Florent Angly
and 1 contributors


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 florent.angly@gmail.com


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 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 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 $community = $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