static double lnchoosek(T1 n, T2 k)
{
ASSERT(std::cout, n >=0);
ASSERT(std::cout, k >=0);
if(n==k or k==0)
return 0;
else
return lfactorial(n)-lfactorial(k)-lfactorial(n-k);
}
T1 dcompois2(T1 x, T2 mean, T3 nu, int give_log = 0) {
T2 logmean = log(mean);
T2 loglambda = compois_calc_loglambda(logmean, nu);
T1 ans = x * loglambda - nu * lfactorial(x);
ans -= compois_calc_logZ(loglambda, nu);
return ( give_log ? ans : exp(ans) );
}
T1 dcompois(T1 x, T2 mode, T3 nu, int give_log = 0) {
T2 loglambda = nu * log(mode);
T1 ans = x * loglambda - nu * lfactorial(x);
ans -= compois_calc_logZ(loglambda, nu);
return ( give_log ? ans : exp(ans) );
}
float pois_logpmf(int k, float lambda) {
return k * log(lambda) - lambda - lfactorial(k);
}
//function to calculate l[P'(D|M)] for a given distribution of bases
double lPDM_mod_fn(int *z, int ind, double pstar)
{
/*'z' is a pointer to a vector of length 5, where the
first 4 elements correspond to each base (with the consensus
as the fourth element z[3]). The final element is
S-z[3]=sum(z[0:2])
'ind' denotes which model (from 0:9) is to be calculated
'pstar' is the overall mutation rate*/
double lPDM = 0.0;
/* switch(ind)*/
/* {*/
/* //Null p1=p2=p3=p3*/
/* case 0 :lPDM=z[4]*log(pstar/3.0)+z[3]*log(1.0-pstar);*/
/* break;*/
/* //Alt that one free pi is different: e.g. p1!=p2=p3 etc. but mutation rate constrained to p**/
/* case 1 :lPDM=-(z[1]+z[2])*log(2.0)+lfactorial(z[0])+lfactorial(z[1]+z[2])-lfactorial(z[4]+1)+z[4]*log(pstar)+z[3]*log(1.0-pstar);*/
/* break;*/
/* case 2 :lPDM=-(z[0]+z[2])*log(2.0)+lfactorial(z[1])+lfactorial(z[0]+z[2])-lfactorial(z[4]+1)+z[4]*log(pstar)+z[3]*log(1.0-pstar);*/
/* break;*/
/* case 3 :lPDM=-(z[0]+z[1])*log(2.0)+lfactorial(z[2])+lfactorial(z[0]+z[1])-lfactorial(z[4]+1)+z[4]*log(pstar)+z[3]*log(1.0-pstar);*/
/* break;*/
/* //Alt that all pis are different but mutation rate constrained to p**/
/* case 4 :lPDM=log(2.0)+lfactorial(z[0])+lfactorial(z[1])+lfactorial(z[2])-lfactorial(z[4]+2)+z[4]*log(pstar)+z[3]*log(1.0-pstar);*/
/* break;*/
/* //Alt that pis are uniform but not constrained to sum to p**/
/* case 5 :lPDM=-z[4]*log(3.0)+lfactorial(z[4])+lfactorial(z[3])-lfactorial(z[3]+z[4]+1);*/
/* break;*/
/* //Alt that one free pi is different: e.g. p1!=p2=p3 etc.*/
/* case 6 :lPDM=-(z[1]+z[2])*log(2.0)+lfactorial(z[1]+z[2])+lfactorial(z[0])+lfactorial(z[3])-log(z[4]+1)-lfactorial(z[4]+z[3]+1);*/
/* break;*/
/* case 7 :lPDM=-(z[0]+z[2])*log(2.0)+lfactorial(z[0]+z[2])+lfactorial(z[1])+lfactorial(z[3])-log(z[4]+1)-lfactorial(z[4]+z[3]+1);*/
