Florent Angly
and 1 contributors


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). Higer gamma diversity values indicate more diverse metacommunities.


This module supports the same diversity metrics provided in Bio::Community::Alpha. In addition, you can use:


Bias-corrected chao2 estimator, which is based on the number of members present in exactly 1 and 2 samples.


First-order jackknife estimator for incidence data.


Second-order jackknife estimator for incidence data.


Incidence-based Coverage Estimator (ICE).


Florent Angly florent.angly@gmail.com


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, bioperl-l@bioperl.org, 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: https://redmine.open-bio.org/projects/bioperl/


Copyright 2011-2014 by Florent Angly <florent.angly@gmail.com>

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 ('observed' by
           default). See L</METRICS> for details.
 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