Florent Angly > Bio-Community > 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 alpha diversity, i.e. the diversity contained within a community. Higer alpha diversity values indicate more diverse communities.

METRICS ^

This module calculates different types of alpha diversity: richness, evenness, dominance and indices. Specifically, the following metrics are supported and can be specified using the type() method:

Richness

Richness is the estimated number of species in a community. Some of these metrics base their estimate on species abundance data and need integer counts.

observed

Observed richness S.

menhinick

Menhinick's richness S/sqrt(n), where n is the total counts (observations).

margalef

Margalef's richness (S-1)/ln(n).

chao1

Bias-corrected chao1 richness, S+n1*(n1-1)/(2*(n2+1)), where n1 and n2 are the number of singletons and doubletons, respectively. Particularly useful for data skewed by low-abundance species, e.g. microbial data.

ace

Abundance-based Coverage Estimator (ACE).

jack1

First-order jackknife richness estimator, S+n1.

jack2

Second-order jackknife richness estimator, S+2*n1-n2.

Evenness

Evenness or equitability, represents how similar in abundance members of a community are.

buzas

Buzas & Gibson's (or Sheldon's) evenness, e^H/S. Ranges from 0 to 1.

heip

Heip's evenness, (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. Note that the Math::GSL::SF module is needed to calculate this metric.

hill_e

Hill's E_2,1 evenness, i.e. Simpson's Reciprocal index divided by e^H.

mcintosh_e

McIntosh's evenness.

camargo

Camargo's eveness. Ranges from 0 to 1.

Dominance

Dominance has the opposite meaning of evenness. It is not strictly speaking a diversity metrics since the higher the dominance, the lower the diversity.

simpson_d

Simpson's Dominance Index D. Ranges from 0 to 1.

berger

Berger-Parker dominance, i.e. the proportion of the most abundant species. Ranges from 0 to 1.

Indices

Indices (accounting for species abundance):

shannon

Shannon-Wiener index H. Emphasizes richness and ranges from 0 to infinity.

simpson

Simpson's Index of Diversity 1-D (or Gini-Simpson index), where D is Simpson's dominance index. 1-D is the probability that two individuals taken randomly are not from the same species. Emphasizes evenness and ranges from 0 to 1.

simpson_r

Simpson's Reciprocal Index 1/D. Ranges from 1 to infinity.

brillouin

Brillouin's index, appropriate for small, completely censused communities. Based on counts, not relative abundance. Note that the Math::GSL::SF module is needed to calculate this metric.

hill

Hill's 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.

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::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 of the desired alpha diversity type ('observed' by default).
           See L</METRICS> for details.
 Returns : String of the desired alpha diversity type.

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. Undef is returned in
           special cases, e.g. when measuring the evenness or dominance in a
           community with no members.
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