Bio::Community::Meta::Beta - Beta diversity or distance separating communities
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;
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).
Qualitative and quantitive measures of beta diversity are available and can be specified with the type() method:
type()
Qualitative metrics are based on the presence or absence of community members only.
The Jaccard distance (between 0 and 1), i.e. the fraction of non-shared species relative to the overall richness of the metacommunity.
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.
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.
The 1-norm, or Manhattan distance, i.e. the sum of difference in abundance for all species.
The 2-norm, or euclidean distance.
The infinity-norm, i.e. the maximum difference in abundance over all species.
Like the euclidean distance, but constrained between 0 and 1.
The Bray-Curtis dissimilarity (or Sørensen quantitative index), which varies between 0 and 1.
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.
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.
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).
Florent Angly florent.angly@gmail.com
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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.
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::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
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
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
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 = $beta->get_beta; Args : None Returns : A number for the beta diversity value
Function: Similar to get_beta(), but return the beta diversity between all pairs of communities in the given metacommunity and also return their average beta diversity. Usage : my ($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};
1 POD Error
The following errors were encountered while parsing the POD:
Non-ASCII character seen before =encoding in 'Sørensen'. Assuming UTF-8
To install Bio::Community, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Community
CPAN shell
perl -MCPAN -e shell install Bio::Community
For more information on module installation, please visit the detailed CPAN module installation guide.