void model_parameters::output_dat(void)
{
ofstream afs("lagrangian_est.dat");
afs<<"# syr " << endl << syr <<endl;
afs<<"# nyr " << endl << nyr <<endl;
afs<<"# sage " << endl << sage <<endl;
afs<<"# nage " << endl << nage <<endl;
afs<<"# smon " << endl << smon <<endl;
afs<<"# nmon " << endl << nmon <<endl;
afs<<"# sarea " << endl << sarea <<endl;
afs<<"# narea " << endl << narea <<endl;
afs<<"# nations " << endl << nations <<endl;
afs<<"# border " << endl << border <<endl;
afs<<"# Ro " << endl << Ro <<endl;
afs<<"# h " << endl << h <<endl;
afs<<"# m " << endl << m <<endl;
afs<<"# fe " << endl << fe <<endl;
afs<<"# q " << endl << q <<endl;
afs<<"# sigR " << endl << sigR <<endl;
afs<<"# weight at age " << endl << wa <<endl;
afs<<"# fecundity at age " << endl << fa <<endl;
afs<<"# vulnerability at age " << endl << va <<endl;
afs<<"# minPos "<< endl << minPos <<endl;
afs<<"# Total effort by country and year " << endl << TotEffyear <<endl;
afs<<"# Total effort by country and month " << endl << TotEffmonth <<endl;
afs<<"# dMinP " << endl << 0.00001 <<endl;
afs<<"# tstp month area catage " << endl << obsCatchNatAge <<endl;
afs<<"# eof " << endl << 999 <<endl;
}
std::string fuzzy::calc_digest ()
{
fuzzy_state * ctx = fuzzy_new () ;
auto_fuzzy_state afs (ctx) ;
if (ctx == 0)
THROW_XDELTA_EXCEPTION_NO_ERRNO ("Out of memory") ;
char_buffer<uchar_t> buff (BUFLEN);
reader_.open_file () ;
while (true ) {
int bytes = reader_.read_file (buff.begin (), (uint32_t)buff.size ());
if (bytes == 0 )
break ;
if (0 != fuzzy_update (afs.ctx, buff.begin (), bytes))
THROW_XDELTA_EXCEPTION ("fuzzy update failed.") ;
}
char result [FUZZY_MAX_RESULT];
if (0 != fuzzy_digest (afs.ctx, result, FUZZY_FLAG_ELIMSEQ))
THROW_XDELTA_EXCEPTION ("fuzzy digest failed.");
reader_.close_file () ;
return std::string(result) ;
}
void rsamplems::readms (string filename){
ifstream inp (filename.c_str());
if (!inp.is_open()){
cerr << "Error reading file "<< filename <<endl;
exit(1);
}
string line;
int linenum = 0;
int chrindex = 0;
int snpindex = 0;
int nsnp = 0;
double totalw = 0;
ofstream snpfs (snpfile.c_str());
int totalsnps = 0;
vector<int> nsegsites (nsamples,0);
int totalnind = 0 ;
vector<int> nind (nsamples,0);
for (int i = 0 ; i < nsamples; i++) {
nind[i] = samples[i];
totalnind += nind[i];
}
char ** snpmat = new char*[totalnind];
int **freq = new int*[nsamples];
double **td = new double *[nsamples];
double **thetaw = new double *[nsamples];
for (int i = 0 ; i < nsamples; i++) {
td[i] = new double[reps];
thetaw[i] = new double[reps];
}
double abba = 0 ;
double baba = 0 ;
double abba2 = 0 ;
double baba2 = 0 ;
double fstnum = 0;
double fstdenom = 0;
vector<double> chrabba = vector<double>(reps,0);
vector<double> chrbaba = vector<double>(reps,0);
vector<double> chrsnps = vector<double>(reps,0);
vector<double> chrfstnum = vector<double> (reps,0);
vector<double> chrfstdenom = vector<double> (reps,0);
vector<double> chrw = vector<double> (reps,0);
int totalnsnps = 0;
int rep = 0 ;
int index = 0;
string id;
double time;
int countmatches = 0;
while ( std::getline (inp, line)){
linenum ++;
io::println ("line = " + line, 2);
char c = line[0];
if (c=='#')
continue;
if (line.empty())
continue;
if (line.find ("time:") ==0 ) {
vector<string> toks;
functions::tokenize (line, toks, " " );
time = atof (toks[1].c_str());
}
if ( line.find ("segsites:")==0) {
string l1 = line.substr(9,line.length()-9);
nsnp = atoi (l1.c_str());
for (int i = 0 ; i < totalnind ; i++) {
snpmat[i] = new char[nsnp];
}
for (int i = 0 ; i < nsamples; i++){
freq[i] = new int[nsnp];
}
io::println ("SNPs = " + tostring(nsnp),2);
}
if ( line.find ("positions:")==0) {
vector<double> genmap ;
vector<double> physmap;
vector<string> snpids;
vector<vector<int> > geno;
vector<vector<int> > haplo;
vector<int> afs ( samples[0]);
chrindex ++;
string l1 = line.substr(10,line.length()-10);
//cout << "l1 = " << l1 << endl;
//
io::println ("rep = " + tostring(rep),2);
//cout << " rep = " << rep << endl;
rep++;
istringstream ss (line.substr(10,line.length()-10));
int count = 0 ;
while (!ss.eof()){
double pos;
ss>>pos;
// cout << pos << endl;
double ppos = pos * length;
double gpos = ppos * rho;
if (count >= nsnp )
break;
count++;
genmap.push_back (gpos);
physmap.push_back (ppos);
id = "snp" + tostring(index);
snpids.push_back (id);
index++;
}
for (int i = 0 ; i < totalnind ; i ++){
string s1, s2;
std::getline (inp, s1);
for (int j = 0 ; j < nsnp ; j++) {
snpmat[i][j] = s1[j];
}
}
vector<int> nsegsites(nsamples,0);
vector<double> pi(nsamples, 0 );
vector<double> h(nsamples,0);
vector<double> th(nsamples,0);
for (int i = 0, t = 0 ; i < nsamples; i++){
for (int j = 0 ; j < nsnp; j++){
freq[i][j] = frequency('1', j, samples[i], snpmat+t);
nsegsites[i] += (freq[i][j] > 0 && freq[i][j] < 1.0);
}
t += samples[i];
}
chrsnps[rep-1] = nsnp;
totalnsnps += nsnp;
for (int j = 0 ; j < nsnp ; j++) {
if (freq[0][j]> 0)
afs[freq[0][j]-1]++;
}
for (int i = 0 ; i < nsamples; i++)
delete[] freq[i];
for (int i = 0 ; i < totalnind; i++)
delete[] snpmat[i];
if (printsnplist) {
for (int j =0 ; j < nsnp; j++){
snpfs << snpids[j] << "\t" << chrindex << "\t" << genmap[j] << "\t" << physmap[j] << endl;
}
}
int dif = 0;
int denom = 0 ;
for (int j = 0 ; j < afs.size() - 1; j++){
int k = j+1;
cout << k << "\t" << afs[j] << endl;
dif += abs(afs[j]-oafs[j]);
denom += oafs[j];
}
countmatches += (dif==0);
double fracmatch = 1 - ((double)dif)/denom;
cout << "rep = " << rep << "\t" << fracmatch << endl;
} // One set of MS sims
if (io::debug >= 2) {
cout << "Next MS sim " <<endl;
}
}
