Bio-Community
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is needed to calculate this metric.
=item hill
Hill's C<N_inf> index, the inverse of the Berger-Parker dominance. Ranges from
1 to infinity.
=item mcintosh
McIntosh's index. Based on counts, not relative abundance.
=back
=head1 AUTHOR
Florent Angly L<florent.angly@gmail.com>
=head1 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,
L<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:
L<https://redmine.open-bio.org/projects/bioperl/>
=head1 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.
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=head2 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
=cut
package Bio::Community::Alpha;
use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use Method::Signatures;
use namespace::autoclean;
use List::Util qw(max);
extends 'Bio::Root::Root';
=head2 community
Function: Get or set the community to process.
Usage : my $community = $alpha->community();
Args : A Bio::Community object
Returns : A Bio::Community object
=cut
has community => (
is => 'ro',
isa => 'Bio::Community',
required => 1,
lazy => 0,
init_arg => '-community',
);
=head2 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.
=cut
has type => (
is => 'rw',
isa => 'AlphaType',
required => 0,
lazy => 1,
default => 'observed',
init_arg => '-type',
);
=head2 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.
=cut
method get_alpha () {
my $metric = '_'.$self->type;
return $self->$metric();
};
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