Florent Angly > Bio-Community-0.001007 > Bio::Community::Meta::Gamma

Download:
Bio-Community-0.001007.tar.gz

Dependencies

Annotate this POD

Website

View/Report Bugs
Source  

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
syntax highlighting: