/dports/biology/migrate/migrate-3.6.11/src/ |
H A D | world.h | 49 extern void create_world (world_fmt ** world, long loci); 50 extern void init_world (world_fmt * world, data_fmt * data, 68 extern void burnin_chain (world_fmt * world); 74 extern void print_simresults (world_fmt * world); 88 extern void precalc_world (world_fmt * world); 90 extern void klone (world_fmt * original, world_fmt * kopie, 92 extern void klone_part (world_fmt * original, world_fmt * kopie, 94 extern void clone_polish (world_fmt * original, world_fmt * kopie); 95 extern long chance_swap_tree (world_fmt * tthis, world_fmt * that); 97 extern void polish_world (world_fmt * world); [all …]
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H A D | migrate_mpi.h | 91 extern void mpi_runloci_worker (world_fmt ** universe, int usize, 104 extern void mpi_results_master (long sendtype, world_fmt * world, 114 extern long pack_result_buffer (MYREAL **buffer, world_fmt * world, 138 extern long pack_bayes_buffer (MYREAL **buffer, world_fmt * world, 148 extern void mpi_startparam_master(world_fmt * world); 149 extern void mpi_startparam_worker(world_fmt * world); 151 extern void mpi_gmax_master(world_fmt * world, long *Gmax); 152 extern void mpi_gmax_worker(world_fmt * world); 154 extern void mpi_send_stop (world_fmt * world); 171 extern long get_filehandle2(void *file, world_fmt *world); [all …]
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H A D | pretty.h | 67 extern void pdf_print_bayestable(world_fmt *world); 72 extern float pdf_loci_histogram(world_fmt *world); 74 extern void pdf_bayes_print_accept(world_fmt *world); 76 extern void pdf_bayes_print_ess(world_fmt *world); 82 extern void pdf_burnin_stops(world_fmt *world, long maxreplicate); 90 extern void pdf_print_eventtime_table(world_fmt *world); 91 extern void pdf_print_time_table(world_fmt *world, 102 extern void pdf_print_profile_title(world_fmt *world); 105 extern void pdf_print_profile_percentile (world_fmt * world); 109 extern void pdf_print_LRT_box(world_fmt* world,char **box,long size, [all …]
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H A D | sequence.h | 48 extern void init_sequences (world_fmt * world, option_fmt * options, 50 extern void init_sequences2 (world_fmt * world, seqmodel_fmt * seq, 52 extern void init_tbl (world_fmt * world, long locus); 53 extern void print_weights (FILE * outfile, world_fmt * world, 55 extern void print_tbl (FILE * outfile, world_fmt * world, 57 extern void print_seqfreqs (FILE * outfile, world_fmt * world, 59 extern MYREAL treelike_seq (world_fmt * world, long locus); 60 extern MYREAL treelike_snp (world_fmt * world, long locus); 67 extern void make_snp (world_fmt * world, option_fmt * options, 70 extern void copy_seq (world_fmt * original, world_fmt * kopie); [all …]
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H A D | bayes.h | 35 extern long bayes_update (world_fmt *world); 36 extern void bayes_free(world_fmt *world); 37 extern void bayes_fill(world_fmt *world, option_fmt *options); 39 extern void bayes_save(world_fmt *world, long step); 40 extern void bayes_stat(world_fmt *world); 43 extern void adjust_bayes_bins(world_fmt * world, long locus); 45 extern void bayes_reset(world_fmt * world); 52 extern void bayes_print_accept(FILE * outfile, world_fmt * world); 53 extern MYREAL probg_treetimes(world_fmt *world); 61 extern MYREAL log_prior_ratio_all(world_fmt *world, MYREAL *newvals); [all …]
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H A D | tree.h | 41 void buildtree (world_fmt *earth, world_fmt * world, option_fmt * options, data_fmt * data, long lo… 45 void fix_times (world_fmt * world, option_fmt * options); 46 void first_smooth (world_fmt * world, long locus); 50 void construct_tymelist (world_fmt * world, timelist_fmt * timevector); 53 MYREAL treelikelihood (world_fmt * world); 54 MYREAL pseudotreelikelihood (world_fmt * world,proposal_fmt * proposal); 60 void print_tree (world_fmt * world, long g, long *filepos); 61 MYREAL find_tipdate(char * id, long pop, world_fmt *world); 67 void swap_tree (world_fmt * tthis, world_fmt * tthat); 69 void free_mignodelet (node * p, world_fmt * world); [all …]
