NAME

Bio::Community::Meta::Beta - Beta diversity or distance separating communities

SYNOPSIS

use Bio::Community::Meta;
use Bio::Community::Meta::Beta;

# Beta diversity of two communities
my $beta = Bio::Community::Meta::Beta->new(
   -metacommunity => Bio::Community::Meta->new(-communities => [$community1, $community2] ),
   -type          => 'euclidean',
);
my $value = $beta->get_beta;

# Beta diversity between all pairs of communities in the given metacommunity
$beta = Bio::Community::Meta::Beta->new(
   -metacommunity => $meta,
   -type          => 'hellinger',
);
my ($average_value, $value_hashref) = $beta->get_all_beta;

DESCRIPTION

The Bio::Community::Beta module quantifies how dissimilar communities are by calculating their beta diversity. The more different communities are, the larger their beta diversity. Some beta diversity metrics are proper distance measures (in the mathematical sense).

Since the relative abundance of community members is not always proportional to member counts (see weights() in Bio::Community::Member and use_weights() in Bio::Community), the beta diversity measured here are always based on relative abundance (as a fractional number between 0 and 1, not as a percentage), even for beta diversity metrics that are usually based on number of observations (counts).

METRICS

Qualitative and quantitive measures of beta diversity are available and can be specified with the type() method:

Qualitative

Qualitative metrics are based on the presence or absence of community members only.

jaccard

The Jaccard distance (between 0 and 1), i.e. the fraction of non-shared species relative to the overall richness of the metacommunity.

sorensen

The Sørensen dissimilarity, or Whittaker's species turnover (between 0 and 1), i.e. the fraction of non-shared species relative to the average richness in the metacommunity.

shared

The percentage of species shared (between 0 and 100), relative to the least rich community. Note: this is the opposite of a beta diversity measure since the higher the percent of species shared, the smaller the beta diversity.

Quantitative

1-norm

The 1-norm, or Manhattan distance, i.e. the sum of difference in abundance for all species.

2-norm (euclidean)

The 2-norm, or euclidean distance.

infinity-norm

The infinity-norm, i.e. the maximum difference in abundance over all species.

hellinger

Like the euclidean distance, but constrained between 0 and 1.

bray-curtis

The Bray-Curtis dissimilarity (or Sørensen quantitative index), which varies between 0 and 1.

morisita-horn

The Morisita-Horn dissimilarity, which varies between 0 and 1. Affected strongly by the abundance of the most abundant species, but not by sample size or richness.

permuted

A beta diversity measure between 0 and 100, representing the percentage of the dominant species in the first community with a permuted abundance rank in the second community. As a special case, when no species are shared (and the percentage permuted is meaningless), undef is returned.

maxiphi

A beta diversity measure between 0 and 1, based on the percentage of species shared and the percentage of top species permuted (that have had a change in abundance rank).

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::Beta object
Usage   : my $beta = Bio::Community::Meta::Beta->new(
             -metacommunity => $meta,
             -type          => 'euclidean',
          );
Args    : -metacommunity : See metacommunity(). This is required!
          -type          : See type().
Returns : a Bio::Community::Meta::Beta object

metacommunity

Function: Get or set the communities to process, given as a metacommunity.
Usage   : my $meta = $beta->metacommunity;
Args    : A Bio::Community::Meta object
Returns : A Bio::Community::Meta object

type

Function: Get or set the beta diversity metric to calculate.
Usage   : my $type = $beta->type;
Args    : String for the desired type of beta diversity ('2-norm' by default).
          See L</METRICS> for details.
Returns : String for the desired type of beta diversity

get_beta

Function: Calculate the beta diversity between two communities. The input
          metacommunity should contain exactly two communities. The distance is
          calculated based on the relative abundance (in %) of the members (not
          their counts).
Usage   : my $value = $beta->get_beta;
Args    : None
Returns : A number for the beta diversity value

get_all_beta

Function: Similar to get_beta(), but return the beta diversity between all pairs
          of communities in the given metacommunity and also return their
          average beta diversity.
Usage   : my ($average, $betas) = $beta->get_all_beta;
Args    : None
Returns : * A number for the average beta diversity
          * A hashref of hashref with the value of all pairwise beta diversities,
            keyed by the community names. To get the beta diversity of a specific
            pair of communities, do:
               my $value = $betas->{$name1}->{$name2};
            or:
               my $value = $betas->{$name2}->{$name1};

cpanm Bio::Community

perl -MCPAN -e shell
install Bio::Community