simplePHENOTYPES — function inventory

Inventory of package-owned R and Rust source at revision 3c000630a5e566640b5eadfd429d0fcbfd5349b9. Generated from the current working tree. R functions were extracted with R's parser; Rust declarations were scanned from src/rust/src/. Source links are pinned to this revision.

This inventory supports the decision about documentation depth. It is not a theory audit. A function count is not a method count: one public function may expose several scientific methods, and one method may require many internal helpers.

Category	Definitions
Public R functions	63
Registered R methods	9
Modern internal R	331
Legacy internal R	44
R-to-Rust bindings	7
Local R helpers	102
Rust implementation	73
Rust tests and test helpers	83

Anonymous R callbacks (351) are excluded from the named list. Vendored crates, generated native registration glue, tests outside Rust source, development scripts, and historical context/ sources are outside scope. Rust test functions are included in their own section. R wrappers and their Rust kernels are separate definitions of the same cross-language interface.

Public R functions 63

User-facing functions exported in NAMESPACE. Worked examples belong in the main book.

R/cross_breed.R 3

Function / method	Enclosing scope	Source
`breed_composition`	—	R/cross_breed.R:27
`crossbreed`	—	R/cross_breed.R:248
`heterosis`	—	R/cross_breed.R:123

R/cross_haplotypes.R 2

Function / method	Enclosing scope	Source
`haplotypes`	—	R/cross_haplotypes.R:206
`population_from_haplotypes`	—	R/cross_haplotypes.R:82

R/cross_map.R 1

Function / method	Enclosing scope	Source
`synthetic_map`	—	R/cross_map.R:77

R/cross_mate.R 2

Function / method	Enclosing scope	Source
`mate`	—	R/cross_mate.R:74
`mating_design`	—	R/cross_mate.R:360

R/cross_mating.R 3

Function / method	Enclosing scope	Source
`cross`	—	R/cross_mating.R:617
`double_haploid`	—	R/cross_mating.R:686
`selfcross`	—	R/cross_mating.R:647

R/cross_pedigree.R 2

Function / method	Enclosing scope	Source
`families`	—	R/cross_pedigree.R:307
`parentage`	—	R/cross_pedigree.R:262

R/cross_population.R 7

Function / method	Enclosing scope	Source
`additive_value`	—	R/cross_population.R:735
`as_population`	—	R/cross_population.R:90
`dosages`	—	R/cross_population.R:621
`genotypic_value`	—	R/cross_population.R:805
`gxe_value`	—	R/cross_population.R:860
`n_individuals`	—	R/cross_population.R:570
`phenotype_value`	—	R/cross_population.R:1004

R/founders_coalescent.R 1

Function / method	Enclosing scope	Source
`founders_coalescent`	—	R/founders_coalescent.R:186

R/grammar_complex.R 1

Function / method	Enclosing scope	Source
`complex_phenotypes`	—	R/grammar_complex.R:64

R/grammar_layers.R 4

Function / method	Enclosing scope	Source
`additive`	—	R/grammar_layers.R:189
`dominance`	—	R/grammar_layers.R:467
`epistasis`	—	R/grammar_layers.R:722
`vqtl`	—	R/grammar_layers.R:914

R/grammar_simulate_phenotype.R 1

Function / method	Enclosing scope	Source
`simulate_phenotype`	—	R/grammar_simulate_phenotype.R:352

R/grammar_threshold.R 3

Function / method	Enclosing scope	Source
`coheritability`	—	R/grammar_threshold.R:180
`cor_ar1`	—	R/grammar_threshold.R:220
`liability_threshold`	—	R/grammar_threshold.R:54

R/grammar_trait.R 1

Function / method	Enclosing scope	Source
`population_trait`	—	R/grammar_trait.R:185

R/io_as_numeric.R 1

Function / method	Enclosing scope	Source
`as_numeric`	—	R/io_as_numeric.R:193

R/io_write.R 7

Function / method	Enclosing scope	Source
`genetic_values`	—	R/io_write.R:1229
`mediation_split`	—	R/io_write.R:1267
`phenotypes_long`	—	R/io_write.R:21
`phenotypes_wide`	—	R/io_write.R:45
`qtn_table`	—	R/io_write.R:1394
`write_phenotypes`	—	R/io_write.R:229
`write_qtn_table`	—	R/io_write.R:353

R/legacy_create_phenotypes.R 1

Function / method	Enclosing scope	Source
`create_phenotypes`	—	R/legacy_create_phenotypes.R:397

R/qc_filter_geno.R 1

Function / method	Enclosing scope	Source
`filter_geno`	—	R/qc_filter_geno.R:167

R/select_blup.R 4

Function / method	Enclosing scope	Source
`a_matrix`	—	R/select_blup.R:61
`predict_ebv`	—	R/select_blup.R:300
`prediction_accuracy`	—	R/select_blup.R:725
`selection_methods`	—	R/select_blup.R:777

R/select_combining.R 2

Function / method	Enclosing scope	Source
`combining_ability`	—	R/select_combining.R:130
`template_effects`	—	R/select_combining.R:371

R/select_ind.R 1

Function / method	Enclosing scope	Source
`select_ind`	—	R/select_ind.R:298

R/select_mabc.R 2

Function / method	Enclosing scope	Source
`mabc_select`	—	R/select_mabc.R:121
`recurrent_parent_recovery`	—	R/select_mabc.R:257

R/select_marker.R 1

Function / method	Enclosing scope	Source
`marker_select`	—	R/select_marker.R:77

R/select_ocs.R 3

Function / method	Enclosing scope	Source
`g_matrix`	—	R/select_ocs.R:44
`optimum_contribution`	—	R/select_ocs.R:180
`sample_parents`	—	R/select_ocs.R:411

R/select_progeny.R 1

Function / method	Enclosing scope	Source
`progeny_test`	—	R/select_progeny.R:91

R/select_schemes.R 4

Function / method	Enclosing scope	Source
`bulk`	—	R/select_schemes.R:144
`pedigree`	—	R/select_schemes.R:263
`recurrent_selection`	—	R/select_schemes.R:350
`single_seed_descent`	—	R/select_schemes.R:102

R/select_usefulness.R 1

Function / method	Enclosing scope	Source
`cross_usefulness`	—	R/select_usefulness.R:103

R/transcriptome_counts.R 1

Function / method	Enclosing scope	Source
`observe_counts`	—	R/transcriptome_counts.R:57

R/transcriptome_layer.R 1

Function / method	Enclosing scope	Source
`transcriptome`	—	R/transcriptome_layer.R:176

R/transcriptome_simulate.R 1

Function / method	Enclosing scope	Source
`simulate_transcriptome`	—	R/transcriptome_simulate.R:221

Function / method	Enclosing scope	Source
`[.Population`	—	R/cross_population.R:588
`print.Population`	—	R/cross_population.R:1166

Function / method	Enclosing scope	Source
`plot.phenotype_sim`	—	R/grammar_plot.R:28

Function / method	Enclosing scope	Source
`print.phenotype_sim`	—	R/grammar_simulate_phenotype.R:1097

