/dports/biology/migrate/migrate-3.6.11/src/ |
H A D | fst.c | 90 long connections = world->numpop * (world->numpop - 1) / 2; in calc_fst() 98 if (world->numpop > 2) in calc_fst() 322 long offset2 = numpop + numpop * (numpop - 1); in solveNm_varm() 323 long offset = numpop; in solveNm_varm() 366 long offset2 = numpop + numpop * (numpop - 1); in solveNm_vartheta() 385 params[numpop] = -999; in solveNm_vartheta() 389 for (i = 1; i < numpop * (numpop - 1); i++) in solveNm_vartheta() 391 params[numpop + i] = params[numpop]; in solveNm_vartheta() 412 long offset2 = numpop + numpop * (numpop - 1); in solveNm_sym() 415 xxx[0] = (MYREAL *) mycalloc (1, sizeof (MYREAL) * numpop * numpop); in solveNm_sym() [all …]
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H A D | aic.c | 88 long i, j, z = numpop; in reshuffle() 90 for (i = 0; i < numpop; i++) in reshuffle() 92 for (j = 0; j < numpop; j++) in reshuffle() 99 pattern[i * numpop + j + space] = ' '; in reshuffle() 335 for (m = nr->numpop; m < nr->numpop2; m++) in fast_aic_score() 367 for (ii = nr->numpop; ii < nr->partsize; ii++) in fast_aic_score() 586 legal_pattern (char *matrix, long numpop) in legal_pattern() argument 596 for (i = 0; i < numpop; i++) in legal_pattern() 602 for (i = numpop; i < numpop * numpop; i++) in legal_pattern() 604 m2mm (i, numpop, &from, &to); in legal_pattern() [all …]
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H A D | migrate_mpi.h | 115 long locus, long maxrep, long numpop); 117 long locus, long maxrep, long numpop); 119 long locus, long maxrep, long numpop); 123 long locus, long maxrep, long numpop); 125 long locus, long maxrep, long numpop); 128 long locus, long maxrep, long numpop); 132 long locus, long maxrep, long numpop); 134 long locus, long maxrep, long numpop); 139 long locus, long maxrep, long numpop); 142 long locus, long maxrep, long numpop); [all …]
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H A D | broyden.c | 376 nr->numpop = world->numpop; in create_nr() 552 const long numpop = nr->world->numpop; in calc_locus_like() local 792 long numpop2 = numpop * numpop; in force_samemigration() 819 long numpop = nr->world->numpop; in param_all_adjust() local 857 if (z < numpop*(numpop-1)) in param_all_adjust() 1030 for (count = numpop; count < numpop * numpop; count++) in check_matrix_arbitrary() 1105 long numpop = nr->numpop; in gradient() local 1203 long numpop = nr->numpop; in gradient_longsum() local 1492 numpop = nr->numpop; in check_symmetric_d() 1505 for (count = numpop; count < numpop * numpop; count++) in check_symmetric_d() [all …]
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H A D | lrt.c | 372 pop = (zi - world->numpop) / (world->numpop - 1); in parse_h0part() 473 long numpop = world->numpop; in set_test_param() local 521 offset = (zi >= world->numpop) ? world->numpop : 0; in set_test_param() 539 offset = (zi >= world->numpop) ? world->numpop : 0; in set_test_param() 541 (zi >= world->numpop) ? world->numpop2 : world->numpop; in set_test_param() 632 zz = (zi - world->numpop) / (world->numpop - 1); in set_test_param() 739 long numpop = world->numpop; 816 offset = (zi >= world->numpop) ? world->numpop : 0; 841 offset = (zi >= world->numpop) ? world->numpop : 0; 843 (zi >= world->numpop) ? world->numpop2 : world->numpop; [all …]
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H A D | world.c | 229 long numpop2 = numpop * numpop; in fill_worldoptions() 488 long numpop2 = numpop * numpop; in fill_worlddata() 582 numpop = data->numpop; in init_world() 591 world->numpop = numpop; in init_world() 592 world->numpop2 = numpop * numpop; in init_world() 916 long numpop = world->numpop; in setup_fluctuate() local 2012 long numpop = world->numpop; in precalc_world() local 2063 long numpop = world->numpop; in reprecalc_world() local 2111 long numpop2 = numpop * numpop; in create_timearchive() 4040 kopie->numpop = original->numpop; in klone() [all …]
