/dports/biology/migrate/migrate-3.6.11/src/ |
H A D | slice.c | 95 oldparam = world->options->mu_rates[world->locus]; in set_slice_param() 96 world->options->mu_rates[world->locus] = newparam; in set_slice_param() 98 recalc_timelist(world, world->options->mu_rates[world->locus] , oldparam); in set_slice_param() 112 oldparam = world->options->mu_rates[world->locus]; in set_multi_slice_param() 113 world->options->mu_rates[world->locus] = newparam[numpop2]; in set_multi_slice_param() 114 recalc_timelist(world, world->options->mu_rates[world->locus] , oldparam); in set_multi_slice_param() 538 newstartval[world->numpop2] = world->options->mu_rates[world->locus]; in expallslice()
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H A D | bayes.c | 422 const MYREAL mu_rate = world->options->mu_rates[locus]; in probg_treetimes() 678 mu = world->options->mu_rates[world->locus]; in log_prior_uni() 947 mu = world->options->mu_rates[world->locus]; in log_prior_mult() 1335 const MYREAL murate = world->options->mu_rates[world->locus]; in uniform_proposal() 1409 world->options->mu_rates[world->locus] = newparam; in uniform_proposal() 1554 const MYREAL murate = world->options->mu_rates[world->locus]; in bayes_update() 1674 recalc_timelist(world, oldparam[which], world->options->mu_rates[world->locus]); in bayes_update() 1683 world->options->mu_rates[world->locus] = oldparam[numpop2]; in bayes_update() 1719 MYREAL murate = world->options->mu_rates[world->locus]; in bayes_save_parameter() 2257 world->options->mu_rates[locus] = options->bayespriorrate->mean; in bayes_fill() [all …]
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H A D | combroyden2.c | 320 MYREAL *mu_rates = world->options->mu_rates; in calc_loci_like() local 340 calc_locus_like (nr, param, lparam, locus) + mu_rates[locus]; in calc_loci_like() 365 MYREAL *mu_rates = world->options->mu_rates; in slow_net_calc_loci_like() local 377 calc_locus_like (nr, param, lparam, locus) + mu_rates[locus]; in slow_net_calc_loci_like()
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H A D | reporter.c | 640 x = world->options->mu_rates[world->locus]; in single_chain_var() 677 x = (double) world->options->mu_rates[world->locus]; in single_chain_var() 773 x = world->options->mu_rates[locus]; in calculate_ess_frombayes() 810 x = (double) world->options->mu_rates[locus]; in calculate_ess_frombayes()
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H A D | menu.c | 2126 options->mu_rates = in menuParameters() 2127 (MYREAL *) myrealloc(options->mu_rates, in menuParameters() 2136 options->mu_rates[count] = atof(temp); in menuParameters() 2137 sum += options->mu_rates[count]; in menuParameters() 2141 options->mu_rates[i] = options->mu_rates[count - 1]; in menuParameters() 2142 sum += options->mu_rates[count]; in menuParameters() 2146 options->mu_rates[i] /= sum; in menuParameters()
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H A D | world.c | 238 if(options->mu_rates == NULL) in fill_worldoptions() 239 options->mu_rates = (MYREAL *) mycalloc (options->muloci, sizeof (MYREAL)); in fill_worldoptions() 265 if(wopt->mu_rates == NULL) in fill_worldoptions() 267 wopt->mu_rates = (MYREAL *) mycalloc (2 * options->muloci, sizeof (MYREAL)); in fill_worldoptions() 269 wopt->lmu_rates = wopt->mu_rates + options->muloci; in fill_worldoptions() 287 if(options->mu_rates[i] <= 0.0) in fill_worldoptions() 289 wopt->mu_rates[i] = 1.0; in fill_worldoptions() 294 wopt->mu_rates[i] = options->mu_rates[i]; in fill_worldoptions() 295 wopt->lmu_rates[i] = log(options->mu_rates[i]); in fill_worldoptions() 1598 if(world->options->mu_rates!=NULL) in free_world() [all …]
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H A D | data.c | 399 options->mu_rates[locus] = 1.0; in get_new_data() 514 options->mu_rates[locus] = 1.0; in get_data() 2794 if(options->mu_rates==NULL) in create_alleles() 2796 options->mu_rates = (MYREAL * ) mycalloc(data->loci,sizeof(MYREAL)); in create_alleles() 2799 options->mu_rates[locus] = z+1; in create_alleles() 2801 delta = options->mu_rates[locus] - mean; in create_alleles() 2811 options->mu_rates[locus] /= mean; in create_alleles()
