Florent Angly
and 1 contributors

NAME

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

SYNOPSIS

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

DESCRIPTION

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.

METRICS

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

chao2

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

jack1_i

First-order jackknife estimator for incidence data.

jack2_i

Second-order jackknife estimator for incidence data.

ice

Incidence-based Coverage Estimator (ICE).

AUTHOR

Florent Angly florent.angly@gmail.com

SUPPORT AND BUGS

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

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.

APPENDIX

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

new

 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

metacommunity

 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

type

 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

get_gamma

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