24  Developer function index

This index covers package-owned R and Rust definitions. Internal functions do not form a stable user API. Scientific algorithms will receive explanations and numerical demonstrations in the relevant chapters; validation, formatting, and storage helpers remain in the reference index.

R-to-Rust wrappers and their compiled kernels are listed separately because they are distinct definitions of the same interface. Local R helpers are scoped to their enclosing functions. Rust test definitions are separate from production code. Anonymous callbacks, vendored dependencies, development scripts, and historical sources in context/ are outside this index.

Use the browser’s find command or book search to locate a function. A standalone searchable inventory provides category filters. Its JSON data are also available for programmatic use.

24.1 Modern internal R

Package-level implementation functions, including scientific algorithms, validation, formatting, I/O, and runtime support.

Definition	Enclosing scope	Source
.draw_qtn	—	R/arch_independent.R:21
.draw_qtn_distinct_chr	—	R/arch_independent.R:56
.draw_qtn_pairs	—	R/arch_independent.R:81
.candidate_markers	—	R/arch_independent.R:114
.candidate_hint	—	R/arch_independent.R:125
.type_occurrence	—	R/arch_independent.R:139
.draw_qtn_ld	—	R/arch_ld.R:62
.apply_ld_phase	—	R/arch_ld.R:245
.ld_user_pairs	—	R/arch_ld.R:279
.ld_check_cross_layer	—	R/arch_ld.R:367
.ld_prior_loci	—	R/arch_ld.R:397
.check_breeds	—	R/cross_breed.R:159
.recycle_by_chr	—	R/cross_map.R:194
.check_plan	—	R/cross_mate.R:260
.cite_isqg	—	R/cross_mating.R:16
.draw_meiosis	—	R/cross_mating.R:53
.check_interference	—	R/cross_mating.R:136
.draw_meiosis_interference	—	R/cross_mating.R:215
.check_meiosis_call	—	R/cross_mating.R:284
.meiosis_layout	—	R/cross_mating.R:332
.mate_many	—	R/cross_mating.R:372
.mate	—	R/cross_mating.R:429
.stable_key	—	R/cross_pedigree.R:25
.key_part	—	R/cross_pedigree.R:42
.key_elements	—	R/cross_pedigree.R:64
.founder_pedigree	—	R/cross_pedigree.R:97
.ensure_pedigree	—	R/cross_pedigree.R:144
.pedigree_union	—	R/cross_pedigree.R:157
.pedigree_ancestors	—	R/cross_pedigree.R:171
.mating_pedigree	—	R/cross_pedigree.R:192
.pedigree_relabel	—	R/cross_pedigree.R:221
.check_pool	—	R/cross_population.R:189
.make_map	—	R/cross_population.R:214
.merge_counted	—	R/cross_population.R:247
.check_counted	—	R/cross_population.R:281
.new_population	—	R/cross_population.R:333
.check_map	—	R/cross_population.R:348
.check_cm_units	—	R/cross_population.R:394
.same_map	—	R/cross_population.R:419
.chr_rank	—	R/cross_population.R:444
.valid_counted	—	R/cross_population.R:467
.check_orientation	—	R/cross_population.R:504
.resolve_geno_qtn	—	R/cross_population.R:636
.geno_marker_names	—	R/cross_population.R:1112
.gxe_args	—	R/cross_population.R:1132
.check_population	—	R/cross_population.R:1206
.check_single	—	R/cross_population.R:1216
.pleio_draw	—	R/effects_pleioarch.R:65
.pleio_check_zero_var	—	R/effects_pleioarch.R:246
.pleio_partition	—	R/effects_pleioarch.R:288
.pleio_check_layout	—	R/effects_pleioarch.R:341
.pleio_user_layout	—	R/effects_pleioarch.R:385
.pleio_single_unit_consequence	—	R/effects_pleioarch.R:412
.pleio_nonadditive_draw	—	R/effects_pleioarch.R:493
.pleio_units	—	R/effects_pleioarch.R:536
.pleio_unit_effects	—	R/effects_pleioarch.R:583
.pleio_total_cor_check	—	R/effects_pleioarch.R:724
.cite_pleioarch	—	R/effects_pleioarch.R:799
.cite_main	—	R/effects_pleioarch.R:814
.pleio_pi_vector	—	R/effects_pleioarch.R:829
.check_pleio_feasible	—	R/effects_pleioarch.R:870
.draw_mvnorm	—	R/effects_pleioarch.R:929
.draw_univariate	—	R/effects_pleioarch.R:944
.pleio_cor_matrix	—	R/effects_pleioarch.R:957
