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POImplementing proximity matrix for clustering
 

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    <p>Please I am a little new to this field so pardon me if the question sound trivial or basic.</p> <p>I have a group of dataset(Bag of words to be specific) and I need to generate a proximity matrix by using their edit distance from each other to find and generate the proximity matrix .</p> <p>I am however quite confused how I will keep track of my data/strings in the matrix. I need the proximity matrix for the purpose of clustering.</p> <p>Or How generally do you approach this kinds of problem in the field. I am using perl and R to implement this.</p> <p>Here is a typical code in perl I have written that reads from a text file containing my bag of words</p> <pre><code>use strict ; use warnings ; use Text::Levenshtein qw(distance) ; main(@ARGV); sub main { my @TokenDistances ; my $Tokenfile = 'TokenDistinct.txt'; my @Token ; my $AppendingCount = 0 ; my @Tokencompare ; my %Levcount = (); open (FH ,"&lt; $Tokenfile" ) or die ("Error opening file . $!"); while(&lt;FH&gt;) { chomp $_; $_ =~ s/^(\s+)$//g; push (@Token , $_ ); } close(FH); @Tokencompare = @Token ; foreach my $tokenWord(@Tokencompare) { my $lengthoffile = scalar @Tokencompare; my $i = 0 ; chomp $tokenWord ; #@TokenDistances = levDistance($tokenWord , \@Tokencompare ); for($i = 0 ; $i &lt; $lengthoffile ;$i++) { if(scalar @TokenDistances == scalar @Tokencompare) { print "Yipeeeeeeeeeeeeeeeeeeeee\n"; } chomp $tokenWord ; chomp $Tokencompare[$i]; #print $tokenWord. " {$Tokencompare[$i]} " . " $TokenDistances[$i] " . "\n"; #$Levcount{$tokenWord}{$Tokencompare[$i]} = $TokenDistances[$i]; $Levcount{$tokenWord}{$Tokencompare[$i]} = levDistance($tokenWord , $Tokencompare[$i] ); } StoreSortedValues ( \%Levcount ,\$tokenWord , \$AppendingCount); $AppendingCount++; %Levcount = () ; } # %Levcount = (); } sub levDistance { my $string1 = shift ; #my @StringList = @{(shift)}; my $string2 = shift ; return distance($string1 , $string2); } sub StoreSortedValues { my $Levcount = shift; my $tokenWordTopMost = ${(shift)} ; my $j = ${(shift)}; my @ListToken; my $Tokenfile = 'LevResult.txt'; if($j == 0 ) { open (FH ,"&gt; $Tokenfile" ) or die ("Error opening file . $!"); } else { open (FH ,"&gt;&gt; $Tokenfile" ) or die ("Error opening file . $!"); } print $tokenWordTopMost; my %tokenWordMaster = %{$Levcount-&gt;{$tokenWordTopMost}}; @ListToken = sort { $tokenWordMaster{$a} cmp $tokenWordMaster{$b} } keys %tokenWordMaster; #@ListToken = keys %tokenWordMaster; print FH "-------------------------- " . $tokenWordTopMost . "-------------------------------------\n"; #print FH map {"$_ \t=&gt; $tokenWordMaster{$_} \n "} @ListToken; foreach my $tokey (@ListToken) { print FH "$tokey=&gt;\t" . $tokenWordMaster{$tokey} . "\n" } close(FH) or die ("Error Closing File. $!"); } </code></pre> <p>the problem is how can I represent the proximity matrix from this and still be able to keep track of which comparison represent which in my matrix.</p>
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    1. COAnd how glad am I that I gave up learning Perl and discovered R instead!
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