NAME

       Bio::PopGen::Simulation::GeneticDrift - A simple genetic drift simulation

SYNOPSIS

         use Bio::PopGen::Simulation::GeneticDrift;
         my $sim = Bio::PopGen::Simulation::GeneticDrift->new(-popsize => 40,
                                                             -alleles => {A => 0.2,
                                                                          B => 0.8});
         for(my $i =0 ;$i < 10; $i++ ) {
           my %f = $sim->next_generation; # get the freqs for each generation
         }

         for(my $i =0 ;$i < 10; $i++ ) {
           # get the allele freqs as part of a Bio::PopGen::Population object
           my $pop = $sim->next_generation('population');
         }

DESCRIPTION

       A very simple 1 locus multi-allele random drift module, start with an initial set of
       allele frequency and simulate what happens over time.

       This isn't really useful for anything in particular yet but will be built upon.

       See Gillespie JH. (1998) "Population Genetics: a Concise guide." The Johns
                     Hopkins University Press, Baltimore, USA.  pp.19-47.

FEEDBACK

   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 email or the web:

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

AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-org

APPENDIX

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

   new
        Title   : new
        Usage   : my $obj = Bio::PopGen::Simulation::GeneticDrift->new();
        Function: Builds a new Bio::PopGen::Simulation::GeneticDrift object
        Returns : an instance of Bio::PopGen::Simulation::GeneticDrift
        Args    : -popsize => starting N
                  -haploid => boolean if we should simulate haploids
                  -alleles => arrayref of the allele names
                  OR
                  -population => L<Bio::PopGen::PopulationI> object to initialize
                                 from some previously defined Population object
                                 (or result from a previous simulation)

   next_generation
        Title   : next_generation
        Usage   : my %generation = $sim->next_generation
        Function: Get the next generation of allele frequencies based on the current
                  generation
        Returns : Hash of allele frequencies
        Args    : 'allelefreqs' or 'population' to get back a hash of allele
                        frequencies (default) OR a L<Bio::PopGen::Population> object

   population_size
        Title   : population_size
        Usage   : $obj->population_size($newval)
        Function:
        Example :
        Returns : value of population_size (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   set_Frequencies_Equivalent
        Title   : set_Frequencies_Equivalent
        Usage   : $sim->set_Frequencies_Equivalent
        Function: Reset the allele frequencies so they are all even
        Returns : none
        Args    : none

   get_Allele_Frequencies
        Title   : get_Allele_Frequencies
        Usage   : my %allele_freqs = $marker->get_Allele_Frequencies;
        Function: Get the alleles and their frequency (set relative to
                  a given population - you may want to create different
                  markers with the same name for different populations
                  with this current implementation
        Returns : Associative array where keys are the names of the alleles
        Args    : none

   add_Allele_Frequency
        Title   : add_Allele_Frequency
        Usage   : $marker->add_Allele_Frequency($allele,$freq)
        Function: Adds an allele frequency
        Returns : None
        Args    : $allele - allele name
                  $freq   - frequency value

   reset_alleles
        Title   : reset_alleles
        Usage   : $marker->reset_alleles();
        Function: Reset the alleles for a marker
        Returns : None
        Args    : None

   validate_Frequencies
        Title   : validate_Frequencies
        Usage   : if( $sim->validate_Frequencies) {}
        Function: Sanity checker that allele frequencies sum to 1 or less
        Returns : boolean
        Args    : -strict => 1 boolean if you want to insure that sum of freqs is 1