Florent Angly > Bio-Community-0.001000 > Bio::Community::Meta::Gamma



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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 florent.angly@gmail.com


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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: https://redmine.open-bio.org/projects/bioperl/


Copyright 2011,2012,2013 by the BioPerl Team bioperl-l@bioperl.org

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:
            * richness: the number of species in the metacommunity
           This defaults to richness
 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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