Function / method	Enclosing scope	Source
`print.combining_ability`	—	R/select_combining.R:331

Function / method	Enclosing scope	Source
`print.ocs`	—	R/select_ocs.R:333

Function / method	Enclosing scope	Source
`c.Population`	—	R/select_schemes.R:25

Function / method	Enclosing scope	Source
`predict.transcriptome_sim`	—	R/transcriptome_simulate.R:789
`print.transcriptome_sim`	—	R/transcriptome_simulate.R:1119

Modern internal R 331

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

R/arch_independent.R 6

Function / method	Enclosing scope	Source
`.candidate_hint`	—	R/arch_independent.R:125
`.candidate_markers`	—	R/arch_independent.R:114
`.draw_qtn`	—	R/arch_independent.R:21
`.draw_qtn_distinct_chr`	—	R/arch_independent.R:56
`.draw_qtn_pairs`	—	R/arch_independent.R:81
`.type_occurrence`	—	R/arch_independent.R:139

R/arch_ld.R 5

Function / method	Enclosing scope	Source
`.apply_ld_phase`	—	R/arch_ld.R:245
`.draw_qtn_ld`	—	R/arch_ld.R:62
`.ld_check_cross_layer`	—	R/arch_ld.R:367
`.ld_prior_loci`	—	R/arch_ld.R:397
`.ld_user_pairs`	—	R/arch_ld.R:279

R/cross_breed.R 1

Function / method	Enclosing scope	Source
`.check_breeds`	—	R/cross_breed.R:159

R/cross_map.R 1

Function / method	Enclosing scope	Source
`.recycle_by_chr`	—	R/cross_map.R:194

R/cross_mate.R 1

Function / method	Enclosing scope	Source
`.check_plan`	—	R/cross_mate.R:260

R/cross_mating.R 8

Function / method	Enclosing scope	Source
`.check_interference`	—	R/cross_mating.R:136
`.check_meiosis_call`	—	R/cross_mating.R:284
`.cite_isqg`	—	R/cross_mating.R:16
`.draw_meiosis`	—	R/cross_mating.R:53
`.draw_meiosis_interference`	—	R/cross_mating.R:215
`.mate`	—	R/cross_mating.R:429
`.mate_many`	—	R/cross_mating.R:372
`.meiosis_layout`	—	R/cross_mating.R:332

R/cross_pedigree.R 9

Function / method	Enclosing scope	Source
`.ensure_pedigree`	—	R/cross_pedigree.R:144
`.founder_pedigree`	—	R/cross_pedigree.R:97
`.key_elements`	—	R/cross_pedigree.R:64
`.key_part`	—	R/cross_pedigree.R:42
`.mating_pedigree`	—	R/cross_pedigree.R:192
`.pedigree_ancestors`	—	R/cross_pedigree.R:171
`.pedigree_relabel`	—	R/cross_pedigree.R:221
`.pedigree_union`	—	R/cross_pedigree.R:157
`.stable_key`	—	R/cross_pedigree.R:25

R/cross_population.R 16

Function / method	Enclosing scope	Source
`.check_cm_units`	—	R/cross_population.R:394
`.check_counted`	—	R/cross_population.R:281
`.check_map`	—	R/cross_population.R:348
`.check_orientation`	—	R/cross_population.R:504
`.check_pool`	—	R/cross_population.R:189
`.check_population`	—	R/cross_population.R:1206
`.check_single`	—	R/cross_population.R:1216
`.chr_rank`	—	R/cross_population.R:444
`.geno_marker_names`	—	R/cross_population.R:1112
`.gxe_args`	—	R/cross_population.R:1132
`.make_map`	—	R/cross_population.R:214
`.merge_counted`	—	R/cross_population.R:247
`.new_population`	—	R/cross_population.R:333
`.resolve_geno_qtn`	—	R/cross_population.R:636
`.same_map`	—	R/cross_population.R:419
`.valid_counted`	—	R/cross_population.R:467

R/effects_pleioarch.R 19

Function / method	Enclosing scope	Source
`.check_pleio_feasible`	—	R/effects_pleioarch.R:870
`.cite_main`	—	R/effects_pleioarch.R:814
`.cite_pleioarch`	—	R/effects_pleioarch.R:799
`.draw_mvnorm`	—	R/effects_pleioarch.R:929
`.draw_univariate`	—	R/effects_pleioarch.R:944
`.pleio_check_layout`	—	R/effects_pleioarch.R:341
`.pleio_check_user_units`	—	R/effects_pleioarch.R:999
`.pleio_check_zero_var`	—	R/effects_pleioarch.R:246
`.pleio_controlled`	—	R/effects_pleioarch.R:1035
`.pleio_cor_matrix`	—	R/effects_pleioarch.R:957
`.pleio_draw`	—	R/effects_pleioarch.R:65
`.pleio_nonadditive_draw`	—	R/effects_pleioarch.R:493
`.pleio_partition`	—	R/effects_pleioarch.R:288
`.pleio_pi_vector`	—	R/effects_pleioarch.R:829
`.pleio_single_unit_consequence`	—	R/effects_pleioarch.R:412
`.pleio_total_cor_check`	—	R/effects_pleioarch.R:724
`.pleio_unit_effects`	—	R/effects_pleioarch.R:583
`.pleio_units`	—	R/effects_pleioarch.R:536
`.pleio_user_layout`	—	R/effects_pleioarch.R:385

R/effects_series.R 2

Function / method	Enclosing scope	Source
`.draw_residual`	—	R/effects_series.R:85
`.effect_series`	—	R/effects_series.R:23

R/founders_coalescent.R 2

Function / method	Enclosing scope	Source
`.coalescent_chromosome`	—	R/founders_coalescent.R:38
`.coalescent_preset`	—	R/founders_coalescent.R:300

R/grammar_layers.R 22

Function / method	Enclosing scope	Source
`.add_layer`	—	R/grammar_layers.R:1102
`.apply_phase`	—	R/grammar_layers.R:1482
`.check_sim`	—	R/grammar_layers.R:997
`.cite_vqtl`	—	R/grammar_layers.R:1459
`.complex_terminal_msg`	—	R/grammar_layers.R:1513
`.dom_hetless`	—	R/grammar_layers.R:1178
`.dom_partial_hetless`	—	R/grammar_layers.R:1194
`.draw_layer`	—	R/grammar_layers.R:1129
`.epi_dead_status`	—	R/grammar_layers.R:1240
`.het_varies`	—	R/grammar_layers.R:1162
`.last_layer_of_type`	—	R/grammar_layers.R:1030
`.one_call_hint`	—	R/grammar_layers.R:1038
`.orthogonal_d_series`	—	R/grammar_layers.R:361
`.orthogonal_hetless_d`	—	R/grammar_layers.R:1214
`.rep_qtn`	—	R/grammar_layers.R:1261
`.require_markers`	—	R/grammar_layers.R:1499
`.resolve_epi_qtn`	—	R/grammar_layers.R:1361
`.resolve_interaction_type`	—	R/grammar_layers.R:1435
`.resolve_n_qtn`	—	R/grammar_layers.R:1007
`.resolve_prop`	—	R/grammar_layers.R:1055
`.resolve_qtn_arg`	—	R/grammar_layers.R:1275
`.warn_monomorphic`	—	R/grammar_layers.R:1335

