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Florent Angly > Bio-Community-0.001005 > Bio::Community::Meta::Gamma



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Source   Latest Release: Bio-Community-0.001008


Bio::Community::Meta::Gamma - Calculate the gamma diversity of a metacommunity


  use Bio::Community::Meta::Gamma;
  my $gamma = Bio::Community::Meta::Gamma->new( -community => $community,
                                                -type      => 'richness'  );
  my $richness = $gamma->get_gamma;


The Bio::Community::Meta::Gamma module calculates the gamma diversity of a group of communities (provided as a metacommunity object). The goal is to support the same diversity metrics provided by Bio::Community::Alpha, but the only metric available at the moment is: richness.

For all these metrics, a higher value means that the community is more diverse.


Florent Angly


User feedback is an integral part of the evolution of this and other Bioperl modules. Please direct usage questions or support issues to the mailing list,, rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

If you have found a bug, please report it on the BioPerl bug tracking system to help us keep track the bugs and their resolution:


Copyright 2011-2014 by Florent Angly <>

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.1 or, at your option, any later version of Perl 5 you may have available.


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Function: Create a new Bio::Community::Meta::Gamma object
 Usage   : my $gamma = Bio::Community::Meta::Gamma->new( ... );
 Args    : -metacommunity : See metacommunity().
           -type          : See type().
 Returns : a new Bio::Community::Meta::Gamma object


 Function: Get or set the communities to process, given as a metacommunity.
 Usage   : my $meta = $gamma->metacommunity;
 Args    : A Bio::Community::Meta object
 Returns : A Bio::Community::Meta object


 Function: Get or set the type of gamma diversity metric to measure.
 Usage   : my $type = $gamma->type;
 Args    : String for the desired type of gamma diversity. The same metrics are
           available as in L<Bio::Community::Alpha>. Default is 'observed'.
 Returns : String for the desired type of gamma diversity


 Function: Calculate the gamma diversity of a community.
 Usage   : my $metric = $gamma->get_gamma;
 Args    : None
 Returns : A number for the gamma diversity measurement
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