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H A D | sequence.c | 2039 if(options->mu_rates == NULL) in find_rates_fromdata() 2041 options->mu_rates = (MYREAL *) mycalloc( loci, sizeof(MYREAL)); in find_rates_fromdata() 2086 … options->mu_rates[locus] = (options->wattersons[locus] + 0.0000001)/data->seq[0]->sites[locus]; in find_rates_fromdata() 2090 delta = options->mu_rates[locus] - mean; in find_rates_fromdata() 2097 options->mu_rates[locus] /= mean; in find_rates_fromdata() 2117 options->segregs[locus] = (long) (options->mu_rates[locus] * mean + 0.5); in find_rates_fromdata_alleles()
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H A D | migration.h | 580 MYREAL *mu_rates; member 887 MYREAL *mu_rates; member
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H A D | options.c | 342 options->mu_rates = NULL; in init_options() 1021 fprintf (file, "%.3f, ", options->mu_rates[i]); in print_options() 1025 fprintf (file, "%.3f\n", options->mu_rates[i]); in print_options() 2048 myfree(options->mu_rates); in destroy_options() 3405 sprintf (fp, "%f ", options->mu_rates[i]); in save_options_buffer() 4506 options->mu_rates = in numbercheck() 4516 options->mu_rates[i] = lastrate; in numbercheck() 4517 musum += options->mu_rates[i]; in numbercheck() 4521 lastrate = options->mu_rates[i] = atof (temp); in numbercheck() 4522 musum += options->mu_rates[i]; in numbercheck() [all …]
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H A D | broyden.c | 569 const MYREAL mu_rate = nr->world->options->mu_rates[locus]; in calc_locus_like() 1114 MYREAL mu_rate = nr->world->options->mu_rates[locus]; in gradient() 1219 MYREAL mu_rate = nr->world->options->mu_rates[locus]; in gradient_longsum() 1617 MYREAL mu_rate = nr->world->options->mu_rates[locus]; in probG() 1697 MYREAL mu_rate = nr->world->options->mu_rates[locus]; in probG_longsum()
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H A D | mcmc1.c | 1366 MYREAL rate = proposal->world->options->mu_rates[proposal->world->locus]; in pre_population() 1861 MYREAL rate = proposal->world->options->mu_rates[proposal->world->locus]; in eventtime() 1949 const MYREAL mu_rate = world->options->mu_rates[world->locus]; in prob_tree()
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H A D | migrate_mpi.c | 861 MYREAL *mu_rates = world->options->mu_rates; in mpi_likelihood_worker() local 881 calc_locus_like (nr, param, lparam, locus) + mu_rates[locus]; in mpi_likelihood_worker() 1479 if(options->mu_rates==NULL) in broadcast_data_worker() 1480 options->mu_rates = (MYREAL *) mycalloc(1+options->muloci, sizeof(MYREAL)); in broadcast_data_worker() 1484 options->mu_rates[i] = atof(temp); in broadcast_data_worker()
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H A D | skyline.c | 255 MYREAL mu_rate = world->options->mu_rates[world->locus]; in calculate_expected_values()
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H A D | main.c | 1040 …print_mutationrate_weights(stdout, options->mu_rates, options->segregs,options->wattersons, data->… in run_sampler() 1041 …print_mutationrate_weights(EARTH->outfile, options->mu_rates, options->segregs,options->wattersons… in run_sampler()
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H A D | tree.c | 1589 * world->options->generation_year * world->options->mu_rates[world->locus]; in fix_times() 1593 …s->meanmu[world->locus],1./world->options->generation_year,world->options->mu_rates[world->locus]); in fix_times() 1642 * world->options->generation_year * world->options->mu_rates[world->locus]+ 1); in upgma() 2454 * world->options->meanmu[locus]) * world->options->mu_rates[locus]; in find_tipdate()
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H A D | pretty.c | 1062 …pdf_print_mutationrate_weights(options->mu_rates, options->segregs, options->wattersons, world->lo… in pdf_master_init() 3480 sprintf(mytext,"%.5f, ", options->mu_rates[i]); in pdf_print_options() 3498 … pdf_printf_next(left_margin + 100 + ii * 60, &page_height,"%.5f", options->mu_rates[i]); in pdf_print_options()
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