/* break;*/
/* case 8 :lPDM=-(z[0]+z[1])*log(2.0)+lfactorial(z[0]+z[1])+lfactorial(z[2])+lfactorial(z[3])-log(z[4]+1)-lfactorial(z[4]+z[3]+1);*/
/* break;*/
/* //Alt that all pis are different*/
/* case 9 :lPDM=log(2.0)+lfactorial(z[0])+lfactorial(z[1])+lfactorial(z[2])+lfactorial(z[3])-log(z[4]+2)-log(z[4]+1)-lfactorial(z[4]+z[3]+1);*/
/* break;*/
/* }*/
int i;
double z1[5];
for(i=0;i<5;i++) z1[i]=(double) z[i];
switch(ind)
{
//Null p1=p2=p3=p/3 where p<=p*
case 0 :lPDM=-z1[4]*log(3.0)-log(pstar)+pbeta(pstar,z1[4]+1,z1[3]+1,1,1)+lbeta(z1[4]+1,z1[3]+1);
break;
//Alt that one free pi is different: e.g. p1!=p2=p3 etc. but mutation rate constrained to be <= p*
case 1 :lPDM=-(z[1]+z[2])*log(2.0)+lfactorial(z[0])+lfactorial(z[1]+z[2])-lfactorial(z[4]+1)-log(pstar)+pbeta(pstar,z1[4]+1,z1[3]+1,1,1)+lbeta(z1[4]+1,z1[3]+1);
break;
case 2 :lPDM=-(z[0]+z[2])*log(2.0)+lfactorial(z[1])+lfactorial(z[0]+z[2])-lfactorial(z[4]+1)-log(pstar)+pbeta(pstar,z1[4]+1,z1[3]+1,1,1)+lbeta(z1[4]+1,z1[3]+1);
break;
case 3 :lPDM=-(z[0]+z[1])*log(2.0)+lfactorial(z[2])+lfactorial(z[0]+z[1])-lfactorial(z[4]+1)-log(pstar)+pbeta(pstar,z1[4]+1,z1[3]+1,1,1)+lbeta(z1[4]+1,z1[3]+1);
break;
//Alt that all pis are different but mutation rate constrained to be <= p*
case 4 :lPDM=log(2.0)+lfactorial(z[0])+lfactorial(z[1])+lfactorial(z[2])-lfactorial(z[4]+2)-log(pstar)+pbeta(pstar,z1[4]+1,z1[3]+1,1,1)+lbeta(z1[4]+1,z1[3]+1);
break;
//Alt p1=p2=p3=p/3 where p>p*
case 5 :lPDM=-z1[4]*log(3.0)-log(1.0-pstar)+pbeta(pstar,z1[4]+1,z1[3]+1,0,1)+lbeta(z1[4]+1,z1[3]+1);
break;
//Alt that one free pi is different: e.g. p1!=p2=p3 etc. but mutation rate constrained to be > p*
case 6 :lPDM=-(z[1]+z[2])*log(2.0)+lfactorial(z[0])+lfactorial(z[1]+z[2])-lfactorial(z[4]+1)-log(1.0-pstar)+pbeta(pstar,z1[4]+1,z1[3]+1,0,1)+lbeta(z1[4]+1,z1[3]+1);
break;
case 7 :lPDM=-(z[0]+z[2])*log(2.0)+lfactorial(z[1])+lfactorial(z[0]+z[2])-lfactorial(z[4]+1)-log(1.0-pstar)+pbeta(pstar,z1[4]+1,z1[3]+1,0,1)+lbeta(z1[4]+1,z1[3]+1);
break;
case 8 :lPDM=-(z[0]+z[1])*log(2.0)+lfactorial(z[2])+lfactorial(z[0]+z[1])-lfactorial(z[4]+1)-log(1.0-pstar)+pbeta(pstar,z1[4]+1,z1[3]+1,0,1)+lbeta(z1[4]+1,z1[3]+1);
break;
//Alt that all pis are different but mutation rate constrained to be > p*
case 9 :lPDM=log(2.0)+lfactorial(z[0])+lfactorial(z[1])+lfactorial(z[2])-lfactorial(z[4]+2)-log(1.0-pstar)+pbeta(pstar,z1[4]+1,z1[3]+1,0,1)+lbeta(z1[4]+1,z1[3]+1);
break;
}
return lPDM;
}
