/* 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); }
/* * Constructor #3 * * The constructor scans the input once and computes * characters probabilities. These probabilities are * used to Huffman-encode run heads. The stream used here * should be the same used in parse(istream& in, ostream& out) * (but it is not necesssary) * * Here Run-heads are Huffman encoded. * */ rle_lz77_v2(istream& in){ auto freqs = get_frequencies(in); RLBWT = rle_bwt(freqs); }