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bin/bc_rarefy  view on Meta::CPAN

=item -ss <sample_size> | -sample_size <sample_size>

Number of members to randomly take at each bootstrap iteration. If omitted, the
sample size defaults to the size (member count) of the smallest community.

=for Euclid:
   sample_size.type: +integer

=item -dt <dist_threshold> | -dist_threshold <dist_threshold>

Keep doing bootstrap iterations until the distance between the current average
community and the average community at the previous iteration becomes less than
the specified threshold. Default: dist_threshold.default

=for Euclid:
   dist_threshold.type: +num
   dist_threshold.default: 1e-3

=item -nr <num_repetitions> | -num_repetitions <num_repetitions>

Perform the specified number of bootstrap iterations instead of a dynamic number
of iterations based on a distance threshold. As a special case, use 'inf' to
assume an infinite number of repetitions.

=for Euclid:
   num_repetitions.type: string

=item -wa <write_average> | -write_average <write_average>

Write the average bootstraped communities (decimals) in addition to the rarefied
communities (integers): 1 is yes, 0 is no. Default: write_average.default

lib/Bio/Community/Tools/Rarefier.pm  view on Meta::CPAN

Bio::Community::Tools::Rarefier - Normalize communities by count

=head1 SYNOPSIS

  use Bio::Community::Tools::Rarefier;

  # Normalize communities in a metacommunity by repeatedly taking 1,000 random members
  my $rarefier = Bio::Community::Tools::Rarefier->new(
     -metacommunity => $meta,
     -sample_size   => 1000,
     -threshold     => 0.001, # stop bootstrap iterations when threshold is reached
  );

  # Rarefied results, with decimal counts
  my $average_community = $rarefier->get_avg_meta->next_community;

  # Round counts to integer numbers
  my $representative_community = $rarefier->get_repr_meta->next_community;
  

  # Alternatively, specify a number of repetitions
  my $rarefier = Bio::Community::Tools::Rarefier->new(
     -metacommunity   => $meta,
     -sample_size     => 1000,
     -num_repetitions => 0.001, # stop after this number of bootstrap iterations
  );

  # ... or assume an infinite number of repetitions
  my $rarefier = Bio::Community::Tools::Rarefier->new(
     -metacommunity   => $meta,
     -sample_size     => 1000,
     -num_repetitions => 'inf',
  );

=head1 DESCRIPTION

lib/Bio/Community/Tools/Rarefier.pm  view on Meta::CPAN

 Function: Get or set the seed used to pick the random members.
 Args    : Positive integer
 Returns : Positive integer

=cut


=head2 verbose

 Function: Get or set verbose mode. In verbose mode, the current number of
           iterations (and beta diversity if a threshold is used) is displayed.
 Usage   : $rarefier->verbose(1);
 Args    : 0 (default) or 1
 Returns : 0 or 1

=cut

has verbose => (
   is => 'rw',
   isa => 'Bool',
   required => 0,