int main(int ac, char **av)
{
Population population;
char *target;
unsigned int epochs = 0;
if (ac == 6 && check_string(av[1]) && check_params(av))
{
target = av[1];
population.setSelectionRate(atof(av[3]));
population.setMutationRate(atof(av[4]));
population.setPoolSize(atoi(av[5]));
population.CreatePopulation(atoi(av[2]), strlen(target));
while (population.getBestFitness() < 100)
{
std::cout << "Epochs: " << epochs++ << std::endl;
population.Evaluate((Fitness)evaluate_sample, target);
population.Selection();
population.Crossover();
population.Mutation();
population.Evaluate((Fitness)evaluate_sample, target);
std::cout << population << std::endl;
}
}
else
std::cerr << "Usage: ./GeneticString \"[a-z](length > 2)\" pop_size(int) select_rate[0.0-1.0] mutation_rate[0.0-1.0] pool_size(int)" << std::endl;
return (0);
}
int main()
{
int NumReps = 1;//this is one parameter to mess with here
string basefilename = "null_1rep_440a_160j_6alleles";
int vs_initial = 500;
int vs_sampled = 500;
int ss_initial = 0;
int ss_sampled = 0;
int end, g, reps, ld_count;
vector <double> ci95_det, ci95_spu, ci99_det, ci99_spu;//for sexual selection
vector <double> vs_ci95_det, vs_ci95_spu, vs_ci99_det, vs_ci99_spu;//vs = viability selection
vector <double> bs95_det, bs95_spu, bs99_det, bs99_spu, fdr_spu, fdr_det;
double ci95d_SE, ci95s_SE, ci99d_SE, ci99s_SE;//standard errors of spurious and detected peaks
double ci95d_m, ci95s_m, ci99d_m, ci99s_m;//means of spurious and detected peaks
double bs95d_SE, bs95s_SE, bs99d_SE, bs99s_SE, fdr_SE, fdrs_SE;//standard errors of spurious and detected peaks
double bs95d_m, bs95s_m, bs99d_m, bs99s_m, fdr_m, fdrs_m;//means of spurious and detected peaks
int peak_n = 0, total_QTL, vs_peak_n = 0;
Population Pop;
ofstream summ;
ofstream Fsts;
ofstream plot_Fsts;
ofstream parameters;
ofstream QTLs;
ofstream peak_summ;
ofstream ld, sig_thresh;
string ldname = basefilename + "_LD.txt";
string QTLname = basefilename + "_QTLs.txt";
string parametername = basefilename + "_Parameters.txt";
string summfilename = basefilename + "_SummStats.txt";
string adultfilename = basefilename + "_AdultSummStats.txt";
string fstfilename = basefilename + "_Fsts.txt";
string fdrfilename = basefilename + "_plot_Fsts.txt";
string peaksummname = basefilename + "_peakSumm.txt";
string sig_threshold_name = basefilename + "_sig_thresholds.txt";
ld.open(ldname.c_str());
summ.open(summfilename.c_str());
Fsts.open(fstfilename.c_str());
plot_Fsts.open(fdrfilename.c_str());
parameters.open(parametername.c_str());
QTLs.open(QTLname.c_str());
sig_thresh.open(sig_threshold_name.c_str());
