Bio::Tools::RandomDistFunctions - A set of routines useful for

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Tools::RandomDistFunctions - A set of routines useful for generating random data in different distributions

SYNOPSIS

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  use Bio::Tools::RandomDistFunctions;
  my $dist = Bio::Tools::RandomDistFunctions->new();
  for my $v ( 1..1000 ) { 
    my $birth_dist = $dist->rand_birth_distribution($lambda);
    # ... do something with the variable
  }

DESCRIPTION

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Most of the code is based on the C implementation of these routines in Mike Sanderson's r8s's package. See http://loco.biosci.arizona.edu/r8s/ for information on his software.

This code tries to be fast and use available faster BigInt and GMP library methods when those modules are available.

FEEDBACK

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Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

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Email jason-at-bioperl.org

CONTRIBUTORS

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Thanks to Mike Sanderson for assistance in the getting this implementation together.

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

birth_distribution

 Title   : rand_birth_distribution
 Usage   : my $randvar = $dist->
            rand_birth_distribution($lambda);
 Function: Returns a random number from a birth process waiting 
           time with a fixed interval
           1.0.  Times are measured from 0=present,1=root;
 Returns : floating point number
 Args    : $lambda ( > 0 )
 References : This is based on code by Mike Sanders in r8s.
              Ross, Stochastic Processes, p. 145 for the density

rand_geometric_distribution

 Title   : rand_geometric_distribution
 Usage   : my $randvar = $dist->rand_geometric_distribution($param);
 Function: Returns a random geometric variate distributed with 
           parameter $param, according to
           c.d.f. 1 - ( 1- param) ^ n 
 Returns : integer
 Args    : $param ( 0 > $param < 1 )

rand_exponentional_distribution

 Title   : rand_exponentional_distribution
 Usage   : my $var = $dist->rand_exponentional_distribution($param);
 Function: Returns a random exponential variate distributed with parameter
           $param, according to c.d.f 1 - e^(-param * x)
 Returns : floating point number 
 Args    : $param ( > 0 )

rand_normal_distribution

 Title   : rand_normal_distribution
 Usage   : my $var = $dist->rand_normal_distribution()
 Function: Returns a random normal (gaussian) variate distributed 
 Returns : floating point number
 Args    : none
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Tools::RandomDistFunctions
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Jason Stajich <jason-at-bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...


package Bio::Tools::RandomDistFunctions;
require Exporter;
use vars qw(%LOADED @EXPORT_OK); use strict;

#use Math::BigFloat lib => 'GMP,Bit::Vector';
#use Math::BigInt lib  => 'GMP,Bit::Vector';
use POSIX;

use base qw(Bio::Root::Root);


sub rand_birth_distribution{
   my ($self,$lambda) = @_;
   if( ! ref($self) && 
       $self !~ /RandomDistFunctions/ ) { 
       $lambda = $self;
   }
   unless( $lambda ) { 
       $self->throw("Cannot call birth_distribution without a valid lambda value (>0)");
   }
   return 1 - (log(rand(1) * (exp($lambda) - 1)+1)/ $lambda); 
}



sub rand_geometric_distribution{
   my ($self,$param) = @_;
   if( ! ref($self) && 
       $self !~ /RandomDistFunctions/ ) { 
       $param = $self;
   }
   unless( $param ) { 
       $self->throw("Cannot call rand_geometric_distribution without a valid param value (>0)");
   }

   my $den;
   if( $param < 1e-8) { 
       $den = (-1 * $param) - ( $param * $param ) / 2;
   } else { 
       $den = log(1 - $param);
   }
   my $z = log(1 - rand(1)) / $den;
   return POSIX::floor($z) + 1;
   # MSanderson comments from r8s code
   # Is this the right truncation of the real-valued expression above?
   # YES
   # Checked by reference to the expected mean of the distribution in
   # 100,000 replicates
   # EX = 1/param Var = (1-param)/param^2 See Olkin, Gleser, and
   # Derman, p. 193ff. Probability Models and Applications, 1980.
}


sub rand_exponentional_distribution {
   my ($self,$param) = @_;
      if( ! ref($self) && 
       $self !~ /RandomDistFunctions/ ) { 
       $param = $self;
   }
   unless( $param ) { 
       $self->throw("Cannot call rand_exponentional_distribution without a valid param value (>0)");
   }
   return log( 1- rand(1)) / $param;
}


sub rand_normal_distribution{
    my $gset;
    my ($rsq,$v1,$v2) = ( 0,0,0);
    do { 
	$v1 = 2 * rand(1) - 1;
	$v2 = 2 * rand(1) - 1;
	$rsq= $v1**2 + $v2 ** 2;
    } while( $rsq >= 1 || $rsq == 0);
    my $fac = sqrt(-2.0 * log($rsq) / $rsq );
    $gset = $v1 * $fac;
    return $v2 * $fac;
}

1;