Bio::Community::Tools::Accumulator - Species accumulation curves
use Bio::Community::Tools::Accumulator; # A collector curve my $collector = Bio::Community::Tools::Accumulator->new( -metacommunity => $meta, -type => 'collector', ); my $numbers = $collector->get_numbers; # or my $strings = $collector->get_strings; # A rarefaction curve, with custom parameters my $rarefaction = Bio::Community::Tools::Accumulator->new( -metacommunity => $meta, -type => 'rarefaction', -num_repetitions => 100, -num_ticks => 8, -tick_spacing => 'linear', -alpha_types => ['simpson', 'shannon'], ); my $numbers = $rarefaction->get_numbers;
This module takes a metacommunity and produces one of two types of species accumulation curves: a rarefaction curve or a collector curve.
In a rarefaction curve, an increasing number of randomly drawn members is sampled from the given communities and alpha diversity is calculated. In a collector curve, an increasing number of communities is randomly drawn and combined and their cumulative alpha diversity is determined.
The average alpha diversity for the different sampling sizes is reported either as array references or a tab-delimited string. Note that no plot is actually drawn.
Florent Angly florent.angly@gmail.com
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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::Accumulator object Usage : my $accumulator = Bio::Community::Tool::Accumulator->new( ); Args : -metacommunity: see metacommunity() -type : 'rarefaction' or 'collector' -num_repetitions : see num_repetitions() -num_ticks : see num_ticks() -tick_spacing : see tick_spacing() -alpha_types : see alpha_types() -seed : see set_seed() Returns : a new Bio::Community::Tools::Accumulator object
Function: Get or set the metacommunity to normalize. Usage : my $meta = $accumulator->metacommunity; Args : A Bio::Community::Meta object Returns : A Bio::Community::Meta object
Function: Get or set the type of accumulation curve to produce. Usage : my $type = $accumulator->type; Args : String of the accumulation type: 'rarefaction' (default) or 'collector' Returns : String of the accumulation type
Function: Get or set the number of num_repetitions to do at each sampling depth. Usage : my $num_repetitions = $accumulator->num_repetitions; Args : positive integer for the number of repetitions Returns : positive integer for the number of repetitions
Function: For rarefaction curves, get or set how many different numbers of individuals to sample, for the smallest community. This number may not always be honored because ticks have to be integer numbers. Usage : my $num_ticks = $accumulator->num_ticks; Args : positive integer for the number of ticks (default: 10) Returns : positive integer for the number of ticks
Function: Get or set the type of spacing between the ticks of a rarefaction curve. Usage : my $tick_spacing = $accumulator->tick_spacing; Args : String, either 'logarithmic' (default) or 'linear' Returns : String
Function: Get or set the type of alpha diversity to calculate. Usage : my $alphas = $accumulator->alpha_types; Args : Arrayref of alpha diversity types (['observed'] by default). See C<type()> in L<Bio::Community::Alpha> for details. Returns : Arrayref of alpha diversity types.
Function: Get or set verbose mode. This displays the number of ticks to use before the accumulation curve itself is computed. Usage : $accumulator->verbose(1); Args : 0 (default) or 1 Returns : 0 or 1
Function: Calculate the accumulation curve and return the numbers. Usage : my $nums = $accumulator->get_numbers; Args : none Returns : A structure containing the average alpha diversity of the communities for each tick value, for each requested alpha type: { alpha_type => [ [tick, alpha1, alpha2, ... ], ... ], ... }
Function: Calculate the accumulation curves and return them as strings. Usage : my $strings = $accumulator->get_strings; Args : none Returns : A arrayref of strings, each of which represents the accumulation curve for a given alpha diversity type.
To install Bio::Community, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Community
CPAN shell
perl -MCPAN -e shell install Bio::Community
For more information on module installation, please visit the detailed CPAN module installation guide.