sig_thresh << "rep\tgen\tnum.fdr.real\tnum.fdr.spur\tnum.99.real\tnum.99.spur\tnum.95.real\tnum.95.spur\tnum.bs99.real\tnum.bs99.spur\tnum.bs95.real\tnum.bs95.spur";
summ << "rep\tgen\tTimepoint\twhich\tMeanLD\t" << "GenVar\t" << "PhenVar\t" << "Heritability\t" << "PopulationSize\t" << "NumMales\t"
<< "NumFem\t" << "SexRatio\t" << "Mean Trait Value\t" << "MaleTraitMean\t" << "FemTraitMean\t" << "Mating Diff\t"
<< "Male m'\t" << "Fem m'" << "\tbs99_real\tbs99_spurious\tci99_real\tci99spurious" << '\n';
parameters << "NumReps\tCarryingCapacity\tMaxFecundity\tMaxEncounters\tAdultSampleSize\tOffSampleSize\tNumGen\tNumSelGen\tNumLoci"
<< "\tNumChrom\tNumQTLs\tMaxNumAlleles\tRecombRate\tMutRate\tMutVar\tEnvVar\tSigma\tbs_reps\tNumforLD\n";
ci95s_m = ci95d_m = ci99d_m = ci99s_m = 0;
bs95d_m = bs95s_m = bs99d_m = bs99s_m = fdr_m = fdrs_m = 0;
bs95d_SE = bs95s_SE = bs99d_SE = bs99s_SE = fdr_SE = fdrs_SE = 0;
vector <double> new_within_chrom_dprime;
double mean_dp_ldistchrom = 0;
//vector <double> adams_avg_dprime;
ld_info returned_data;
for (reps = 0; reps < NumReps; reps++)
{
Pop.SetParameters();
Pop.Initialize(Pop.prior_qtl);
cout << "Started rep " << reps + 1 << '\n';
if (reps == 0)
{
ld << "rep\tgen\t" << "Avg_perchrom_ldDp\t" << "PairwiseD\t" << "Dprime\t"
<< "long_dist_d\t" << "long_distDprime";
total_QTL = Pop.NumQTLs*Pop.NumChrom;
QTLs << "reps";
for (int c = 0; c < Pop.NumChrom; c++)
{
new_within_chrom_dprime.push_back(0);
// adams_avg_dprime.push_back(0);
ld << "\tchrom_" << c << "_D" << "\tchrom_" << c << "_ldDp";
for (int cc = 0; cc < Pop.NumQTLs; cc++)
QTLs << '\t' << c << "." << cc;
}
QTLs << '\n';
ld << '\n';
parameters << NumReps << '\t' << Pop.CarryingCapacity << '\t' << Pop.MaximumFecundity << '\t' << Pop.MaximumEncounters << '\t'
<< Pop.pAdultSample << '\t' << Pop.ProgSample << '\t' << Pop.Generations << '\t' << Pop.NumSelGen << '\t' << Pop.NumMarkers << '\t'
<< Pop.NumChrom << '\t' << Pop.NumQTLs << '\t' << Pop.NumAlleles << '\t' << Pop.RecombRate << '\t' << Pop.MutationRate << '\t'
<< Pop.MutationalVariance << '\t' << Pop.EnvironmentalVariance << '\t' << Pop.sigma << '\t' << Pop.bs_replicates << '\t' << Pop.NumLD << '\n';
}
QTLs << reps;
for (int c = 0; c < Pop.NumChrom; c++)
{
for (int cc = 0; cc < Pop.NumQTLs; cc++)
QTLs << '\t' << Pop.Locations[c].LociOnChrom[cc];
}
QTLs << '\n';
for (g = 0; g < Pop.Generations; g++)
{
Pop.PopulationSize = Pop.DeterminePopSize();
Pop.Mating(ss_initial);//random mating if 0
if (Pop.popExtinct == true)
{
cout << "Extinct Generation " << g + 1 << '\n';
break;
}
Pop.Mutation();
Pop.SelectionOnPhenotypes(vs_initial);//none if 0
Pop.DensityRegulation();
Pop.PopulationSize = Pop.DeterminePopSize();
Pop.CalcMeanTraitValues();
Pop.AdultSumm();