R/grammar_plot.R 6

Function / method	Enclosing scope	Source
`.plot_cor`	—	R/grammar_plot.R:144
`.plot_effects`	—	R/grammar_plot.R:114
`.plot_genetic_target`	—	R/grammar_plot.R:135
`.plot_hist`	—	R/grammar_plot.R:106
`.plot_variance`	—	R/grammar_plot.R:85
`.var_budget_matrix`	—	R/grammar_plot.R:71

R/grammar_realize.R 32

Function / method	Enclosing scope	Source
`.Random.seed_safe`	—	R/grammar_realize.R:1023
`.ad_partition`	—	R/grammar_realize.R:872
`.ad_report`	—	R/grammar_realize.R:842
`.apply_vqtl`	—	R/grammar_realize.R:599
`.avg_effect`	—	R/grammar_realize.R:182
`.breeding_value_matrix`	—	R/grammar_realize.R:236
`.bv_from_effects`	—	R/grammar_realize.R:316
`.check_h2_complete`	—	R/grammar_realize.R:1132
`.component_raw`	—	R/grammar_realize.R:484
`.correlated_residuals`	—	R/grammar_realize.R:924
`.epi_unit_column`	—	R/grammar_realize.R:579
`.genetic_matrix`	—	R/grammar_realize.R:125
`.genetic_value_matrix`	—	R/grammar_realize.R:394
`.has_genetic_transcriptome`	—	R/grammar_realize.R:377
`.layer_qtn_effect`	—	R/grammar_realize.R:648
`.layer_scaled_effects`	—	R/grammar_realize.R:343
`.layer_sd`	—	R/grammar_realize.R:549
`.mediation_budget`	—	R/grammar_realize.R:730
`.orthogonal_var_split`	—	R/grammar_realize.R:778
`.realize_phenotype`	—	R/grammar_realize.R:35
`.realized_h2`	—	R/grammar_realize.R:1078
`.resid_cor_factor`	—	R/grammar_realize.R:951
`.restore_seed`	—	R/grammar_realize.R:1034
`.scaled_component`	—	R/grammar_realize.R:557
`.seeded_residual`	—	R/grammar_realize.R:1010
`.sim_reps`	—	R/grammar_realize.R:1113
`.trait_mean`	—	R/grammar_realize.R:1173
`.transcriptome_matrix`	—	R/grammar_realize.R:410
`.tx_raw`	—	R/grammar_realize.R:454
`.validate_rep`	—	R/grammar_realize.R:659
`.validate_resid_cor`	—	R/grammar_realize.R:965
`.variance_budget`	—	R/grammar_realize.R:671

R/grammar_simulate_phenotype.R 27

Function / method	Enclosing scope	Source
`.build_one_call`	—	R/grammar_simulate_phenotype.R:767
`.check_arch_args`	—	R/grammar_simulate_phenotype.R:611
`.expand_prop`	—	R/grammar_simulate_phenotype.R:1342
`.expression_foundation`	—	R/grammar_simulate_phenotype.R:963
`.fmt_int`	—	R/grammar_simulate_phenotype.R:1268
`.geno_cols`	—	R/grammar_simulate_phenotype.R:991
`.geno_label`	—	R/grammar_simulate_phenotype.R:561
`.is_one_call`	—	R/grammar_simulate_phenotype.R:760
`.layer_seed`	—	R/grammar_simulate_phenotype.R:1079
`.marker_maf_ref`	—	R/grammar_simulate_phenotype.R:1050
`.marker_stats_ref`	—	R/grammar_simulate_phenotype.R:1022
`.min_ind_reason`	—	R/grammar_simulate_phenotype.R:904
`.n_word`	—	R/grammar_simulate_phenotype.R:902
`.normalize_geno`	—	R/grammar_simulate_phenotype.R:795
`.print_ad_report`	—	R/grammar_simulate_phenotype.R:1287
`.print_reps_note`	—	R/grammar_simulate_phenotype.R:1237
`.print_threshold_note`	—	R/grammar_simulate_phenotype.R:1214
`.qtn_count_label`	—	R/grammar_simulate_phenotype.R:1361
`.select_individuals`	—	R/grammar_simulate_phenotype.R:922
`.small_expr`	—	R/grammar_simulate_phenotype.R:583
`.total_genetic_prop`	—	R/grammar_simulate_phenotype.R:1317
`.total_variance_prop`	—	R/grammar_simulate_phenotype.R:1333
`.validate_count`	—	R/grammar_simulate_phenotype.R:694
`.validate_flag`	—	R/grammar_simulate_phenotype.R:725
`.validate_proportion`	—	R/grammar_simulate_phenotype.R:748
`.validate_reps`	—	R/grammar_simulate_phenotype.R:711
`.validate_seed`	—	R/grammar_simulate_phenotype.R:735

R/grammar_threshold.R 3

Function / method	Enclosing scope	Source
`.apply_threshold`	—	R/grammar_threshold.R:117
`.liability_table`	—	R/grammar_threshold.R:102
`.threshold_cuts`	—	R/grammar_threshold.R:140

R/grammar_trait.R 9

Function / method	Enclosing scope	Source
`.epi_itype`	—	R/grammar_trait.R:299
`.epi_locus_centers`	—	R/grammar_trait.R:310
`.freeze_trait`	—	R/grammar_trait.R:34
`.frozen_layer_ignored`	—	R/grammar_trait.R:249
`.pop_trait`	—	R/grammar_trait.R:110
`.shared_trait`	—	R/grammar_trait.R:117
`.simulate_from_trait`	—	R/grammar_trait.R:202
`.trait_layers_on`	—	R/grammar_trait.R:129
`.variance_budget_frozen`	—	R/grammar_trait.R:266

R/io_detect_format.R 12

Function / method	Enclosing scope	Source
`.call_to_letters`	—	R/io_detect_format.R:52
`.check_unique_ids`	—	R/io_detect_format.R:388
`.detect_df_format`	—	R/io_detect_format.R:157
`.fill_missing_ids`	—	R/io_detect_format.R:415
`.gds_needed`	—	R/io_detect_format.R:67
`.het_to_letters`	—	R/io_detect_format.R:27
`.hmp_header_match`	—	R/io_detect_format.R:151
`.sniff_text_signature`	—	R/io_detect_format.R:129
`assemble_output`	—	R/io_detect_format.R:373
`compute_flip`	—	R/io_detect_format.R:342
`detect_format`	—	R/io_detect_format.R:82
`parse_hapmap_chars_to_raw`	—	R/io_detect_format.R:223

R/io_format_conversion.R 2

Function / method	Enclosing scope	Source
`.label_hash`	—	R/io_format_conversion.R:277
`format_conversion`	—	R/io_format_conversion.R:51

