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enumerate.c
186 lines (167 loc) · 4.57 KB
/
enumerate.c
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#include <stdio.h>
#include <math.h>
#include <stddef.h>
#include <stdlib.h>
#include <time.h>
#define min(x, y) (((x) < (y)) ? x : y)
#define RLIM 200 /* maximum sample size */
#define KLIMIT 40 /* maximum number of alleles */
int r_obs[KLIMIT]; /* observed configuration */
int r[KLIMIT]; /* sample configuration */
int k; /* number of allelic classes */
int r_tot; /* number of copies sampled= n */
int r_top; /* highest value of r[i] */
int alpha[RLIM]; /* here so it will be set to zero */
double tot_sum; /* sum of all coefficients */
double sig_sum; /* sum of significant coefficients */
double F_sig_sum; /* sum for significant F values */
double F_obs; /* homozygosity observed
*/
double obs_value; /* coefficient for r_obs */
long double factors[RLIM]; /* contains factorials */
int Fsig, Esig;
int main(int argc, char *argv[]) {
int i;
void config(int rt, int rmax, int ic);
double ewens_form(int *r, int r_tot, double *mpt);
double F(int *r), multiplicity;
double theta_est(int k_obs, int n);
void print_config(int *r);
long start_time, finish_time, net_time;
void fill_factors();
start_time = time(NULL);
if (argc == 1) {
printf("Specify the configuration on the command line\n");
exit(0);
}
k = argc - 1;
for (i=1; i<=k; i++) {
r_obs[i] = atoi(argv[i]);
r_tot += r_obs[i];
}
F_obs = F(r_obs);
printf("\nn = %d, k = %d, theta = %g, F = %g\n",
r_tot, k, theta_est(k, r_tot), F_obs);
if (r_tot >= RLIM) {
printf("n = %d is too large..\n", r_tot);
exit(0);
}
if (k >= KLIMIT) {
printf("k = %d is too large.\n", k);
exit(0);
}
for (i=1;
i<k; i++)
if (r_obs[i] < r_obs[i+1]) {
print_config(r_obs);
printf(" is not a valid configuration.\n");
exit(0);
}
r_top = r_tot - 1;
Fsig = Esig = 0;
fill_factors();
obs_value = ewens_form(r_obs, r_obs[1], &multiplicity);
config(r_tot, r_tot-k+1, 1);
print_config(r_obs);
printf(": P_E = %g, ", sig_sum / tot_sum);
printf("P_H = %g\n", F_sig_sum / tot_sum);
finish_time = time(NULL);
net_time = time(NULL) - start_time;
if (net_time < 60)
printf("Program took %ld seconds\n", net_time);
else
printf("Program took %4.2f minutes\n", net_time / 60.0);
return 0;
} /* end, main */
void config(int rt, int rmax, int ic) {
int r1, i;
double ewens_form(int *r, int r_top, double *mpt), test_value;
double F(int *r), F_test, multiplicity;
void print_config(int *r);
if (ic == k - 1)
for (i=min(rmax,rt-1); i>=((rt%2)?(rt+1)/2:rt/2); i--) {
r[ic] = i;
r[ic+1] = rt - i;
test_value = ewens_form(r, r_top, &multiplicity);
tot_sum += multiplicity * test_value;
F_test = F(r);
if (test_value <= obs_value)
sig_sum += multiplicity * test_value;
if (F_test <= F_obs)
F_sig_sum += multiplicity * test_value;
}
else {
for(r1=((rt%k)?rt/k+1:rt/k);r1<=(min(rmax,rt-k+ic+1));r1++) {
if (ic == 1)
r_top = r1;
r[ic] = r1;
config(rt-r1, r1, ic+1);
}
}
} /* end, config */
void fill_factors() {
int i;
factors[0] = 1.0;
for(i=1; i<=r_tot; i++)
factors[i] = i * factors[i-1];
}
void print_config(int *r) {
int i;
printf("(");
for (i=1; i<k; i++)
printf("%d,", r[i]);
printf("%d)", r[k]);
} /* end, print_config */
double ewens_form(int *r, int r_top, double *mpt) {
int i;
void print_alpha(int a[RLIM], int r_top);
double coef;
for (i=1; i<=r_top; i++)
alpha[i] = 0;
for(i=1; i<=k; i++)
alpha[r[i]]++;
coef = 1.0;
*mpt = factors[r_tot];
for (i=1; i<=r_top; i++)
if (alpha[i]) {
coef *= 1.0 / pow(i, alpha[i]);
*mpt /= factors[alpha[i]];
}
return coef;
} /* end, ewens_form */
double F(int *r) {
int i;
double sum;
sum = 0.0;
for (i=1; i<=k; i++) sum += r[i] * r[i];
return sum / (r_tot * r_tot);
}
double theta_est(int k_obs, int n) {
/* Estimates theta = 4N*mu using formula 9.26 in Ewens' book */
double kval(double theta, int n);
double xlow, xhigh, xmid;
double eps;
eps = 0.00001;
xlow = 0.1;
while (kval(xlow, n) > k_obs)
xlow /= 10.0;
xhigh = 10.0;
while (kval(xhigh, n) < k_obs)
xhigh *= 10.0;
while ((xhigh - xlow) > eps) {
xmid = (xhigh + xlow) / 2.0;
if (kval(xmid, n) > k_obs)
xhigh = xmid;
else
xlow = xmid;
}
return xmid;
} /* end, theta_est */
double kval(double x, int n) {
int i;
double sum;
sum = 0.0;
for (i=0; i<n; i++)
sum += x / (i + x);
return sum;
}