void main(int argc,char **argv)
{ int i,j,n,dist,c;
double density,r;
long seed=0;
short **con;
short *labeled;
if((argc != 3 && argc != 5) || (density=atof(argv[2])) >1 || density < 0 ||
(n=atoi(argv[1])) <= 1){
fprintf(stderr,"USAGE: %s <number of nodes> <density> [-R <rand seed>]\n"
"Density is a fraction in (0,1] giving the proability of any of\n"
"the n*(n-1)/2 possible edges being in the graph\n"
"OUTPUT table of numbers representing lower triangular matrix\n"
"of a distance matrix for a set of n nodes with costs in 1--1000\n"
"Disconnected nodes have a cost of n*1000\n",
argv[0]);
exit(1);
}
if(argc == 5){
seed = atol(argv[1]);
seed_all(seed);
}else
seed = seed_time(); /* initialise random number generator */
con = (short **)malloc(n * sizeof(short *));
labeled = (short *)malloc(n * sizeof(short));
do{ /* keep generating until a connected graph exists */
for(i=0;i<n;i++) labeled[i] = FALSE;
labeled[n-1] = TRUE;
for(i=n-1;i>0;i--){
con[i] = (short *)malloc(i * sizeof(short));
for(j=0;j<i;j++){
r = rand2();
con[i][j] = (r < density); /* nodes i & j connected */
if(labeled[i] && con[i][j]) labeled[j] = TRUE;
if(labeled[j] && con[i][j]) labeled[i] = TRUE;
}
}
do{ /* check if there are any other reachable unlabeled nodes */
c = FALSE;
for(i=0;i<n;i++)
for(j=0;j<i;j++)
if(con[i][j]){
if(!labeled[i] && labeled[j]) c = labeled[i] = TRUE;
if(labeled[i] && !labeled[j]) c = labeled[j] = TRUE;
}
}while(c);
c=TRUE; /* connected */
for(i=0;i<n;i++) c = (c && labeled[i]);
}while(!c); /* try again if graph is not connected */
for(i=0;i<n;i++){
for(j=0;j<i;j++)
printf("%d%c",((con[i][j]) ? irand2(999)+1 : (n*1000)),
( ((j+1)%10) ? ' ' : '\n'));
printf("\n");
}
}
void main(int argc,char **argv)
{ int i,n;
if(argc != 2 || (n=atoi(argv[1])) <= 1){
fprintf(stderr,"USAGE: %s <number of nodes>\n"
"OUTPUT: table of numbers representing lower triangular matrix\n"
"of a totaly random distance matrix.\n",argv[0]);
exit(1);
}
seed_time();
for(i=0;i<n*(n-1)/2;i++)
printf("%d%c",irand2(500)+1,( (i%10) ? ' ' : '\n'));
}
size_t select_random(size_t lo, size_t hi)
{
static bool first = true;
if (first) {
// This is a copy of the way GalSim seeds its random number generator using urandom first,
// and then if that fails, using the time.
// Except we just use this to seed the std rand function, not a boost rng.
// Should be fine for this purpose.