.pleio_check_user_units	—	R/effects_pleioarch.R:999
.pleio_controlled	—	R/effects_pleioarch.R:1035
.effect_series	—	R/effects_series.R:23
.draw_residual	—	R/effects_series.R:85
.coalescent_chromosome	—	R/founders_coalescent.R:38
.coalescent_preset	—	R/founders_coalescent.R:300
.orthogonal_d_series	—	R/grammar_layers.R:361
.check_sim	—	R/grammar_layers.R:997
.resolve_n_qtn	—	R/grammar_layers.R:1007
.last_layer_of_type	—	R/grammar_layers.R:1030
.one_call_hint	—	R/grammar_layers.R:1038
.resolve_prop	—	R/grammar_layers.R:1055
.add_layer	—	R/grammar_layers.R:1102
.draw_layer	—	R/grammar_layers.R:1129
.het_varies	—	R/grammar_layers.R:1162
.dom_hetless	—	R/grammar_layers.R:1178
.dom_partial_hetless	—	R/grammar_layers.R:1194
.orthogonal_hetless_d	—	R/grammar_layers.R:1214
.epi_dead_status	—	R/grammar_layers.R:1240
.rep_qtn	—	R/grammar_layers.R:1261
.resolve_qtn_arg	—	R/grammar_layers.R:1275
.warn_monomorphic	—	R/grammar_layers.R:1335
.resolve_epi_qtn	—	R/grammar_layers.R:1361
.resolve_interaction_type	—	R/grammar_layers.R:1435
.cite_vqtl	—	R/grammar_layers.R:1459
.apply_phase	—	R/grammar_layers.R:1482
.require_markers	—	R/grammar_layers.R:1499
.complex_terminal_msg	—	R/grammar_layers.R:1513
.var_budget_matrix	—	R/grammar_plot.R:71
.plot_variance	—	R/grammar_plot.R:85
.plot_hist	—	R/grammar_plot.R:106
.plot_effects	—	R/grammar_plot.R:114
.plot_genetic_target	—	R/grammar_plot.R:135
.plot_cor	—	R/grammar_plot.R:144
.realize_phenotype	—	R/grammar_realize.R:35
.genetic_matrix	—	R/grammar_realize.R:125
.avg_effect	—	R/grammar_realize.R:182
.breeding_value_matrix	—	R/grammar_realize.R:236
.bv_from_effects	—	R/grammar_realize.R:316
.layer_scaled_effects	—	R/grammar_realize.R:343
.has_genetic_transcriptome	—	R/grammar_realize.R:377
.genetic_value_matrix	—	R/grammar_realize.R:394
.transcriptome_matrix	—	R/grammar_realize.R:410
.tx_raw	—	R/grammar_realize.R:454
.component_raw	—	R/grammar_realize.R:484
.layer_sd	—	R/grammar_realize.R:549
.scaled_component	—	R/grammar_realize.R:557
.epi_unit_column	—	R/grammar_realize.R:579
.apply_vqtl	—	R/grammar_realize.R:599
.layer_qtn_effect	—	R/grammar_realize.R:648
.validate_rep	—	R/grammar_realize.R:659
.variance_budget	—	R/grammar_realize.R:671
.mediation_budget	—	R/grammar_realize.R:730
.orthogonal_var_split	—	R/grammar_realize.R:778
.ad_report	—	R/grammar_realize.R:842
.ad_partition	—	R/grammar_realize.R:872
.correlated_residuals	—	R/grammar_realize.R:924
.resid_cor_factor	—	R/grammar_realize.R:951
.validate_resid_cor	—	R/grammar_realize.R:965
.seeded_residual	—	R/grammar_realize.R:1010
.Random.seed_safe	—	R/grammar_realize.R:1023
.restore_seed	—	R/grammar_realize.R:1034
.realized_h2	—	R/grammar_realize.R:1078
.sim_reps	—	R/grammar_realize.R:1113
.check_h2_complete	—	R/grammar_realize.R:1132
.trait_mean	—	R/grammar_realize.R:1173
.geno_label	—	R/grammar_simulate_phenotype.R:561
.small_expr	—	R/grammar_simulate_phenotype.R:583
.check_arch_args	—	R/grammar_simulate_phenotype.R:611
.validate_count	—	R/grammar_simulate_phenotype.R:694
.validate_reps	—	R/grammar_simulate_phenotype.R:711
.validate_flag	—	R/grammar_simulate_phenotype.R:725
.validate_seed	—	R/grammar_simulate_phenotype.R:735
.validate_proportion	—	R/grammar_simulate_phenotype.R:748
.is_one_call	—	R/grammar_simulate_phenotype.R:760
.build_one_call	—	R/grammar_simulate_phenotype.R:767
.normalize_geno	—	R/grammar_simulate_phenotype.R:795
.n_word	—	R/grammar_simulate_phenotype.R:902
.min_ind_reason	—	R/grammar_simulate_phenotype.R:904
.select_individuals	—	R/grammar_simulate_phenotype.R:922
.expression_foundation	—	R/grammar_simulate_phenotype.R:963
.geno_cols	—	R/grammar_simulate_phenotype.R:991
.marker_stats_ref	—	R/grammar_simulate_phenotype.R:1022
.marker_maf_ref	—	R/grammar_simulate_phenotype.R:1050