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H A D | uep.h | 40 extern void destroy_uep(world_fmt * world, long storesize); 46 extern void update_uep (node * p, world_fmt * world); 47 extern void check_uep_root (node * p, world_fmt * world); 50 extern void store_uep (world_fmt * world); 51 extern MYREAL pseudo_ueplikelihood (world_fmt * world, 53 extern MYREAL ueplikelihood (world_fmt * world); 59 extern void show_uep_store (world_fmt * world); 62 extern void analyze_uep (world_fmt * world); 64 extern void update_uepanc (world_fmt * world); 65 extern void setup_uep (world_fmt * world, option_fmt * options); [all …]
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H A D | reporter.h | 43 extern void convergence_check (world_fmt * world, boolean progress); 44 extern void calc_chain_s(MYREAL *cs, MYREAL *cm, world_fmt *world, long replicate); 45 extern void convergence_check_bayes (world_fmt *world, long maxreplicate); 46 extern void chain_means (MYREAL *thischainmeans, world_fmt * world); 47 extern void convergence_progress(FILE *file, world_fmt *world); 48 extern MYREAL single_chain_var(world_fmt *world, long T, MYREAL *variance, MYREAL *autoc, MYREAL *e… 50 extern void print_bayes_ess(FILE *file, world_fmt *world, long numparam, int offset, 52 extern void calculate_ess_frombayes(world_fmt *world, long T, MYREAL *params, long locus, MYREAL *a… 53 extern void collect_ess_values(world_fmt *world); 54 extern void collect_acceptance(world_fmt *world);
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H A D | profile.h | 35 extern boolean print_profile_likelihood_driver (long which, world_fmt * world, 37 extern void print_profile_likelihood (long which, world_fmt * world, long *gmaxptr); 38 extern long print_profile_percentile (world_fmt * world); 39 extern void allocate_profile_percentiles (world_fmt * world); 40 extern void destroy_profile_percentiles (world_fmt * world); 41 extern void print_profile_title (world_fmt * world); 43 extern long choose_profile_parameters (world_fmt * world, long *profilelist);
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H A D | migevents.h | 39 extern void setup_mighist (world_fmt * world, option_fmt * options); 40 extern void destroy_mighist (world_fmt * world); 45 extern void setup_event_events (world_fmt * world, option_fmt * options); 46 extern void destroy_event_events (world_fmt * world); 47 extern void print_mighist_output (FILE * out, world_fmt * world, MYREAL *sums, boolean mrca); 48 extern void print_event_values(world_fmt * world); 49 extern void store_events (world_fmt * world, timelist_fmt * ltl, long np, long rep);
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H A D | options.h | 82 void fillup_custm (long len, world_fmt * world, option_fmt * options); 84 void set_param (world_fmt * world, data_fmt * data, option_fmt * options, long locus); 91 long save_parmfile (option_fmt * options, world_fmt * world, data_fmt *data); 93 void print_menu_options (world_fmt * world, option_fmt * options, data_fmt * data); 94 void print_options (FILE * file, world_fmt * world, option_fmt * options, data_fmt * data); 139 void synchronize_param (world_fmt * world, option_fmt * options); 145 void resynchronize_param (world_fmt * world); 159 void reorder_populations(world_fmt *world, option_fmt *options, data_fmt *data);
