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Searched refs:mu_rates (Results 1 – 17 of 17) sorted by relevance

/dports/biology/migrate/migrate-3.6.11/src/
H A Dslice.c95 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()
H A Dbayes.c422 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()
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H A Dcombroyden2.c320 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()
H A Dreporter.c640 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()
H A Dmenu.c2126 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()
H A Dworld.c238 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()
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H A Ddata.c399 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()
H A Dsequence.c2039 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()
H A Dmigration.h580 MYREAL *mu_rates; member
887 MYREAL *mu_rates; member
H A Doptions.c342 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()
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H A Dbroyden.c569 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()
H A Dmcmc1.c1366 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()
H A Dmigrate_mpi.c861 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()
H A Dskyline.c255 MYREAL mu_rate = world->options->mu_rates[world->locus]; in calculate_expected_values()
H A Dmain.c1040 …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()
H A Dtree.c1589 * 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()
H A Dpretty.c1062 …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()