Bio::Community::Meta - A metacommunity, or group of communities
use Bio::Community::Meta; my $meta = Bio::Community::Meta->new( -name => 'alpine' ); # Get communities from somewhere and ... $meta->add_communities( [$community1, $community2, $community3] ); print "Metacommunity contains:\n"; print " ".$meta->get_communities_count." communities\n"; print " ".$meta->get_richness." species\n"; print " ".$meta->get_members_count." individuals\n";
The Bio::Community::Meta module represent metacommunities, or groups of communities. This object holds several Bio::Community objects, for example tree communities found at different sites of a forest. Random access to any of the communities is provided. However, the communities can also be accessed sequentially, in the order they were given. This makes Bio::Community::Meta capable of representing communities along a natural gradient.
Florent Angly firstname.lastname@example.org
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, email@example.com, 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 2011-2014 by Florent Angly <firstname.lastname@example.org>
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 object Usage : my $meta = Bio::Community::Meta->new( ... ); Args : -name : See name() -communities : See add_communities() -identify_members_by: See identify_members_by() Returns : A new Bio::Community::Meta object
Function: Get or set the name of the metacommunity Usage : $meta->name('estuary_salinity_gradient'); my $name = $meta->name(); Args : String for the name Returns : String for the name
Function: Get or set how members are handled. In the Bio::Community modules, members with the same ID are considered identical, no matter what their description or taxonomy is. If the communities added to the metacommunity come from different sources or files, the IDs of the members are unsafe because the same member in different communities will likely have a different ID and be interpreted as a different member, whereas different members may have the same ID and be counted as the same. To work around this, you can specify to look at the desc() of the members and give the same ID to members that have the same description. Usage : $meta->identify_members_by('desc'); Args : String, either 'id' or 'desc' Returns : String, either 'id' (default) or 'desc'
Function: Add communities to a metacommunity. Communities have to have distinct names. Do not change the name of a community after you have added it! Usage : $meta->add_communities([$community1, $community2]); Args : An arrayref of Bio::Community objects to add Returns : 1 on success
Function: Remove a community from a metacommunity Usage : $meta->remove_community($community); Args : A Bio::Community to remove Returns : 1 on success
Function: Access the next community in the metacommunity (in the order the communities were added). Usage : my $member = $meta->next_community(); Args : None Returns : A Bio::Community object
Function: Generate a list of all communities in the metacommunity. Usage : my $communities = $meta->get_all_communities(); Args : None Returns : An arrayref of Bio::Community objects
Function: Generate a community that is the sum of all the members of the communities. If sampling effort was unequal between your communities, you may consider using L<Bio::Community::Tools::Rarefier>. Usage : my $metacommunity = $meta->get_metacommunity(); Args : None Returns : A new Bio::Community object
Function: Fetch a community based on its name Usage : my $community = $meta->get_community_by_name('prairie'); Args : String of the community name to look for Returns : A Bio::Community object or undef if the community was not found
Function: Get the total number of communities in the metacommunity Usage : my $nof_communities = $meta->get_communities_count(); Args : None Returns : Integer for the count
Function: Generate a list of all members in the metacommunity. Every member appears only once in this list, even if the member is present in multiple communities. Remember that members with the same ID are considered the same member. Usage : my $members = $meta->get_all_members(); Args : None Returns : An arrayref of Bio::Community::Member objects
Function: Calculate the total count of members in the metacommunity. Usage : my $nof_individuals = $meta->get_members_count; Args : None Returns : Integer for the count
Function: Calculate the richness of the metacommunity (number of different types of members). This is a form of gamma diversity. Usage : my $gamma_richness = $meta->get_richness(); Args : None Returns : Integer for the richness