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H A D | tools.h | 80 extern void start_node_collection(world_fmt *world); 81 extern void stop_node_collection(world_fmt *world); 82 extern void collect_nodelet(world_fmt *world, node *p); 83 extern node * dispense_nodelet(world_fmt *world); 84 extern void swap_node_collection(world_fmt * tthis, world_fmt * that); 110 extern void init_files (world_fmt * world, data_fmt * data, 112 extern void exit_files (world_fmt * world, data_fmt * data, 119 extern long read_savesum (world_fmt * world, option_fmt * options, 121 extern void write_savesum (world_fmt * world); 132 extern void record_warnings(world_fmt * world, const char *fmt, ...); [all …]
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H A D | skyline.h | 34 …, MYREAL interval, MYREAL age, long from, long to, long * lineages, long numpop, world_fmt *world); 35 extern void setup_expected_events (world_fmt * world, option_fmt * options); 36 extern void destroy_expected_events (world_fmt * world); 37 extern void print_expected_values(world_fmt * world, option_fmt *options); 38 extern void debug_skyline(world_fmt *world, char text[]);
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H A D | combroyden.h | 45 extern long estimateParameter (long rep, long G, world_fmt * world, 61 extern void set_replicates (world_fmt * world, long repkind, long rep, 63 extern void prepare_broyden (long kind, world_fmt * world, 69 extern void setup_parameter0_standard (world_fmt * world, nr_fmt * nr, 76 extern long maximize (MYREAL **thisparam, world_fmt * world, 82 extern long do_profiles (world_fmt * world, nr_fmt * nr, MYREAL *likes, 85 world_fmt * world, nr_fmt * nr);
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H A D | main.c | 248 void run_one_update (world_fmt * world); 250 void run_updates (world_fmt ** universe, 344 world_fmt **universe; in main() 405 universe = (world_fmt **) mycalloc (HEATED_CHAIN_NUM, sizeof (world_fmt *)); in main() 449 universe = (world_fmt **) myrealloc (universe, usize * sizeof (world_fmt *)); in main() 1400 analyze_olddata (world_fmt * world, in analyze_olddata() 2094 run_one_update (world_fmt * world) in run_one_update() 2128 run_updates (world_fmt ** universe, in run_updates() 2230 run_steps (world_fmt ** universe, in run_steps() 2288 run_chains (world_fmt ** universe, in run_chains() [all …]
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H A D | histogram.h | 31 extern void read_from_bayesmdim_minimal_info(znzFile mdimfile, world_fmt *world,option_fmt *options… 32 extern void read_bayes_fromfile(znzFile mdimfile, world_fmt *world, option_fmt *options, char **fil… 34 extern void read_from_bayesmdim_minimal_info(FILE *mdimfile, world_fmt *world,option_fmt *options, … 35 extern void read_bayes_fromfile(FILE *mdimfile, world_fmt *world, option_fmt *options, char **files…
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H A D | world.c | 177 void klone (world_fmt * original, world_fmt * kopie, 179 void klone_part (world_fmt * original, world_fmt * kopie, 181 void clone_polish (world_fmt * original, world_fmt * kopie); 182 long chance_swap_tree (world_fmt * tthis, world_fmt * that); 215 (*world) = (world_fmt *) mycalloc (1, sizeof (world_fmt)); in create_world() 2664 world_fmt *world=EARTH; in print_fluctuate() 4026 klone (world_fmt * original, world_fmt * kopie, in klone() 4151 klone_part (world_fmt * original, world_fmt * kopie, in klone_part() 4208 clone_polish (world_fmt * original, world_fmt * kopie) in clone_polish() 4235 chance_swap_tree (world_fmt * tthis, world_fmt * that) in chance_swap_tree() [all …]
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H A D | bayes.c | 138 void bayes_combine_loci(world_fmt * world); 153 extern void print_bf_values(world_fmt * world); 380 MYREAL probg_treetimes(world_fmt *world) in probg_treetimes() 1023 MYREAL calculate_prior(world_fmt *world) in calculate_prior() 1536 bayes_update (world_fmt * world) in bayes_update() 1956 void bayes_save(world_fmt *world, long step) in bayes_save() 2272 void bayes_reset(world_fmt * world) in bayes_reset() 2285 void bayes_free(world_fmt *world) in bayes_free() 2318 void bayes_stat(world_fmt *world) in bayes_stat() 2606 bayes_progress(world_fmt *world, long ten) in bayes_progress() [all …]