R/io_read_formats.R 23

Function / method	Enclosing scope	Source
`.add_counted_column`	—	R/io_read_formats.R:133
`.allele_label`	—	R/io_read_formats.R:177
`.apply_coding`	—	R/io_read_formats.R:18
`.as_pos`	—	R/io_read_formats.R:187
`.counted_allele`	—	R/io_read_formats.R:84
`.counted_col_values`	—	R/io_read_formats.R:124
`.has_counted_col`	—	R/io_read_formats.R:107
`.n_meta`	—	R/io_read_formats.R:116
`.normalize_numeric_schema`	—	R/io_read_formats.R:297
`.plink_cm`	—	R/io_read_formats.R:823
`.read_gds_to_raw`	—	R/io_read_formats.R:497
`.vcf_classify_gt`	—	R/io_read_formats.R:541
`.vcf_scan_calls`	—	R/io_read_formats.R:590
`.vcf_warn_dropped`	—	R/io_read_formats.R:560
`.write_numeric`	—	R/io_read_formats.R:160
`handle_bed`	—	R/io_read_formats.R:839
`handle_finalreport`	—	R/io_read_formats.R:925
`handle_gds`	—	R/io_read_formats.R:780
`handle_hapmap`	—	R/io_read_formats.R:200
`handle_numeric`	—	R/io_read_formats.R:322
`handle_ped`	—	R/io_read_formats.R:880
`handle_table`	—	R/io_read_formats.R:379
`handle_vcf`	—	R/io_read_formats.R:639

R/io_write.R 34

Function / method	Enclosing scope	Source
`.canonical_path`	—	R/io_write.R:563
`.causal_markers`	—	R/io_write.R:926
`.check_path_arg`	—	R/io_write.R:399
`.commit_staged`	—	R/io_write.R:805
`.companion_paths`	—	R/io_write.R:507
`.dosage_block`	—	R/io_write.R:979
`.export_sim`	—	R/io_write.R:966
`.file_rename`	—	R/io_write.R:685
`.json_classed_elements`	—	R/io_write.R:1139
`.json_escape`	—	R/io_write.R:1166
`.json_vec`	—	R/io_write.R:1158
`.json_vec_elements`	—	R/io_write.R:1111
`.marker_json_objects`	—	R/io_write.R:1072
`.marker_meta`	—	R/io_write.R:900
`.preflight_paths`	—	R/io_write.R:650
`.qtn_table_reps`	—	R/io_write.R:435
`.qtn_var`	—	R/io_write.R:1288
`.random_token`	—	R/io_write.R:691
`.remove_stage_dirs`	—	R/io_write.R:741
`.require_jsonlite`	—	R/io_write.R:388
`.resolve_reps`	—	R/io_write.R:411
`.sibling_path`	—	R/io_write.R:491
`.stage_dir`	—	R/io_write.R:721
`.staged_write`	—	R/io_write.R:770
`.staging_ext`	—	R/io_write.R:703
`.tx_qtn_var`	—	R/io_write.R:1328
`.unicode_nfd`	—	R/io_write.R:588
`.whole_to_integer`	—	R/io_write.R:1057
`.with_c_numeric`	—	R/io_write.R:472
`.write_json_rows`	—	R/io_write.R:456
`.write_marker_file`	—	R/io_write.R:999
`.write_qtn_table_to`	—	R/io_write.R:371
`.write_split_markers`	—	R/io_write.R:941
`.write_target`	—	R/io_write.R:611

R/qc_filter_geno.R 13

Function / method	Enclosing scope	Source
`.check_maf_arg`	—	R/qc_filter_geno.R:449
`.cite_ld`	—	R/qc_filter_geno.R:1190
`.ld_prune`	—	R/qc_filter_geno.R:490
`.ld_spec`	—	R/qc_filter_geno.R:423
`.ld_sweep`	—	R/qc_filter_geno.R:524
`.plink_blocks_chrom`	—	R/qc_filter_geno.R:1066
`.plink_blocks_classify`	—	R/qc_filter_geno.R:978
`.plink_calc_lnlike`	—	R/qc_filter_geno.R:884
`.plink_calc_lnlike_quantile`	—	R/qc_filter_geno.R:952
`.plink_cubic_roots`	—	R/qc_filter_geno.R:902
`.plink_em_hethet`	—	R/qc_filter_geno.R:822
`.plink_hap_rsq`	—	R/qc_filter_geno.R:796
`.subset_population_markers`	—	R/qc_filter_geno.R:396

R/qc_ld_methods.R 1

Function / method	Enclosing scope	Source
`.gabriel_blocks`	—	R/qc_ld_methods.R:23

R/select_blup.R 7

Function / method	Enclosing scope	Source
`.blup_variances`	—	R/select_blup.R:656
`.check_pheno_matrix`	—	R/select_blup.R:427
`.check_relationship`	—	R/select_blup.R:587
`.founder_inbreeding`	—	R/select_blup.R:113
`.gblup_marker_effects`	—	R/select_blup.R:695
`.mt_variances`	—	R/select_blup.R:467
`.predict_ebv_mt`	—	R/select_blup.R:515

R/select_bqp.R 6

Function / method	Enclosing scope	Source
`.bqp_check_args`	—	R/select_bqp.R:104
`.bqp_g`	—	R/select_bqp.R:85
`.bqp_inputs`	—	R/select_bqp.R:36
`.bqp_solve`	—	R/select_bqp.R:130
`.cite_bqp`	—	R/select_bqp.R:16
`.sel_bqp`	—	R/select_bqp.R:220

R/select_combining.R 5

Function / method	Enclosing scope	Source
`.check_ad`	—	R/select_combining.R:226
`.check_distinct`	—	R/select_combining.R:212
`.decompose_ca`	—	R/select_combining.R:310
`.expected_cross_means`	—	R/select_combining.R:244
`.simulate_cross_means`	—	R/select_combining.R:260

R/select_ind.R 14

Function / method	Enclosing scope	Source
`.check_direction`	—	R/select_ind.R:618
`.check_trait_index`	—	R/select_ind.R:603
`.combined_score`	—	R/select_ind.R:858
`.criterion_values`	—	R/select_ind.R:630
`.index_score`	—	R/select_ind.R:753
`.index_weights`	—	R/select_ind.R:799
`.quadratic_index_score`	—	R/select_ind.R:713
`.resolve_keep`	—	R/select_ind.R:559
`.resolve_n_per_family`	—	R/select_ind.R:503
`.sel_among_family`	—	R/select_ind.R:967
`.sel_top`	—	R/select_ind.R:910
`.sel_within_family`	—	R/select_ind.R:917
`.select_culling`	—	R/select_ind.R:1004
`.selection_result`	—	R/select_ind.R:984

R/select_mabc.R 9

Function / method	Enclosing scope	Source
`.mabc_check_flanks`	—	R/select_mabc.R:364
`.mabc_check_weights`	—	R/select_mabc.R:471
`.mabc_founders`	—	R/select_mabc.R:295
`.mabc_interval`	—	R/select_mabc.R:442
`.mabc_markers`	—	R/select_mabc.R:318
`.mabc_parse_interval`	—	R/select_mabc.R:401
`.mabc_recovery`	—	R/select_mabc.R:457
`.mabc_require_informative`	—	R/select_mabc.R:343
`.mabc_weights`	—	R/select_mabc.R:508