try {
seed_urandom();
} catch(...) {
seed_time();
}
first = false;
}
if (lo == hi) {
return lo;
} else {
size_t mid = int((rand() / RAND_MAX) * (hi-lo+1)) + lo;
if (mid > hi) mid = hi; // Just in case rand() == RAND_MAX
return mid;
}
}
int main (int argc, char **argv)
{
// Default simulation parameters
char filename[100] = "";
double Tmax = 10000; // length of simulation
double Tsample = 1000; // time of first sample (and intervals)
int sampleSize = 10; // number of seqs sampled
double dt = 1.0; // time-step
// Default epidemiological parameters
int hostPopSize = 10000;
int N0 = 10; // initial viral pop size
double gamma = 0.1; // decay of immunity
double beta = 0.5; // transmission rate
double delta = 0.1; // recovery rate
// Default sequence parameters
double kappa = 3.0;
double mut_rate = 1e-5;
int Ld = 0;
int Lb = 2;
double sb = 0.01;
double sd = 1e-3;
double sigma = 1.0;
// User-specified arguments
int opt_char;
while ((opt_char = getopt(argc, argv, "ho:T:S:Z:t:H:N:g:b:d:L:u:k:l:a:s:c:")) != -1)
{
switch (opt_char)
{
case 'h':
printf("%s\n", helpStr);
exit(0);
break;
case 'o':
strcpy(filename, optarg);
break;
case 'T':
if ((Tmax = strtod(optarg, NULL)) <= 0.0)
{
fprintf (stderr, "Invalid -T parameter: %s\n", optarg);
exit(1);
}
break;
case 'S':
if ((Tsample = strtod(optarg, NULL)) <= 0.0)
{
fprintf (stderr, "Invalid -S parameter: %s\n", optarg);
exit(1);
}
break;
case 'Z':
sampleSize = atoi(optarg);
break;
case 't':
if ((dt = strtod(optarg, NULL)) <= 0.0)
{
fprintf (stderr, "Invalid -t parameter: %s\n", optarg);
exit(1);
}
break;
case 'N':
if ((N0 = atoi(optarg)) <= 0)
{
fprintf (stderr, "Invalid -N parameter: %s\n", optarg);
exit(1);
}
break;
case 'H':
if ((hostPopSize = atoi(optarg)) <= 0)
{
fprintf (stderr, "Invalid -H parameter: %s\n", optarg);
exit(1);
}
break;
case 'g':
if ((gamma = strtod(optarg, NULL)) < 0.0)
{
fprintf (stderr, "Invalid -g parameter: %s\n", optarg);
exit(1);
}
break;
case 'b':
if ((beta = strtod(optarg, NULL)) <= 0.0)
{
fprintf (stderr, "Invalid -b parameter: %s\n", optarg);
exit(1);
}
break;
case 'd':
if ((delta = strtod(optarg, NULL)) <= 0.0)
{
fprintf (stderr, "Invalid -d parameter: %s\n", optarg);
exit(1);
}
break;
case 'L':
if ((Ld = atoi(optarg)) < 0)
{
fprintf (stderr, "Invalid -L parameter: %s\n", optarg);
exit(1);
}
break;
case 'u':
if ((mut_rate = strtod(optarg, NULL)) < 0.0)
{
fprintf (stderr, "Invalid -u parameter: %s\n", optarg);
exit(1);
}
break;
case 'k':
if ((kappa = strtod(optarg, NULL)) < 0.0)
{
fprintf (stderr, "Invalid -k parameter: %s\n", optarg);
exit(1);
}
break;
case 'l':
if ((Lb = atoi(optarg)) < 0)
{
fprintf (stderr, "Invalid -l parameter: %s\n", optarg);
exit(1);
}
break;
case 'a':
sb = strtod(optarg, NULL);
break;
case 's':
sd = strtod(optarg, NULL);
break;
case 'c':
if ((sigma = strtod(optarg, NULL)) < 0.0)
{
fprintf (stderr, "Invalid -c parameter: %s\n", optarg);
exit(1);
}
break;
case '?':
fprintf (stderr, "Unrecognized argument\n");
exit(1);
}
}
if (filename[0] == '\0')
{
fprintf (stderr, "Output filename (option -o) must be specified\n");
exit(1);
}
FILE *outfile;
if ((outfile = fopen(filename, "w")) == NULL)
{
fprintf (stderr, "Cannot open %s\n", filename);
exit(1);
}
seed_time();
codonString::init_trans_matrix (kappa);
codonString viralPop(N0, Lb, Ld, sb, sd, sigma);
double t = 0.0;
int N = 0;
while ((N = viralPop.popSize()) > 0 && t < Tmax)
{
viralPop.mutate(mut_rate * dt);
viralPop.transmit(beta * dt, hostPopSize);
viralPop.recover(rbinom(N, delta * dt));
if (gamma > 0)
viralPop.immuneDecay(gamma * dt);
if (fmod(t, Tsample) < 1e-4)
viralPop.printSample(outfile, t, sampleSize);
t += dt;
}
fclose(outfile);
}