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H A D | profile.c | 170 j = (which - world->numpop) % (world->numpop - 1); in choose_profile_parameters() 171 i = (which - world->numpop) / (world->numpop - 1); in choose_profile_parameters() 187 j = (which - world->numpop) % (world->numpop - 1); in choose_profile_parameters() 188 i = (which - world->numpop) / (world->numpop - 1); in choose_profile_parameters() 249 j = (which - world->numpop) % (world->numpop - 1); in print_profile_likelihood_driver() 250 i = (which - world->numpop) / (world->numpop - 1); in print_profile_likelihood_driver() 266 j = (which - world->numpop) % (world->numpop - 1); in print_profile_likelihood_driver() 267 i = (which - world->numpop) / (world->numpop - 1); in print_profile_likelihood_driver() 300 world->numpop * world->numpop; in print_profile_likelihood() 372 1 : world->numpop * world->numpop; in print_profile_table() [all …]
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H A D | tools.h | 135 extern void set_paramstr(char *paramstr, long j, long numpop, boolean usem); 143 extern long mstart (long pop, long numpop); 144 extern long mend (long pop, long numpop); 145 extern long mm2m (long frompop, long topop, long numpop); 146 extern void m2mm (long i, long numpop, long *frompop, long *topop); 147 extern long m2mml (long i, long numpop); 148 extern long m2mml2 (long i, long topop, long numpop); 149 extern long mmstart (long pop, long numpop); 150 extern long mmend (long pop, long numpop); 151 extern long mml2m (long pos, long numpop);
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H A D | bayes.c | 386 const long numpop = world->numpop; in probg_treetimes() local 664 long numpop = world->numpop; in log_prior_uni() local 665 long start = ((numparam <= numpop || numpop==1) ? 0 : numpop); in log_prior_uni() 931 long numpop = world->numpop; in log_prior_mult() local 932 long start = ((numparam <= numpop || numpop==1) ? 0 : numpop); in log_prior_mult() 1025 const long numpop = world->numpop; in calculate_prior() local 1714 long numpop = world->numpop; in bayes_save_parameter() local 3054 long numpop = world->numpop; in print_param_order() local 3308 long numpop2 = numpop * numpop; in print_bayes_credibility() 4301 for(i=numpop;i<numpop*numpop; ++i) in bayes_set_param() [all …]
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H A D | data.c | 160 long numpop = data->numpop; in destroy_data() local 174 for(pop=0; pop < numpop ; pop++) in destroy_data() 220 for(pop=0;pop < data->numpop; pop++) in destroy_data() 256 for(pop=0; pop < data->numpop; pop++) in shuffle_data() 528 long numpop = (*data)->numpop; in init_data_structure1() local 2024 if(pop<data->numpop-1) in print_random_subset() 2909 long numpop2 = numpop * numpop; in read_geofile() 2925 for (i = 0; i < numpop; i++) in read_geofile() 2965 for(pop=0;pop<data->numpop;pop++) in read_date_fromfile() 3000 for(pop=0;pop<data->numpop;pop++) in read_date_fromfile() [all …]
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H A D | uep.c | 78 world->numpop, world->loci); in setup_uep() 242 (*ueplike)[i] = (*ueplike)[0] + i * numpop; in alloc_ueplike() 387 for (pop = 0; pop < world->numpop; pop++) in make_uep_values() 610 for (pop = 0; pop < world->numpop; ++pop) in print_uep() 626 for (pop = 0; pop < world->numpop; ++pop) in print_uep() 642 for (pop = 0; pop < world->numpop; ++pop) in print_uep() 676 for (pop = 0; pop < world->numpop; pop++) in calc_uep_popprob() 737 for (pop = 0; pop < world->numpop; pop++) in calc_uep_timeprob() 794 for (i = 0; i < world->numpop; ++i) in show_uep_store() 846 half = world->numpop * world->data->uepsites; in print_ancestor() [all …]
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H A D | tools.c | 1397 data->numpop = world->numpop; in read_savesum() 3128 return numpop + pop * numpop - pop; in mstart() 3135 return numpop + pop * numpop - pop + numpop - 1; in mend() 3152 return pop * numpop + numpop; in mmend() 3168 return numpop + topop * (numpop - 1) + frompop; in mm2m() 3190 (*topop) = (long) (i - numpop) / (numpop - 1); in m2mm() 3191 (*frompop) = i - numpop - (*topop) * (numpop - 1); in m2mm() 3211 topop = (long) (i - numpop) / (numpop - 1); in m2mml() 3212 frompop = i - numpop - (topop) * (numpop - 1); in m2mml() 3244 frompop = i - numpop - (topop) * (numpop - 1); in m2mml2() [all …]
