| /dports/biology/migrate/migrate-3.6.11/src/ |
| H A D | pretty.c | 1690 if(!strchr("c", bayes->custm2[j0])) in pdf_bayes_print_accept()
1705 if(!strchr("0c", bayes->custm2[j0])) in pdf_bayes_print_accept()
1790 if(!strchr("c", world->options->custm2[j0])) in pdf_bayes_print_ess()
1802 if(!strchr("0c", bayes->custm2[j0])) in pdf_bayes_print_ess()
3007 pdf_printf(lx, *page_height, 'L', " %c", world->options->custm2[z]); in pdf_print_connection_table()
3034 char *custm2 = world->options->custm2; in pdf_print_param_order() local
3052 if((pa0 == pa) && (custm2[pa0] == '*')) in pdf_print_param_order()
3064 pdf_printf(left_margin+190, *page_height,'L',"[%c]",custm2[pa0]); in pdf_print_param_order()
3081 if((pa0==pa) && (custm2[pa0]=='*')) in pdf_print_param_order()
3108 pdf_printf(left_margin+190, *page_height,'L',"[%c]",custm2[pa0]); in pdf_print_param_order()
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| H A D | world.c | 304 wopt->custm2 = wopt->custm + (numpop2 + 2); in fill_worldoptions()
310 sprintf (wopt->custm2, "%-*.*s", (int) optnumpop2, (int) optnumpop2, options->custm2); in fill_worldoptions()
650 …setup_bayes_map(world->bayes->map, world->options->custm2, world->numpop, world->numpop2, world->n… in init_world()
1230 char save_a = world->options->custm2[world->numpop2]; in print_alpha_curve()
1236 world->options->custm2[world->numpop2] = 'c'; in print_alpha_curve()
1379 world->options->custm2[world->numpop2] = save_a; in print_alpha_curve()
2038 world->design0list[pop] += world->options->custm2[i] == '0' ? 1 : 0; in precalc_world()
2091 world->design0list[thatpop] += world->options->custm2[i] == '0' ? 1 : 0; in reprecalc_world()
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| H A D | bayes.c | 351 if(options->custm2[i]!='0') in bayes_check_and_fix_param()
1984 long n = strlen(custm2); in setup_bayes_map()
1995 switch(custm2[i]) in setup_bayes_map()
2268 bayes->custm2 = world->options->custm2; in bayes_fill()
3058 char *custm2 = world->options->custm2; in print_param_order() local
3095 if((pa0==pa) && (custm2[pa0]=='*')) in print_param_order()
3111 custm2[pa0]); in print_param_order()
4266 char migtype = custm2[which]; in bayes_set_param()
4295 if(custm2[i]=='m') in bayes_set_param()
4303 if(custm2[i]=='m') in bayes_set_param()
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| H A D | options.c | 1622 world->bayes->custm2 = world->options->custm2; in synchronize_param()
1980 if (check == custm2[i]) in scan_connect()
1997 if (custm2[i] == 'm') in set_partmean_mig()
2006 if (custm2[i] == 'm') in set_partmean_mig()
2065 myfree(options->custm2); in destroy_options()
5987 options->custm2 = in read_custom_migration()
6027 options->custm2[z] = '\0'; in read_custom_migration()
6085 options->custm2 = in read_custom_migration_worker()
6121 options->custm2[z] = '\0'; in read_custom_migration_worker()
6220 options->custm2 = in fillup_custm()
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| H A D | broyden.c | 768 char *custm2 = wopt->custm2; in force_sametheta() local
771 if (custm2[i] == 'm') in force_sametheta()
781 if (custm2[i] == 'm') in force_sametheta()
794 char *custm2 = wopt->custm2; in force_samemigration() local
798 if (custm2[i] == 'm') in force_samemigration()
808 if (custm2[i] == 'm') in force_samemigration()
835 custm = wopt->custm2; in param_all_adjust()
1005 custm = wopt->custm2; in check_matrix_arbitrary()
1150 if(nr->world->options->custm2[i]=='S') in gradient()
1373 char *custm = nr->world->options->custm2; in calc_same_d()
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| H A D | combroyden2.c | 255 if (strpbrk (world->options->custm2, "0c")) in estimateParameter()
258 && world->options->custm2[world->numpop2] == 'c') in estimateParameter()
1014 p = world->options->custm2; in do_profiles()
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| H A D | histogram.c | 79 options->custm2 = (char *) myrealloc(options->custm2, sizeof(char) * (strlen(input)+1)); in read_from_bayesmdim_minimal_info()
80 strcpy(options->custm2,input+9); in read_from_bayesmdim_minimal_info()
81 printf("%i> custom2 = %s\n",myID, options->custm2); in read_from_bayesmdim_minimal_info()