double mean_new_longdist_d, mean_new_longdist_dprime;
mean_new_longdist_d = mean_new_longdist_dprime = 0;
Pop.AvgLD = 0;
Pop.avg_pairwise_d = 0;
Pop.avg_longdist_d = 0;
mean_dp_ldistchrom = 0;
ld_count = 0;
while (ld_count < Pop.NumLD)
{
returned_data = Pop.AdultPopLD(randnum(Pop.NumChrom), randnum(Pop.NumChrom), randnum(Pop.NumMarkers), randnum(Pop.NumMarkers));
if (returned_data.dprime != -5)
{
mean_new_longdist_d = mean_new_longdist_d + returned_data.d;
mean_new_longdist_dprime = mean_new_longdist_dprime + returned_data.dprime;
ld_count++;
}
}
mean_new_longdist_d = mean_new_longdist_d / Pop.NumLD;
mean_new_longdist_dprime = mean_new_longdist_dprime / Pop.NumLD;
for (int c = 0; c < Pop.NumChrom; c++)
{
for (int cc = 0; cc < Pop.NumMarkers - 1; cc++)
{//Pairwise
returned_data = Pop.AdultPopLD(c, c, cc, cc + 1);
Pop.avg_pairwise_d = Pop.avg_pairwise_d + returned_data.d;
Pop.AvgLD = Pop.AvgLD + returned_data.dprime;
}
//adams_avg_dprime[c] = 0;
Pop.avg_d[c] = 0;
ld_count = 0;
new_within_chrom_dprime[c] = 0;
while (ld_count < 100)
{//random within-chromosomes
returned_data = Pop.AdultPopLD(c, c, randnum(Pop.NumMarkers), randnum(Pop.NumMarkers));
if (returned_data.dprime != -5)
{
Pop.avg_d[c] = Pop.avg_d[c] + returned_data.d;
new_within_chrom_dprime[c] = new_within_chrom_dprime[c] + returned_data.dprime;
mean_dp_ldistchrom = mean_dp_ldistchrom + returned_data.dprime;
ld_count++;
}
}
Pop.avg_d[c] = Pop.avg_d[c] / 100;
new_within_chrom_dprime[c] = new_within_chrom_dprime[c] / 100;
}
mean_dp_ldistchrom = mean_dp_ldistchrom / (Pop.NumChrom * 100);
Pop.AvgLD = Pop.AvgLD / (Pop.NumChrom * Pop.NumMarkers);
Pop.avg_pairwise_d = Pop.avg_pairwise_d / (Pop.NumChrom * Pop.NumMarkers);
ld << reps << '\t' << g << '\t' << mean_dp_ldistchrom << '\t' << Pop.avg_pairwise_d << '\t' << Pop.AvgLD
<< '\t' << mean_new_longdist_d << '\t' << mean_new_longdist_dprime;
for (int c = 0; c < Pop.NumChrom; c++)
{
ld << '\t' << Pop.avg_d[c] << '\t' << new_within_chrom_dprime[c];
}
ld << '\n';
if ((g + 1) % 100 == 0)
cout << "Generation " << g + 1 << " complete. ";
}//end of generations
cout << '\n';
if (!Pop.popExtinct)
{
int Q;
for (g = 0; g < Pop.NumSelGen; g++)
{
Pop.PopulationSize = Pop.DeterminePopSize();
if (Pop.PopulationSize == 0)
Pop.popExtinct = true;
else
{
cout << "Sample Gen " << g + 1 << ", ";
Pop.StandardizeGenotypes();
Pop.Mating(ss_sampled);//mate choice
Pop.Mutation();
//Sample the new population
Pop.SamplePop();
//calculate stats
//Pop.SampleFsts();
Pop.POFst();
Pop.CalcFstChiSq(Pop.F_Marker);
Pop.BenjaminiHochbergFDR(Pop.Psig);
Pop.CalcLD();
for (int c = 0; c < Pop.NumChrom; c++)
{
for (int cc = 0; cc < Pop.NumMarkers - 1; cc++)
{//Pairwise
