pbf::Population Class Reference

Population class. More...

#include <population.hpp>

Public Member Functions
	Population (const size_t initial_size, std::random_device::result_type seed, const double carrying_capacity=1e3, const double recruitment_coef=2.0, const double negative_binom_k=-1.0)
	Constructor.
void	run (const int_fast32_t simulating_duration, const std::vector< size_t > &sample_size_adult={1u, 1u}, const std::vector< size_t > &sample_size_juvenile={1u, 1u}, const int_fast32_t recording_duration=1)
	Main iteration.
std::ostream &	write_sample_family (std::ostream &ost) const
std::ostream &	write_demography (std::ostream &) const
	Write demography_.
std::ostream &	write (std::ostream &) const
	Write subpopulations_ and juveniles_subpops_ for debugging.

Private Member Functions
void	reproduce ()
	give birth to children
void	reproduce (uint_fast32_t location, size_t popsize)
void	survive (int_fast32_t season)
	Evaluate survival.
void	migrate ()
	Evaluate migration. Individuals in juveniles_subpops_ moves to subpopulations_.
void	sample (std::vector< std::vector< std::shared_ptr< Individual > > > *subpops, const std::vector< size_t > &sample_sizes)
	Sample individuals.
void	append_demography (int_fast32_t season)
	Append current state to demography_.
std::vector< std::vector< uint_fast32_t > >	count (int_fast32_t season) const
	Count individuals for each location and age.
size_t	num_subpops () const noexcept
	Return size of subpopulations_.

Private Attributes
std::vector< std::vector< std::shared_ptr< Individual > > >	subpopulations_
	Individual array for each subpopulation.
std::vector< std::vector< std::shared_ptr< Individual > > >	juveniles_subpops_
std::vector< std::vector< uint_fast32_t > >	juveniles_demography_ = {}
	Counts of juveniles of the year: [[number for each location] for each season].
std::vector< std::map< int_fast32_t, std::vector< std::shared_ptr< Individual > > > >	loc_year_samples_ = {}
	Samples: [{capture_year => individuals} for each location].
std::map< std::pair< int_fast32_t, int_fast32_t >, std::vector< std::vector< uint_fast32_t > > >	demography_ = {}
	(year, season) => [[count for each age] for each location]
int_fast32_t	year_ = 0
std::unique_ptr< URBG >	engine_
	Uniform Random Bit Generator.
const double	carrying_capacity_
	\(K\): carrying capacity used in reproduce()
const double	recruitment_coef_
	\(r\): coefficient used in reproduce()
const double	k_nbinom_

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

Detailed Description

Population class.

Member Function Documentation

reproduce()

void pbf::Population::reproduce ( uint_fast32_t location, size_t popsize )

private

Append new individuals to juveniles_subpops_ at location. 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.

write_sample_family()

std::ostream & pbf::Population::write_sample_family

(

std::ostream &

ost

)

const

Construct and write tree from loc_year_samples_. Serial IDs are assigned to sampled individuals. IDs larger than sample size are assigned to unsampled ancestors.

Member Data Documentation

juveniles_subpops_

std::vector<std::vector<std::shared_ptr<Individual> > > pbf::Population::juveniles_subpops_

private

First-year individuals separated for sample(). Note that it becomes empty in migrate().

year_

int_fast32_t pbf::Population::year_ = 0

private

Current time.

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

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