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H A D | migevents.c | 127 const long endpop = (mrca ? world->numpop : numpop2); in print_mighist_output() 289 …for (pop = (world->options->mighist_all ? 0 : world->numpop); pop < (mrca ? world->numpop : world… in print_mighist_output() 294 m2mm(pop,world->numpop,&frompop,&topop); in print_mighist_output() 367 pop = mm2m(from, to, numpop); in calculate_event_values() 455 long numpop2 = numpop * numpop; in print_event_values_list() 461 if(pop < numpop) in print_event_values_list() 467 m2mm(pop,numpop,&frompop,&topop); in print_event_values_list() 552 long numpop = world->numpop; in print_event_values_tofile() local 570 if(pop < numpop) in print_event_values_tofile() 576 m2mm(pop,numpop,&frompop,&topop); in print_event_values_tofile() [all …]
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H A D | skyline.c | 65 long numpop) in waiting_theta() argument 70 for(i=0;i<numpop; i++) in waiting_theta() 92 long numpop, in waiting_M() argument 100 for(i=0;i<numpop; i++) in waiting_M() 233 long numpop, in calculate_expected_values() argument 295 pop = mm2m(from, to, numpop); in calculate_expected_values() 425 long numpop2 = numpop * numpop; in print_expected_values_list() 431 if(pop < numpop) in print_expected_values_list() 437 m2mm(pop,numpop,&frompop,&topop); in print_expected_values_list() 527 long numpop = world->numpop; in print_expected_values_tofile() local [all …]
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H A D | mcmc1.c | 469 allocate_lineages (ntl, 0, numpop); in new_localtimelist() 490 allocate_lineages (ntl, 0, numpop); in new_localtimelist_new() 514 (*proposal)->numpop = world->numpop; in new_proposal() 607 (*proposal)->numpop = world->numpop; in set_new_proposal() 844 for(jj = 1;jj < proposal->numpop; jj++) in construct_localtimelist() 1029 long numpop = proposal->numpop; in migrate() local 1032 if (i > MIGRATION_LIMIT * numpop || numpop < 2) in migrate() 1042 if(tmp < numpop) in migrate() 1183 msta = mstart (to, proposal->numpop); in migration_from_old() 1184 msto = mend (to, proposal->numpop); in migration_from_old() [all …]
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H A D | reporter.c | 390 long numpop = world->numpop; in print_bayes_ess() local 417 if(pa0 < numpop) in print_bayes_ess() 972 long numpop = world->numpop; in calc_s() local 982 startkm = numpop; in calc_s() 984 startl = startp + numpop; in calc_s() 1045 long numpop = world->numpop; in calc_s2() local 1055 startkm = numpop; in calc_s2() 1057 startl = startp + numpop; in calc_s2() 1148 long numpop = world->numpop; in chain_means_ml() local 1149 long numpop2 = numpop * numpop; in chain_means_ml() [all …]
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H A D | histogram.c | 87 sscanf (input+3, "%li %li %li %li %li %i", &world->loci, &world->numpop, in read_from_bayesmdim_minimal_info() 90 printf("%i> numpop = %li\n",myID, world->numpop); in read_from_bayesmdim_minimal_info() 96 data->numpop = world->numpop; in read_from_bayesmdim_minimal_info() 97 options->newpops_numpop = world->numpop; in read_from_bayesmdim_minimal_info() 104 data->popnames = (char **) mymalloc (sizeof (char *) * world->numpop); in read_from_bayesmdim_minimal_info() 105 for (pop = 0; pop < world->numpop; pop++) in read_from_bayesmdim_minimal_info() 124 data->numpop = world->numpop; in read_from_bayesmdim_minimal_info() 134 for(i = 0; i < world->numpop; i++) in get_fullbinsum() 140 for(i = world->numpop; i < world->numpop2; i++) in get_fullbinsum()
