25 Equation and implementation index
25.1 Evidence for the worked chapter
Package definitions, algebraic consequences, and literature claims need different forms of evidence. The first chapter uses package normalization rules and directly derived sample identities. These are linked to source and executable checks below.
| Claim | Evidence type and provenance | Executable check |
|---|---|---|
| Additive score and layer normalization (Equation A.1) | Package definition; .component_raw, .genetic_matrix |
first-variance |
| Residual normalization and phenotype assembly (Equation A.2) | Package definition for the stated one-layer example; .draw_residual, .realize_phenotype |
first-variance |
| Sample variance identity and realized ratio (Equation 1.1; Equation A.4) | Algebraic consequence; derived in Appendix A; derivation in Appendix A | first-variance, ratio-counterexample |
| Same-input, same-environment reproducibility | Executable API contract; .layer_seed |
first-reproduce |
| Text export and reload demonstration | Executable API contract; write_phenotypes, write_qtn_table |
first-export |
| Exact sample calibration is a different residual-generation design | Algebraic projection argument; proposed design only; Projection argument in the first chapter; not a package option | Algebraic projection argument |
| AlphaSimR 2.1.0 residual generation | Official software documentation and installed source; optional compare_alphasimr.R; AlphaSimR setPheno/addError source and official documentation | dev/book/compare_alphasimr.R (optional) |
| Random residual mode leaves normal draws unstandardized | Package definition and normal sampling model; .draw_residual, .correlated_residuals, .apply_vqtl |
first-random-residuals |
| Additive score and geometric effect series (Equation 5.1, Equation 5.2) | Package definition; .component_raw, .effect_series |
additive-effects, additive-model |
| Marginal var_explained and its non-additivity across markers (Equation 5.3) | Package definition plus algebraic variance expansion; .qtn_var |
additive-var-explained, additive-mice |
| Positional repulsion phase and layer sub-seeding | Package definition; .apply_phase, .layer_seed |
additive-phase, additive-reps |
| Dominance (heterozygote indicator) and centered-product epistasis components (Equation 6.1) | Package definition, rebuilt by hand; .component_raw, .epi_unit_column |
nonadditive-rebuild, nonadditive-epistasis-rebuild |
| Additive-dominance covariance on shared loci, -(2p-1)2pq, and Var(g)=pi_A+pi_D+2Cov (Equation 6.2, Equation 6.3) | Algebraic derivation; package ad_report; .genetic_matrix |
nonadditive-ad-report, nonadditive-rebuild |
| Orthogonal genotypic model: average effect alpha = a + d(1-2p), breeding value, emergent A/D split (Equation 6.4) | Literature (Falconer 1985; Falconer & Mackay 1996 page unverified; Fisher 1918) and package definition; .avg_effect, .breeding_value_matrix, .orthogonal_var_split |
nonadditive-orthogonal, nonadditive-degree |
| PleioArch shared covariance, MAF scaling, and realized correlation as a random ratio (Equation 7.1) | Package implementation of Prado et al. (in preparation); page unverified; .pleio_draw |
multitrait-pleiotropy, multitrait-spread |
| Attainability cor^2 <= pi_1 pi_2 and PSD generalization (Equation 7.2) | Reference implementation constraint; PSD generalization algebraic; .check_pleio_feasible |
multitrait-infeasible |
| Co-heritability = r_G h1 h2 and phenotypic correlation decomposition (Equation 7.3) | Literature (Falconer & Mackay 1996, correlated response; from roxygen) and algebraic derivation; coheritability, .correlated_residuals |
multitrait-coheritability, multitrait-resid-cor |
| LD architecture: distinct linked loci, composite r2 window, ld_phase sign control | Package design (DECISION-014); r2 as Pearson on dosages, page unverified; .draw_qtn_ld |
multitrait-ld, multitrait-ld-phase |
| Liability-threshold category rule (Equation 8.1) | Package definition; model attributed to Wright 1934 and Falconer 1965 in roxygen; .apply_threshold, .liability_table |
binary-liability, binary-threshold |
| Cut points are normal quantiles on the sample-standardized liability, not sample quantiles (Equation 8.2) | Package definition; .threshold_cuts |
binary-threshold, binary-replications |
| All variance quantities of a thresholded trait stay on the liability scale | Package definition; .liability_table, coheritability |
binary-model, binary-two-traits |
| Case/control sampling changes genetic and liability variances (selection on the output) | Algebraic consequence; sampling done outside the package; Selection on the liability through the label; argument in the binary chapter | binary-ascertainment |
| vQTL loading and log-linear heterogeneous residual (Equation 9.1; Equation 9.2); equation map V2-grammar-19/20 | Package definition; .apply_vqtl |
complex-classes, complex-replications, complex-random |
| vQTL share is residual, enters realized H2 denominator only; residual budget 1 - sum(layers) - sum(vqtl); map V2-grammar-9/14 | Package definition; .realize_phenotype, .realized_h2 |
complex-vqtl, complex-stack |
| complex_phenotypes() genetic value is the rescaled sum of inputs’ genetic values with a fresh common residual | Package definition; complex_phenotypes |
complex-combine, complex-correlation |
| Genetic correlation of a combined model is the variance-weighted average of input correlations (Equation 9.3) | Algebraic derivation, assumes uncorrelated inputs; derivation in the complex chapter | complex-correlation |
| F1 heterozygous at informative loci; F2 1:2:1; DH homozygous (gamete construction) | Package definition; cross, selfcross, double_haploid |
cross-f1-het, cross-f2, cross-dh |
| Heterozygosity under selfing H_t = H_0/2^t (Equation 10.3) | Algebraic consequence of single-locus Mendelian transmission; equation map V2-crossing-10 (Falconer & Mackay 1996 ch. 5, page unverified); selfcross, mate |
cross-selfing |
| Poisson count-location meiosis gives Haldane r(d) = (1 - e^{-2d})/2 (Equation 10.1) | Package definition (isqg-parity draws) and property of the Poisson process; equation map V2-crossing-3/4/9 (Haldane 1919, page unverified); .draw_meiosis |
cross-interference |
| Default gamma interference r(d) formula (Equation 10.2), nu = 2.6, p = 0 | Package definition as documented in ?cross (derived and checked in package tests, not copied from McPeek & Speed 1995 / Housworth & Stahl 2003); .draw_meiosis_interference |
cross-linkage, cross-interference |
| Seeded meiosis is reproducible; R draws, Rust pure (DECISION-012) | Executable API contract; .draw_meiosis |
cross-reproduce |
| Fixed-scale additive and total genotypic value (Equation 11.1, Equation 11.2) | Package definition; equation map V2-crossing-13/14 (Falconer & Mackay 1996, page unverified); additive_value, genotypic_value |