.layer_seed	—	R/grammar_simulate_phenotype.R:1079
.print_threshold_note	—	R/grammar_simulate_phenotype.R:1214
.print_reps_note	—	R/grammar_simulate_phenotype.R:1237
.fmt_int	—	R/grammar_simulate_phenotype.R:1268
.print_ad_report	—	R/grammar_simulate_phenotype.R:1287
.total_genetic_prop	—	R/grammar_simulate_phenotype.R:1317
.total_variance_prop	—	R/grammar_simulate_phenotype.R:1333
.expand_prop	—	R/grammar_simulate_phenotype.R:1342
.qtn_count_label	—	R/grammar_simulate_phenotype.R:1361
.liability_table	—	R/grammar_threshold.R:102
.apply_threshold	—	R/grammar_threshold.R:117
.threshold_cuts	—	R/grammar_threshold.R:140
.freeze_trait	—	R/grammar_trait.R:34
.pop_trait	—	R/grammar_trait.R:110
.shared_trait	—	R/grammar_trait.R:117
.trait_layers_on	—	R/grammar_trait.R:129
.simulate_from_trait	—	R/grammar_trait.R:202
.frozen_layer_ignored	—	R/grammar_trait.R:249
.variance_budget_frozen	—	R/grammar_trait.R:266
.epi_itype	—	R/grammar_trait.R:299
.epi_locus_centers	—	R/grammar_trait.R:310
.het_to_letters	—	R/io_detect_format.R:27
.call_to_letters	—	R/io_detect_format.R:52
.gds_needed	—	R/io_detect_format.R:67
detect_format	—	R/io_detect_format.R:82
.sniff_text_signature	—	R/io_detect_format.R:129
.hmp_header_match	—	R/io_detect_format.R:151
.detect_df_format	—	R/io_detect_format.R:157
parse_hapmap_chars_to_raw	—	R/io_detect_format.R:223
compute_flip	—	R/io_detect_format.R:342
assemble_output	—	R/io_detect_format.R:373
.check_unique_ids	—	R/io_detect_format.R:388
.fill_missing_ids	—	R/io_detect_format.R:415
format_conversion	—	R/io_format_conversion.R:51
.label_hash	—	R/io_format_conversion.R:277
.apply_coding	—	R/io_read_formats.R:18
.counted_allele	—	R/io_read_formats.R:84
.has_counted_col	—	R/io_read_formats.R:107
.n_meta	—	R/io_read_formats.R:116
.counted_col_values	—	R/io_read_formats.R:124
.add_counted_column	—	R/io_read_formats.R:133
.write_numeric	—	R/io_read_formats.R:160
.allele_label	—	R/io_read_formats.R:177
.as_pos	—	R/io_read_formats.R:187
handle_hapmap	—	R/io_read_formats.R:200
.normalize_numeric_schema	—	R/io_read_formats.R:297
handle_numeric	—	R/io_read_formats.R:322
handle_table	—	R/io_read_formats.R:379
.read_gds_to_raw	—	R/io_read_formats.R:497
.vcf_classify_gt	—	R/io_read_formats.R:541
.vcf_warn_dropped	—	R/io_read_formats.R:560
.vcf_scan_calls	—	R/io_read_formats.R:590
handle_vcf	—	R/io_read_formats.R:639
handle_gds	—	R/io_read_formats.R:780
.plink_cm	—	R/io_read_formats.R:823
handle_bed	—	R/io_read_formats.R:839
handle_ped	—	R/io_read_formats.R:880
handle_finalreport	—	R/io_read_formats.R:925
.write_qtn_table_to	—	R/io_write.R:371
.require_jsonlite	—	R/io_write.R:388
.check_path_arg	—	R/io_write.R:399
.resolve_reps	—	R/io_write.R:411
.qtn_table_reps	—	R/io_write.R:435
.write_json_rows	—	R/io_write.R:456
.with_c_numeric	—	R/io_write.R:472
.sibling_path	—	R/io_write.R:491
.companion_paths	—	R/io_write.R:507
.canonical_path	—	R/io_write.R:563
.unicode_nfd	—	R/io_write.R:588
.write_target	—	R/io_write.R:611
.preflight_paths	—	R/io_write.R:650
.file_rename	—	R/io_write.R:685
.random_token	—	R/io_write.R:691
.staging_ext	—	R/io_write.R:703
.stage_dir	—	R/io_write.R:721
.remove_stage_dirs	—	R/io_write.R:741
.staged_write	—	R/io_write.R:770
.commit_staged	—	R/io_write.R:805
.marker_meta	—	R/io_write.R:900
.causal_markers	—	R/io_write.R:926
.write_split_markers	—	R/io_write.R:941
.export_sim	—	R/io_write.R:966
.dosage_block	—	R/io_write.R:979
.write_marker_file	—	R/io_write.R:999
.whole_to_integer	—	R/io_write.R:1057
.marker_json_objects	—	R/io_write.R:1072
.json_vec_elements	—	R/io_write.R:1111
.json_classed_elements	—	R/io_write.R:1139
.json_vec	—	R/io_write.R:1158
.json_escape	—	R/io_write.R:1166
.qtn_var	—	R/io_write.R:1288
