#include <population.hpp>

Public Types
using	param_type = PopulationParams
	Alias.

Public Member Functions
	Population (size_t size, size_t num_founders=1)
	constructor
	Population (const Population &other)=default
	default copy constructor
	~Population ()
	destructor
bool	evolve (size_t max_generations, size_t record_interval, Recording flags=Recording::activity\|Recording::fitness, size_t t_hyperactivate=0u)
	return false if TE is extinct
std::ostream &	write_summary (std::ostream &) const
	write summary in JSON format
std::ostream &	write_fasta_individual (std::ostream &, size_t i) const
	count identicals and write FASTA for i-th individual
std::ostream &	write_fasta (std::ostream &, size_t num_individuals=-1u) const
	call write_fasta_individual() repeatedly

Static Public Member Functions
static void	param (const param_type &p)
	Set PARAM_.
static const param_type &	param ()
	Get PARAM_.
static void	seed (std::mt19937_64::result_type value)
	Set SEEDER_ seed.

Static Public Attributes
static constexpr double	THETA = 0.01
	\(\theta = 4N\mu\), population mutation rate
static constexpr double	RHO = 20000
	\(\rho = 4Nc\), population recombination rate

Private Member Functions
std::vector< double >	step (double previous_max_fitness=1.0)
	proceed one generation and return fitness record
void	eval_species_distance ()
	find farthest element, count species, and cause speciation if qualified
bool	is_extinct () const
	return true if no TE exists in gametes_
void	write_activity (std::ostream &, size_t time, bool header) const
	summarize and write activity

Private Attributes
std::vector< Haploid >	gametes_
	vector of chromosomes, not individuals

Static Private Attributes
static param_type	PARAM_
	Parameters shared among instances.
static std::mt19937_64	SEEDER_
	seed generator for Haploid::URBG

Friends
std::ostream &	operator<< (std::ostream &ost, const Population &pop)
	shortcut << Population::gametes_

Detailed Description

The documentation for this class was generated from the following files:

Public Types