trait-fixed-scale, trait-same-ranking, trait-genotypic |
| var_e = V_A,ref (1 - h2)/h2 and h2_t = V_A,t/(V_A,t + var_e) (Equation 11.3, Equation 11.4) | Package definition plus algebraic derivation; equation map V2-crossing-15; phenotype_value |
trait-var-e |
| Carried population trait keeps base loci, effects, scale and var_e (refit = FALSE) | Package definition; population_trait |
trait-carry, trait-inherit |
| Entry means: residual divided by sqrt(reps), n_reps repeats realization (Equation 11.5) | Package definition; algebraic Var(ybar) = V_G + V_E/r; .draw_residual |
trait-replication |
| G x E phenotype y = A + s w + e, w = sigma_w Phi^{-1}(env) (Equation 11.6) | Package definition reproducing AlphaSimR 2.1.0 source per roxygen; gxe_value, phenotype_value |
trait-gxe |
| Expected breed composition recursion (Equation 12.1); backcross 1/2, 3/4, 7/8, 15/16 | Package definition; equation map V2-crossing-16; breed_composition |
mating-composition, mating-crossbreed, mating-three-way |
| Mating design pair counts (factorial, half/full diallel, nested, random) | Package definition; equation map V2-crossing-C3 (Griffing 1956 per roxygen); mating_design |
mating-design |
| Realized and expected F1 heterosis (Equation 12.2, Equation 12.3); inbred-line special case; backcross retention condition h_A = 2p_A(1-p_A) | Package definition and package derivation; equation map V2-crossing-17/18/20 (Falconer & Mackay 1996 H_F1 = sum d y^2, page unverified); heterosis, .expected_cross_means |
mating-heterosis |
| Expression model, cis/trans blend and residual blend (Equation 18.1; Equation 18.2; Equation 18.3) | Package definition; map V2-transcriptome-1,3,4,6,8; simulate_transcriptome |
expression-h2, expression-fixed-h2, expression-coexpression |
| Cis window rule (same chromosome, within cis_window of TSS) | Package definition; map V2-transcriptome-3; simulate_transcriptome |
expression-cis |
| Genetic expression reconstructable from truth tables with reference-centered dosage; budget closes | Package definition; map V2-transcriptome-2,10,11,13; simulate_transcriptome, predict.transcriptome_sim |
expression-reconstruct, expression-budget, expression-predict-reference |
| Realized expression heritability includes 2Cov(G,R); allocation equals target on reference (Equation 18.4) | Algebraic consequence of the sample-variance identity; map V2-transcriptome-9; simulate_transcriptome |
expression-h2, expression-fixed-h2, expression-predict |
| Epistatic share is a marginal blend weight; realized share differs by covariance | Package definition; map V2-transcriptome-7; simulate_transcriptome |
expression-epistasis |
| mimic matches per-gene mean and variance exactly; GREML h2 is a distribution-level calibration | Package definition; map V2-transcriptome-14,15,16,17,18,19; .tx_grm, .greml_h2, .tx_estimate_factors, .tx_estimate_kappa |
expression-mimic |
| NB count model: log mu = log L + alpha + sigma z, Var = mu + phi mu^2, Poisson at phi = 0 (Equation 18.5) | Package definition; edgeR parameterization (McCarthy et al. 2012; Robinson & Smyth 2008; pages unverified); map V2-transcriptome-20; observe_counts |
expression-counts, expression-library-size |
| Expression layer score and scaling to prop (Equation 19.1) | Package definition; map V2-transcriptome-21; .tx_raw, .transcriptome_matrix |
mediation-reconstruct |
| Mediation split: same sd(E_g) denominator gives additive decomposition; three shares sum to the realized component share (Equation 19.2) | Package definition plus sample-variance identity; map V2-transcriptome-22; .mediation_budget, mediation_split |
mediation-split, mediation-reconstruct, mediation-genes |
| Genetic value = marker layers + genetic-mediated part; real expression source contributes zero (Equation 19.3) | Package definition; map V2-transcriptome-23; .genetic_value_matrix, .realized_h2 |
mediation-genetic-values, mediation-real |
| Per-gene var_explained is marginal (c w_g)^2 / V_P | Package definition; map V2-transcriptome-24; .tx_qtn_var |
mediation-qtn |
| Allele frequency and MAF definition (Equation 3.1); monomorphic/MAF/heterozygosity filters | Package definition following PLINK –maf semantics (equation map V2-io-formats-1..3); filter_geno |
input-filter-maf |
| Frequency-based orientation and tie rule (first-listed allele kept on a tie); counted-allele record | Package convention (V2-io-formats-10, 11, 12); compute_flip, numericalize_core |
input-counted, input-reference, input-counted-column, input-coding |
| Composite genotype r2 and pruning decision, lower-MAF marker dropped (Equation 3.2) | Package definition; PLINK 1.9 –indep-pairwise (V2-io-formats-4, 5, 6); .ld_sweep |
input-filter-ld |
| Haplotypic r2 with exact two-locus ML phase (Equation 3.3) | Literature: Hill & Robertson 1968 (page unverified), Gaunt et al. 2007 (page unverified); PLINK port (V2-io-formats-7, C2, C3); .plink_hap_rsq, .plink_em_hethet |
input-filter-pairphase |
| VIF pruning; singular-window handling unverifiable vs PLINK | PLINK –indep, Purcell et al. 2007 (V2-io-formats-8); .ld_sweep |
input-filter-ld |
| Gabriel blocks reproduce PLINK –blocks; tag-per-block is a package convenience | Literature: Gabriel et al. 2002 (method page unverified); V2-io-formats-9, C5, C6; .gabriel_blocks |
input-filter-blocks |
| Heterozygote phasing rule cis=1[x>=0], trans=1[x>0] (Equation 4.1) | Package convention (V2-crossing-1); as_population |
founders-human |
| Dosage = cis + trans - 1 (Equation 4.2) | isqg genotype_num convention (V2-crossing-2); dosages, population_from_haplotypes |
founders-haplotypes, founders-from-haplotypes |
| Synthetic map local-rate model (Equation 4.3), monotone cM in bp, target length | Package definition; Gaussian form phenomenological; Bauer et al. 2013 cited by roxygen for pattern/scale only; synthetic_map |
founders-mice-map, founders-map-shape, founders-map-options |
| Coalescent founders: SMC’ model, theta/rho/history units, AlphaSimR runMacs presets, seeded Rust PRNG reproducibility | Package documentation and references as given in ?founders_coalescent (Marjoram & Wall 2006; Chen et al. 2009; Hudson 2002; Gaynor et al. 2021); algorithm not verified in the book; founders_coalescent, coalescent_chromosome_core |
founders-coalescent, founders-coalescent-presets |
| OCS objective and group coancestry (Equation 15.1) | Package definition; literature: Meuwissen 1997 J Anim Sci 75:934-940 (verified; page unverified); optimum_contribution, .frank_wolfe, .tune_lambda |
optimization-ocs-check, optimization-frontier, optimization-target |
| Genomic relationship matrix (Equation 15.2) | Literature: VanRaden 2008 J Dairy Sci 91:4414-4423 method 1 (paper verified; page unverified); g_matrix |
optimization-g |
| Largest-remainder allocation vs multinomial draws; realized coancestry not preserved exactly | Package definition; sample_parents |
optimization-parents, optimization-parents-coancestry |
