Main class that implements simulation. More...

#include <population.hpp>

Public Member Functions
	Population (const Parameters &)
	Constructor.

void	run ()
	Main iteration.

std::ostream &	write_sample_family (std::ostream &ost) const
	Construct and write tree from SubPopulation::samples. Serial IDs are assigned to sampled individuals. IDs larger than sample size are assigned to unsampled ancestors.

std::ostream &	write_demography (std::ostream &) const
	Write SubPopulation::demography.

std::ostream &	write (std::ostream &) const
	Write subpopulations_ for debugging.

Private Types
using	PairDestDist = std::pair<uint_fast32_t, std::discrete_distribution<uint_fast32_t>>
	Alias for readability.

Private Member Functions
void	reproduce ()
	give birth to children

void	reproduce_lognormal ()
	Reproduce according to constant lognormal distribution. Total recruitment is calculated first, and then split it.

void	reproduce_logistic ()
	Reproduce according to population size and carrying capacity.

void	reproduce_impl (SubPopulation &, const std::vector< uint_fast32_t > &litter_sizes)
	Append new individuals to SubPopulation::juveniles. The expected number of children for each adult is proportional to its weight. All the females are evaluated for recruitment, whereas males are stochastically chosen.

std::vector< uint_fast32_t >	litter_sizes_logistic (const std::vector< ShPtrIndividual > &females, size_t popsize)
	Calculate stochastic litter sizes proportional to female weight.

void	survive (int_fast32_t season)
	Evaluate survival.

double	death_rate (const int_fast32_t age, const int_fast32_t season) const
	Finite death rate per quarter year: \( d = 1 - \exp(- M - eF) \).

void	migrate ()
	Evaluate migration. Merge SubPopulation::juveniles to SubPopulation::adults.

uint_fast32_t	destination (int_fast32_t age, uint_fast32_t loc)
	Generate random number for new location.

void	sample (SubPopulation &subpops, size_t n_adults, size_t n_juveniles)
	Move individuals to SubPopulation::samples.

size_t	sample (std::vector< ShPtrIndividual > &src, std::vector< ShPtrIndividual > &dst, size_t n)
	Implementation of sample().

void	init_demography (int_fast32_t duration)
	Initialize SubPopulation::demography.

void	record_demography (int_fast32_t season)
	Record current state to SubPopulation::demography.

std::vector< double >	weights (const std::vector< ShPtrIndividual > &) const
	For male selection.

void	propagate_params ()
	Call all the init* functions.

void	init_migration ()
	Prepare MIGRATION_DESTINATION_.

void	init_mortality ()
	Prepare NATURAL_MORTALITY_, FISHING_MORTALITY_, FISHING_COEF_.

void	init_weight ()
	Prepare WEIGHT_FOR_AGE_.

bool	is_ready () const
	Test if dependent variables are ready.

Private Attributes
Parameters	params_
	Store the values from command line and json.

std::vector< double >	NATURAL_MORTALITY_ {}
	elongated version of Parameters::natural_mortality

std::vector< double >	FISHING_MORTALITY_ {}
	elongated version of Parameters::fishing_mortality

std::vector< double >	FISHING_COEF_ {}
	elongated version of Parameters::fishing_coef

std::vector< double >	WEIGHT_FOR_AGE_ {}
	year version of Parameters::weight_for_age

std::vector< std::vector< PairDestDist > >	MIGRATION_DESTINATION_ {}
	Discrete distributions for migrate()

std::vector< SubPopulation >	subpopulations_ {}
	Array of SubPopulation.

int_fast32_t	year_ {0}
	Current time.

std::unique_ptr< URBG >	engine_ {nullptr}
	Uniform Random Bit Generator.

Static Private Attributes
static constexpr int_fast32_t	MAX_AGE = 80
	No individual lives longer than this.

Friends
std::ostream &	operator<< (std::ostream &ost, const Population &pop)
	Shortcut for Population::write(ost)

Detailed Description

Main class that implements simulation.

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

src/population.hpp
src/population.cpp

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

Friends

Detailed Description