You still haven't said anything about your application domain. From a Perl perspective there seem to be not hard choices to make - the issue is more to do with how you use the result than how you calculate it.

Hi,
I have check the similarity values between two sequences (values). Absoultely in bioinformatics.. still I couldn't able to find out the exact behaviour of this
When you run the example,

#!c:\perl\bin\perl
use strict;
use warnings;
use Statistics::Shannon;
use Data::Dumper;
my @data1=(1,3,2,4,6);  
my @data2=(2,3,2,3,6); 
my $data=[(@data1,@data2)];
my $base_index=2;
my $shannon=Statistics::Shannon->new($data,$base_index);
my $output=$shannon->index;

print Dumper($shannon);

__OUTPUT___
$VAR1 = bless( {
                 'shannon' => {
                                '2.71828182845905' => '1.4681399390162
+1'
                              },
                 'min' => 1,
                 'max' => 4,
                 'data' => {
                             '6' => 2,
                             '4' => 1,
                             '1' => 1,
                             '3' => 3,
                             '2' => 4
                           },
                 'update' => sub { "DUMMY" },
                 'sum' => 11
               }, 'Statistics::Shannon' );
[download]

I got this result.
if you look into the perldoc of Statistics::Shannon ,
It says that  $base_index denoted for the logerthemic specification. But the dumer output denotes that  $base_index also added up with the data and hence it shows  '2' => 4 { 4 denotes the count of value '2' in the list } .
Anyone can please help me out ??.
-kulls

You are passing $base_index as an additional data set. If you wish to retreive the index you use the index member and pass an optional base. Changling your last few lines to:

my $shannon=Statistics::Shannon->new($data,);
my $output=$shannon->index ($base_index);

print "Index: $output\n";

print Dumper($shannon);
[download]

Prints:

Index: 2.17095059445467
$VAR1 = bless( {
                 'shannon' => {
                                '2' => '1.50478828368119'
                              },
                 'min' => 1,
                 'max' => 3,
                 'data' => {
                             '6' => 2,
                             '4' => 1,
                             '1' => 1,
                             '3' => 3,
                             '2' => 3
                           },
                 'update' => sub { "DUMMY" },
                 'sum' => 10
               }, 'Statistics::Shannon' );
[download]

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DWIM is Perl's answer to Gödel