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;
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).
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. 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
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.