| Usefulness U = mu + i sigma with normal-theory intensity (Equation 15.3) | Literature: Zhong & Jannink 2007 Genetics 177:567-576; Lehermeier et al. 2017 Genetics 207:1651-1661 (verified; pages unverified); intensity Falconer & Mackay 1996 (author-year); cross_usefulness, .intensity_from_p, .additive_model |
optimization-usefulness, optimization-usefulness-check |
| Recurrent-allele score and weighted recovery (Equation 16.1; Equation 16.2) | Package definition; .mabc_founders, .mabc_recovery, .mabc_weights, recurrent_parent_recovery |
markers-mabc, markers-drag, markers-weights |
| Expected recovery 1 - 2^-(t+1) in an unselected backcross cohort (Equation 16.3) | Mendelian derivation; attributed to Frisch & Melchinger 2005 Genetics 170:909-917 (paper verified; location unverified); recurrent_parent_recovery |
markers-mabc, markers-foreground |
| Foreground / recombinant / background lexicographic staging | Package definition; literature: Frisch & Melchinger 2001 Crop Sci 41:1485-1494 (verified; page unverified); mabc_select |
markers-mabc-record |
| MAS feasibility rule and staged pyramid (DECISION-029); Mendelian 1/64 and (3/4)^3 expectations | Package definition; algebraic expectation under independent assortment; marker_select |
markers-pyramid, markers-staged |
| Marker index as rank_on (Lande & Thompson 1990 Genetics 124:743-756, verified; page unverified) | Literature; oracle weights are a package convention; additive_value, marker_select |
markers-index |
| Expected cross mean per locus (Equation 17.1) | Package derivation from Falconer & Mackay 1996 genotypic values (page unverified); .expected_cross_means |
programs-diallel, programs-diallel-sim |
| GCA/SCA decomposition: factorial (Sprague & Tatum 1942, page unverified) and diallel method 4 (Griffing 1956, page unverified) (Equation 17.2; Equation 17.3) | Literature; sums-to-zero properties checked; .decompose_ca, combining_ability |
programs-diallel-check, programs-topcross |
| template_effects reproduces genetic_values up to a constant | Package definition; template_effects, .layer_scaled_effects, genotypic_value |
programs-template-check |
| Progeny-test accuracy sqrt(n h2 / (4 + (n-1) h2)) (Equation 17.4) | Package derivation of a classical result (no page asserted); worked example violates its assumptions (illustrative); progeny_test |
programs-progeny |
| Scheme definitions (SSD, bulk, pedigree, recurrent selection) and trait carry-over across generations | Package definition; Bernardo 2020 cited by roxygen without page; single_seed_descent, bulk, pedigree, recurrent_selection, population_trait |
programs-schemes, programs-schemes-compare, programs-population-trait, programs-recurrent, programs-recurrent-cycles |
| Long/wide table layouts and QTN table columns are package definitions | Package definition; phenotypes_long, phenotypes_wide, qtn_table |
output-long-wide, output-counts, output-truth |
| vary_qtn = TRUE gives distinct architectures per replication; rep selects them | Executable API contract; genetic_values, qtn_table |
output-vary-qtn |
| Text export reads back to ~1e-14 relative; JSON reads back exactly | Package definition (writer precision, ?write_phenotypes); write_phenotypes, write_qtn_table |
output-roundtrip, output-write-qtn |
| split_markers causal set is the union over selected replications; causal + noncausal = input markers | Package definition; write_phenotypes |
output-split, output-split-read, output-split-json |
| Legacy residual variance sigma_e^2 = V_G (1 - h2) / h2 with sample V_G (Equation 21.1) | Package definition; equation map V1-core-linkage-7 (F&M page unverified); phenotypes |
legacy-ratio |
| Grammar owes legacy no bit-parity: same seed, different markers and values, comparable variance ratio | Executable API contract; DECISION-009; create_phenotypes, .layer_seed |
legacy-parity, legacy-ratio |
| Legacy LD summary is a signed composite LD coefficient; grammar ld_r2 is a squared correlation | Package definition; equation map V1-core-linkage-15 (UNVERIFIABLE primary source); qtn_linkage |
legacy-ld, legacy-ld-v2 |
| Known-variance mixed model and GLS/BLUP solution (Equation 13.1; Equation 13.2) | Package definition; Henderson 1975 (page unverified) per equation map V2-prediction-C1/4/5; predict_ebv, .blup_variances |
prediction-ebv, prediction-custom-k |
| Reliability 1 - PEV/(K_ii sigma_A^2) (Equation 13.3) | Package definition; equation map V2-prediction-6; predict_ebv |
prediction-ebv |
| Tabular pedigree relationship matrix (Equation 13.4) | Package definition; Emik & Terrill 1949 and Wright 1922 (page unverified) per V2-prediction-1/2; a_matrix |
prediction-amatrix |
| VanRaden method-1 genomic relationship with ridge and base_freq (Equation 13.5) | Package definition; VanRaden 2008 (page unverified) per V2-prediction-C3; g_matrix |
prediction-gmatrix, prediction-gmatrix-options, prediction-amatrix |
| Accuracy = cor(ebv, truth), slope of truth on prediction (Equation 13.6) | Package definition; V2-prediction-8; prediction_accuracy |
prediction-accuracy, prediction-design, prediction-multitrait |
| Multi-trait BLUP with known G0, R0 raises accuracy for an unrecorded trait | Executed demonstration; Henderson & Quaas 1976 per roxygen; predict_ebv |
prediction-multitrait |
| Selection differential, realized intensity and large-N intensity (Equation 14.1) | Package definition; Falconer & Mackay 1996 (page unverified) per V2-selection-1..4; select_ind, .resolve_keep |
selection-mass, selection-intensity |
| Breeder’s equation R = h2 S for additive mass selection, checked as genetic selection differential and as progeny mean | Literature (V2-selection-5, page unverified) with executed check; select_ind |
selection-response, selection-progeny |
| Lush combined index weights (Equation 14.2) | Package definition; Lush 1947 (verified) per V2-selection-10; .combined_score |
selection-family |
| Smith-Hazel index b = P^-1 G a; quadratic index scores true BVs | Package definition; Smith 1936, Hazel 1943 (V2-selection-8), Ceron-Rojas 2026 (art. no. unverified, V2-selection-9); .index_weights, .quadratic_index_score |
selection-multitrait |
| Independent culling, simultaneous and sequential | Package definition; Hazel & Lush 1942 (verified) per V2-selection-13/C4; .select_culling |
selection-culling |
| BQP relatedness-penalized selection reduces to truncation at lambda = 0 and lowers mean relatedness as lambda grows | Package definition; Montesinos-Lopez et al. 2025 per roxygen; heuristic solver; .bqp_solve |
selection-bqp |
25.2 Existing equation map
The repository’s original equation-to-code PDF is retained as an archival reference. Its audit was performed at c511c6f, with locations subsequently remapped to e666a2c. That provenance does not establish that every formula or source page is verified against the current implementation.
