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=head1 NAME |
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Text::NSP::Measures::2D::Fisher::twotailed - Perl module implementation of the two-sided |
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Fisher's exact test. |
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=head1 SYNOPSIS |
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=head3 Basic Usage |
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use Text::NSP::Measures::2D::Fisher::twotailed; |
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my $npp = 60; my $n1p = 20; my $np1 = 20; my $n11 = 10; |
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$twotailed_value = calculateStatistic( n11=>$n11, |
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n1p=>$n1p, |
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np1=>$np1, |
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npp=>$npp); |
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if( ($errorCode = getErrorCode())) |
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{ |
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print STDERR $errorCode." - ".getErrorMessage(); |
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} |
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else |
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{ |
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print getStatisticName."value for bigram is ".$twotailed_value; |
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} |
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=head1 DESCRIPTION |
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Assume that the frequency count data associated with a bigram |
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is stored in a 2x2 contingency table: |
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word2 ~word2 |
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word1 n11 n12 | n1p |
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~word1 n21 n22 | n2p |
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-------------- |
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np1 np2 npp |
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where n11 is the number of times occur together, and |
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n12 is the number of times occurs with some word other than |
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word2, and n1p is the number of times in total that word1 occurs as |
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the first word in a bigram. |
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The fishers exact tests are calculated by fixing the marginal totals |
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and computing the hypergeometric probabilities for all the possible |
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contingency tables, |
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A twotailed fishers test is calculated by adding the probabilities of |
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all the contingency tables with probabilities less than the probability |
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of the observed table. The twotailed fishers test tells us how likely |
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it would be to observe an contingency table which is less probable than |
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the current table. |
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=head2 Methods |
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=over |
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=cut |
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package Text::NSP::Measures::2D::Fisher::twotailed; |
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use Text::NSP::Measures::2D::Fisher; |
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use strict; |
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use Carp; |
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use warnings; |
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no warnings 'redefine'; |
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require Exporter; |
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our ($VERSION, @EXPORT, @ISA); |
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@ISA = qw(Exporter); |
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@EXPORT = qw(initializeStatistic calculateStatistic |
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getErrorCode getErrorMessage getStatisticName); |
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$VERSION = '0.97'; |
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=item calculateStatistic() - This method calculates the twotailed |
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Fisher value |
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INPUT PARAMS : $count_values .. Reference of an array containing |
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the count values computed by the |
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count.pl program. |
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RETURN VALUES : $twotailed .. Twotailed Fisher value. |
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=cut |
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sub calculateStatistic |
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{ |
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my %values = @_; |
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my $probabilities; |
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# computes and returns the observed and marginal values from |
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# the frequency combination values. returns 0 if there is an |
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# error in the computation or the values are inconsistent. |
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if( !(Text::NSP::Measures::2D::Fisher::getValues(\%values)) ) |
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{ |
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return; |
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} |
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my $final_limit = ($n1p < $np1) ? $n1p : $np1; |
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my $n11_org = $n11; |
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my $n11_start = $n1p + $np1 - $npp; |
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if($n11_start<0) |
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{ |
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$n11_start = 0; |
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} |
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if( !($probabilities = Text::NSP::Measures::2D::Fisher::computeDistribution($n11_start, $final_limit))) |
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{ |
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return; |
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} |
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my $value; |
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my $ttfisher=0; |
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foreach $value (sort { $a <=> $b } values %$probabilities) |
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{ |
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if($value > $probabilities->{$n11_org}) |
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{ |
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next; |
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} |
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$ttfisher += exp($value); |
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} |
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return $ttfisher; |
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} |
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=item getStatisticName() - Returns the name of this statistic |
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INPUT PARAMS : none |
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RETURN VALUES : $name .. Name of the measure. |
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=cut |
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sub getStatisticName |
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{ |
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return "Two Tailed Fisher"; |
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} |
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1; |
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__END__ |