returned_data = Pop.AdultPopLD(c, c, cc, cc + 1);
Pop.avg_pairwise_d = Pop.avg_pairwise_d + returned_data.d;
Pop.AvgLD = Pop.AvgLD + returned_data.dprime;
}
}
Pop.AvgLD = Pop.AvgLD / (Pop.NumChrom * Pop.NumMarkers);
//Pop.LongDistLD();
Pop.QTLFstCalcs();
Pop.GeneticVariance();
Pop.WeightedFst(Pop.F_Marker, 0);
Pop.CalculateFstCIs(Pop.F_Marker);
Pop.bootstrap_resampling(Pop.F_Marker);
Pop.PeakDetector();
ci95d_m = ci95d_m + Pop.ci_detected95;
ci95s_m = ci95s_m + Pop.ci_spurious95;
ci99d_m = ci99d_m + Pop.ci_detected;
ci99s_m = ci99s_m + Pop.ci_spurious;
bs95d_m = bs95d_m + Pop.bs_detected95;
bs95s_m = bs95s_m + Pop.bs_spurious95;
bs99d_m = bs99d_m + Pop.bs_detected;
bs99s_m = bs99s_m + Pop.bs_spurious;
fdr_m = fdr_m + Pop.fdr_det;
fdrs_m = fdrs_m + Pop.fdr_spur;
ci95_det.push_back(Pop.ci_detected95);
ci95_spu.push_back(Pop.ci_spurious95);
ci99_det.push_back(Pop.ci_detected);
ci99_spu.push_back(Pop.ci_spurious);
bs95_det.push_back(Pop.bs_detected95);
bs95_spu.push_back(Pop.bs_spurious95);
bs99_det.push_back(Pop.bs_spurious);
bs99_spu.push_back(Pop.bs_detected);
fdr_det.push_back(Pop.fdr_det);
fdr_spu.push_back(Pop.fdr_spur);
sig_thresh << '\n' << reps << '\t' << g << '\t' << Pop.fdr_det << '\t' << Pop.fdr_spur << '\t' << Pop.ci_detected << '\t' << Pop.ci_spurious << '\t'
<< Pop.ci_detected95 << '\t' << Pop.ci_spurious95 << '\t' << Pop.bs_detected << '\t' << Pop.bs_spurious << '\t' << Pop.bs_detected95 << '\t'
<< Pop.bs_spurious95;
peak_n++;
if (g == 0 && reps == 0)
{
Fsts << "TotalNumPolymorphicLoci:" << Pop.NumPolymorphicLoci << '\n';
Fsts << "NumSampledAdults:" << Pop.pAdultSample << '\n';
Fsts << "NumSampledOffspring:" << Pop.ProgSample << '\n';
Fsts << "NumSampledGenerations:" << Pop.NumSelGen << '\n' << '\n';
Fsts << "Label\tGeneration\t" << "Chrom\t" << "Locus\t" << "QTL?\t" << "GenVar\t" << "Fst\t" << "WeightedFst\t" << "ChiSqP\t"
<< "ExpAdultHet\t" << "ExpOffHet\t" << "Ht\t" << "Hs\t" << "A.p1\t" << "O.p1\t" << "A.LD\t" << "O.LD\t"
<< "Fst.Q\t" << "QAHet\t" << "QOffHet\t" << "QHt\t" << "QHs\n";
plot_Fsts << "Rep\tGen\t" << "FDRCrit\t" << "Smooth99\t" << "Smooth98\t" << "Smooth95\t" << "Smooth90\t" << "Smooth80\t"
<< "bs99\tbs98\tbs95\tbs90\tbs80";
for (int l = 0; l < Pop.NumChrom; l++)
{
for (int ll = 0; ll < Pop.NumMarkers; ll++)
{
if (Pop.SampledLoci[l].LociOnChrom[ll] == 1)
plot_Fsts << '\t' << l << "." << ll;
}
}
plot_Fsts << '\n';
}
plot_Fsts << reps << '\t' << g << "a\t" << Pop.CriticalValue << '\t' << Pop.SmoothedCritValue99 << '\t' << Pop.SmoothedCritValue98 << '\t'
<< Pop.SmoothedCritValue95 << '\t' << Pop.SmoothedCritValue90 << '\t' << Pop.SmoothedCritValue80