.tx_qtn_var	—	R/io_write.R:1328
.subset_population_markers	—	R/qc_filter_geno.R:396
.ld_spec	—	R/qc_filter_geno.R:423
.check_maf_arg	—	R/qc_filter_geno.R:449
.ld_prune	—	R/qc_filter_geno.R:490
.ld_sweep	—	R/qc_filter_geno.R:524
.plink_hap_rsq	—	R/qc_filter_geno.R:796
.plink_em_hethet	—	R/qc_filter_geno.R:822
.plink_calc_lnlike	—	R/qc_filter_geno.R:884
.plink_cubic_roots	—	R/qc_filter_geno.R:902
.plink_calc_lnlike_quantile	—	R/qc_filter_geno.R:952
.plink_blocks_classify	—	R/qc_filter_geno.R:978
.plink_blocks_chrom	—	R/qc_filter_geno.R:1066
.cite_ld	—	R/qc_filter_geno.R:1190
.gabriel_blocks	—	R/qc_ld_methods.R:23
.founder_inbreeding	—	R/select_blup.R:113
.check_pheno_matrix	—	R/select_blup.R:427
.mt_variances	—	R/select_blup.R:467
.predict_ebv_mt	—	R/select_blup.R:515
.check_relationship	—	R/select_blup.R:587
.blup_variances	—	R/select_blup.R:656
.gblup_marker_effects	—	R/select_blup.R:695
.cite_bqp	—	R/select_bqp.R:16
.bqp_inputs	—	R/select_bqp.R:36
.bqp_g	—	R/select_bqp.R:85
.bqp_check_args	—	R/select_bqp.R:104
.bqp_solve	—	R/select_bqp.R:130
.sel_bqp	—	R/select_bqp.R:220
.check_distinct	—	R/select_combining.R:212
.check_ad	—	R/select_combining.R:226
.expected_cross_means	—	R/select_combining.R:244
.simulate_cross_means	—	R/select_combining.R:260
.decompose_ca	—	R/select_combining.R:310
.resolve_n_per_family	—	R/select_ind.R:503
.resolve_keep	—	R/select_ind.R:559
.check_trait_index	—	R/select_ind.R:603
.check_direction	—	R/select_ind.R:618
.criterion_values	—	R/select_ind.R:630
.quadratic_index_score	—	R/select_ind.R:713
.index_score	—	R/select_ind.R:753
.index_weights	—	R/select_ind.R:799
.combined_score	—	R/select_ind.R:858
.sel_top	—	R/select_ind.R:910
.sel_within_family	—	R/select_ind.R:917
.sel_among_family	—	R/select_ind.R:967
.selection_result	—	R/select_ind.R:984
.select_culling	—	R/select_ind.R:1004
.mabc_founders	—	R/select_mabc.R:295
.mabc_markers	—	R/select_mabc.R:318
.mabc_require_informative	—	R/select_mabc.R:343
.mabc_check_flanks	—	R/select_mabc.R:364
.mabc_parse_interval	—	R/select_mabc.R:401
.mabc_interval	—	R/select_mabc.R:442
.mabc_recovery	—	R/select_mabc.R:457
.mabc_check_weights	—	R/select_mabc.R:471
.mabc_weights	—	R/select_mabc.R:508
.allocate_slots	—	R/select_ocs.R:473
.validate_coancestry_matrix	—	R/select_ocs.R:509
.check_G_ids	—	R/select_ocs.R:539
.dosage_from	—	R/select_ocs.R:558
.frank_wolfe	—	R/select_ocs.R:594
.tune_lambda	—	R/select_ocs.R:652
.check_tandem	—	R/select_schemes.R:420
.check_tandem_range	—	R/select_schemes.R:432
.check_backed	—	R/select_schemes.R:449
.bulk_counts	—	R/select_schemes.R:470
.as_founder_pop	—	R/select_schemes.R:477
.check_phenotyper	—	R/select_schemes.R:500
.self_each	—	R/select_schemes.R:514
.intermate	—	R/select_schemes.R:534
.relabel	—	R/select_schemes.R:557
.intensity_from_p	—	R/select_usefulness.R:161
.additive_model	—	R/select_usefulness.R:170
.additive_gv	—	R/select_usefulness.R:221
.resolve_pairs	—	R/select_usefulness.R:234
.warn_heterozygous_parents	—	R/select_usefulness.R:275
.make_family	—	R/select_usefulness.R:297
.tx_count_par	—	R/transcriptome_counts.R:130
.attach_expression	—	R/transcriptome_layer.R:11
.tx_cor_design_warning	—	R/transcriptome_layer.R:300
.tx_grm	—	R/transcriptome_mimic.R:24
.greml_h2	—	R/transcriptome_mimic.R:53
.tx_estimate_factors	—	R/transcriptome_mimic.R:111
.tx_estimate_kappa	—	R/transcriptome_mimic.R:149
.tx_mimic_calibrate	—	R/transcriptome_mimic.R:188
.tx_mimic_scale	—	R/transcriptome_simulate.R:985
.tx_ratio	—	R/transcriptome_simulate.R:1010
.tx_pergene	—	R/transcriptome_simulate.R:1020
.tx_synthetic_coords	—	R/transcriptome_simulate.R:1043
.tx_check_annotation	—	R/transcriptome_simulate.R:1093
.onAttach	—	R/zzz.R:1
.unwrap_extendr	—	R/zzz.R:32

