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Searched refs:world_fmt (Results 1 – 25 of 61) sorted by relevance

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/dports/biology/migrate/migrate-3.6.11/src/
H A Dworld.h49 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);
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H A Dmigrate_mpi.h91 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);
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H A Dpretty.h67 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,
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H A Dsequence.h48 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);
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H A Dbayes.h35 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);
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H A Dtree.h41 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);
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H A Duep.h40 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);
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H A Dreporter.h43 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);
H A Dprofile.h35 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);
H A Dmigevents.h39 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);
H A Doptions.h82 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);
H A Dtools.h80 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, ...);
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H A Dskyline.h34 …, 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[]);
H A Dcombroyden.h45 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);
H A Dmain.c248 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()
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H A Dhistogram.h31 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…
H A Dworld.c177 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()
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H A Dbayes.c138 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()
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H A Ddata.h60 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,
H A Dcorrelation.h34 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);
H A Dcorrelation.c67 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()
H A Dtree.c196 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()
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H A Dsequence.c62 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()
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H A Dmenu.h53 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);
H A Dslice.h29 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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