<< '\t' << Pop.bsCritValue99 << '\t' << Pop.bsCritValue98 << '\t' << Pop.bsCritValue95 << '\t' << Pop.bsCritValue90
<< '\t' << Pop.bsCritValue80;
for (int w = 0; w < Pop.NumChrom; w++)
{
for (int x = 0; x < Pop.NumSampledLoci; x++)
{
plot_Fsts << '\t' << Pop.F_Marker.WeightedFst[w].LociOnChrom[x];
if (Pop.QTLtracker[w].LociOnChrom[int(Pop.F_Marker.Locus[w].LociOnChrom[x])] == 1)
{
for (int q = 0; q < Pop.NumQTLs; q++)
{
if (Pop.Locations[w].LociOnChrom[q] == Pop.F_Marker.Locus[w].LociOnChrom[x])
Q = q;
}
Fsts << g << "_A-O\t" << w << '\t';
Fsts << Pop.F_Marker.Locus[w].LociOnChrom[x] << '\t';
Fsts << "YES\t" << Pop.GenetVars[w].LociOnChrom[Q] << '\t';
Fsts << Pop.F_Marker.FstValue[w].LociOnChrom[x] << '\t';
Fsts << Pop.F_Marker.WeightedFst[w].LociOnChrom[x] << '\t';
Fsts << Pop.F_Marker.PValue[w].LociOnChrom[x] << '\t';
Fsts << Pop.AdultHet[w].LociOnChrom[x] << '\t';
Fsts << Pop.OffHet[w].LociOnChrom[x] << '\t';
Fsts << Pop.TotHet[w].LociOnChrom[x] << '\t';
Fsts << Pop.HetS[w].LociOnChrom[x] << '\t';
Fsts << Pop.AFreq1[w].LociOnChrom[x] << '\t';
Fsts << Pop.MFreq1[w].LociOnChrom[x] << '\t';
Fsts << Pop.OFreq1[w].LociOnChrom[x] << '\t';
Fsts << Pop.ALD[w].LociOnChrom[int(Pop.F_Marker.Locus[w].LociOnChrom[x])] << '\t';
Fsts << Pop.OLD[w].LociOnChrom[int(Pop.F_Marker.Locus[w].LociOnChrom[x])] << '\t';
Fsts << Pop.F_QTL.FstValue[w].LociOnChrom[Q] << '\t';
Fsts << Pop.QAdultHet[w].LociOnChrom[Q] << '\t';
Fsts << Pop.QOffHet[w].LociOnChrom[Q] << '\t';
Fsts << Pop.QTotHet[w].LociOnChrom[Q] << '\t';
Fsts << Pop.QHs[w].LociOnChrom[Q] << '\t';
Fsts << '\n';
}
else{
if (Pop.F_Marker.FstValue[w].LociOnChrom[x] > 0)
{
Fsts << g << "_A-O\t" << w << '\t';
Fsts << Pop.F_Marker.Locus[w].LociOnChrom[x] << '\t';
Fsts << "NO\t" << 0 << '\t';
Fsts << Pop.F_Marker.FstValue[w].LociOnChrom[x] << '\t';
Fsts << Pop.F_Marker.WeightedFst[w].LociOnChrom[x] << '\t';
Fsts << Pop.F_Marker.PValue[w].LociOnChrom[x] << '\t';
Fsts << Pop.AdultHet[w].LociOnChrom[x] << '\t';
Fsts << Pop.OffHet[w].LociOnChrom[x] << '\t';
Fsts << Pop.TotHet[w].LociOnChrom[x] << '\t';
Fsts << Pop.HetS[w].LociOnChrom[x] << '\t';
Fsts << Pop.AFreq1[w].LociOnChrom[x] << '\t';
Fsts << Pop.MFreq1[w].LociOnChrom[x] << '\t';
Fsts << Pop.OFreq1[w].LociOnChrom[x] << '\t';
Fsts << Pop.ALD[w].LociOnChrom[int(Pop.F_Marker.Locus[w].LociOnChrom[x])] << '\t';
Fsts << Pop.OLD[w].LociOnChrom[int(Pop.F_Marker.Locus[w].LociOnChrom[x])] << '\t';
for (int out = 0; out < 5; out++)
Fsts << "0\t";
Fsts << '\n';
}
}
}
}
plot_Fsts << '\n';
Pop.AdultSumm();
summ << reps << '\t' << g << "\tAO\tAdults\t" << Pop.meanLD << '\t' << Pop.GenVar << '\t' << Pop.PhenVar << '\t' << Pop.Heritability << '\t'
<< Pop.PopulationSize << '\t' << Pop.malN << '\t' << Pop.femN << '\t' << Pop.adultRatio << '\t'
