Florent Angly
and 1 contributors


Bio::Community::Tools::Transformer - Arbitrary transformation of member counts


  use Bio::Community::Tools::Transformer;

  # Hellinger-transform the counts of community members in a metacommunity
  my $transformer = Bio::Community::Tools::Transformer->new(
     -metacommunity => $meta,
     -type          => 'hellinger',

  my $transformed_meta = $summarizer->get_transformed_meta;


This module takes a metacommunity and transform the count of the community members it contains. Several transformation methods are available: identity, binary, or hellinger.


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::Tool::Transformer object
 Usage   : my $transformer = Bio::Community::Tool::Transformer->new( );
 Args    : -metacommunity: see metacommunity()
           -type         : see type()
 Returns : a new Bio::Community::Tools::Transformer object


 Function: Get or set the metacommunity to normalize.
 Usage   : my $meta = $transformer->metacommunity;
 Args    : A Bio::Community::Meta object
 Returns : A Bio::Community::Meta object


 Function: Get or set the type of transformation that is to be applied to member
           counts (not relative abundance):
            * identity  : Keep the counts as-is
            * binary    : Assign 1 if member is present, 0 if absent
            * relative  : Set count of member equal to its relative abundance (%)
            * chisquare : Chi-square transformation
            * chord     : Chord transformation
            * hellinger : Hellinger transformation
 Usage   : my $type = $transformer->type;
 Args    : identity, binary, relative, chisquare, chord, or hellinger
 Returns : identity, binary, relative, chisquare, chord, or hellinger


 Function: Calculate and return a transformed metacommunity.
 Usage   : my $meta = $transformer->get_transformed_meta;
 Args    : none
 Returns : a new Bio::Community::Meta object