24.2 Legacy internal R

Private helpers supporting the frozen create_phenotypes() engine.

Definition	Enclosing scope	Source
base_line_multi_traits	—	R/legacy_Base_line_multi_traits.R:68
.check_cor_inputs	—	R/legacy_Base_line_multi_traits.R:373
base_line_single_trait	—	R/legacy_Base_line_single_trait.R:20
genotypes	—	R/legacy_Genotypes.R:56
phenotypes	—	R/legacy_Phenotypes.R:20
qtn_linkage	—	R/legacy_QTN_linkage.R:26
.ld_pair	—	R/legacy_QTN_linkage.R:1850
.ld_key	—	R/legacy_QTN_linkage.R:1859
.ld_contract_stop	—	R/legacy_QTN_linkage.R:1869
.ld_check_indirect	—	R/legacy_QTN_linkage.R:1895
.ld_direct_violation	—	R/legacy_QTN_linkage.R:1955
.ld_check_direct	—	R/legacy_QTN_linkage.R:1993
.ld_max_attempts	—	R/legacy_QTN_linkage.R:2019
.ld_attempt_seed	—	R/legacy_QTN_linkage.R:2036
.ld_search_stop	—	R/legacy_QTN_linkage.R:2045
.ld_run_attempt	—	R/legacy_QTN_linkage.R:2061
.ld_give_up_now	—	R/legacy_QTN_linkage.R:2101
.ld_emit_warnings	—	R/legacy_QTN_linkage.R:2109
.ld_search_giveup	—	R/legacy_QTN_linkage.R:2119
.qtn_linkage_checked	—	R/legacy_QTN_linkage.R:2132
qtn_partially_pleiotropic	—	R/legacy_QTN_partially_pleiotropic.R:60
.partial_spec_labels	—	R/legacy_QTN_partially_pleiotropic.R:794
.partial_assemble	—	R/legacy_QTN_partially_pleiotropic.R:804
.partial_qtn_matrix	—	R/legacy_QTN_partially_pleiotropic.R:839
.check_partial_disjoint	—	R/legacy_QTN_partially_pleiotropic.R:851
.check_partial_counts	—	R/legacy_QTN_partially_pleiotropic.R:870
qtn_pleiotropic	—	R/legacy_QTN_pleiotropic.R:70
check_in	—	R/legacy_check_in.R:69
.v1_validate_basic	—	R/legacy_check_in.R:1162
.v1_validate_ld	—	R/legacy_check_in.R:1223
.v1_validate_seed_arith	—	R/legacy_check_in.R:1262
.v1_validate_cor	—	R/legacy_check_in.R:1361
.v1_validate_effects	—	R/legacy_check_in.R:1410
.v1_rng_capture	—	R/legacy_check_in.R:1456
.v1_rng_restore	—	R/legacy_check_in.R:1479
.v1_check_qtn_capacity	—	R/legacy_check_in.R:1504
.v1_check_vqtl_sd	—	R/legacy_check_in.R:1542
.v1_check_vqtl_baseline	—	R/legacy_check_in.R:1567
constraint	—	R/legacy_constraint.R:20
genetic_effect	—	R/legacy_genetic_effect.R:70
.check_effect_length	—	R/legacy_genetic_effect.R:219
make_pd	—	R/legacy_make_pd.R:46
qtn_from_user	—	R/legacy_qtn_from_user.R:27
vQTL	—	R/legacy_vQTL.R:67

