/
jaan_simulation.h
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/
jaan_simulation.h
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#ifndef JAAN_SIMULATION_H
#define JAAN_SIMULATION_H
#include <vector>
#include <random>
#include "jaan_parameters.h"
#include "jaan_habitat.h"
#include "jaan_individual.h"
class Simulation
{
public:
Simulation();
void run(
std::mt19937& generator,
const Parameters& p,
const std::vector<Habitat>& habitat_list,
const char stats_file[],
const char hist_file[]);
void output_data(
std::ofstream& stats,
std::ofstream& histograms,
Parameters p,
const std::vector<Individual>& population,
const std::vector<int>& location,
int g);
void statistics(
std::ofstream& stats,
const std::vector<Individual>& population,
const std::vector<int>& location);
void histogram(
std::ofstream& histograms,
const Parameters& p,
const std::vector<Individual>& population);
std::vector<Individual> create_next_gen(
std::mt19937& generator,
const Parameters& p,
const std::vector<Habitat>& habitat_list,
const std::vector<Individual>& population,
std::vector<int>& location);
int pick_mother(
std::mt19937& generator,
const std::vector<double>& female_viab_dist,
const std::vector<int>& mates_in_hab);
int pick_father(
std::mt19937& generator,
const Habitat& habitat,
const std::vector<int> mates_in_hab,
const std::vector<double>& quals,
const std::vector<double>& male_viab_dist,
const std::vector<Individual>& population,
const double& m_pref);
void crt_female_viability(
const std::vector<Habitat>& habitat_list,
const std::vector<double>& preferences,
const std::vector<double>& quals,
const std::vector<int>& location,
std::vector<double>& viab_dist);
void crt_male_viability(
const std::vector<Habitat>& habitat_list,
const std::vector<double>& traits,
const std::vector<double>& quals,
const std::vector<int>& location,
std::vector<double>& viab_dist);
void mutate_populace(
std::mt19937& generator,
const Parameters& p,
std::vector<Individual>& population);
void mutate_pref_populace(
std::mt19937& generator,
const double& pref_mu,
const double& scale_pref,
std::vector<Individual>& population);
void mutate_trt_populace(
std::mt19937& generator,
const double& trt_mu,
const double& scale_trt,
std::vector<Individual>& population);
void mutate_qual_populace(
std::mt19937& generator,
const double& qual_mu,
const double& scale_qual,
std::vector<Individual>& population);
void setup_initial_population(
std::mt19937& generator,
const Parameters& p,
std::vector<Individual>& population,
std::vector<int>& location);
void setup_output_titles(
std::ofstream& stats,
std::ofstream& histograms,
const Parameters& p,
const std::vector<Habitat>& habitat_list,
const std::vector<Individual>& population,
const std::vector<int>& location,
const std::vector<int>& location0);
};
void migration(
std::mt19937& generator,
const double& migration_rate,
std::vector<int>& location);
void setup_histogram_titles(
std::ofstream& histograms,
const Parameters p);
void create_histogram(
const int& n_genes,
const double& ind_character,
const double& scale,
std::vector<double>& hist);
void output_histogram(
std::ofstream& histograms,
const double& n_genes,
const std::vector<double>& hist);
std::vector<double> collect_prefs(const std::vector<Individual>& population);
std::vector<double> collect_trts(const std::vector<Individual>& population);
std::vector<double> collect_quals(const std::vector<Individual>& population);
double compute_square(const double& x);
double sum(const std::vector<double>& v);
std::vector<double> square_vector(const std::vector<double>& v);
double variance_calc(
const std::vector<double>& v,
const int pop);
double covariance_calc(
const std::vector<double>& v1,
const std::vector<double>& v2,
const int pop);
#endif // JAAN_SIMULATION_H