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Noble Ape Simulation 0.689 (Carbon Mac OS and Source Code branch)
01-08-2009
The Noble Ape Simulation creates a random environment and simulates the ape inhabitants' cognitive processes. It features the Ocelot landscape rendering engine. License: MIT/X Consortium License Changes:|
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Bio::PopGen::Simulation::GeneticDrift(3pm) User Contributed Perl Documentation Bio::PopGen::Simulation::GeneticDrift(3pm) 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 perl v5.14.2 2012-03-02 Bio::PopGen::Simulation::GeneticDrift(3pm)