R/select_ocs.R 6

Function / method	Enclosing scope	Source
`.allocate_slots`	—	R/select_ocs.R:473
`.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
`.validate_coancestry_matrix`	—	R/select_ocs.R:509

R/select_schemes.R 9

Function / method	Enclosing scope	Source
`.as_founder_pop`	—	R/select_schemes.R:477
`.bulk_counts`	—	R/select_schemes.R:470
`.check_backed`	—	R/select_schemes.R:449
`.check_phenotyper`	—	R/select_schemes.R:500
`.check_tandem`	—	R/select_schemes.R:420
`.check_tandem_range`	—	R/select_schemes.R:432
`.intermate`	—	R/select_schemes.R:534
`.relabel`	—	R/select_schemes.R:557
`.self_each`	—	R/select_schemes.R:514

R/select_usefulness.R 6

Function / method	Enclosing scope	Source
`.additive_gv`	—	R/select_usefulness.R:221
`.additive_model`	—	R/select_usefulness.R:170
`.intensity_from_p`	—	R/select_usefulness.R:161
`.make_family`	—	R/select_usefulness.R:297
`.resolve_pairs`	—	R/select_usefulness.R:234
`.warn_heterozygous_parents`	—	R/select_usefulness.R:275

R/transcriptome_counts.R 1

Function / method	Enclosing scope	Source
`.tx_count_par`	—	R/transcriptome_counts.R:130

R/transcriptome_layer.R 2

Function / method	Enclosing scope	Source
`.attach_expression`	—	R/transcriptome_layer.R:11
`.tx_cor_design_warning`	—	R/transcriptome_layer.R:300

R/transcriptome_mimic.R 5

Function / method	Enclosing scope	Source
`.greml_h2`	—	R/transcriptome_mimic.R:53
`.tx_estimate_factors`	—	R/transcriptome_mimic.R:111
`.tx_estimate_kappa`	—	R/transcriptome_mimic.R:149
`.tx_grm`	—	R/transcriptome_mimic.R:24
`.tx_mimic_calibrate`	—	R/transcriptome_mimic.R:188

R/transcriptome_simulate.R 5

Function / method	Enclosing scope	Source
`.tx_check_annotation`	—	R/transcriptome_simulate.R:1093
`.tx_mimic_scale`	—	R/transcriptome_simulate.R:985
`.tx_pergene`	—	R/transcriptome_simulate.R:1020
`.tx_ratio`	—	R/transcriptome_simulate.R:1010
`.tx_synthetic_coords`	—	R/transcriptome_simulate.R:1043

R/zzz.R 2

Function / method	Enclosing scope	Source
`.onAttach`	—	R/zzz.R:1
`.unwrap_extendr`	—	R/zzz.R:32

Local R helpers 102

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

R/arch_independent.R 1

Function / method	Enclosing scope	Source
`make_one`	.draw_qtn_pairs	R/arch_independent.R:94

R/arch_ld.R 5

Function / method	Enclosing scope	Source
`chr_block`	.draw_qtn_ld	R/arch_ld.R:91
`per_trait`	.ld_prior_loci	R/arch_ld.R:398
`r2_pair`	.draw_qtn_ld	R/arch_ld.R:128
`r_pair`	.draw_qtn_ld	R/arch_ld.R:121
`window_partners`	.draw_qtn_ld	R/arch_ld.R:102

R/cross_breed.R 2

Function / method	Enclosing scope	Source
`gen_cross`	crossbreed	R/cross_breed.R:278
`record`	crossbreed	R/cross_breed.R:271

R/cross_haplotypes.R 1

Function / method	Enclosing scope	Source
`zero_one`	population_from_haplotypes	R/cross_haplotypes.R:143

R/cross_mate.R 5

Function / method	Enclosing scope	Source
`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
`pick`	mate	R/cross_mate.R:126
`try_slot`	mating_design	R/cross_mate.R:432

R/cross_mating.R 2

Function / method	Enclosing scope	Source
`num1`	.check_interference	R/cross_mating.R:167
`sub`	.check_interference	R/cross_mating.R:144

R/cross_pedigree.R 5

Function / method	Enclosing scope	Source
`digit_strand`	.founder_pedigree	R/cross_pedigree.R:110
`pid`	parentage	R/cross_pedigree.R:271
`pid`	families	R/cross_pedigree.R:315
`st`	.mating_pedigree	R/cross_pedigree.R:203
`strand_part`	.founder_pedigree	R/cross_pedigree.R:113

R/cross_population.R 2

Function / method	Enclosing scope	Source
`close_to`	.same_map	R/cross_population.R:420
`draw`	phenotype_value	R/cross_population.R:1078

R/effects_pleioarch.R 5

Function / method	Enclosing scope	Source
`as_units`	.pleio_unit_effects	R/effects_pleioarch.R:588
`fmt`	.pleio_total_cor_check	R/effects_pleioarch.R:749
`pick`	.pleio_total_cor_check	R/effects_pleioarch.R:741
`scale_idx`	.pleio_draw	R/effects_pleioarch.R:202
`spec_rows`	.pleio_units	R/effects_pleioarch.R:557

R/founders_coalescent.R 1

Function / method	Enclosing scope	Source
`per_chr`	founders_coalescent	R/founders_coalescent.R:202

R/grammar_layers.R 10

Function / method	Enclosing scope	Source
`as_idx`	.resolve_qtn_arg	R/grammar_layers.R:1280
`build`	additive	R/grammar_layers.R:291
`build`	dominance	R/grammar_layers.R:565
`build`	epistasis	R/grammar_layers.R:790
`build`	vqtl	R/grammar_layers.R:959
`eff_for`	additive	R/grammar_layers.R:287
`eff_for`	dominance	R/grammar_layers.R:521
`eff_for`	epistasis	R/grammar_layers.R:788
`to_idx`	.resolve_epi_qtn	R/grammar_layers.R:1366
`to_mat`	.resolve_epi_qtn	R/grammar_layers.R:1382

R/grammar_realize.R 2

Function / method	Enclosing scope	Source
`loci`	.ad_partition	R/grammar_realize.R:873
`scaled`	.ad_partition	R/grammar_realize.R:879

R/grammar_simulate_phenotype.R 2

Function / method	Enclosing scope	Source
`fmt`	print.phenotype_sim	R/grammar_simulate_phenotype.R:1102
`walk`	.small_expr	R/grammar_simulate_phenotype.R:585

R/io_detect_format.R 2

Function / method	Enclosing scope	Source
`.rows`	parse_hapmap_chars_to_raw	R/io_detect_format.R:302
`is_letter`	parse_hapmap_chars_to_raw	R/io_detect_format.R:238

R/io_read_formats.R 2

Function / method	Enclosing scope	Source
`find_col`	handle_finalreport	R/io_read_formats.R:949
`grab`	handle_vcf	R/io_read_formats.R:715

R/io_write.R 5

Function / method	Enclosing scope	Source
`block`	qtn_table	R/io_write.R:1417
`enc`	.json_classed_elements	R/io_write.R:1140
`gene_block`	qtn_table	R/io_write.R:1442
`rollback`	.commit_staged	R/io_write.R:816
`write_pheno`	write_phenotypes	R/io_write.R:246