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H A D | migrate_mpi.c | 1607 for (pop = 0; pop < data->numpop * data->numpop; pop++) in pack_databuffer() 1898 for (i = 0; i < data->numpop * data->numpop; i++) in unpack_databuffer() 1912 for (pop = 0; pop < data->numpop * data->numpop; pop++) in unpack_databuffer() 2544 const long np2 = numpop * numpop; in unpack_skyline_buffer() 3271 long numpop2plus = numpop * numpop + 2 * numpop; in unpack_single_sumfile_buffer() 3306 long numpop2 = numpop * numpop; in pack_single_sumfile_buffer() 3352 long numpop2 = numpop * numpop; in pack_sumfile_buffer() 3393 long numpop = world->numpop; in mpi_results_master() local 3451 long numpop = world->numpop; in mpi_results_worker() local 4647 long numpop = world->numpop; [all …]
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H A D | priors.c | 266 long numpop = world->numpop; in log_prior_gamma() local 267 long start = ((numparam <= numpop || numpop==1) ? 0 : numpop); in log_prior_gamma() 268 long stop = ((start == numpop) ? world->numpop2 : numpop); in log_prior_gamma() 351 world->numpop=1; in main()
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H A D | options.c | 668 if (options->numpop > data->numpop) in print_menu_options() 822 if(world->numpop > 1) in print_options() 848 if(world->numpop > 1) in print_options() 1445 long numpop = world->numpop; in set_mig_ownstart() local 1453 if ((iitest = mm2m (j, i, numpop) - numpop) < options->nummg) in set_mig_ownstart() 1463 iitest += numpop; in set_mig_ownstart() 1501 1.0 / world->param0[(i - world->numpop) / (world->numpop)]; in set_mig_fststart() 6015 z = numpop; in read_custom_migration() 6109 z = numpop; in read_custom_migration_worker() 6223 z = world->numpop; in fillup_custm() [all …]
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H A D | uep.h | 32 long ****ueprootstore, long numpop, long loci); 35 long numpop, long loci); 63 extern void alloc_uepanc (long ***uepanc, long size, long numpop, long loci);
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/dports/biology/recombine/recombine1.41/ |
H A D | getmsatdata.c | 16 void setupmsatdata(msatdata **ms, long numpop, long numloci, in setupmsatdata() argument 24 (*ms)->popnames = (char **)calloc(numpop,sizeof(char *)); in setupmsatdata() 26 for(i = 1; i < numpop; i++) in setupmsatdata() 29 (*ms)->numpop = numpop; in setupmsatdata() 32 (*ms)->numind = (long *)calloc(numpop,sizeof(long)); in setupmsatdata() 33 for(i = 0; i < numpop; i++) (*ms)->numind[i] = numind; in setupmsatdata() 35 (*ms)->msats = (long ****)calloc(numpop,sizeof(long ***)); in setupmsatdata() 42 for(i = 1; i < numpop; i++) { in setupmsatdata() 49 (long **)calloc(numpop*numind*numloci,sizeof(long *)); in setupmsatdata() 52 for(i = 0; i < numpop; i++) in setupmsatdata() [all …]
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H A D | getdata.c | 78 return(data->msptr->numpop); in getdata_numpop() 82 return(data->dnaptr->numpop); in getdata_numpop() 778 long numloci, long numpop) in setupdnadata() argument 787 for(i = 1; i < numpop; i++) in setupdnadata() 790 (*dna)->numpop = numpop; in setupdnadata() 819 for(i = 1; i < numpop; i++) { in setupdnadata() 833 for(i = 0; i < numpop; i++) in setupdnadata() 843 for(i = 0; i < numpop; i++) in setupdnadata() 856 for(i = 0; i < numpop; i++) in setupdnadata() 920 numpop = getdata_numpop(op,data); in printdnadata() [all …]
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H A D | getdata.h | 12 void setupdata(data_fmt *data, char datatype, long numpop, long numloci, 48 long numpop); 61 void readtruehaps(option_struct *op, data_fmt *hap, long numpop, long 64 long numpop, long numloci, long numind, long *numsites);
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/dports/biology/migrate/migrate-3.6.11/contribution/ |
H A D | combine-sumfiles | 168 ($loci, $numpop, $replicates, $replicatenum, 178 $numpop2 = $numpop * $numpop; 184 printf SUMFILE "$loci $numpop $numpop2 1 $replicatenum\n"; 248 ($loci, $numpop, $replicates, $replicatenum, 258 $numpop2 = $numpop * $numpop; 319 ($loci, $numpop, $replicates, $replicatenum, 324 $numpop2 = $numpop * $numpop; 380 ($loci, $numpop, $replicates, $replicatenum, 383 $numpop2 = $numpop * $numpop; 444 print "N-pop " . $numpop; [all …]
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