The table below reproduces the topic, function, and location index from Appendix B of its Markdown source. Locations are historical; use the developer index for the current function definitions. Individual claims still require reconciliation and primary-source review before they are used as validated theory in new chapters. In particular, an archival entry labeled “page unverified” remains unverified.
| Ver | Group | Topic | Function | Location |
|---|---|---|---|---|
| V2 | v2-grammar | Layer scaling to prop | .genetic_matrix |
R/grammar_realize.R:139-161 (146) |
| V2 | v2-grammar | Additive component | .component_raw |
R/grammar_realize.R:498-509 (500), centred 432 |
| V2 | v2-grammar | Orthogonal genotypic value | .component_raw |
R/grammar_realize.R:501-507 (506) |
| V2 | v2-grammar | Dominance component | .component_raw |
R/grammar_realize.R:510 |
| V2 | v2-grammar | Epistasis unit column | .epi_unit_column |
R/grammar_realize.R:579-589 (586, 588) |
| V2 | v2-grammar | Epistasis component | .component_raw |
R/grammar_realize.R:511-529 (524) |
| V2 | v2-grammar | Geometric effect series | .effect_series |
R/effects_series.R:23-72 (64) |
| V2 | v2-grammar | Repulsion phase | .apply_phase |
R/grammar_layers.R:1482-1490 (1487) |
| V2 | v2-grammar | Residual budget | .realize_phenotype |
R/grammar_realize.R:55-59 (59) |
| V2 | v2-grammar | Residual draw | .draw_residual |
R/effects_series.R:85-102 (99) |
| V2 | v2-grammar | Phenotype | .realize_phenotype |
R/grammar_realize.R:96 |
| V2 | v2-grammar | Requested budget identity | .resolve_prop, .add_layer, .check_h2_complete |
R/grammar_layers.R:1085-1098, 1102-1115; R/grammar_realize.R:1153-1166 |
| V2 | v2-grammar | One-call split | .build_one_call |
R/grammar_simulate_phenotype.R:767-780 (769) |
| V2 | v2-grammar | Realized H² | .realized_h2 |
R/grammar_realize.R:1078-1106 (716-720) |
| V2 | v2-grammar | Average effect of substitution | .avg_effect |
R/grammar_realize.R:182-184 (183) |
| V2 | v2-grammar | Breeding value | .breeding_value_matrix |
R/grammar_realize.R:282-303 (227-235) |
| V2 | v2-grammar | Orthogonal split | .orthogonal_var_split, .variance_budget |
R/grammar_realize.R:778-794 (646-650), 536-551 |
| V2 | v2-grammar | HWE theory (check only) | — (audit check) | — |
| V2 | v2-grammar | vQTL loading | .apply_vqtl |
R/grammar_realize.R:605-618 (616) |
| V2 | v2-grammar | vQTL residual | .apply_vqtl |
R/grammar_realize.R:627-641 |
| V2 | v2-grammar | Transcriptome score | .tx_raw, .transcriptome_matrix |
R/grammar_realize.R:454-476 (470, 473, 475), 308-338 |
| V2 | v2-grammar | Mediation split | .mediation_budget |
R/grammar_realize.R:738-750 (604-606) |
| V2 | v2-grammar | Complex combination | complex_phenotypes |
R/grammar_complex.R:122-134 (123, 127), 96-107 (99) |
| V2 | v2-grammar | MAF | .marker_maf_ref |
R/grammar_simulate_phenotype.R:1022-1052 (1040, 1044) |
| V2 | v2-grammar | Sub-seed | .layer_seed |
R/grammar_simulate_phenotype.R:1079-1094 (1083, 1092) |
| V2 | v2-grammar | Per-QTN variance | .qtn_var |
R/io_write.R:1288-1312 (217-218) |
| V2 | v2-grammar | Fixed-scale phenotype | phenotype_value |
R/cross_population.R:1004-1104 (1061) |
| V2 | v2-grammar | Genetic correlation (plot) | .plot_cor |
R/grammar_plot.R:144-162 (150) |
| V2 | v2-grammar (codex) | PleioArch shared covariance | .pleio_draw, .pleio_nonadditive_draw |
R/effects_pleioarch.R:65-93 (sigma at 78-80), 345-358 (356-357) |
| V2 | v2-grammar (codex) | PleioArch effect allocation (non-additive) | .pleio_unit_effects, .draw_mvnorm |
R/effects_pleioarch.R:583-690 (535-537), 780-800 |
| V2 | v2-grammar (codex) | PleioArch attainability | .check_pleio_feasible |
R/effects_pleioarch.R:870-917 |
| V2 | v2-grammar (codex) | Total pleiotropic correlation target | .pleio_total_cor_check |
R/effects_pleioarch.R:724-788 (roxygen 543-574) |
| V2 | v2-grammar (codex) | Additive MAF effect scaling | .pleio_draw |
R/effects_pleioarch.R:201-217 (144-149) |
| V2 | v2-grammar (codex) | LD window (two-trait linked distinct loci) | .draw_qtn_ld |
R/arch_ld.R:62-225 (window 69-95, sampling 105-175) |
| V2 | v2-effects-arch | Pleiotropic covariance | .pleio_draw, .pleio_nonadditive_draw |
effects_pleioarch.R:90-91, :504-505 |
| V2 | v2-effects-arch | Trait-specific variance | .pleio_draw, .pleio_unit_effects |
:197-199, :685 |
| V2 | v2-effects-arch | Major/minor split | .pleio_draw, .draw_mvnorm |
:195-196, :934 |
| V2 | v2-effects-arch | MVN draw | .draw_mvnorm |
:929-939 |
| V2 | v2-effects-arch | Univariate draw | .draw_univariate |
:944-949 |
| V2 | v2-effects-arch | Shared-unit count | .pleio_partition |
:291-292, 320 |
| V2 | v2-effects-arch | Attainability (2 traits) | .check_pleio_feasible |
:876-890 |
| V2 | v2-effects-arch | Attainability (n traits) | .check_pleio_feasible |
:898-915 |
| V2 | v2-effects-arch | Allele -> genotype scaling | .pleio_draw; .marker_maf_ref |
:201-217; grammar_simulate_phenotype.R:1040-1044 |
| V2 | v2-effects-arch | Non-additive normaliser | .pleio_unit_effects; .epi_unit_column |
:601-604, 686; grammar_realize.R:579-589; dominance design :518 vs grammar_realize.R:510 |
| V2 | v2-effects-arch | Effective per-component target | .pleio_unit_effects |
:659-664 |
| V2 | v2-effects-arch | Total-correlation target | .pleio_total_cor_check |
:754-759 |
| V2 | v2-effects-arch | Layer rescale (context) | .genetic_matrix |
grammar_realize.R:144-146 |
| V2 | v2-effects-arch | Few-unit attenuation | doc claim | :26-28; grammar_simulate_phenotype.R:318-320 |
| V2 | v2-effects-arch | Complete-LD ensemble mean | doc claim | :28-30; DECISIONS.md 023 Scope |
| V2 | v2-effects-arch | Geometric effect series | .effect_series |
effects_series.R:55, 64 |
| V2 | v2-effects-arch | Repulsion phase | .apply_phase |
grammar_layers.R:1482-1490 |
| V2 | v2-effects-arch | Residual draw | .draw_residual |
effects_series.R:85-102 |
| V2 | v2-effects-arch | LD measure | window_partners, r2_pair |
