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.IX Title "Bio::PopGen::Simulation::GeneticDrift 3pm"
.TH Bio::PopGen::Simulation::GeneticDrift 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
Bio::PopGen::Simulation::GeneticDrift \- A simple genetic drift simulation
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 7
\&  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(\*(Aqpopulation\*(Aq); 
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.PP
This isn't really useful for anything in particular yet but will be
built upon.
.PP
See Gillespie \s-1JH.\s0 (1998) \*(L"Population Genetics: a Concise guide.\*(R" The Johns
              Hopkins University Press, Baltimore, \s-1USA.\s0  pp.19\-47.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason-at-bioperl-dot-org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 11
\& 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)
.Ve
.SS "next_generation"
.IX Subsection "next_generation"
.Vb 7
\& 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    : \*(Aqallelefreqs\*(Aq or \*(Aqpopulation\*(Aq to get back a hash of allele 
\&                 frequencies (default) OR a L<Bio::PopGen::Population> object
.Ve
.SS "population_size"
.IX Subsection "population_size"
.Vb 6
\& 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)
.Ve
.SS "set_Frequencies_Equivalent"
.IX Subsection "set_Frequencies_Equivalent"
.Vb 5
\& Title   : set_Frequencies_Equivalent
\& Usage   : $sim\->set_Frequencies_Equivalent
\& Function: Reset the allele frequencies so they are all even
\& Returns : none
\& Args    : none
.Ve
.SS "get_Allele_Frequencies"
.IX Subsection "get_Allele_Frequencies"
.Vb 8
\& 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
.Ve
.SS "add_Allele_Frequency"
.IX Subsection "add_Allele_Frequency"
.Vb 6
\& 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
.Ve
.SS "reset_alleles"
.IX Subsection "reset_alleles"
.Vb 5
\& Title   : reset_alleles
\& Usage   : $marker\->reset_alleles();
\& Function: Reset the alleles for a marker
\& Returns : None
\& Args    : None
.Ve
.SS "validate_Frequencies"
.IX Subsection "validate_Frequencies"
.Vb 5
\& 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
.Ve