population.hpp

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#pragma once
#ifndef PBT_POPULATION_HPP_
#define PBT_POPULATION_HPP_
 
#include "random_fwd.hpp"
 
#include <cstdint>
#include <iosfwd>
#include <vector>
#include <map>
#include <memory>
 
 
namespace pbf {
 
class Individual;
 
class Population {
  public:
    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);
    ~Population();
 
    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);
 
    std::ostream& write_sample_family(std::ostream& ost) const;
    std::ostream& write_demography(std::ostream&) const;
    std::ostream& write(std::ostream&) const;
    friend std::ostream& operator<<(std::ostream&, const Population&);
 
  private:
    void reproduce();
 
    void reproduce(uint_fast32_t location, size_t popsize);
 
    void survive(int_fast32_t season);
 
    void migrate();
 
    void sample(std::vector<std::vector<std::shared_ptr<Individual>>>* subpops,
                const std::vector<size_t>& sample_sizes);
 
    void append_demography(int_fast32_t season);
 
    std::vector<std::vector<uint_fast32_t>> count(int_fast32_t season) const;
 
    size_t num_subpops() const noexcept {return subpopulations_.size();}
 
    std::vector<std::vector<std::shared_ptr<Individual>>> subpopulations_;
    std::vector<std::vector<std::shared_ptr<Individual>>> juveniles_subpops_;
    std::vector<std::vector<uint_fast32_t>> juveniles_demography_ = {};
    std::vector<std::map<int_fast32_t, std::vector<std::shared_ptr<Individual>>>> loc_year_samples_ = {};
    std::map<std::pair<int_fast32_t, int_fast32_t>, std::vector<std::vector<uint_fast32_t>>> demography_ = {};
 
 
    const double carrying_capacity_;
    const double recruitment_coef_;
    const double k_nbinom_;
    int_fast32_t year_ = 0;
    std::unique_ptr<URBG> engine_;
};
 
} // namespace pbf
 
#endif /* PBT_POPULATION_HPP_ */