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 email@example.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, firstname.lastname@example.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 <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 ('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