24.3 R-to-Rust bindings

Seven R wrappers for compiled Rust entry points; these are not seven additional scientific methods.

Definition	Enclosing scope	Source
numericalize_core	—	R/extendr-wrappers.R:33
meiosis_core	—	R/extendr-wrappers.R:55
mate_haplotypes_core	—	R/extendr-wrappers.R:82
mate_many_core	—	R/extendr-wrappers.R:110
gamete_masks_core	—	R/extendr-wrappers.R:125
stable_hash_core	—	R/extendr-wrappers.R:131
coalescent_chromosome_core	—	R/extendr-wrappers.R:143

24.4 Local R helpers

Named functions defined inside another function. Scope identifies the enclosing function; these are not independently callable package functions.

Definition	Enclosing scope	Source
make_one	.draw_qtn_pairs	R/arch_independent.R:94
chr_block	.draw_qtn_ld	R/arch_ld.R:91
window_partners	.draw_qtn_ld	R/arch_ld.R:102
r_pair	.draw_qtn_ld	R/arch_ld.R:121
r2_pair	.draw_qtn_ld	R/arch_ld.R:128
per_trait	.ld_prior_loci	R/arch_ld.R:398
record	crossbreed	R/cross_breed.R:271
gen_cross	crossbreed	R/cross_breed.R:278
zero_one	population_from_haplotypes	R/cross_haplotypes.R:143
pick	mate	R/cross_mate.R:126
ids_of	mating_design	R/cross_mate.R:369
key_of	mating_design	R/cross_mate.R:380
ok	mating_design	R/cross_mate.R:430
try_slot	mating_design	R/cross_mate.R:432
sub	.check_interference	R/cross_mating.R:144
num1	.check_interference	R/cross_mating.R:167
digit_strand	.founder_pedigree	R/cross_pedigree.R:110
strand_part	.founder_pedigree	R/cross_pedigree.R:113
st	.mating_pedigree	R/cross_pedigree.R:203
pid	parentage	R/cross_pedigree.R:271
pid	families	R/cross_pedigree.R:315
close_to	.same_map	R/cross_population.R:420
draw	phenotype_value	R/cross_population.R:1078
scale_idx	.pleio_draw	R/effects_pleioarch.R:202
spec_rows	.pleio_units	R/effects_pleioarch.R:557
as_units	.pleio_unit_effects	R/effects_pleioarch.R:588
pick	.pleio_total_cor_check	R/effects_pleioarch.R:741
fmt	.pleio_total_cor_check	R/effects_pleioarch.R:749
per_chr	founders_coalescent	R/founders_coalescent.R:202
eff_for	additive	R/grammar_layers.R:287
build	additive	R/grammar_layers.R:291
eff_for	dominance	R/grammar_layers.R:521
build	dominance	R/grammar_layers.R:565
eff_for	epistasis	R/grammar_layers.R:788
build	epistasis	R/grammar_layers.R:790
build	vqtl	R/grammar_layers.R:959
as_idx	.resolve_qtn_arg	R/grammar_layers.R:1280
to_idx	.resolve_epi_qtn	R/grammar_layers.R:1366
to_mat	.resolve_epi_qtn	R/grammar_layers.R:1382
loci	.ad_partition	R/grammar_realize.R:873
scaled	.ad_partition	R/grammar_realize.R:879
walk	.small_expr	R/grammar_simulate_phenotype.R:585
fmt	print.phenotype_sim	R/grammar_simulate_phenotype.R:1102
is_letter	parse_hapmap_chars_to_raw	R/io_detect_format.R:238
.rows	parse_hapmap_chars_to_raw	R/io_detect_format.R:302
grab	handle_vcf	R/io_read_formats.R:715
find_col	handle_finalreport	R/io_read_formats.R:949
write_pheno	write_phenotypes	R/io_write.R:246
rollback	.commit_staged	R/io_write.R:816
enc	.json_classed_elements	R/io_write.R:1140
block	qtn_table	R/io_write.R:1417
gene_block	qtn_table	R/io_write.R:1442
numify	genotypes	R/legacy_Genotypes.R:69
numeric_df	genotypes	R/legacy_Genotypes.R:79
read_one	genotypes	R/legacy_Genotypes.R:122
pair_ld	.ld_check_indirect	R/legacy_QTN_linkage.R:1922
out	.ld_check_indirect	R/legacy_QTN_linkage.R:1930
differs	.ld_check_indirect	R/legacy_QTN_linkage.R:1935
chk	.check_partial_counts	R/legacy_QTN_partially_pleiotropic.R:875
chk_eff	.check_partial_counts	R/legacy_QTN_partially_pleiotropic.R:889
whole1	.v1_validate_basic	R/legacy_check_in.R:1165
ok	.v1_validate_ld	R/legacy_check_in.R:1224
worst_of	.v1_validate_seed_arith	R/legacy_check_in.R:1285
ok	.v1_validate_seed_arith	R/legacy_check_in.R:1294
accepted	.v1_validate_seed_arith	R/legacy_check_in.R:1331
chk	.v1_validate_effects	R/legacy_check_in.R:1414
g	.v1_check_qtn_capacity	R/legacy_check_in.R:1505
cleanup_outputs	create_phenotypes	R/legacy_create_phenotypes.R:552
note	filter_geno	R/qc_filter_geno.R:304
whole	.ld_spec	R/qc_filter_geno.R:429
lg	.ld_sweep	R/qc_filter_geno.R:578
sg	.ld_sweep	R/qc_filter_geno.R:579
ls	.ld_sweep	R/qc_filter_geno.R:585
ss	.ld_sweep	R/qc_filter_geno.R:590
is_pruned	.ld_sweep	R/qc_filter_geno.R:591
set_pruned	.ld_sweep	R/qc_filter_geno.R:592
maf_of	.ld_sweep	R/qc_filter_geno.R:593
cor_sub	.ld_sweep	R/qc_filter_geno.R:594
is_singular	.ld_sweep	R/qc_filter_geno.R:600
win_at	.ld_sweep	R/qc_filter_geno.R:605
clq	.plink_blocks_classify	R/qc_filter_geno.R:1005
counts_of	.plink_blocks_chrom	R/qc_filter_geno.R:1076
bad	.founder_inbreeding	R/select_blup.R:114
one	.mt_variances	R/select_blup.R:474
ok	.blup_variances	R/select_blup.R:683
m	selection_methods	R/select_blup.R:778
obj_of	.bqp_solve	R/select_bqp.R:134
feas_of	.bqp_solve	R/select_bqp.R:137
pen_of	.bqp_solve	R/select_bqp.R:182
p2	.index_weights	R/select_ind.R:813
coan_at	.tune_lambda	R/select_ocs.R:664
done	.tune_lambda	R/select_ocs.R:668
bad	.check_backed	R/select_schemes.R:450
draw	observe_counts	R/transcriptome_counts.R:95
build	transcriptome	R/transcriptome_layer.R:259
draw	transcriptome / build	R/transcriptome_layer.R:260
negll	.greml_h2	R/transcriptome_mimic.R:76
run	simulate_transcriptome	R/transcriptome_simulate.R:405
z1	simulate_transcriptome / run	R/transcriptome_simulate.R:492
draw_resid	predict.transcriptome_sim	R/transcriptome_simulate.R:892
z1	predict.transcriptome_sim / draw_resid	R/transcriptome_simulate.R:893
draw	.tx_synthetic_coords	R/transcriptome_simulate.R:1062

