//sfs input is here the untransformed, e.g length=dim
void bfgs(double *sfs,Matrix<double> *GL1){
double p[dim-1];
for(int i=1;i<dim;i++)
p[i-1] = sfs[i]/sfs[0];
//initialize the stuff needed for the bfgs
double para[dim-1]; /* parameters */
double min[dim-1]; /* lower bound */
double max[dim-1]; /* upper bound */
int nbd[dim-1]; /* boundary constraint option; nbd[i] = 0 or 1 or 2 or 3; see bfgs.h for details */
int noisy=-1; /* bigger value produces more detailed output */
for (int i=0; i<dim-1; i++){
min[i] = 0.0000001;
max[i] = 10.0;
nbd[i] = 2;
}
double fnmax ;
if(noGrad==0)
fnmax= findmax_bfgs( dim-1, p,NULL, lik1_bfgs, lik1_grad_bfgs_master, min, max, nbd, noisy );
else
fnmax= findmax_bfgs( dim-1, p,NULL, lik1_bfgs,NULL, min, max, nbd, noisy );
//tranform back
double ts=1;
for(int i=0;i<dim-1;i++)
ts += p[i];
sfs[0]=1.0/ts;
for(int i=0;i<dim-1;i++)
sfs[i+1]=p[i]/ts;
}
double frequency::likeNoFixedMinor_bfgs(double *loglikes,int numInds,int major){
bfgs_vars bv;
bv.loglikes = loglikes;
bv.numInds = numInds;
bv.major=major;
bv.indF=indF;
double start[1] = {0.01};
double lbound[1] = {0};
double ubound[1] = {1};
int lims[1] = {2};
double res=findmax_bfgs(1,start,(void*) &bv,likeNoFixedMinor_wrapper,NULL,lbound,ubound,lims,-1);
//fprintf(stderr,"%f\n",res);
//fprintf(stderr,"%s\t like %f isoptim is: %f\n",__FUNCTION__,res,start[0]);
return start[0];
}
double run_optim_full_calcA2(const genome &g,const std::vector<perChr>&pc,para&p){
toOptim2 *to = new toOptim2(g,pc);
double tsk[4];//tmparray used of saving stackpointers
to->tsk = tsk;
double pars[2]; pars[0]=myRand(0,1);pars[1]=myRand(0,1-pars[0]);
//fix last pars
double lbd[2]={0.000001,0.000001};
double ubd[2]={0.999999,0.999999};
int nbd[2]={2,2};
double opt= -findmax_bfgs(2,pars,(void *)to, bfgs_call_full_calcA2,NULL,lbd, ubd,nbd, -1);
p.k0=pars[0];
p.k1=pars[1];
p.k2=1-pars[0]-pars[1];
p.a=calculateA(p.k0,p.k1,p.k2,PHI);
return opt;
}
double run_optim_k2zero_calcA2(const genome &g,const std::vector<perChr>&pc,para&p){
toOptim2 *to = new toOptim2(g,pc);
double tsk[4];//tmparray used of saving stackpointers
to->tsk = tsk;
double pars[1]={myRand(0,1)};
// fprintf(stderr,"pars=%f\n",pars[0]);
double lbd[1]={0.000001};
double ubd[1]={0.999999};
int nbd[1]={2};
double opt= -findmax_bfgs(1,pars,(void *)to, bfgs_call_k2zero_calcA2,NULL,lbd, ubd,nbd, -1);
p.k0=pars[0];
p.k1=1-p.k0;
p.k2=0;
p.a=calculateA(p.k0,p.k1,p.k2,PHI);
return opt;
}
double frequency::likeFixedMinor_bfgs(double *loglikes,int numInds){
bfgs_vars *bv = new bfgs_vars;
bv->loglikes = loglikes;
bv->numInds = numInds;
bv->indF = indF;
double start[1] = {0.01};
double lbound[1] = {0};
double ubound[1] = {1};
int lims[1] = {2};
double res=findmax_bfgs(1,start,bv,&likeFixedMinor_wrapper,NULL,lbound,ubound,lims,-1);
//fprintf(stderr,"%s\t like %f isoptim is: %f\n",__FUNCTION__,res,start[0]);
delete bv;
return start[0];
}
double run_optim_full2(const genome &g,const std::vector<perChr>&pc,para&p){
toOptim2 *to = new toOptim2(g,pc);
double tsk[4];//tmparray used of saving stackpointers
to->tsk = tsk;
double pars[3];pars[0]=myRand(alim[0],alim[1]); pars[1]=myRand(0,1);pars[2]=myRand(0,1-pars[1]);
//double pars[3];pars[0]=myRand(alim[0],alim[1]); pars[1]=myRand(0,1);pars[2]=1-pars[1];pars[2]=0;
// double pars[3]={0.045854, 0.823746,0.176254};
//fix last pars
double lbd[3]={alim[0],0.000001,0.000001};
double ubd[3]={alim[1],0.999999,0.999999};
int nbd[3]={2,2,2};
double opt= -findmax_bfgs(3,pars,(void *)to, bfgs_call_full2,NULL,lbd, ubd,nbd, -1);
p.a=pars[0];
p.k0=pars[1];
p.k1=pars[2];
p.k2=1-pars[1]-pars[2];
return opt;
}