arch_ld.R:111, 124-126 |
| V2 | v2-effects-arch | Direct pair choice | .draw_qtn_ld |
arch_ld.R:149-160 (:151-152); partner :73-74 |
| V2 | v2-effects-arch | Indirect flanks | .draw_qtn_ld |
arch_ld.R:161-197 |
| V2 | v2-effects-arch | Layer sub-seed | .layer_seed |
grammar_simulate_phenotype.R:1083-1093 |
| V2 | v2-effects-arch | Gabriel blocks tag | .gabriel_blocks |
qc_ld_methods.R:24-29, 38-43 |
| V2 | v2-effects-arch (codex) | Zero-variance correlation guard | .pleio_check_zero_var() |
R/effects_pleioarch.R:246-275 |
| V2 | v2-effects-arch (codex) | Shared/specific unit count (clamped) | .pleio_partition() |
R/effects_pleioarch.R:288-329 (clamp :291-292) |
| V2 | v2-effects-arch (codex) | One shared unit | .pleio_single_unit_consequence() |
R/effects_pleioarch.R:412-441 |
| V2 | v2-effects-arch (codex) | Correlation input expansion | .pleio_cor_matrix() |
R/effects_pleioarch.R:957-986 |
| V2 | v2-effects-arch (codex) | Pleiotropic-share argument mapping | .pleio_pi_vector() |
R/effects_pleioarch.R:829-860 |
| V2 | v2-effects-arch (codex) | Architecture-specific QTN sampling | .draw_qtn() |
R/arch_independent.R:21-45 |
| V2 | v2-effects-arch (codex) | Distinct-chromosome allocation | .draw_qtn_distinct_chr() |
R/arch_independent.R:56-75 |
| V2 | v2-effects-arch (codex) | Epistatic-set sampling | .draw_qtn_pairs() |
R/arch_independent.R:81-103 |
| V2 | v2-effects-arch (codex) | Candidate-marker rule | .candidate_markers() |
R/arch_independent.R:114-134 |
| V2 | v2-effects-arch (codex) | Layer occurrence index | .type_occurrence() |
R/arch_independent.R:139-141 |
| V2 | v2-crossing | Heterozygote phasing | as_population |
R/cross_population.R:176-177 |
| V2 | v2-crossing | Dosage from strands | dosages |
R/cross_population.R:623; genome.rs:273-278 |
| V2 | v2-crossing | Crossover count | .draw_meiosis |
R/cross_mating.R:53-56 (dispatch), Poisson branch :77-78; gamma model :215-275; default .INTERFERENCE_DEFAULT :117 (DECISION-047); cM\(\rightarrow\)M :339,341 |
| V2 | v2-crossing | Chiasma positions | .draw_meiosis |
R/cross_mating.R:79-87 |
| V2 | v2-crossing | Strand choice | .draw_meiosis |
R/cross_mating.R:90 |
| V2 | v2-crossing | Ancestry mask | chromosome_mask, breaks_at |
src/rust/src/meiosis.rs:49-51, 63-72 |
| V2 | v2-crossing | Gamete | recombine |
meiosis.rs:224-237 |
| V2 | v2-crossing | Cross / self / DH | mate_haplotypes |
meiosis.rs:350-371; events per progeny R/cross_mating.R:345 |
| V2 | v2-crossing | Recombination fraction (implied, verified) | — (property of the Poisson process) | verified e4.R/e5.R; tests/testthat/test-cross.R:179-202 (file runs under simplePHENOTYPES.interference = "poisson", :13) |
| V2 | v2-crossing | Heterozygosity under selfing | selfcross (doc) |
R/cross_mating.R:627-629; verified e1.R E3 |
| V2 | v2-crossing | Synthetic map rate | synthetic_map |
R/cross_map.R:157 |
| V2 | v2-crossing | Synthetic map integration | synthetic_map |
R/cross_map.R:168-173, :133 |
| V2 | v2-crossing | Additive value (fixed scale) | additive_value |
R/cross_population.R:746 |
| V2 | v2-crossing | Genotypic value | genotypic_value |
R/cross_population.R:821 |
| V2 | v2-crossing | Residual from h² | phenotype_value |
R/cross_population.R:1061 |
| V2 | v2-crossing | Breed composition | breed_composition |
R/cross_breed.R:37-43 |
| V2 | v2-crossing | Realized heterosis | heterosis |
R/cross_breed.R:135-139, 152 |
| V2 | v2-crossing | Expected F1 heterosis | heterosis + .expected_cross_means |
R/cross_breed.R:140-150; R/select_combining.R:244-255 |
| V2 | v2-crossing | Per-locus cross mean | .expected_cross_means |
R/select_combining.R:249-254 |
| V2 | v2-crossing | Retention fractions (doc only) | roxygen | R/cross_breed.R:68-72; docs/SPEC-block3b.md §7 |
| V2 | v2-crossing | Rotation sire sequence | crossbreed |
R/cross_breed.R:302-305 |
| V2 | v2-crossing | Pedigree key | .mating_pedigree, .stable_key |
R/cross_pedigree.R:25-37 (.stable_key), :42-59 (.key_part), :205-207 (mating key); hash.rs:12-23 |
| V2 | v2-crossing | Generation | .mating_pedigree |
R/cross_pedigree.R:208-209 |
| V2 | v2-crossing | A-matrix (other group, consistency only) | a_matrix |
R/select_blup.R:69-90 |
| V2 | v2-crossing (codex) | Average-effect vs genotypic-value distinction (doc) | roxygen of genotypic_value (implemented in select_ind(on = "bv"), other group) |
R/cross_population.R:774-780 (verified: α text at 776-777) |
| V2 | v2-crossing (codex) | Full-sib family identity | families |
R/cross_pedigree.R:307-336 (verified: families <- at 307, closes at 336) |
| V2 | v2-crossing (codex) | Mating designs (counts) | mating_design |
R/cross_mate.R:360-486 (verified: mating_design <- at 229; file is 350 lines) |
| V2 | v2-crossing (codex) | Within-family relationship validation (test) | test helper .icc |
tests/testthat/test-family-relationship.R:1-58 (verified: 58 lines, .icc at 26, targets at 52-57) |
| V2 | v2-rust-core | Crossover count (count-location) | .draw_meiosis |
R R/cross_mating.R:77-78; isqg Genetics.cpp:44,84; Rust: none (input counts) |
| V2 | v2-rust-core | Chiasma locations | .draw_meiosis |
R :79-87; isqg Genetics.cpp:86-97 |
| V2 | v2-rust-core | Strand raffle | .draw_meiosis / chromosome_mask |
R :90; Rust meiosis.rs:68-70; isqg :74-75 |
| V2 | v2-rust-core | Breakpoint rank | breaks_at |
Rust meiosis.rs:49-51; isqg Genetics.cpp:67 |
| V2 | v2-rust-core | Ancestry mask | chromosome_mask, Bits::toggle_from, flip_all |
Rust meiosis.rs:63-72, genome.rs:69-87; isqg :58-70 (XOR loop), :74-75 (flip) |
| V2 | v2-rust-core | Gamete assembly | recombine |
Rust meiosis.rs:224-237; isqg Genetics.cpp:356 |
| V2 | v2-rust-core | Cross | mate_haplotypes |
Rust meiosis.rs:359-369; R .mate cross_mating.R:345,453,460-467 |
| V2 | v2-rust-core | Self | selfcross \(\rightarrow\) .mate(parent, parent) |
R cross_mating.R:647-652; Rust same path |
| V2 | v2-rust-core | Doubled haploid | mate_haplotypes (Dh) |