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| H A D | priors.c | 277 if(!strchr("0c", world->options->custm2[i])) in log_prior_gamma()
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| H A D | migration.h | 372 char * custm2; //pointer to the world->options->custm2; member
419 char *custm2; /*custom migration matrix: theta on diagonal */ member
901 char *custm2; member
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| H A D | profile.c | 118 long set_df (long which, char *custm2, long numpop, long numpop2);
146 switch (world->options->custm2[which]) in choose_profile_parameters()
225 switch (world->options->custm2[which]) in print_profile_likelihood_driver()
1037 custm2, in profile_max_percentiles()
1148 custm2, in profile_max_spline()
1446 char *custm2 = world->options->custm2; in set_profile_param() local
1458 p = world->options->custm2; in set_profile_param()
1471 switch (custm2[which]) in set_profile_param()
1874 set_df (long which, char *custm2, long numpop, long numpop2) in set_df() argument
1884 ch = custm2[i]; in set_df()
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| H A D | reporter.c | 395 char *custm2 = world->options->custm2; in print_bayes_ess() local
419 if((pa0 == pa) && (custm2[pa0] == '*')) in print_bayes_ess()
429 "Theta",pa0+1, pa+1, custm2[pa0],autocorr[pa],effsample[pa]); in print_bayes_ess()
437 if((pa0==pa) && (custm2[pa0]=='*')) in print_bayes_ess()
448 offset, offset, " ", "M", frompop+1, topop+1, custm2[pa0], autocorr[pa], effsample[pa]); in print_bayes_ess()
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| H A D | tools.c | 1365 … options->custm2 = (char *) myrealloc(options->custm2, sizeof(char) * (strlen(input)+1)); in read_savesum()
1366 strcpy(options->custm2,input+6); in read_savesum()
1536 fprintf (sumfile,"Mode2=%s\n",world->options->custm2); in write_savesum()
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| H A D | lrt.c | 517 if(custm[el][0] != world->options->custm2[zi]) in set_test_param()
535 if(custm[el][0] != world->options->custm2[zi]) in set_test_param()
575 if(custm[el][0] != world->options->custm2[zi]) in set_test_param()
593 if(custm[el][0] != world->options->custm2[zi]) in set_test_param()
613 if(custm[el][0] != world->options->custm2[zi]) in set_test_param()
617 if(custm[el][0] != world->options->custm2[zi]) in set_test_param()
810 if(tmp[0] != world->options->custm2[zi])
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| H A D | slice.c | 90 bayes_set_param(world->param0,newparam,which,world->options->custm2, world->numpop); in set_slice_param()
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| H A D | options.h | 81 long scan_connect (char *custm2, long start, long stop, int check);
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| H A D | bayes.h | 41 extern long setup_bayes_map(longpair *map, char *custm2, long numpop, long numpop2, long size);
56 extern void bayes_set_param(MYREAL *param, MYREAL newparam, long which, char *custm2, long numpop);
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| H A D | gammalike.c | 108 nr->world->options->custm2[nr->world->numpop2]='c'; in gamma_loci_like_iterative()
136 nr->world->options->custm2[nr->world->numpop2]=save_a; in gamma_loci_like_iterative()
159 nr->world->options->custm2[nr->world->numpop2]='c'; in gamma_loci_like_new_notworking()
211 nr->world->options->custm2[nr->world->numpop2]=save_a; in gamma_loci_like_new_notworking()
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| H A D | aic.c | 322 char *custm2 = nr->world->options->custm2; in fast_aic_score() local
341 savecustm2 = custm2[m]; in fast_aic_score()
342 custm2[m] = migtype; in fast_aic_score()
365 custm2[m] = savecustm2; in fast_aic_score()
371 custm2[best[ii].numparam] = migtype; in fast_aic_score()
425 char *custm2 = nr->world->options->custm2; in print_progress_aic() local
509 char *custm2 = nr->world->options->custm2; in aic_score() local
522 if (nr->world->options->custm2[which] == 'm') in aic_score()
529 savecustm2 = custm2[m]; in aic_score()
530 custm2[m] = migtype; in aic_score()
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