<< Pop.allphenavg << '\t' << Pop.malphenavg << '\t' << Pop.femphenavg << '\t' << Pop.allDiff << '\t'
<< Pop.maleDiff << '\t' << Pop.femDiff << '\t' << Pop.bs_detected << '\t' << Pop.bs_spurious << '\t'
<< Pop.ci_detected << '\t' << Pop.ci_spurious << '\n';
Pop.SelectionOnPhenotypes(vs_sampled);
Pop.OffSumm();
summ << reps << '\t' << g << "\tAO\tOff\t" << '\t' << Pop.GenVar << '\t' << Pop.PhenVar << '\t' << Pop.Heritability << '\t'
<< Pop.PopulationSize << '\t' << Pop.malN << '\t' << Pop.femN << '\t' << Pop.offRatio << '\t'
<< Pop.allphenavg << '\t' << Pop.malphenavg << '\t' << Pop.femphenavg << '\t' << Pop.allDiff << '\t'
<< Pop.maleDiff << '\t' << Pop.femDiff << '\t' << '\t' << '\t' << '\t' << '\n';
//population continues
Pop.DensityRegulation();
Pop.CalcMeanTraitValues();
Pop.PopulationSize = Pop.DeterminePopSize();
//compare current adults to previous progeny
Pop.SamplePop();
Pop.POFst();
//Pop.SampleFsts();
Pop.CalcFstChiSq(Pop.F_Marker);
Pop.BenjaminiHochbergFDR(Pop.Psig);
Pop.CalcLD();
for (int c = 0; c < Pop.NumChrom; c++)
{
for (int cc = 0; cc < Pop.NumMarkers - 1; cc++)
{//Pairwise
returned_data = Pop.AdultPopLD(c, c, cc, cc + 1);
Pop.avg_pairwise_d = Pop.avg_pairwise_d + returned_data.d;
Pop.AvgLD = Pop.AvgLD + returned_data.dprime;
}
}
Pop.AvgLD = Pop.AvgLD / (Pop.NumChrom * Pop.NumMarkers);
//Pop.LongDistLD();
Pop.QTLFstCalcs();
Pop.GeneticVariance();
Pop.WeightedFst(Pop.F_Marker, 0);
Pop.CalculateFstCIs(Pop.F_Marker);
Pop.bootstrap_resampling(Pop.F_Marker);
Pop.PeakDetector();
for (int w = 0; w < Pop.NumChrom; w++)
{
for (int x = 0; x < Pop.NumSampledLoci; x++)
{
if (Pop.QTLtracker[w].LociOnChrom[int(Pop.F_Marker.Locus[w].LociOnChrom[x])] == 1)
{
for (int q = 0; q < Pop.NumQTLs; q++)
{
if (Pop.Locations[w].LociOnChrom[q] == Pop.F_Marker.Locus[w].LociOnChrom[x])
Q = q;
}
Fsts << g << "_O-A\t" << w << '\t';
Fsts << Pop.F_Marker.Locus[w].LociOnChrom[x] << '\t';
Fsts << "YES\t" << Pop.GenetVars[w].LociOnChrom[Q] << '\t';
Fsts << Pop.F_Marker.FstValue[w].LociOnChrom[x] << '\t';
Fsts << Pop.F_Marker.WeightedFst[w].LociOnChrom[x] << '\t';
Fsts << Pop.F_Marker.PValue[w].LociOnChrom[x] << '\t';
Fsts << Pop.AdultHet[w].LociOnChrom[x] << '\t';
Fsts << Pop.OffHet[w].LociOnChrom[x] << '\t';
Fsts << Pop.TotHet[w].LociOnChrom[x] << '\t';
Fsts << Pop.HetS[w].LociOnChrom[x] << '\t';
Fsts << Pop.AFreq1[w].LociOnChrom[x] << '\t';
Fsts << Pop.MFreq1[w].LociOnChrom[x] << '\t';
Fsts << Pop.OFreq1[w].LociOnChrom[x] << '\t';
Fsts << Pop.ALD[w].LociOnChrom[int(Pop.F_Marker.Locus[w].LociOnChrom[x])] << '\t';
Fsts << Pop.OLD[w].LociOnChrom[int(Pop.F_Marker.Locus[w].LociOnChrom[x])] << '\t';