Rust meiosis.rs:263-269,351-358; R cross_mating.R:686-691 |
| V2 | v2-rust-core | Genotype projection | write_genotype, dosages |
Rust genome.rs:273-284; R cross_population.R:623 (cis + trans - 1) |
| V2 | v2-rust-core | Founder phasing | as_population |
R cross_population.R:176-177 |
| V2 | v2-rust-core | Map units | .mate |
R cross_mating.R:339,341 |
| V2 | v2-rust-core | Haldane map function (consequence, tested only) | — | test tests/testthat/test-cross.R:179-202; auditor T2–T4 |
| V2 | v2-rust-core | Numericalization — orientation | compute_flip |
R io_detect_format.R:362-364; reference mode :354-359 |
| V2 | v2-rust-core | Numericalization — codes | numericalize_core |
Rust numeric.rs:76-88,135-180 |
| V2 | v2-rust-core | Pedigree key hash | fnv1a_128, .stable_key |
Rust hash.rs:12-23; R cross_pedigree.R:22-59 |
| V2 | v2-rust-core (codex) | Public ingestion dispatch | as_numeric() |
R/io_as_numeric.R:192-207 (verified: if (is.character(x) && is.null(dim(x))) at :198, format_conversion(...) at :206) |
| V2 | v2-rust-core (codex) | Genetic-model post-transform (split out of Fable’s single “codes” row) | numericalize_core() |
src/rust/src/numeric.rs:149-180 (verified: match model at :156, "Dom" :157, "Left" :164, "Right" :171, default :178) |
| V2 | v2-selection | Truncation count from prop | .resolve_keep |
R/select_ind.R:574 |
| V2 | v2-selection | Selection intensity (large N) | .resolve_keep |
R/select_ind.R:585–587 |
| V2 | v2-selection | Selection differential | select_ind |
R/select_ind.R:460, 482 |
| V2 | v2-selection | Realized intensity | select_ind, .select_culling |
R/select_ind.R:461–478, 1089–1090 |
| V2 | v2-selection | Response (documented, tested here) | roxygen only | R/select_ind.R:16–21 |
| V2 | v2-selection | Average effect | .avg_effect |
R/grammar_realize.R:182–184 |
| V2 | v2-selection | Breeding value | .breeding_value_matrix |
R/grammar_realize.R:236–305 (loop 282–303) |
| V2 | v2-selection | Smith–Hazel index | .index_score, .index_weights |
R/select_ind.R:769–782; 799–842 |
| V2 | v2-selection | QGSI | .quadratic_index_score |
R/select_ind.R:737, 744–747 |
| V2 | v2-selection | Lush combined index | .combined_score |
R/select_ind.R:867, 872–877, 889–902 |
| V2 | v2-selection | Within-family allocation | .sel_within_family |
R/select_ind.R:939–949 |
| V2 | v2-selection | Among-family | .sel_among_family |
R/select_ind.R:968–978 |
| V2 | v2-selection | Independent culling | .select_culling |
R/select_ind.R:1067–1081 |
| V2 | v2-selection | Index : culling : tandem | roxygen; test-culling.R:71–89 | R/select_ind.R:157–164 |
| V2 | v2-selection | Bulk pool | bulk |
R/select_schemes.R:156–169; .bulk_counts :470–472 |
| V2 | v2-selection | Pedigree family size | pedigree |
R/select_schemes.R:304–307 |
| V2 | v2-selection | Tandem schedule | pedigree, recurrent_selection |
R/select_schemes.R:291, 398 |
| V2 | v2-selection | Intermating | .intermate |
R/select_schemes.R:542–545 |
| V2 | v2-selection (codex) | General index response (context, not implemented) | roxygen only | R/select_ind.R:16-21 |
| V2 | v2-selection (codex) | Singular Smith–Hazel extension | .index_weights |
R/select_ind.R:799-830 |
| V2 | v2-selection (codex) | Selfed / DH family BV correlation | select_ind() docs (family_relationship) |
R/select_ind.R:94-98 |
| V2 | v2-selection (codex) | Sequential culling | .select_culling |
R/select_ind.R:1067-1074 |
| V2 | v2-selection (codex) | Population pooling | c.Population |
R/select_schemes.R:25-68 |
| V2 | v2-selection (codex) | Single seed descent | single_seed_descent |
R/select_schemes.R:102-118 |
| V2 | v2-selection (codex) | Recurrent-selection cycle | recurrent_selection, .intermate |
R/select_schemes.R:387-410; 354-370 |
| V2 | v2-selection (codex) | Scheme RNG threading | all four wrappers, .self_each, .intermate |
R/select_schemes.R:111, 155, 283, 384; 521; 544 |
| V2 | v2-ocs-usefulness-marker | Genomic relationship | g_matrix |
R/select_ocs.R:71–92 |
| V2 | v2-ocs-usefulness-marker | Genomic inbreeding | g_matrix (doc) |
R/select_ocs.R:16, 42–43 |
| V2 | v2-ocs-usefulness-marker | OCS objective | optimum_contribution, .frank_wolfe |
R/select_ocs.R:105–108, 601–624 |
| V2 | v2-ocs-usefulness-marker | Group coancestry | optimum_contribution, .tune_lambda |
R/select_ocs.R:319, 666 |
| V2 | v2-ocs-usefulness-marker | FW gradient / duality gap | .frank_wolfe |
R/select_ocs.R:601–607 |
| V2 | v2-ocs-usefulness-marker | Away-step and line search | .frank_wolfe |
R/select_ocs.R:609–625 |
| V2 | v2-ocs-usefulness-marker | Penalty tuning | .tune_lambda |
R/select_ocs.R:652–718 |
| V2 | v2-ocs-usefulness-marker | Parent sampling | sample_parents |
R/select_ocs.R:429–441; .allocate_slots :473–494 |
| V2 | v2-ocs-usefulness-marker | Usefulness | cross_usefulness |
R/select_usefulness.R:142–144 |
| V2 | v2-ocs-usefulness-marker | Selection intensity | .intensity_from_p |
R/select_usefulness.R:161–163 |
| V2 | v2-ocs-usefulness-marker | Fixed additive score | .additive_model, .additive_gv |
R/select_usefulness.R:204–209, 228 |
| V2 | v2-ocs-usefulness-marker | Average effect | .avg_effect |
R/grammar_realize.R:182–184 |
| V2 | v2-ocs-usefulness-marker | MAS feasibility | marker_select |
R/select_marker.R:116–119 |
| V2 | v2-ocs-usefulness-marker | MARS/oracle index | additive_value (documented in marker_select) |
R/cross_population.R:735–747; doc R/select_marker.R:20–33 |
| V2 | v2-ocs-usefulness-marker | Recurrent-allele score | .mabc_founders |
R/select_mabc.R:311 |
| V2 | v2-ocs-usefulness-marker | Recovery | .mabc_recovery |
R/select_mabc.R:464 |
| V2 | v2-ocs-usefulness-marker | Expected recovery | doc only | R/select_mabc.R:25–31, 227–229 |
| V2 | v2-ocs-usefulness-marker | Interval weights | .mabc_weights |
R/select_mabc.R:520–529 |
| V2 | v2-ocs-usefulness-marker | Foreground / recombinant / background staging | mabc_select |
R/select_mabc.R:170–177, 194 |
