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/dports/biology/migrate/migrate-3.6.11/src/
H A Dfst.c90 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()
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H A Daic.c88 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()
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H A Dmigrate_mpi.h115 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);
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H A Dbroyden.c376 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()
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H A Dlrt.c372 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;
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H A Dworld.c229 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()
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H A Dprofile.c170 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()
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H A Dtools.h135 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);
H A Dbayes.c386 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()
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H A Ddata.c160 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()
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H A Duep.c78 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()
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H A Dtools.c1397 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()
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H A Dmigevents.c127 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()
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H A Dskyline.c65 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
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H A Dmcmc1.c469 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()
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H A Dreporter.c390 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()
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H A Dhistogram.c87 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()
H A Dmigrate_mpi.c1607 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;
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H A Dpriors.c266 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()
H A Doptions.c668 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()
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H A Duep.h32 long ****ueprootstore, long numpop, long loci);
35 long numpop, long loci);
63 extern void alloc_uepanc (long ***uepanc, long size, long numpop, long loci);
/dports/biology/recombine/recombine1.41/
H A Dgetmsatdata.c16 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()
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H A Dgetdata.c78 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()
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H A Dgetdata.h12 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);
/dports/biology/migrate/migrate-3.6.11/contribution/
H A Dcombine-sumfiles168 ($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;
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