Florent Angly > Bio-Community-0.001005 > Bio::Community::Meta::Beta

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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 ^

Calculate how dissimilar communities are by calculating their beta diversity. The more different communities are, the larger their beta diversity. Some beta diversity metrics are a distance measure (in the mathematical sense). Qualitative (presence/absence) and qualitative measures of beta diversity are available: see type().

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).

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.

           Qualitative (presence/absence):
            * 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: 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).

 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};
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