/* Function to be called from R */
void R_epidemics(int *seqLength, double *mutRate, int *npop, int *nHostPerPop, double *beta, int *nStart, int *t1, int *t2, int *Nsample, int *Tsample, int *duration, int *nbnb, int *listnb, double *pdisp){
int i, nstep, counter_sample = 0, tabidx;
/* Initialize random number generator */
int j;
time_t t;
t = time(NULL); // time in seconds, used to change the seed of the random generator
gsl_rng * rng;
const gsl_rng_type *typ;
gsl_rng_env_setup();
typ=gsl_rng_default;
rng=gsl_rng_alloc(typ);
gsl_rng_set(rng,t); // changes the seed of the random generator
/* transfer simulation parameters */
struct param * par;
par = (struct param *) malloc(sizeof(struct param));
par->L = *seqLength;
par->mu = *mutRate;
par->muL = par->mu * par->L;
par->rng = rng;
par->npop = *npop;
par->popsizes = nHostPerPop;
par->beta = *beta;
par->nstart = *nStart;
par->t1 = *t1;
par->t2 = *t2;
par->t_sample = Tsample;
par->n_sample = *Nsample;
par->duration = *duration;
par->cn_nb_nb = nbnb;
par->cn_list_nb = listnb;
par->cn_weights = pdisp;
/* check/print parameters */
check_param(par);
print_param(par);
/* dispersal matrix */
struct network *cn = create_network(par);
/* print_network(cn, TRUE); */
/* group sizes */
struct ts_groupsizes * grpsizes = create_ts_groupsizes(par);
/* initiate population */
struct metapopulation * metapop;
metapop = create_metapopulation(par);
/* get sampling schemes (timestep+effectives) */
translate_dates(par);
struct table_int *tabdates = get_table_int(par->t_sample, par->n_sample);
printf("\n\nsampling at timesteps:");
print_table_int(tabdates);
/* create sample */
struct sample ** samplist = (struct sample **) malloc(tabdates->n * sizeof(struct sample *));
struct sample *samp;
/* MAKE METAPOPULATION EVOLVE */
nstep = 0;
while(get_total_nsus(metapop)>0 && (get_total_ninf(metapop)+get_total_nexp(metapop))>0 && nstep<par->duration){
nstep++;
/* age metapopulation */
age_metapopulation(metapop, par);
/* process infections */
for(j=0;j<get_npop(metapop);j++){
process_infections(get_populations(metapop)[j], metapop, cn, par);
}
/* draw samples */
if((tabidx = int_in_vec(nstep, tabdates->items, tabdates->n)) > -1){ /* TRUE if step must be sampled */
samplist[counter_sample++] = draw_sample(metapop, tabdates->times[tabidx], par);
}
fill_ts_groupsizes(grpsizes, metapop, nstep);
}
/* we stopped after 'nstep' steps */
if(nstep < par->duration){
printf("\nEpidemics ended at time %d, before last sampling time (%d).\n", nstep, par->duration);
} else {
/* printf("\n\n-- FINAL METAPOPULATION --"); */
/* print_metapopulation(metapop, FALSE); */
/* merge samples */
samp = merge_samples(samplist, tabdates->n, par);
/* write sample to file */
printf("\n\nWriting sample to file 'out-sample.txt'\n");
write_sample(samp);
/* free memory */
free_sample(samp);
}
/* write group sizes to file */
printf("\n\nPrinting group sizes to file 'out-popsize.txt'\n");
write_ts_groupsizes(grpsizes);
/* free memory */
free_metapopulation(metapop);
free_param(par);
for(i=0;i<counter_sample;i++) free_sample(samplist[i]);
free(samplist);
free_table_int(tabdates);
free_network(cn);
free_ts_groupsizes(grpsizes);
}
int main(int argc, char *argv[])
{
FILE *fp = NULL;
int i;
int modules_loaded;
int dither = 0;
const char *sample_bank_fn = "sample_bank.bin";
struct pimp_sample_bank master_sample_bank;
struct serializer s;
pimp_sample_bank_init(&master_sample_bank);
serializer_init(&s);
modules_loaded = 0;
for (i = 1; i < argc; ++i)
{
const char *arg = argv[i];
if (arg[0] == '-')
{
if (strlen(arg) < 2) print_usage();
switch (arg[1])
{
case 'd':
case 'D':
dither = 1;
break;
default: print_usage();
}
}
else
{
struct pimp_module *mod;
const char *ifn = arg;
struct pimp_sample_bank sample_bank;
pimp_sample_bank_init(&sample_bank);
/* load module */
if (isatty(STDOUT_FILENO)) printf("loading %s...\n", ifn);
mod = load_module(ifn, &sample_bank);
if (NULL != mod)
{
char ofn[256];
modules_loaded++;
/* generate output filename */
strncpy(ofn, ifn, 256);
strncat(ofn, ".bin", 256);
/* dump sample data */
merge_samples(&master_sample_bank, &sample_bank, mod);
/* dump module */
if (isatty(STDOUT_FILENO)) printf("dumping %s...\n", ofn);
dump_module(mod, ofn);
}
}
}
if (0 == modules_loaded)
{
fprintf(stderr, "%s: No input files\n", argv[0]);
exit(EXIT_FAILURE);
}
if (isatty(STDOUT_FILENO)) printf("dumping %s\n", sample_bank_fn);
fp = fopen(sample_bank_fn, "wb");
if (NULL == fp)
{
perror(sample_bank_fn);
exit(EXIT_FAILURE);
}