Fsts << Pop.F_QTL.FstValue[w].LociOnChrom[Q] << '\t';
Fsts << Pop.QAdultHet[w].LociOnChrom[Q] << '\t';
Fsts << Pop.QOffHet[w].LociOnChrom[Q] << '\t';
Fsts << Pop.QTotHet[w].LociOnChrom[Q] << '\t';
Fsts << Pop.QHs[w].LociOnChrom[Q] << '\t';
Fsts << '\n';
}
else{
if (Pop.F_Marker.FstValue[w].LociOnChrom[x] > 0)
{
Fsts << g << "_O-A\t" << w << '\t' << Pop.SampledLoci[w].LociOnChrom[x] << '\t';
Fsts << "NO\t" << 0 << '\t';
Fsts << Pop.F_Marker.FstValue[w].LociOnChrom[x] << '\t';
Fsts << Pop.F_Marker.WeightedFst[w].LociOnChrom[x] << '\t';
Fsts << Pop.F_Marker.PValue[w].LociOnChrom[x] << '\t';
Fsts << Pop.AdultHet[w].LociOnChrom[x] << '\t';
Fsts << Pop.OffHet[w].LociOnChrom[x] << '\t';
Fsts << Pop.TotHet[w].LociOnChrom[x] << '\t';
Fsts << Pop.HetS[w].LociOnChrom[x] << '\t';
Fsts << Pop.AFreq1[w].LociOnChrom[x] << '\t';
Fsts << Pop.MFreq1[w].LociOnChrom[x] << '\t';
Fsts << Pop.OFreq1[w].LociOnChrom[x] << '\t';
Fsts << Pop.ALD[w].LociOnChrom[int(Pop.F_Marker.Locus[w].LociOnChrom[x])] << '\t';
Fsts << Pop.OLD[w].LociOnChrom[int(Pop.F_Marker.Locus[w].LociOnChrom[x])] << '\t';
for (int out = 0; out < 5; out++)
Fsts << "0\t";
Fsts << '\n';
}
}
}
}
Pop.AdultSumm();
summ << reps << '\t' << g << "\tOA\tAdult\t" << Pop.meanLD << '\t' << Pop.GenVar << '\t' << Pop.PhenVar << '\t' << Pop.Heritability << '\t'
<< Pop.PopulationSize << '\t' << Pop.malN << '\t' << Pop.femN << '\t' << Pop.adultRatio << '\t'
<< Pop.allphenavg << '\t' << Pop.malphenavg << '\t' << Pop.femphenavg << '\t' << Pop.allDiff << '\t'
<< Pop.maleDiff << '\t' << Pop.femDiff << '\t' << Pop.bs_detected << '\t' << Pop.bs_spurious << '\t'
<< Pop.ci_detected << '\t' << Pop.ci_spurious << '\n';
Pop.OffSumm();
summ << reps << '\t' << g << "\tOA\tOff\t" << '\t' << Pop.GenVar << '\t' << Pop.PhenVar << '\t' << Pop.Heritability << '\t'
<< Pop.PopulationSize << '\t' << Pop.malN << '\t' << Pop.femN << '\t' << Pop.offRatio << '\t'
<< Pop.allphenavg << '\t' << Pop.malphenavg << '\t' << Pop.femphenavg << '\t' << Pop.allDiff << '\t'
<< Pop.maleDiff << '\t' << Pop.femDiff << '\t' << '\t' << '\t' << '\t' << '\n';
}//run five times with MC and track it each time
}
}
cout << "Done rep " << reps + 1 << '\n';
Pop.DeInitialize();
}//end of reps
//calculate the summary stats regarding the peaks
peak_summ.open(peaksummname.c_str());
peak_summ << "Name\t" << "which\t" << "AvgRatioReal_99\t" << "RealSE_99\t" << "AvgRatioSpur_99\t" << "SpuriousSE_99\t"
<< "AvgRatioReal_95\t" << "Real_SE_95\t" << "AvgRatioSpur_95\t" << "SpuriousSE_95\t" << "TotalNumQTLs\t" << "TotalN\n";
//calculate summary stats for sexual selection
ci95d_m = (ci95d_m / peak_n); //peak_n is the number of reps & generations that cis are calculated for.
