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 email@example.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 2011-2014 by Florent Angly <email@example.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. 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