fwrite(master_sample_bank.data, 1, master_sample_bank.size, fp);
fclose(fp);
fp = NULL;
serializer_deinit(&s);
return 0;
}
/* all-in-one function testing epidemics growth, summary statistics, etc. */
void test_epidemics(int seqLength, double mutRate, int npop, int *nHostPerPop, double beta, int nStart, int t1, int t2, int Nsample, int *Tsample, int duration, int *nbnb, int *listnb, double *pdisp){
int i, j, nstep=0, tabidx, counter_sample = 0;
/* Initialize random number generator */
time_t t;
t = time(NULL); // time in seconds, used to change the seed of the random generator
gsl_rng * rng;
const gsl_rng_type *typ;
gsl_rng_env_setup();
typ=gsl_rng_default;
rng=gsl_rng_alloc(typ);
gsl_rng_set(rng,t); // changes the seed of the random generator
/* transfer simulation parameters */
struct param * par;
par = (struct param *) malloc(sizeof(struct param));
par->L = seqLength;
par->mu = mutRate;
par->muL = par->mu * par->L;
par->rng = rng;
par->npop = npop;
par->npop = npop;
par->popsizes = nHostPerPop;
par->beta = beta;
par->nstart = nStart;
par->t1 = t1;
par->t2 = t2;
par->t_sample = Tsample;
par->n_sample = Nsample;
par->duration = duration;
par->cn_nb_nb = nbnb;
par->cn_list_nb = listnb;
par->cn_weights = pdisp;
/* check/print parameters */
check_param(par);
print_param(par);
/* dispersal matrix */
struct network *cn = create_network(par);
/* group sizes */
struct ts_groupsizes * grpsizes = create_ts_groupsizes(par);
/* initiate population */
struct metapopulation * metapop;
metapop = create_metapopulation(par);
/* get sampling schemes (timestep+effectives) */
translate_dates(par);
struct table_int *tabdates = get_table_int(par->t_sample, par->n_sample);
printf("\n\nsampling at timesteps:");
print_table_int(tabdates);
/* create sample */
struct sample ** samplist = (struct sample **) malloc(tabdates->n * sizeof(struct sample *));
struct sample *samp;
/* MAKE METAPOPULATION EVOLVE */
nstep = 0;
while(get_total_nsus(metapop)>0 && (get_total_ninf(metapop)+get_total_nexp(metapop))>0 && nstep<par->duration){
nstep++;
/* age metapopulation */
age_metapopulation(metapop, par);
/* process infections */
for(j=0;j<get_npop(metapop);j++){
process_infections(get_populations(metapop)[j], metapop, cn, par);
}
/* draw samples */
if((tabidx = int_in_vec(nstep, tabdates->items, tabdates->n)) > -1){ /* TRUE if step must be sampled */
samplist[counter_sample++] = draw_sample(metapop, tabdates->times[tabidx], par);
}
fill_ts_groupsizes(grpsizes, metapop, nstep);
}
/* we stopped after 'nstep' steps */
if(nstep < par->duration){
printf("\nEpidemics ended at time %d, before last sampling time (%d).\n", nstep, par->duration);
} else {
printf("\n\n-- FINAL METAPOPULATION --");
print_metapopulation(metapop, TRUE);
/* test samples */
for(i=0;i<tabdates->n;i++) {
printf("\nsample %d\n", i);
print_sample(samplist[i], TRUE);
}
samp = merge_samples(samplist, tabdates->n, par) ;
print_sample(samp, TRUE);
/* test allele listing */
struct snplist *snpbilan;
snpbilan = list_snps(samp, par);
print_snplist(snpbilan);
/* test allele frequencies */
struct allfreq *freq;
freq = get_frequencies(samp, par);
print_allfreq(freq);
/* test Hs*/
double Hs = hs(samp,par);
printf("\nHs = %0.3f\n", Hs);
/* test Hs full genome */
Hs = hs_full_genome(samp,par);
printf("\nHs (full genome) = %0.5f\n", Hs);
/* test nb of snps */
int nball = nb_snps(samp,par);
printf("\nnumber of SNPs = %d\n", nball);
/* test mean nb of snps */
double temp = mean_nb_snps(samp);
printf("\nmean number of SNPs = %.2f\n", temp);
/* test var nb of snps */
temp = var_nb_snps(samp);
printf("\nvariance of number of alleles = %.2f\n", temp);
/* test pairwise distances */
struct distmat_int *mat = pairwise_dist(samp, par);
print_distmat_int(mat);
/* test mean pairwise distances */
temp = mean_pairwise_dist(samp,par);
printf("\nmean pairwise distance: %.2f", temp);
/* test variance of pairwise distances */
temp = var_pairwise_dist(samp,par);
printf("\nvar pairwise distance: %.2f", temp);
/* test Fst */
temp = fst(samp,par);
printf("\nfst: %.2f", temp);
printf("\n\n");
/* free memory */
free_sample(samp);
free_snplist(snpbilan);
free_allfreq(freq);
free_distmat_int(mat);
}
/* write group sizes to file */
printf("\n\nPrinting group sizes to file 'out-popsize.txt'");
write_ts_groupsizes(grpsizes);
/* free memory */
free_metapopulation(metapop);
free_param(par);
for(i=0;i<counter_sample;i++) free_sample(samplist[i]);
free(samplist);
free_table_int(tabdates);
free_network(cn);
free_ts_groupsizes(grpsizes);
}