| V2 | v2-ocs-usefulness-marker (codex) | Ridge blend of G | g_matrix |
R/select_ocs.R:25-26, 44-50, 93-95 |
| V2 | v2-ocs-usefulness-marker (codex) | MABC foreground feasibility | mabc_select |
R/select_mabc.R:168-174 |
| V2 | v2-prediction | Tabular relationship (off-diagonal) | a_matrix |
R/select_blup.R:73-79 |
| V2 | v2-prediction | Inbreeding / diagonal | a_matrix |
R/select_blup.R:80-88 |
| V2 | v2-prediction | Variance ratio | predict_ebv, .blup_variances |
R/select_blup.R:365, :676-681 |
| V2 | v2-prediction | GLS mean | predict_ebv |
R/select_blup.R:376-386 |
| V2 | v2-prediction | BLUP of u | predict_ebv |
R/select_blup.R:387-388 |
| V2 | v2-prediction | PEV / reliability | predict_ebv |
R/select_blup.R:395-398 |
| V2 | v2-prediction | GBLUP marker back-solve | .gblup_marker_effects |
R/select_blup.R:695-703 |
| V2 | v2-prediction | Accuracy / bias | prediction_accuracy |
R/select_blup.R:752-761 |
| V2 | v2-prediction | Expected cross mean (one locus) | .expected_cross_means |
R/select_combining.R:244-255 |
| V2 | v2-prediction | Tester-referenced average effect | combining_ability (doc) |
R/select_combining.R:30-37 |
| V2 | v2-prediction | Topcross / factorial GCA, SCA | .decompose_ca |
R/select_combining.R:321-324 |
| V2 | v2-prediction | Diallel GCA (method 4) | .decompose_ca |
R/select_combining.R:312-316 |
| V2 | v2-prediction | Diallel SCA (method 4) | .decompose_ca |
R/select_combining.R:317-318 |
| V2 | v2-prediction | Broad-sense residual for simulated crosses | phenotype_value via .simulate_cross_means |
R/cross_population.R:1061; R/select_combining.R:290-293 |
| V2 | v2-prediction | Realized-scale template effects | .layer_scaled_effects \(\leftarrow\) template_effects |
R/grammar_realize.R:364; R/select_combining.R:400-406 |
| V2 | v2-prediction | Progeny-test expected mean | progeny_test (doc) |
R/select_progeny.R:17-35 |
| V2 | v2-prediction | Progeny-test accuracy | progeny_test (doc) |
R/select_progeny.R:37-53 |
| V2 | v2-prediction | Mate sampling | progeny_test |
R/select_progeny.R:121-135 |
| V2 | v2-prediction | Family mean | progeny_test |
R/select_progeny.R:149-150 |
| V2 | v2-prediction (codex) | Known-variance mixed model (the model BLUP solves) | predict_ebv |
R/select_blup.R:174-181 (roxygen), :300-321 (inputs) |
| V2 | v2-prediction (codex) | Supplied-covariance validation (correlation-scale PSD test) | .check_relationship |
R/select_blup.R:587-650 (scaling :630-632, eigen :640, tolerance :644-645) |
| V2 | v2-prediction (codex) | VanRaden method-1 genomic relationship (consumed by GBLUP) | predict_ebv \(\rightarrow\) g_matrix |
R/select_blup.R:337-343 (Codex wrote 168-173); R/select_ocs.R:44-98 (Codex wrote 44-92; core at :83, 90-92) |
| V2 | v2-prediction (codex) | Progeny-test RNG draw order (reproducibility contract) | progeny_test |
R/select_progeny.R:113-114 (seed), :132 (mates), :138 (meioses), :144-145 (residual) |
| V2 | v2-transcriptome | Expression model | simulate_transcriptome |
R/transcriptome_simulate.R:616-618 |
| V2 | v2-transcriptome | Reference-centered dosage | simulate_transcriptome |
:308-310; predict :845-847 |
| V2 | v2-transcriptome | cis score | simulate_transcriptome |
:501-511 |
| V2 | v2-transcriptome | trans factor | simulate_transcriptome |
:451-471, :512 |
| V2 | v2-transcriptome | Standardization | z1 |
:492-496 |
| V2 | v2-transcriptome | Additive genetic score | simulate_transcriptome |
:548-578 |
| V2 | v2-transcriptome | Epistatic blend | simulate_transcriptome |
:522-572 |
| V2 | v2-transcriptome | Residual | simulate_transcriptome |
:585-595 |
| V2 | v2-transcriptome | Realized heritability | simulate_transcriptome, predict |
:619-628; :943-948 |
| V2 | v2-transcriptome | Effective coefficients | simulate_transcriptome |
:636-646, :666, :673, :684 |
| V2 | v2-transcriptome | Genetic budget | simulate_transcriptome |
:651-658 |
| V2 | v2-transcriptome | Realized cis fraction | simulate_transcriptome |
:659-661; predict :950 |
| V2 | v2-transcriptome | Cross-population genetic value | predict.transcriptome_sim |
:829-848, :860-886 |
| V2 | v2-transcriptome | Mimic affine | simulate_transcriptome |
:602-616 |
| V2 | v2-transcriptome | GRM | .tx_grm |
R/transcriptome_mimic.R:24-30 |
| V2 | v2-transcriptome | REML objective | .greml_h2 |
R/transcriptome_mimic.R:76-84 |
| V2 | v2-transcriptome | GREML heritability | .greml_h2 |
R/transcriptome_mimic.R:94-97 |
| V2 | v2-transcriptome | Factor count | .tx_estimate_factors |
R/transcriptome_mimic.R:111-119 |
| V2 | v2-transcriptome | kappa proxy | .tx_estimate_kappa |
R/transcriptome_mimic.R:149-172 (roxygen :120-148); called at R/transcriptome_simulate.R:395 |
| V2 | v2-transcriptome | NB observation | observe_counts |
R/transcriptome_counts.R:75-80, :98-102 |
| V2 | v2-transcriptome | Layer score | .tx_raw, .transcriptome_matrix |
R/grammar_realize.R:454-476, :414-440 |
| V2 | v2-transcriptome | Mediation split | .tx_raw(which="genetic"), .mediation_budget, mediation_split |
R/grammar_realize.R:458-476, :730-761; R/io_write.R:1267-1270 |
| V2 | v2-transcriptome | Realized H2 | .genetic_value_matrix, .realized_h2 |
R/grammar_realize.R:394-400, :1078-1106 |
| V2 | v2-transcriptome | Per-gene share | .tx_qtn_var |
R/io_write.R:1328-1345 |
| V2 | v2-transcriptome | Layer sub-seed | .layer_seed, transcriptome |
R/grammar_simulate_phenotype.R:1079-1092; R/transcriptome_layer.R:257-276 |
| V2 | v2-transcriptome (codex) | Single-component LMM (model statement) | .greml_h2 |
R/transcriptome_mimic.R:32-53 (roxygen), fit :58-97 |
| V2 | v2-transcriptome (codex) | Calibration metrics | benchmark 01 | benchmarks/01_h2_calibration.R:61-62 (h2), :93-94 (cis) |
| V2 | v2-transcriptome (codex) | Marginal eQTL scan | scan_one |
benchmarks/02_eqtl_recovery.R:61-80 (\(r\) at :75, best rank :80) |
| V2 | v2-transcriptome (codex) | Co-expression rank test | benchmark 03 | benchmarks/03_coexpression_fp_control.R:55-70 |