R/legacy_Genotypes.R 3

Function / method	Enclosing scope	Source
`numeric_df`	genotypes	R/legacy_Genotypes.R:79
`numify`	genotypes	R/legacy_Genotypes.R:69
`read_one`	genotypes	R/legacy_Genotypes.R:122

R/legacy_QTN_linkage.R 3

Function / method	Enclosing scope	Source
`differs`	.ld_check_indirect	R/legacy_QTN_linkage.R:1935
`out`	.ld_check_indirect	R/legacy_QTN_linkage.R:1930
`pair_ld`	.ld_check_indirect	R/legacy_QTN_linkage.R:1922

R/legacy_QTN_partially_pleiotropic.R 2

Function / method	Enclosing scope	Source
`chk`	.check_partial_counts	R/legacy_QTN_partially_pleiotropic.R:875
`chk_eff`	.check_partial_counts	R/legacy_QTN_partially_pleiotropic.R:889

R/legacy_check_in.R 7

Function / method	Enclosing scope	Source
`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
`ok`	.v1_validate_ld	R/legacy_check_in.R:1224
`ok`	.v1_validate_seed_arith	R/legacy_check_in.R:1294
`whole1`	.v1_validate_basic	R/legacy_check_in.R:1165
`worst_of`	.v1_validate_seed_arith	R/legacy_check_in.R:1285

R/legacy_create_phenotypes.R 1

Function / method	Enclosing scope	Source
`cleanup_outputs`	create_phenotypes	R/legacy_create_phenotypes.R:552

R/qc_filter_geno.R 14

Function / method	Enclosing scope	Source
`clq`	.plink_blocks_classify	R/qc_filter_geno.R:1005
`cor_sub`	.ld_sweep	R/qc_filter_geno.R:594
`counts_of`	.plink_blocks_chrom	R/qc_filter_geno.R:1076
`is_pruned`	.ld_sweep	R/qc_filter_geno.R:591
`is_singular`	.ld_sweep	R/qc_filter_geno.R:600
`lg`	.ld_sweep	R/qc_filter_geno.R:578
`ls`	.ld_sweep	R/qc_filter_geno.R:585
`maf_of`	.ld_sweep	R/qc_filter_geno.R:593
`note`	filter_geno	R/qc_filter_geno.R:304
`set_pruned`	.ld_sweep	R/qc_filter_geno.R:592
`sg`	.ld_sweep	R/qc_filter_geno.R:579
`ss`	.ld_sweep	R/qc_filter_geno.R:590
`whole`	.ld_spec	R/qc_filter_geno.R:429
`win_at`	.ld_sweep	R/qc_filter_geno.R:605

R/select_blup.R 4

Function / method	Enclosing scope	Source
`bad`	.founder_inbreeding	R/select_blup.R:114
`m`	selection_methods	R/select_blup.R:778
`ok`	.blup_variances	R/select_blup.R:683
`one`	.mt_variances	R/select_blup.R:474

R/select_bqp.R 3

Function / method	Enclosing scope	Source
`feas_of`	.bqp_solve	R/select_bqp.R:137
`obj_of`	.bqp_solve	R/select_bqp.R:134
`pen_of`	.bqp_solve	R/select_bqp.R:182

R/select_ind.R 1

Function / method	Enclosing scope	Source
`p2`	.index_weights	R/select_ind.R:813

R/select_ocs.R 2

Function / method	Enclosing scope	Source
`coan_at`	.tune_lambda	R/select_ocs.R:664
`done`	.tune_lambda	R/select_ocs.R:668

R/select_schemes.R 1

Function / method	Enclosing scope	Source
`bad`	.check_backed	R/select_schemes.R:450

R/transcriptome_counts.R 1

Function / method	Enclosing scope	Source
`draw`	observe_counts	R/transcriptome_counts.R:95

R/transcriptome_layer.R 2

Function / method	Enclosing scope	Source
`build`	transcriptome	R/transcriptome_layer.R:259
`draw`	transcriptome / build	R/transcriptome_layer.R:260

R/transcriptome_mimic.R 1

Function / method	Enclosing scope	Source
`negll`	.greml_h2	R/transcriptome_mimic.R:76

R/transcriptome_simulate.R 5

Function / method	Enclosing scope	Source
`draw`	.tx_synthetic_coords	R/transcriptome_simulate.R:1062
`draw_resid`	predict.transcriptome_sim	R/transcriptome_simulate.R:892
`run`	simulate_transcriptome	R/transcriptome_simulate.R:405
`z1`	simulate_transcriptome / run	R/transcriptome_simulate.R:492
`z1`	predict.transcriptome_sim / draw_resid	R/transcriptome_simulate.R:893

Rust implementation 73

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

src/rust/src/coalescent.rs 29

Function / method	Enclosing scope	Source
`Demography::epoch`	Demography	src/rust/src/coalescent.rs:131
`Demography::new`	Demography	src/rust/src/coalescent.rs:108
`Demography::next_change`	Demography	src/rust/src/coalescent.rs:138
`Fenwick::find`	Fenwick	src/rust/src/coalescent.rs:182
`Fenwick::new`	Fenwick	src/rust/src/coalescent.rs:153
`Fenwick::rebuild`	Fenwick	src/rust/src/coalescent.rs:202
`Fenwick::set`	Fenwick	src/rust/src/coalescent.rs:160
`Fenwick::total`	Fenwick	src/rust/src/coalescent.rs:171
`Rng::below`	Rng	src/rust/src/coalescent.rs:77
`Rng::exp1`	Rng	src/rust/src/coalescent.rs:72
`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
`Tree::branch_len`	Tree	src/rust/src/coalescent.rs:391
`Tree::float_time`	Tree	src/rust/src/coalescent.rs:429
`Tree::insert_internal`	Tree	src/rust/src/coalescent.rs:525
`Tree::kingman`	Tree	src/rust/src/coalescent.rs:258
`Tree::leaf_bits`	Tree	src/rust/src/coalescent.rs:642
`Tree::mutate`	Tree	src/rust/src/coalescent.rs:656
`Tree::recombine`	Tree	src/rust/src/coalescent.rs:569
`Tree::refresh_len`	Tree	src/rust/src/coalescent.rs:398
`Tree::remove_internal`	Tree	src/rust/src/coalescent.rs:514
`Tree::sample_lineage_at`	Tree	src/rust/src/coalescent.rs:536
`Tree::sample_point`	Tree	src/rust/src/coalescent.rs:419
`Tree::tmrca`	Tree	src/rust/src/coalescent.rs:407
`Tree::total_length`	Tree	src/rust/src/coalescent.rs:403
`coalescent_chromosome_core`	—	src/rust/src/coalescent.rs:770
`simulate_chromosome`	—	src/rust/src/coalescent.rs:684
`splitmix64`	—	src/rust/src/coalescent.rs:31

