127 | ok=false; |
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128 | } |
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129 | } |
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130 | |
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131 | *error << "testing FoldChange" << std::endl; |
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132 | statistics::FoldChange fold_change(true); |
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133 | |
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134 | *error << "testing tScore" << std::endl; |
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135 | statistics::tScore t_score(true); |
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136 | |
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137 | *error << "testing Pearson" << std::endl; |
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138 | statistics::Pearson pearson(true); |
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139 | |
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140 | *error << "testing WilcoxonFoldChange" << std::endl; |
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141 | statistics::WilcoxonFoldChange wfc(true); |
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142 | |
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143 | *error << "testing SAM" << std::endl; |
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144 | statistics::SAM sam(1.0,true); |
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145 | |
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146 | |
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147 | if (ok) |
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148 | return 0; |
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149 | return -1; |
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150 | } |
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