1 | // $Id: Fisher.cc 865 2007-09-10 19:41:04Z peter $ |
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2 | |
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3 | /* |
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4 | Copyright (C) 2004 Jari Häkkinen, Peter Johansson |
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5 | Copyright (C) 2005 Peter Johansson |
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6 | Copyright (C) 2006 Jari Häkkinen, Peter Johansson |
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7 | Copyright (C) 2007 Peter Johansson |
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8 | |
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9 | This file is part of the yat library, http://trac.thep.lu.se/trac/yat |
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10 | |
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11 | The yat library is free software; you can redistribute it and/or |
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12 | modify it under the terms of the GNU General Public License as |
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13 | published by the Free Software Foundation; either version 2 of the |
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14 | License, or (at your option) any later version. |
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15 | |
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16 | The yat library is distributed in the hope that it will be useful, |
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17 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
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18 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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19 | General Public License for more details. |
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20 | |
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21 | You should have received a copy of the GNU General Public License |
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22 | along with this program; if not, write to the Free Software |
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23 | Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA |
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24 | 02111-1307, USA. |
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25 | */ |
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26 | |
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27 | #include "Fisher.h" |
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28 | #include "utility.h" |
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29 | |
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30 | #include <gsl/gsl_cdf.h> |
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31 | #include <gsl/gsl_randist.h> |
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32 | |
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33 | namespace theplu { |
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34 | namespace yat { |
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35 | namespace statistics { |
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36 | |
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37 | |
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38 | Fisher::Fisher() |
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39 | : a_(0), b_(0), c_(0), d_(0), oddsratio_(1.0) |
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40 | { |
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41 | } |
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42 | |
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43 | |
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44 | Fisher::~Fisher() |
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45 | { |
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46 | } |
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47 | |
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48 | |
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49 | bool Fisher::calculate_p_exact(void) const |
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50 | { |
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51 | return ( a_<minimum_size_ || b_<minimum_size_ || |
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52 | c_<minimum_size_ || d_<minimum_size_); |
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53 | } |
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54 | |
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55 | double Fisher::Chi2() const |
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56 | { |
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57 | double a,b,c,d; |
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58 | expected(a,b,c,d); |
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59 | return (a-a_)*(a-a_)/a + (b-b_)*(b-b_)/b + |
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60 | (c-c_)*(c-c_)/c + (d-d_)*(d-d_)/d; |
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61 | } |
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62 | |
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63 | |
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64 | void Fisher::expected(double& a, double& b, double& c, double& d) const |
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65 | { |
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66 | double N = a_+b_+c_+d_; |
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67 | a =((a_+b_)*(a_+c_)) / N; |
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68 | b =((a_+b_)*(b_+d_)) / N; |
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69 | c =((c_+d_)*(a_+c_)) / N; |
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70 | d =((c_+d_)*(b_+d_)) / N; |
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71 | } |
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72 | |
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73 | |
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74 | u_int& Fisher::minimum_size(void) |
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75 | { |
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76 | return minimum_size_; |
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77 | } |
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78 | |
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79 | |
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80 | const u_int& Fisher::minimum_size(void) const |
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81 | { |
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82 | return minimum_size_; |
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83 | } |
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84 | |
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85 | |
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86 | double Fisher::oddsratio(const u_int a, |
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87 | const u_int b, |
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88 | const u_int c, |
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89 | const u_int d) |
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90 | { |
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91 | // If a column sum or a row sum is zero, the table is nonsense |
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92 | if ((a==0 || d==0) && (c==0 || b==0)){ |
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93 | throw std::runtime_error("runtime_error: Table in Fisher is not valid\n"); |
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94 | } |
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95 | |
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96 | oddsratio_=(a*d)/(b*d); |
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97 | return oddsratio_; |
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98 | } |
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99 | |
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100 | |
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101 | double Fisher::p_value() const |
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102 | { |
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103 | if (oddsratio_>1.0) |
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104 | return 2*p_value_one_sided(); |
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105 | if (oddsratio_<1.0){ |
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106 | // If oddsratio is less than unity |
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107 | // Two-sided p-value is |
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108 | // P(X <= oddsratio) + P(X >= 1/oddsratio) = |
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109 | // P(X <= oddsratio) + P(X <= oddsratio) |
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110 | // 2 * (P(X < oddsratio) + P(X = oddsratio)) |
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111 | // 2 * (1 - P(X >= oddsratio) + P(X = oddsratio)) |
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112 | if (calculate_p_exact()) |
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113 | return 2*(1-p_value_one_sided()+ |
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114 | gsl_ran_hypergeometric_pdf(a_,a_+b_,c_+d_, a_+c_) |
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115 | ); |
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116 | // if p is calculated approximatively correction is not needed |
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117 | return 2*(1-p_value_one_sided()); |
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118 | |
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119 | } |
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120 | return 1.0; |
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121 | } |
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122 | |
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123 | |
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124 | double Fisher::p_value_one_sided() const |
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125 | { |
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126 | if ( calculate_p_exact() ) |
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127 | return p_value_exact(); |
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128 | return p_value_approximative(); |
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129 | } |
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130 | |
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131 | |
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132 | double Fisher::p_value_approximative() const |
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133 | { |
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134 | return gsl_cdf_chisq_Q(Chi2(), 1.0); |
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135 | } |
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136 | |
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137 | double Fisher::p_value_exact() const |
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138 | { |
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139 | // Since the calculation is symmetric and cdf_hypergeometric_P |
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140 | // loops up to k we choose the smallest number to be k and mirror |
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141 | // the matrix. This choice makes the p-value two-sided. |
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142 | |
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143 | if (a_<b_ && a_<c_ && a_<d_) |
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144 | return statistics::cdf_hypergeometric_P(a_,a_+b_,c_+d_,a_+c_); |
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145 | else if (b_<a_ && b_<c_ && b_<d_) |
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146 | return statistics::cdf_hypergeometric_P(b_,a_+b_,c_+d_,b_+d_); |
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147 | else if (c_<a_ && c_<b_ && c_<d_) |
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148 | return statistics::cdf_hypergeometric_P(c_,c_+d_,a_+b_,a_+c_); |
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149 | |
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150 | return statistics::cdf_hypergeometric_P(d_,c_+d_,a_+b_,b_+d_); |
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151 | |
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152 | } |
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153 | |
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154 | |
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155 | }}} // of namespace statistics, yat, and theplu |
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