NAME

Bio::Community::Meta - A metacommunity, or group of communities

SYNOPSIS

  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";

DESCRIPTION

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.

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 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

name

 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

identify_members_by

 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'

add_communities

 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

remove_community

 Function: Remove a community from a metacommunity
 Usage   : $meta->remove_community($community);
 Args    : A Bio::Community to remove
 Returns : 1 on success

next_community

 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

get_all_communities

 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

get_community_by_name

 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

get_communities_count

 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

get_all_members

 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

get_members_count

 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

get_richness

 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

cpanm Bio::Community

perl -MCPAN -e shell
install Bio::Community