24.5 Rust implementation

Functions and associated methods in the package-owned Rust source. Rust pub visibility does not make a function part of the exported R API.

Definition	Enclosing scope	Source
splitmix64	—	src/rust/src/coalescent.rs:31
Rng::new	Rng	src/rust/src/coalescent.rs:40
Rng::next_u64	Rng	src/rust/src/coalescent.rs:51
Rng::unif	Rng	src/rust/src/coalescent.rs:67
Rng::exp1	Rng	src/rust/src/coalescent.rs:72
Rng::below	Rng	src/rust/src/coalescent.rs:77
Demography::new	Demography	src/rust/src/coalescent.rs:108
Demography::epoch	Demography	src/rust/src/coalescent.rs:131
Demography::next_change	Demography	src/rust/src/coalescent.rs:138
Fenwick::new	Fenwick	src/rust/src/coalescent.rs:153
Fenwick::set	Fenwick	src/rust/src/coalescent.rs:160
Fenwick::total	Fenwick	src/rust/src/coalescent.rs:171
Fenwick::find	Fenwick	src/rust/src/coalescent.rs:182
Fenwick::rebuild	Fenwick	src/rust/src/coalescent.rs:202
Tree::kingman	Tree	src/rust/src/coalescent.rs:258
Tree::branch_len	Tree	src/rust/src/coalescent.rs:391
Tree::refresh_len	Tree	src/rust/src/coalescent.rs:398
Tree::total_length	Tree	src/rust/src/coalescent.rs:403
Tree::tmrca	Tree	src/rust/src/coalescent.rs:407
Tree::sample_point	Tree	src/rust/src/coalescent.rs:419
Tree::float_time	Tree	src/rust/src/coalescent.rs:429
Tree::remove_internal	Tree	src/rust/src/coalescent.rs:514
Tree::insert_internal	Tree	src/rust/src/coalescent.rs:525
Tree::sample_lineage_at	Tree	src/rust/src/coalescent.rs:536
Tree::recombine	Tree	src/rust/src/coalescent.rs:569
Tree::leaf_bits	Tree	src/rust/src/coalescent.rs:642
Tree::mutate	Tree	src/rust/src/coalescent.rs:656
simulate_chromosome	—	src/rust/src/coalescent.rs:684
coalescent_chromosome_core	—	src/rust/src/coalescent.rs:770
Bits::zeros	Bits	src/rust/src/genome.rs:33
Bits::len	Bits	src/rust/src/genome.rs:41
Bits::get	Bits	src/rust/src/genome.rs:46
Bits::set	Bits	src/rust/src/genome.rs:53
Bits::toggle_from	Bits	src/rust/src/genome.rs:69
Bits::flip_all	Bits	src/rust/src/genome.rs:82
Bits::parse_strand	Bits	src/rust/src/genome.rs:109
Bits::to_code	Bits	src/rust/src/genome.rs:139
Bits::clear_tail	Bits	src/rust/src/genome.rs:149
Bits::tail_is_clean	Bits	src/rust/src/genome.rs:166
GenomeLayout::try_new	GenomeLayout	src/rust/src/genome.rs:189
GenomeLayout::n_chr	GenomeLayout	src/rust/src/genome.rs:241
GenomeLayout::n_loci	GenomeLayout	src/rust/src/genome.rs:246
GenomeLayout::chr_positions	GenomeLayout	src/rust/src/genome.rs:251
GenomeLayout::chr_offset	GenomeLayout	src/rust/src/genome.rs:256
GenomeLayout::chr_len	GenomeLayout	src/rust/src/genome.rs:263
write_genotype	—	src/rust/src/genome.rs:273
fnv1a_128	—	src/rust/src/hash.rs:16
stable_hash_core	—	src/rust/src/hash.rs:28
breaks_at	—	src/rust/src/meiosis.rs:49
chromosome_mask	—	src/rust/src/meiosis.rs:63
EventStream::try_new	EventStream	src/rust/src/meiosis.rs:99
EventStream::n_events	EventStream	src/rust/src/meiosis.rs:185
EventStream::slot	EventStream	src/rust/src/meiosis.rs:190
EventStream::block	EventStream	src/rust/src/meiosis.rs:195
EventStream::flip	EventStream	src/rust/src/meiosis.rs:201
genome_mask	—	src/rust/src/meiosis.rs:207
recombine	—	src/rust/src/meiosis.rs:224
Design::parse	Design	src/rust/src/meiosis.rs:251
Design::events_per_progeny	Design	src/rust/src/meiosis.rs:264
Parents::parse	Parents	src/rust/src/meiosis.rs:281
progeny_count	—	src/rust/src/meiosis.rs:299
mate_haplotypes	—	src/rust/src/meiosis.rs:324
mate_core	—	src/rust/src/meiosis.rs:383
mate_many	—	src/rust/src/meiosis.rs:425
meiosis_core	—	src/rust/src/meiosis.rs:562
gamete_masks_core	—	src/rust/src/meiosis.rs:601
mate_haplotypes_core	—	src/rust/src/meiosis.rs:642
mate_many_core	—	src/rust/src/meiosis.rs:701
coding	—	src/rust/src/numeric.rs:8
parse_model	—	src/rust/src/numeric.rs:28
size_arg	—	src/rust/src/numeric.rs:42
numericalize	—	src/rust/src/numeric.rs:66
numericalize_core	—	src/rust/src/numeric.rs:221

24.6 Rust tests and test helpers

Verification code, separated from implemented methods. Includes the test-specific Bits::tail_is_clean definition.

