1 | #ifndef _theplu_yat_statistics_fisher_ |
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2 | #define _theplu_yat_statistics_fisher_ |
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3 | |
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4 | // $Id: Fisher.h 683 2006-10-11 22:20:36Z jari $ |
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5 | |
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6 | /* |
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7 | Copyright (C) The authors contributing to this file. |
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8 | |
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9 | This file is part of the yat library, http://lev.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 "Score.h" |
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28 | #include "yat/utility/vector.h" |
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29 | |
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30 | #include <cmath> |
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31 | |
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32 | namespace theplu { |
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33 | namespace yat { |
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34 | namespace statistics { |
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35 | /** |
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36 | @brief Fisher's exact test. |
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37 | |
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38 | Fisher's Exact test is a procedure that you can use for data |
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39 | in a two by two contingency table: \f[ \begin{tabular}{|c|c|} |
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40 | \hline a&b \tabularnewline \hline c&d \tabularnewline \hline |
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41 | \end{tabular} \f] Fisher's Exact Test is based on exact |
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42 | probabilities from a specific distribution (the hypergeometric |
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43 | distribution). There's really no lower bound on the amount of |
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44 | data that is needed for Fisher's Exact Test. You do have to |
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45 | have at least one data value in each row and one data value in |
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46 | each column. If an entire row or column is zero, then you |
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47 | don't really have a 2 by 2 table. But you can use Fisher's |
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48 | Exact Test when one of the cells in your table has a zero in |
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49 | it. Fisher's Exact Test is also very useful for highly |
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50 | imbalanced tables. If one or two of the cells in a two by two |
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51 | table have numbers in the thousands and one or two of the |
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52 | other cells has numbers less than 5, you can still use |
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53 | Fisher's Exact Test. For very large tables (where all four |
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54 | entries in the two by two table are large), your computer may |
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55 | take too much time to compute Fisher's Exact Test. In these |
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56 | situations, though, you might as well use the Chi-square test |
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57 | because a large sample approximation (that the Chi-square test |
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58 | relies on) is very reasonable. If all elements are larger than |
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59 | 10 a Chi-square test is reasonable to use. |
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60 | |
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61 | @note The statistica assumes that each column and row sum, |
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62 | respectively, are fixed. Just because you have a 2x2 table, this |
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63 | assumtion does not necessarily match you experimental upset. See |
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64 | e.g. Barnard's test for alternative. |
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65 | */ |
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66 | |
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67 | class Fisher : public Score |
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68 | { |
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69 | |
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70 | public: |
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71 | /// |
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72 | /// Default Constructor. |
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73 | /// |
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74 | Fisher(bool absolute=true); |
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75 | |
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76 | /// |
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77 | /// Destructor |
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78 | /// |
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79 | virtual ~Fisher(void) {}; |
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80 | |
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81 | |
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82 | /// |
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83 | /// @return Chi2 score |
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84 | /// |
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85 | double Chi2(void) const; |
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86 | |
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87 | /// |
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88 | /// Cutoff sets the limit whether a value should go into the left |
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89 | /// or the right row. @see score |
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90 | /// |
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91 | /// @return reference to cutoff for row |
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92 | /// |
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93 | inline double& value_cutoff(void) { return value_cutoff_; } |
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94 | |
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95 | /// |
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96 | /// Calculates the expected values under the null hypothesis. |
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97 | /// a' = (a+c)(a+b)/(a+b+c+d) |
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98 | /// |
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99 | void expected(double& a, double& b, double& c, double& d) const; |
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100 | |
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101 | /// |
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102 | /// minimum_size is the threshold for when the p-value calculation |
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103 | /// is performed using a Chi2 approximation. |
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104 | /// |
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105 | /// @return reference to minimum_size |
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106 | /// |
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107 | inline u_int& minimum_size(void){ return minimum_size_; } |
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108 | |
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109 | /// |
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110 | /// If absolute, the p-value is the two-sided p-value. If all |
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111 | /// elements in table is at least minimum_size, a Chi2 |
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112 | /// approximation is used. |
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113 | /// |
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114 | /// @return p-value |
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115 | /// |
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116 | /// @note in weighted case, approximation Chi2 is always used. |
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117 | /// |
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118 | double p_value() const; |
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119 | |
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120 | /// |
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121 | /// Function calculating score from 2x2 table for which the |
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122 | /// elements are calculated as follows \n |
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123 | /// target.binary(i) sample i in group a or c otherwise in b or d |
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124 | /// \f$ value(i) > \f$ value_cutoff() sample i in group a or b |
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125 | /// otherwise c or d\n |
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126 | /// |
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127 | /// @return odds ratio. If absolute_ is true and odds ratio is |
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128 | /// less than unity 1 divided by odds ratio is returned |
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129 | /// |
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130 | double score(const classifier::Target& target, |
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131 | const utility::vector& value); |
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132 | |
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133 | /// |
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134 | /// Weighted version of score. Each element in 2x2 table is |
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135 | /// calculated as \f$ \sum w_i \f$, so when each weight is |
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136 | /// unitary the same table is created as in the unweighted version |
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137 | /// |
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138 | /// @return odds ratio |
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139 | /// |
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140 | /// @see score |
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141 | /// |
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142 | double score(const classifier::Target& target, |
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143 | const classifier::DataLookupWeighted1D& value); |
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144 | |
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145 | |
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146 | /// |
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147 | /// Weighted version of score. Each element in 2x2 table is |
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148 | /// calculated as \f$ \sum w_i \f$, so when each weight is |
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149 | /// unitary the same table is created as in the unweighted version |
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150 | /// |
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151 | /// @return odds ratio |
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152 | /// |
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153 | /// @see score |
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154 | /// |
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155 | double score(const classifier::Target& target, |
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156 | const utility::vector& value, |
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157 | const utility::vector& weight); |
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158 | |
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159 | /// |
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160 | /// \f$ \frac{ad}{bc} \f$ |
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161 | /// |
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162 | /// @return odds ratio. If absolute_ is true and odds ratio is |
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163 | /// less than unity, 1 divided by odds ratio is returned |
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164 | /// |
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165 | double score(const u_int a, const u_int b, |
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166 | const u_int c, const u_int d); |
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167 | |
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168 | |
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169 | private: |
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170 | double oddsratio(const double a, const double b, |
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171 | const double c, const double d); |
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172 | |
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173 | // two-sided |
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174 | double p_value_approximative(void) const; |
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175 | //two-sided |
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176 | double p_value_exact(void) const; |
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177 | |
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178 | double a_; |
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179 | double b_; |
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180 | double c_; |
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181 | double d_; |
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182 | u_int minimum_size_; |
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183 | double oddsratio_; |
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184 | double value_cutoff_; |
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185 | }; |
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186 | |
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187 | }}} // of namespace statistics, yat, and theplu |
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188 | |
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189 | #endif |
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