#include "parameters.h" Parameters::Parameters() { //Simulation simNr = 10016; reps =5; gens =500; //Landscape K = 50; // carrying capacity // Chromosome and Biology of Mutations R = 10; // length of the chromosome //---> recombination COd = 1.0; //---> mutational effects, number of mutations shape_mut = 1.0; // ->shape parameter k (or alpha) mean_mut = 0.01; // -> mean parameter u, mean = shape parameter* scale parameter (in R) -> scale= mean/shape initial_nMut = 0; // initiate individuals with mutations s_const = 0; // if selection coef constant for deleterious mutations mean_hd = 0.37; // mean dominance effect for mildly deleterious mutations Ud = 1.0; // number of deleterious mutations occuring in offspring --> currently with 1, gives error when 0 Ub = 0.05; // number of beneficial mutations Ur = 0.05; // probability of del mut reversing (backmutation) neut_mu = 1.0; // probability of neutral mutation occuring per individual per generation -> per locus mutation rate = neut_mu/2 neut_Veffect = 1.0; // variance from which to sample neutral mutation value, should be chosen so Vm is exactly 1 //-> Vm= 2*nloci*neut_mu*neut_effect=1 // Condition add_error = true; // if noise is added to condition sd_error = 0.01; // if 0, then add_error has to be false // Survival dens_ind_sel = true; // density independent survival strength_sel = 1.0; // determining the shape of the function how deleterious mutations affect survival, 1 is linear // Sexual selection deme_size = 1; // deme size, number of competing males alpha = 1.0; //male-male competition //---> offspring production fecundity_selection = false; r = 4.0; // number of offspring fec_par = 1.0; noff_det = 1; // output pop_slim = true; out_pop_interval = 10; // interval for population output every X generations out_pop_interval2 = 2000; // new pop interval out_ind_interval = 100000; // interval indivudal output every X generations out_ind_interval2 = 100000; // new ind interval out2_limit = 2000; // limit when to switch to new output interval mutout_on = 0; dload_out_start =1; // for popmut output dload_interval =100000; // for dirft load output full_mutmap_interval = 1; // full_mutmap_start = 1000; out_Ne = 0; out_Ne_start = 1000; out_Ne_interval = 10; W_critical = 0.6; // make model deterministic seed = 2.0; } /* void Parameters::outPara(string name) { ofstream out; out.open(name.c_str()); //Simulation out << "SimNr\t" << simNr << endl; // simulation ID out << "rep\t" << reps << endl; //replicates out << "gen\t" << gens << endl; //generations out << "determ\t" << DET << endl; // determinisitc model out << "dominance\t" << DOM << endl; // dominance model out << "benmut\t" << BENMUT << endl; // beneficial mutations modelled out << "revmut\t" << BACKMUT << endl; // reverse mutations modelled // Landscape out << "seed\t" << seed << endl; //set seed for deterministic model out << "K\t" << K << endl; //carrying capacity // Genetics out << "R\t" << R << endl; //length of chromosome out << "COlength\t" << COd << endl; //length of CO region out << "initMut\t" << initial_nMut << endl; //initial number of mutations present out << "shapeMut_effect\t" << shape_mut << endl; //shape parameter of mutational effect distribution out << "meanMut_effect\t" << mean_mut << endl; //mean of mutational effect distribution-> scale= mean/shape out << "Udel\t" << Ud << endl; //number of del mut per generation per genom out << "Uben\t" << Ub << endl; //number of benefical mut per generation per genom out << "Urev\t" << Ur << endl; //number of reverse mut per gen/per genom out << "mean_hd\t" << mean_hd << endl; //goes into determining domiance coef h via calculation of k, mean domiance // Condition out << "c_error\t" << add_error << endl; // add random error to condition out << "c_sderror\t" << sd_error << endl; //width of error distribution //Suvivial out << "dens_ind_sel\t" << dens_ind_sel << endl; //is natural selection density independent out << "strength_nat_sel\t" << strength_sel << endl; //strength of nat selection // Sexual selection out << "deme_size\t" << deme_size << endl; //males in a deme out << "alpha\t" << alpha << endl; //potential for mate monoplisation // Offspring production out << "fec_sel\t" << fecundity_selection << endl; //fecundity selection true out << "mean_fec\t" << r << endl; //mean number of offspring out << "fec_par\t" << fec_par << endl; //scaling fecundity to condition // output variables out << "out_ind1\t" << out_ind_interval << endl; // out << "out_ind2\t" << out_ind_interval2 << endl; // out << "out_pop1\t" << out_pop_interval << endl; // out << "out_pop2\t" << out_pop_interval2 << endl; // out << "out_limit\t" << out2_limit << endl; // out << "mutout_on\t" << mutout_on << endl; // out << "out_start\t" << out_start << endl; // out << "Popmut_interval\t" << PopMut_interval << endl; // out.close(); } */ void Parameters::outPara(string name) { ofstream out; out.open(name.c_str()); //Simulation out << "SimNr\t" << "rep\t" //replicates << "gen\t" //generations << "determ\t" // determinisitc model << "dominance\t" // dominance model << "benmut\t" // beneficial mutations modelled << "revmut\t" // reverse mutations modelled << "delmut\t" // reverse mutations modelled // Landscape << "seed\t" //set seed for deterministic model << "K\t" //carrying capacity // Genetics << "R\t" //length of chromosome << "COlength\t" //length of CO region << "initMut\t" //initial number of mutations present << "shapeMut_effect\t" //shape parameter of mutational effect distribution << "meanMut_effect\t" //mean of mutational effect distribution-> scale= mean/shape << "constant_s\t" // if cosntant s true << "Udel\t" //number of del mut per generation per genom << "Uben\t" //number of benefical mut per generation per genom << "Urev\t" //number of reverse mut per gen/per genom << "mean_hd\t" //goes into determining domiance coef h via calculation of k, mean domiance << "neut_mu\t" // << "neut_Veffect\t" // // Condition << "c_error\t" // add random error to condition << "c_sderror\t" //width of error distribution //Suvivial << "dens_ind_sel\t" //is natural selection density independent << "strength_nat_sel\t" //strength of nat selection // Sexual selection << "deme_size\t" //males in a deme << "alpha\t" //potential for mate monoplisation // Offspring production << "fec_sel\t" //fecundity selection true << "mean_fec\t" //mean number of offspring << "fec_par\t" //scaling fecundity to condition << "noff_det\t" //fecudnity a constant // output variables << "out_ind1\t" // << "out_ind2\t" // << "out_pop1\t" // << "out_pop2\t" // << "out_limit\t" // << "mutout_on\t" // << "out_start\t" // << "Popmut_interval\t" // << "out_Ne\t" // << "out_Ne_start\t" // << "out_Ne_interval\t" << endl; // // INPUT VARIABLES //Simulation out << simNr << "\t" // simulation ID << reps << "\t" //replicates << gens << "\t" //generations << DET << "\t" // determinisitc model << DOM << "\t" // dominance model << BENMUT << "\t" // beneficial mutations modelled << BACKMUT << "\t" // reverse mutations modelled << DELMUT << "\t" // reverse mutations modelled // Landscape << seed << "\t" //set seed for deterministic model << K << "\t" //carrying capacity // Genetics << R << "\t" //length of chromosome << COd << "\t" //length of CO region << initial_nMut << "\t" //initial number of mutations present << shape_mut << "\t" //shape parameter of mutational effect distribution << mean_mut << "\t" //mean of mutational effect distribution-> scale= mean/shape << s_const << "\t" // constant s coef << Ud << "\t"//number of del mut per generation per genom << Ub << "\t" //number of benefical mut per generation per genom << Ur << "\t" //number of reverse mut per gen/per genom << mean_hd << "\t" //goes into determining domiance coef h via calculation of k, mean domiance << neut_mu << "\t" // << neut_Veffect << "\t" // // Condition << add_error << "\t" // add random error to condition << sd_error << "\t" //width of error distribution //Suvivial << dens_ind_sel << "\t" //is natural selection density independent << strength_sel << "\t" //strength of nat selection // Sexual selection << deme_size << "\t" //males in a deme << alpha << "\t" //potential for mate monoplisation // Offspring production << fecundity_selection << "\t" //fecundity selection true << r << "\t"//mean number of offspring << fec_par << "\t" //scaling fecundity to condition << noff_det << "\t"//mean number of offspring // output variables << out_ind_interval << "\t" // << out_ind_interval2 << "\t" // << out_pop_interval << "\t" // << out_pop_interval2 << "\t" // << out2_limit << "\t" // << mutout_on << "\t" // << dload_out_start << "\t" // << dload_interval << "\t" // << out_Ne << "\t" // << out_Ne_start << "\t" // << out_Ne_interval << endl; // out.close(); } Parameters::~Parameters() { }