pbf::Population Class Reference

Main class that implements simulation. More...

#include <population.hpp>

Public Member Functions
	Population (const Parameters &)
	Constructor.
void	run ()
	The main loop of simulation.
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<int_fast32_t, std::discrete_distribution<int_fast32_t>>
	Alias for readability.

Private Member Functions
void	reproduce ()
	Call reproduce_impl() via reproduce_lognormal() or reproduce_logistic() depending on Parameters::med_recruitment. 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. All the SubPopulation::adults are evaluated regardless of age. Currently, the breeding places are hardcoded to subpopulations 0 and 1.
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 (const int_fast32_t loc, std::vector< int_fast32_t > litter_sizes)
	Call survive_juvenile() and append survived ones to SubPopulation::juveniles. "Juveniles" are sampled from first-year individuals died in the final season.
std::vector< int_fast32_t >	litter_sizes_logistic (const std::vector< ShPtrIndividual > &females, int_fast32_t popsize)
	Calculate stochastic litter sizes proportional to female weight.
std::vector< double >	survive_juvenile (std::vector< int_fast32_t > &litter_sizes, std::array< std::vector< int_fast32_t >, 4 > &demography_y, const int_fast32_t sample_size)
	Evaluate and record survival of juveniles.
int_fast32_t	sample_size_juvenile (int_fast32_t loc) const
	Return sample size of juveniles at location loc in current year_.
void	survive (int_fast32_t season)
	Evaluate survival using death_rate(). "Adults" are sampled from individuals died in the final season.
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.
int_fast32_t	destination (int_fast32_t age, int_fast32_t loc)
	Generate random number for new location.
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() based on Parameters::migration_matrices.
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.

Member Function Documentation

run()

void pbf::Population::run

(

)

The main loop of simulation.

1. reproduce() includes sampling from dead juveniles.
2. for each season:
   • record_demography()
   • survive() includes sampling from dead adults.
3. migrate()

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

• src/population.hpp
• src/population.cpp