src/rust/src/genome.rs 17

Function / method	Enclosing scope	Source
`Bits::clear_tail`	Bits	src/rust/src/genome.rs:149
`Bits::flip_all`	Bits	src/rust/src/genome.rs:82
`Bits::get`	Bits	src/rust/src/genome.rs:46
`Bits::len`	Bits	src/rust/src/genome.rs:41
`Bits::parse_strand`	Bits	src/rust/src/genome.rs:109
`Bits::set`	Bits	src/rust/src/genome.rs:53
`Bits::tail_is_clean`	Bits	src/rust/src/genome.rs:166
`Bits::to_code`	Bits	src/rust/src/genome.rs:139
`Bits::toggle_from`	Bits	src/rust/src/genome.rs:69
`Bits::zeros`	Bits	src/rust/src/genome.rs:33
`GenomeLayout::chr_len`	GenomeLayout	src/rust/src/genome.rs:263
`GenomeLayout::chr_offset`	GenomeLayout	src/rust/src/genome.rs:256
`GenomeLayout::chr_positions`	GenomeLayout	src/rust/src/genome.rs:251
`GenomeLayout::n_chr`	GenomeLayout	src/rust/src/genome.rs:241
`GenomeLayout::n_loci`	GenomeLayout	src/rust/src/genome.rs:246
`GenomeLayout::try_new`	GenomeLayout	src/rust/src/genome.rs:189
`write_genotype`	—	src/rust/src/genome.rs:273

src/rust/src/hash.rs 2

Function / method	Enclosing scope	Source
`fnv1a_128`	—	src/rust/src/hash.rs:16
`stable_hash_core`	—	src/rust/src/hash.rs:28

src/rust/src/meiosis.rs 20

Function / method	Enclosing scope	Source
`Design::events_per_progeny`	Design	src/rust/src/meiosis.rs:264
`Design::parse`	Design	src/rust/src/meiosis.rs:251
`EventStream::block`	EventStream	src/rust/src/meiosis.rs:195
`EventStream::flip`	EventStream	src/rust/src/meiosis.rs:201
`EventStream::n_events`	EventStream	src/rust/src/meiosis.rs:185
`EventStream::slot`	EventStream	src/rust/src/meiosis.rs:190
`EventStream::try_new`	EventStream	src/rust/src/meiosis.rs:99
`Parents::parse`	Parents	src/rust/src/meiosis.rs:281
`breaks_at`	—	src/rust/src/meiosis.rs:49
`chromosome_mask`	—	src/rust/src/meiosis.rs:63
`gamete_masks_core`	—	src/rust/src/meiosis.rs:601
`genome_mask`	—	src/rust/src/meiosis.rs:207
`mate_core`	—	src/rust/src/meiosis.rs:383
`mate_haplotypes`	—	src/rust/src/meiosis.rs:324
`mate_haplotypes_core`	—	src/rust/src/meiosis.rs:642
`mate_many`	—	src/rust/src/meiosis.rs:425
`mate_many_core`	—	src/rust/src/meiosis.rs:701
`meiosis_core`	—	src/rust/src/meiosis.rs:562
`progeny_count`	—	src/rust/src/meiosis.rs:299
`recombine`	—	src/rust/src/meiosis.rs:224

src/rust/src/numeric.rs 5

Function / method	Enclosing scope	Source
`coding`	—	src/rust/src/numeric.rs:8
`numericalize`	—	src/rust/src/numeric.rs:66
`numericalize_core`	—	src/rust/src/numeric.rs:221
`parse_model`	—	src/rust/src/numeric.rs:28
`size_arg`	—	src/rust/src/numeric.rs:42

Rust tests and test helpers 83

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

src/rust/src/coalescent.rs 23

Function / method	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
`between_deme_pair_tmrca_is_join_plus_half`	test configuration	src/rust/src/coalescent.rs:1167
`check_split_invariants`	test configuration	src/rust/src/coalescent.rs:1125
`extreme_history_sizes_are_errors_not_panics`	test configuration	src/rust/src/coalescent.rs:1034
`harmonic`	test configuration	src/rust/src/coalescent.rs:832
`kingman_length_mean_is_harmonic`	test configuration	src/rust/src/coalescent.rs:876
`kingman_tmrca_mean_constant_size`	test configuration	src/rust/src/coalescent.rs:857
`lineage_sampler_is_uniform_over_the_lineages_at_tau`	test configuration	src/rust/src/coalescent.rs:1058
`marginal_tree_follows_the_demography_after_recombination`	test configuration	src/rust/src/coalescent.rs:958
`overflowing_rates_are_errors_not_hangs`	test configuration	src/rust/src/coalescent.rs:1028
`pair_tmrca_under_a_size_change`	test configuration	src/rust/src/coalescent.rs:894
`reservoir_keeps_the_requested_number_in_order`	test configuration	src/rust/src/coalescent.rs:1014
`seeded_runs_reproduce`	test configuration	src/rust/src/coalescent.rs:1005
`smc_prime_keeps_the_marginal_tree_kingman`	test configuration	src/rust/src/coalescent.rs:929
`split_inputs_are_validated`	test configuration	src/rust/src/coalescent.rs:1227
`split_keeps_demes_isolated_until_the_join`	test configuration	src/rust/src/coalescent.rs:1151
`tree_at_end`	test configuration	src/rust/src/coalescent.rs:916
`tree_stays_consistent_through_recombination`	test configuration	src/rust/src/coalescent.rs:977
`two_locus_correlation_is_smc_prime_not_smc`	test configuration	src/rust/src/coalescent.rs:1088
`unif_and_below_are_in_range`	test configuration	src/rust/src/coalescent.rs:847
`within_deme_sample_before_a_late_join_is_kingman`	test configuration	src/rust/src/coalescent.rs:1205
`xoshiro_reference_stream`	test configuration	src/rust/src/coalescent.rs:837

src/rust/src/genome.rs 15

Function / method	Enclosing scope	Source
`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
`code_round_trips_ascending`	test configuration	src/rust/src/genome.rs:363
`flip_all_is_an_involution_and_keeps_tail_clean`	test configuration	src/rust/src/genome.rs:307
`genotype_is_symmetric_in_the_two_strands_only_for_homozygotes`	test configuration	src/rust/src/genome.rs:396
`genotype_uses_loci_major_layout`	test configuration	src/rust/src/genome.rs:374
`layout_rejects_empty_chromosome_na_and_no_chromosomes`	test configuration	src/rust/src/genome.rs:418
`layout_rejects_mismatched_counts`	test configuration	src/rust/src/genome.rs:410
`layout_rejects_non_finite_and_decreasing_positions_but_allows_ties`	test configuration	src/rust/src/genome.rs:426
`layout_slices_chromosomes_in_order`	test configuration	src/rust/src/genome.rs:446
`strands_must_match_the_layout_and_the_binary_alphabet`	test configuration	src/rust/src/genome.rs:436
`toggle_from_at_or_past_n_is_a_noop`	test configuration	src/rust/src/genome.rs:338
`toggle_from_covers_the_suffix_only`	test configuration	src/rust/src/genome.rs:324
`toggle_from_twice_cancels`	test configuration	src/rust/src/genome.rs:351