Definition	Enclosing scope	Source
Tree::lineages_at	test configuration	src/rust/src/coalescent.rs:413
Tree::lineages_crossing	test configuration	src/rust/src/coalescent.rs:502
harmonic	test configuration	src/rust/src/coalescent.rs:832
xoshiro_reference_stream	test configuration	src/rust/src/coalescent.rs:837
unif_and_below_are_in_range	test configuration	src/rust/src/coalescent.rs:847
kingman_tmrca_mean_constant_size	test configuration	src/rust/src/coalescent.rs:857
kingman_length_mean_is_harmonic	test configuration	src/rust/src/coalescent.rs:876
pair_tmrca_under_a_size_change	test configuration	src/rust/src/coalescent.rs:894
tree_at_end	test configuration	src/rust/src/coalescent.rs:916
smc_prime_keeps_the_marginal_tree_kingman	test configuration	src/rust/src/coalescent.rs:929
marginal_tree_follows_the_demography_after_recombination	test configuration	src/rust/src/coalescent.rs:958
tree_stays_consistent_through_recombination	test configuration	src/rust/src/coalescent.rs:977
seeded_runs_reproduce	test configuration	src/rust/src/coalescent.rs:1005
reservoir_keeps_the_requested_number_in_order	test configuration	src/rust/src/coalescent.rs:1014
overflowing_rates_are_errors_not_hangs	test configuration	src/rust/src/coalescent.rs:1028
extreme_history_sizes_are_errors_not_panics	test configuration	src/rust/src/coalescent.rs:1034
lineage_sampler_is_uniform_over_the_lineages_at_tau	test configuration	src/rust/src/coalescent.rs:1058
two_locus_correlation_is_smc_prime_not_smc	test configuration	src/rust/src/coalescent.rs:1088
check_split_invariants	test configuration	src/rust/src/coalescent.rs:1125
split_keeps_demes_isolated_until_the_join	test configuration	src/rust/src/coalescent.rs:1151
between_deme_pair_tmrca_is_join_plus_half	test configuration	src/rust/src/coalescent.rs:1167
within_deme_sample_before_a_late_join_is_kingman	test configuration	src/rust/src/coalescent.rs:1205
split_inputs_are_validated	test configuration	src/rust/src/coalescent.rs:1227
Bits::from_code	test configuration	src/rust/src/genome.rs:94
Bits::tail_is_clean	test configuration	src/rust/src/genome.rs:159
all_ones_via_flip_all_keeps_the_tail_clean	test configuration	src/rust/src/genome.rs:294
flip_all_is_an_involution_and_keeps_tail_clean	test configuration	src/rust/src/genome.rs:307
toggle_from_covers_the_suffix_only	test configuration	src/rust/src/genome.rs:324
toggle_from_at_or_past_n_is_a_noop	test configuration	src/rust/src/genome.rs:338
toggle_from_twice_cancels	test configuration	src/rust/src/genome.rs:351
code_round_trips_ascending	test configuration	src/rust/src/genome.rs:363
genotype_uses_loci_major_layout	test configuration	src/rust/src/genome.rs:374
genotype_is_symmetric_in_the_two_strands_only_for_homozygotes	test configuration	src/rust/src/genome.rs:396
layout_rejects_mismatched_counts	test configuration	src/rust/src/genome.rs:410
layout_rejects_empty_chromosome_na_and_no_chromosomes	test configuration	src/rust/src/genome.rs:418
layout_rejects_non_finite_and_decreasing_positions_but_allows_ties	test configuration	src/rust/src/genome.rs:426
strands_must_match_the_layout_and_the_binary_alphabet	test configuration	src/rust/src/genome.rs:436
layout_slices_chromosomes_in_order	test configuration	src/rust/src/genome.rs:446
empty_input_is_the_offset_basis	test configuration	src/rust/src/hash.rs:44
prime_is_two_pow_88_plus_two_pow_8_plus_0x3b	test configuration	src/rust/src/hash.rs:49
known_answer_vectors	test configuration	src/rust/src/hash.rs:54
distinct_inputs_differ_and_repeat_equally	test configuration	src/rust/src/hash.rs:68
pos	test configuration	src/rust/src/meiosis.rs:770
layout	test configuration	src/rust/src/meiosis.rs:774
stream	test configuration	src/rust/src/meiosis.rs:778
breaks_counts_positions_at_or_below_the_chiasma	test configuration	src/rust/src/meiosis.rs:788
a_chiasma_exactly_on_a_marker_leaves_it_upstream	test configuration	src/rust/src/meiosis.rs:797
zero_chiasmata_gives_all_zero_or_all_one_by_the_flip	test configuration	src/rust/src/meiosis.rs:807
one_chiasma_toggles_the_downstream_segment_inclusively	test configuration	src/rust/src/meiosis.rs:816
a_chiasma_upstream_of_the_first_marker_toggles_everything	test configuration	src/rust/src/meiosis.rs:826
two_chiasmata_restore_the_intervening_segment	test configuration	src/rust/src/meiosis.rs:834
duplicate_chiasmata_cancel_and_order_is_irrelevant	test configuration	src/rust/src/meiosis.rs:841
single_locus_chromosome	test configuration	src/rust/src/meiosis.rs:854
event_stream_slices_ragged_blocks_in_order	test configuration	src/rust/src/meiosis.rs:863
err_of	test configuration	src/rust/src/meiosis.rs:881
event_stream_rejects_a_count_chiasmata_mismatch	test configuration	src/rust/src/meiosis.rs:889
event_stream_rejects_negative_and_na_counts	test configuration	src/rust/src/meiosis.rs:901
event_stream_rejects_non_binary_flips	test configuration	src/rust/src/meiosis.rs:910
event_stream_rejects_ragged_shapes	test configuration	src/rust/src/meiosis.rs:919
event_stream_rejects_non_finite_and_out_of_range_chiasmata	test configuration	src/rust/src/meiosis.rs:926
chiasma_range_is_per_chromosome	test configuration	src/rust/src/meiosis.rs:944
genome_mask_concatenates_chromosomes_ascending	test configuration	src/rust/src/meiosis.rs:952
recombine_picks_cis_where_the_mask_is_set	test configuration	src/rust/src/meiosis.rs:960
dh_progeny_are_fully_homozygous	test configuration	src/rust/src/meiosis.rs:968
cross_takes_cis_from_the_first_parent	test configuration	src/rust/src/meiosis.rs:977
events_are_consumed_progeny_major	test configuration	src/rust/src/meiosis.rs:989
dh_haplotypes_are_segments_of_the_parent_strands_not_the_mask	test configuration	src/rust/src/meiosis.rs:1002
mate_core_agrees_with_mate_haplotypes	test configuration	src/rust/src/meiosis.rs:1024
the_event_budget_must_match_n_prog_exactly	test configuration	src/rust/src/meiosis.rs:1037
progeny_count_rejects_na_and_negative	test configuration	src/rust/src/meiosis.rs:1057
parents_must_match_the_layout	test configuration	src/rust/src/meiosis.rs:1065
design_parsing_and_event_budget	test configuration	src/rust/src/meiosis.rs:1074
entry_points_return_errors_not_panics	test configuration	src/rust/src/meiosis.rs:1085
bits_to_i32	test configuration	src/rust/src/meiosis.rs:1151
mate_many_equals_sequential_mate_haplotypes	test configuration	src/rust/src/meiosis.rs:1159
mate_many_rejects_inconsistent_inputs	test configuration	src/rust/src/meiosis.rs:1225
mate_many_core_returns_errors_not_panics	test configuration	src/rust/src/meiosis.rs:1254
run	test configuration	src/rust/src/numeric.rs:253
additive_101_unflipped_and_flipped	test configuration	src/rust/src/numeric.rs:266
each_snp_uses_its_own_flip	test configuration	src/rust/src/numeric.rs:284
full_valid_grid_matches_an_independent_mapper	test configuration	src/rust/src/numeric.rs:293
malformed_inputs_are_errors_not_defaults	test configuration	src/rust/src/numeric.rs:362
size_args_reject_na_and_negative	test configuration	src/rust/src/numeric.rs:385