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H A D | data.h | 60 void get_data (FILE * infile, data_fmt * data, option_fmt * options, world_fmt *world); 61 void print_data (world_fmt * world, option_fmt * options, 63 void print_spectra(world_fmt * world, option_fmt * options,data_fmt * data); 64 void print_data_summary (FILE * file, world_fmt * world,
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H A D | correlation.h | 34 void covariance_bayes(world_fmt *world, long locus); 35 void covariance_bayes2(world_fmt *world, long locus, MYREAL *params); 36 void covariance_summary(world_fmt *world);
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H A D | correlation.c | 67 void covarianceBayes(world_fmt *world, long T, MYREAL *params, long offset, long locus, MYREAL ***c… in covarianceBayes() 123 void correlationBayes(world_fmt *world, long locus, MYREAL **cov, MYREAL ***corr) in correlationBayes() 140 void covariance_bayes(world_fmt *world, long locus) in covariance_bayes() 152 void covariance_summary(world_fmt *world) in covariance_summary() 208 world_fmt *world; in main() 209 world = (world_fmt *) calloc(1,sizeof(world_fmt)); in main()
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H A D | tree.c | 196 void sankoff (world_fmt * world); 205 void copy_tree (world_fmt * original, world_fmt * kopie); 206 node *copy_node (world_fmt * original, node * o, world_fmt * kopie, 208 void copy_node_content (world_fmt * original, world_fmt * kopie, node * o, 210 void swap_tree (world_fmt * tthis, world_fmt * tthat); 246 buildtree (world_fmt *earth, world_fmt * world, option_fmt * options, data_fmt * data, in buildtree() 1811 sankoff (world_fmt * world) in sankoff() 5208 copy_tree (world_fmt * original, world_fmt * kopie) in copy_tree() 5214 copy_node (world_fmt * original, node * o, world_fmt * kopie, node * last) in copy_node() 5268 copy_node_content (world_fmt * original, world_fmt * kopie, node * o, in copy_node_content() [all …]
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H A D | sequence.c | 62 void init_tbl (world_fmt * world, long locus); 67 MYREAL treelike_seq (world_fmt * world, long locus); 68 MYREAL treelike_snp (world_fmt * world, long locus); 83 void inputoptions (world_fmt *earth, world_fmt * world, option_fmt * options, data_fmt * data, 98 void init_sequences_aliases (world_fmt * earth, world_fmt * world, option_fmt * options, 152 init_sequences_aliases (world_fmt *earth, world_fmt * world, option_fmt * options, in init_sequences_aliases() 1282 inputoptions (world_fmt *earth, world_fmt * world, option_fmt * options, data_fmt * data, in inputoptions() 1470 init_tbl (world_fmt * world, long locus) in init_tbl() 1620 treelike_seq (world_fmt * world, long locus) in treelike_seq() 1778 treelike_snp (world_fmt * world, long locus) in treelike_snp() [all …]
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H A D | menu.h | 53 void print_menu_accratio (long a, long b, world_fmt *world); 59 long print_title (world_fmt * world, option_fmt * options); 67 void get_menu (option_fmt * options, world_fmt *world, data_fmt *data);
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H A D | slice.h | 29 extern MYREAL slice (MYREAL *startval, long which, world_fmt * world, MYREAL (*func) (MYREAL, MYRE… 30 extern MYREAL expslice (MYREAL *startval, long which, world_fmt * world, MYREAL (*func) (MYREAL, M… 31 extern void expallslice (MYREAL *values, MYREAL *rateval, long which, world_fmt * world);
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