Florent Angly > Bio-Community > Bio::Community::Tools::Sampler

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NAME ^

Bio::Community::Tools::Sampler - Sample organisms according to their abundance

SYNOPSIS ^

  use Bio::Community::Tools::Sampler;

  # Sample members from a reference community 
  my $sampler = Bio::Community::Tools::Sampler->new( -community => $ref_community );
  my $member1 = $sampler->get_rand_member();
  my $member2 = $sampler->get_rand_member();

  # Or sample 100 members in one step
  my $rand_community = $sampler->get_rand_community( 100 );

DESCRIPTION ^

Pick individuals at random (without replacement) from a community.

Note that the sampling is done based on relative abundances, and is hence affected by weights. If you need to sample based on counts instead, simply set $community->use_weights(0), before using Bio::Community::Tools::Sampler.

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::Tool::Sampler object
 Usage   : my $sampler = Bio::Community::Tool::Sampler->new( );
 Args    : -community: See community().
           -seed     : See set_seed().
 Returns : a new Bio::Community::Tools::Sampler object

community

 Function: Get or set the community to sample from.
 Usage   : my $community = $sampler->community();
 Args    : a Bio::Community object
 Returns : a Bio::Community object

get_seed, set_seed

 Usage   : $sampler->set_seed(1234513451);
 Function: Get or set the seed used to pick the random members.
 Args    : Positive integer
 Returns : Positive integer

get_rand_member

 Function: Get a random member from a community (sample with replacement).
 Usage   : my $member = $sampler->get_rand_member();
 Args    : None
 Returns : A Bio::Community::Member object

get_rand_community

 Function: Create a community from random members of a community
 Usage   : my $community = $sampler->get_rand_community(1000);
 Args    : Number of members (positive integer)
 Returns : A Bio::Community object
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