Florent Angly > Bio-Community-0.001000 > Bio::Community::Alpha

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NAME ^

Bio::Community::Alpha - Calculate the alpha diversity of a community

SYNOPSIS ^

  use Bio::Community::Alpha;
  
  my $alpha = Bio::Community::Alpha->new( -community => $community,
                                          -type      => 'observed'  );
  my $richness = $alpha->get_alpha;

DESCRIPTION ^

The Bio::Community::Alpha module calculates the alpha diversity within a community. The goal is to support many different alpha diversity metrics, but the only metric available at the moment is: richness.

For all these metrics, a higher value means that the community is more diverse.

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 2011,2012,2013 by the BioPerl Team bioperl-l@bioperl.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.

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::Alpha object
 Usage   : my $alpha = Bio::Community::Alpha->new( ... );
 Args    : -community : See community().
           -type      : See type().
 Returns : a new Bio::Community::Alpha object

community

 Function: Get or set the community to process.
 Usage   : my $community = $alpha->community();
 Args    : A Bio::Community object
 Returns : A Bio::Community object

type

 Function: Get or set the type of alpha diversity metric to measure.
 Usage   : my $type = $alpha->type;
 Args    : String for the desired type of alpha diversity ('observed' by default).

           Richness (or estimated number of species):
            * observed :  C<S>
            * menhinick:  C<S/sqrt(n)>, where C<n> is the total counts (observations).
            * margalef : C<(S-1)/ln(n)>
            * chao1    : Bias-corrected chao1 richness, C<S+n1*(n1-1)/(2*(n2+1))>
                         where C<n1> and C<n2> are the number of singletons and
                         doubletons, respectively. Particularly useful for data
                         skewed toward the low-abundance species, e.g. microbial.
                         Based on counts, not relative abundance.
            * ace      : Abundance-based Coverage Estimator (ACE). Based on
                         counts, not relative abundance.

           Evenness (or equitability):
            * buzas      : Buzas & Gibson's (or Sheldon's) evenness, C<e^H/S>.
                           Ranges from 0 to 1.
            * heip       : Heip's evenness, C<(e^H-1)/(S-1)>. Ranges from 0 to 1.
            * shannon_e  : Shannon's evenness, or the Shannon-Wiener index
                           divided by the maximum diversity possible in the
                           community. Ranges from 0 to 1.
            * simpson_e  : Simpson's evenness, or the Simpson's Index of Diversity
                           divided by the maximum diversity possible in the
                           community. Ranges from 0 to 1.
            * brillouin_e: Brillouin's evenness, or the Brillouin's index divided
                           by the maximum diversity possible in the community.
                           Ranges from 0 to 1.
            * hill_e     : Hill's C<E_2,1> evenness, i.e. Simpson's Reciprocal
                           index divided by C<e^H>.
            * mcintosh_e : McIntosh's evenness.
            * camargo    : Camargo's eveness. Ranges from 0 to 1.

           Indices (accounting for species abundance):
            * shannon  : Shannon-Wiener index C<H>. Emphasizes richness. Ranges
                         from 0 to infinity.
            * simpson  : Simpson's Index of Diversity C<1-D>, where C<D> is
                         Simpson's dominance index. C<1-D> is the probability
                         that two individuals taken randomly are not from the
                         same species. Emphasizes evenness. Ranges from 0 to 1.
            * simpson_r: Simpson's Reciprocal Index C<1/D>. Ranges from 1 to
                         infinity.
            * brillouin: Brillouin's index, appropriate for small, completely
                         censused communities. Based on counts, not relative
                         abundance.
            * hill     : Hill's C<N_inf> index, the inverse of the Berger-Parker
                         dominance. Ranges from 1 to infinity.
            * mcintosh : McIntosh's index. Based on counts, not relative abundance.

           Dominance (B<not> diversity metrics since the higher their value, the
           lower the diversity):
            * simpson_d: Simpson's Dominance Index C<D>. Ranges from 0 to 1.
            * berger   : Berger-Parker dominance, i.e. the proportion of the most
                         abundant species. Ranges from 0 to 1.

 Returns : String for the desired type of alpha diversity.

get_alpha

 Function: Calculate the alpha diversity of a community.
 Usage   : my $metric = $alpha->get_alpha;
 Args    : None
 Returns : A number for the alpha diversity measurement
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