ci95s_m = (ci95s_m / peak_n);
ci99d_m = (ci99d_m / peak_n);
ci99s_m = (ci99s_m / peak_n);
ci95d_SE = 0;
ci95s_SE = 0;
ci99d_SE = 0;
ci99s_SE = 0;
for (int c = 0; c < peak_n; c++)
{
ci95d_SE = ci95d_SE + ((ci95_det[c]) - ci95d_m)*((ci95_det[c]) - ci95d_m);
ci95s_SE = ci95s_SE + ((ci95_spu[c]) - ci95s_m)*((ci95_spu[c]) - ci95s_m);
ci99d_SE = ci99d_SE + ((ci99_det[c]) - ci99d_m)*((ci99_det[c]) - ci99d_m);
ci99s_SE = ci99s_SE + ((ci99_spu[c]) - ci99s_m)*((ci99_spu[c]) - ci99s_m);
}
ci95d_SE = sqrt(ci95d_SE / peak_n);
ci95s_SE = sqrt(ci95s_SE / peak_n);
ci99s_SE = sqrt(ci99s_SE / peak_n);
ci99d_SE = sqrt(ci99d_SE / peak_n);
peak_summ << basefilename << "\tSmooth\t" << ci99d_m << '\t' << ci99d_SE << '\t' << ci99s_m << '\t' << ci99s_SE
<< '\t' << ci95d_m << '\t' << ci95d_SE << '\t' << ci95s_m << '\t' << ci95s_SE << '\t'
<< total_QTL << '\t' << peak_n << '\n';
//calculate summary stats for sexual selection
bs95d_m = (bs95d_m / peak_n) / total_QTL; //peak_n is the number of reps & generations that cis are calculated for.
bs95s_m = (bs95s_m / peak_n) / total_QTL;
bs99d_m = (bs99d_m / peak_n) / total_QTL;
bs99s_m = (bs99s_m / peak_n) / total_QTL;
fdrs_m = (fdrs_m / peak_n) / total_QTL;
fdr_m = (fdr_m / peak_n) / total_QTL;
bs95d_SE = 0;
bs95s_SE = 0;
bs99d_SE = 0;
bs99s_SE = 0;
fdrs_SE = 0;
fdr_SE = 0;
for (int c = 0; c < peak_n; c++)
{
bs95d_SE = bs95d_SE + ((bs95_det[c] / total_QTL) - bs95d_m)*((bs95_det[c] / total_QTL) - bs95d_m);
bs95s_SE = bs95s_SE + ((bs95_spu[c] / total_QTL) - bs95s_m)*((bs95_spu[c] / total_QTL) - bs95s_m);
bs99d_SE = bs99d_SE + ((bs99_det[c] / total_QTL) - bs99d_m)*((bs99_det[c] / total_QTL) - bs99d_m);
bs99s_SE = bs99s_SE + ((bs99_spu[c] / total_QTL) - bs99s_m)*((bs99_spu[c] / total_QTL) - bs99s_m);
fdr_SE = fdr_SE + ((fdr_det[c] / total_QTL) - fdr_m)*((fdr_det[c] / total_QTL) - fdr_m);
fdrs_SE = fdrs_SE + ((fdr_spu[c] / total_QTL) - fdrs_m)*((fdr_spu[c] / total_QTL) - fdrs_m);
}
bs95d_SE = sqrt(bs95d_SE / peak_n);
bs95s_SE = sqrt(bs95s_SE / peak_n);
bs99s_SE = sqrt(bs99s_SE / peak_n);
bs99d_SE = sqrt(bs99d_SE / peak_n);
fdr_SE = sqrt(fdr_SE / peak_n);
fdrs_SE = sqrt(fdrs_SE / peak_n);
peak_summ << basefilename << "\tStacksBS\t" << bs99d_m << '\t' << bs99d_SE << '\t' << bs99s_m << '\t' << bs99s_SE
<< '\t' << bs95d_m << '\t' << bs95d_SE << '\t' << bs95s_m << '\t' << bs95s_SE << '\n'
<< "\tFDR\t\t\t\t\t" << fdr_m << '\t' << fdr_SE << '\t' << fdrs_m << '\t' << fdrs_SE << '\n';
peak_summ.close();
summ.close();
Fsts.close();
QTLs.close();
parameters.close();
plot_Fsts.close();
cout << "Finished! Input integer to quit\n";
cin >> end;
return 0;
}