src/rust/src/hash.rs 4

Function / method	Enclosing scope	Source
`distinct_inputs_differ_and_repeat_equally`	test configuration	src/rust/src/hash.rs:68
`empty_input_is_the_offset_basis`	test configuration	src/rust/src/hash.rs:44
`known_answer_vectors`	test configuration	src/rust/src/hash.rs:54
`prime_is_two_pow_88_plus_two_pow_8_plus_0x3b`	test configuration	src/rust/src/hash.rs:49

src/rust/src/meiosis.rs 35

Function / method	Enclosing scope	Source
`a_chiasma_exactly_on_a_marker_leaves_it_upstream`	test configuration	src/rust/src/meiosis.rs:797
`a_chiasma_upstream_of_the_first_marker_toggles_everything`	test configuration	src/rust/src/meiosis.rs:826
`bits_to_i32`	test configuration	src/rust/src/meiosis.rs:1151
`breaks_counts_positions_at_or_below_the_chiasma`	test configuration	src/rust/src/meiosis.rs:788
`chiasma_range_is_per_chromosome`	test configuration	src/rust/src/meiosis.rs:944
`cross_takes_cis_from_the_first_parent`	test configuration	src/rust/src/meiosis.rs:977
`design_parsing_and_event_budget`	test configuration	src/rust/src/meiosis.rs:1074
`dh_haplotypes_are_segments_of_the_parent_strands_not_the_mask`	test configuration	src/rust/src/meiosis.rs:1002
`dh_progeny_are_fully_homozygous`	test configuration	src/rust/src/meiosis.rs:968
`duplicate_chiasmata_cancel_and_order_is_irrelevant`	test configuration	src/rust/src/meiosis.rs:841
`entry_points_return_errors_not_panics`	test configuration	src/rust/src/meiosis.rs:1085
`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_non_finite_and_out_of_range_chiasmata`	test configuration	src/rust/src/meiosis.rs:926
`event_stream_rejects_ragged_shapes`	test configuration	src/rust/src/meiosis.rs:919
`event_stream_slices_ragged_blocks_in_order`	test configuration	src/rust/src/meiosis.rs:863
`events_are_consumed_progeny_major`	test configuration	src/rust/src/meiosis.rs:989
`genome_mask_concatenates_chromosomes_ascending`	test configuration	src/rust/src/meiosis.rs:952
`layout`	test configuration	src/rust/src/meiosis.rs:774
`mate_core_agrees_with_mate_haplotypes`	test configuration	src/rust/src/meiosis.rs:1024
`mate_many_core_returns_errors_not_panics`	test configuration	src/rust/src/meiosis.rs:1254
`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
`one_chiasma_toggles_the_downstream_segment_inclusively`	test configuration	src/rust/src/meiosis.rs:816
`parents_must_match_the_layout`	test configuration	src/rust/src/meiosis.rs:1065
`pos`	test configuration	src/rust/src/meiosis.rs:770
`progeny_count_rejects_na_and_negative`	test configuration	src/rust/src/meiosis.rs:1057
`recombine_picks_cis_where_the_mask_is_set`	test configuration	src/rust/src/meiosis.rs:960
`single_locus_chromosome`	test configuration	src/rust/src/meiosis.rs:854
`stream`	test configuration	src/rust/src/meiosis.rs:778
`the_event_budget_must_match_n_prog_exactly`	test configuration	src/rust/src/meiosis.rs:1037
`two_chiasmata_restore_the_intervening_segment`	test configuration	src/rust/src/meiosis.rs:834
`zero_chiasmata_gives_all_zero_or_all_one_by_the_flip`	test configuration	src/rust/src/meiosis.rs:807

src/rust/src/numeric.rs 6

Function / method	Enclosing scope	Source
`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
`run`	test configuration	src/rust/src/numeric.rs:253
`size_args_reject_na_and_negative`	test configuration	src/rust/src/numeric.rs:385

Function / method	Enclosing scope	Source
`.ld_attempt_seed`	—	R/legacy_QTN_linkage.R:2036
`.ld_check_direct`	—	R/legacy_QTN_linkage.R:1993
`.ld_check_indirect`	—	R/legacy_QTN_linkage.R:1895
`.ld_contract_stop`	—	R/legacy_QTN_linkage.R:1869
`.ld_direct_violation`	—	R/legacy_QTN_linkage.R:1955
`.ld_emit_warnings`	—	R/legacy_QTN_linkage.R:2109
`.ld_give_up_now`	—	R/legacy_QTN_linkage.R:2101
`.ld_key`	—	R/legacy_QTN_linkage.R:1859
`.ld_max_attempts`	—	R/legacy_QTN_linkage.R:2019
`.ld_pair`	—	R/legacy_QTN_linkage.R:1850
`.ld_run_attempt`	—	R/legacy_QTN_linkage.R:2061
`.ld_search_giveup`	—	R/legacy_QTN_linkage.R:2119
`.ld_search_stop`	—	R/legacy_QTN_linkage.R:2045
`.qtn_linkage_checked`	—	R/legacy_QTN_linkage.R:2132
`qtn_linkage`	—	R/legacy_QTN_linkage.R:26

Function / method	Enclosing scope	Source
`.check_cor_inputs`	—	R/legacy_Base_line_multi_traits.R:373
`base_line_multi_traits`	—	R/legacy_Base_line_multi_traits.R:68

Function / method	Enclosing scope	Source
`.check_partial_counts`	—	R/legacy_QTN_partially_pleiotropic.R:870
`.check_partial_disjoint`	—	R/legacy_QTN_partially_pleiotropic.R:851
`.partial_assemble`	—	R/legacy_QTN_partially_pleiotropic.R:804
`.partial_qtn_matrix`	—	R/legacy_QTN_partially_pleiotropic.R:839
`.partial_spec_labels`	—	R/legacy_QTN_partially_pleiotropic.R:794
`qtn_partially_pleiotropic`	—	R/legacy_QTN_partially_pleiotropic.R:60

Function / method	Enclosing scope	Source
`.v1_check_qtn_capacity`	—	R/legacy_check_in.R:1504
`.v1_check_vqtl_baseline`	—	R/legacy_check_in.R:1567
`.v1_check_vqtl_sd`	—	R/legacy_check_in.R:1542
`.v1_rng_capture`	—	R/legacy_check_in.R:1456
`.v1_rng_restore`	—	R/legacy_check_in.R:1479
`.v1_validate_basic`	—	R/legacy_check_in.R:1162
`.v1_validate_cor`	—	R/legacy_check_in.R:1361
`.v1_validate_effects`	—	R/legacy_check_in.R:1410
`.v1_validate_ld`	—	R/legacy_check_in.R:1223
`.v1_validate_seed_arith`	—	R/legacy_check_in.R:1262
`check_in`	—	R/legacy_check_in.R:69

Function / method	Enclosing scope	Source
`.check_effect_length`	—	R/legacy_genetic_effect.R:219
`genetic_effect`	—	R/legacy_genetic_effect.R:70

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

simplePHENOTYPES: all named functions

Public R functions 63

Registered R methods 9

Modern internal R 331

Legacy internal R 44

R-to-Rust bindings 7

Local R helpers 102

Rust implementation 73

Rust tests and test helpers 83