| V2 | v2-transcriptome (codex) | Benchmark-04 mediation target | benchmark 04 | benchmarks/04_mediation_recovery.R:9-12, 89-90, 114-116 |
| V2 | v2-transcriptome (codex) | TWAS Pearson test | cor_p |
benchmarks/05_twas_power.R:103-112 (\(t\) at :110, \(p\) at :111) |
| V2 | v2-transcriptome (codex) | Bonferroni threshold | benchmark 05 | benchmarks/05_twas_power.R:114, 146-147 |
| V2 | v2-io-formats | Allele frequency / MAF | filter_geno |
R/qc_filter_geno.R:290-297 |
| V2 | v2-io-formats | Monomorphic / MAF filters | filter_geno |
:311, :314, :318 |
| V2 | v2-io-formats | Heterozygosity | filter_geno |
:301, :322, :324 |
| V2 | v2-io-formats | Composite (genotypic) \(r^2\) | .ld_sweep |
:556-565 |
| V2 | v2-io-formats | Pruning decision | .ld_sweep |
:532, :663, :665-668 |
| V2 | v2-io-formats | Window / step | .ld_prune, .ld_sweep |
:492-506, :605-617 (win_at), :737-782 (slide) |
| V2 | v2-io-formats | Haplotypic \(r^2\) | .plink_hap_rsq, .plink_em_hethet, .plink_cubic_roots |
:796-809 (r² at :808), :822-879, :902-943 |
| V2 | v2-io-formats | VIF | .ld_sweep (vif branch) |
:683-736 (solve :697,:721; test :725) |
| V2 | v2-io-formats | Gabriel block MAF floor / tag | .gabriel_blocks |
R/qc_ld_methods.R:25, :40 |
| V2 | v2-io-formats | Major-allele flip (frequency) | compute_flip |
R/io_detect_format.R:362-364 |
| V2 | v2-io-formats | Reference flip | compute_flip |
:359 |
| V2 | v2-io-formats | Numeric coding | numericalize_core |
src/rust/src/numeric.rs:76-76, :138-145, :156-178 |
| V2 | v2-io-formats | HWE | — | — |
| V2 | v2-io-formats | Missing-rate filter | — | — |
| V2 | v2-io-formats (codex) | Raw genotype parsing and coding dispatch | parse_hapmap_chars_to_raw(), .apply_coding() |
R/io_detect_format.R:223-326; R/io_read_formats.R:18-194 |
| V2 | v2-io-formats (codex) | Exact two-locus ML cubic | .plink_em_hethet() |
R/qc_filter_geno.R:822-879 |
| V2 | v2-io-formats (codex) | Two-locus haplotype log-likelihood | .plink_calc_lnlike() |
R/qc_filter_geno.R:884-894 |
| V2 | v2-io-formats (codex) | Cubic real roots | .plink_cubic_roots() |
R/qc_filter_geno.R:902-943 |
| V2 | v2-io-formats (codex) | D’ likelihood surface and class codes | .plink_calc_lnlike_quantile(), .plink_blocks_classify() |
R/qc_filter_geno.R:952-966, :978-1053 |
| V2 | v2-io-formats (codex) | Gabriel/Haploview block acceptance | .plink_blocks_chrom(), .gabriel_blocks() |
R/qc_filter_geno.R:1066-1180; R/qc_ld_methods.R:23-46 |
| V2 | v2-io-formats (codex) | Per-QTN marginal realized variance share | .qtn_var(), qtn_table() |
R/io_write.R:1288-1312; :1400-1403 |
| V2 | v2-io-formats (codex) | Per-gene transcriptome marginal share | .tx_qtn_var() |
R/io_write.R:1328-1345 |
| V2 | v2-io-formats (codex) | PLINK fixture allele serialization | fixture generator | data-raw/plink_parity_fixtures.R:26-34 |
| V1 | v1-core-linkage | Additive genetic value | genetic_effect |
legacy_genetic_effect.R:109-112 |
| V1 | v1-core-linkage | Dominance value | genetic_effect |
:61-75 |
| V1 | v1-core-linkage | Epistatic value | genetic_effect |
:77-89 |
| V1 | v1-core-linkage | Centering | genetic_effect |
:93 |
| V1 | v1-core-linkage | Degree of dominance | check_in |
legacy_check_in.R:274 |
| V1 | v1-core-linkage | Geometric series | check_in |
:786-788, 796-798, 810-812, 823-825 |
| V1 | v1-core-linkage | Residual variance | phenotypes |
legacy_Phenotypes.R:216, 650, 1065, 1511 |
| V1 | v1-core-linkage | Single-trait phenotype | phenotypes |
:669-674, 1517-1522 |
| V1 | v1-core-linkage | Multi-trait residual | phenotypes |
:238-245, 1080-1086 |
| V1 | v1-core-linkage | Null trait (h2=0) | phenotypes |
:533-534, 86-92 |
| V1 | v1-core-linkage | Realized heritability | phenotypes |
:248-251, 336, 675-676, 876 |
| V1 | v1-core-linkage | Per-QTN PVE | phenotypes |
:260-268, 685-693 |
| V1 | v1-core-linkage | Residual seed | phenotypes |
:234, 665, 1076, 1513; 82, 529, 924, 1374 |
| V1 | v1-core-linkage | LD-QTN seed | qtn_linkage |
legacy_QTN_linkage.R:110, 383, 645, 971, 1220, 1243, 1455, 1479 |
| V1 | v1-core-linkage | LD measure | qtn_linkage |
:150-151, 176-177, 1025-1028, 1270-1273 |
| V1 | v1-core-linkage | Indirect selection | qtn_linkage |
:125-212 |
| V1 | v1-core-linkage | Direct selection | qtn_linkage |
:1229-1308 (fixed), :978-1062, 1465-1546 (unfixed) |
| V1 | v1-core-linkage | MAF | constraint, qtn_linkage, qtn_from_user |
legacy_constraint.R:47-50; QTN_linkage.R:314-317; qtn_from_user.R:237-240 |
| V1 | v1-core-linkage | Genetic correlation (given cor) |
base_line_multi_traits (not in group) |
legacy_Base_line_multi_traits.R:167-183 |
| V1 | v1-core-linkage (codex) | Heterozygote eligibility indicator | constraint() (correct); create_phenotypes() guard (wrong code) |
legacy_constraint.R:28-42; legacy_create_phenotypes.R:100-102, 848-935 |
| V1 | v1-core-linkage (codex) | Reported residual “sample correlation” | phenotypes() |
legacy_Phenotypes.R:483-491, 1335-1343 (verified: matrix(0,...) at :484/:1336, cov2cor at :488/:1340) |
| V1 | v1-core-linkage (codex) | QTN anchor sampling without replacement | qtn_linkage() |
legacy_QTN_linkage.R:109-113, 382-386, 644-648, 970-974, 1219-1223, 1454-1458 (verified: while (s <= 10 & border) at :109,382,644,970,1219,1454; sample(index, ...) at :113,386,648,974,1223,1458) |
| V1 | v1-core-linkage (codex) | User marker resolution and order | qtn_from_user() |
legacy_qtn_from_user.R:1358-1388 (add), :1447-1460 (dom), :1517-1530 (epi), :1589-1602 (var) (verified: selected_snps <- genotypes$snp %in% i at :1361, 1450, 1520, 1592) |
| V1 | v1-core-linkage (codex) | Epistatic interaction diagnostic expansion | qtn_from_user() |
legacy_qtn_from_user.R:1582-1605 (verified: e_len <- lengths(QTN_list$epi)/epi_interaction at :1532, each = epi_interaction at :1541, each = e_len[i] at :1544) |
| V1 | v1-core-linkage (codex) | (reconciler-added) Direct-LD acceptance sentinel | qtn_linkage() |
legacy_QTN_linkage.R:1269-1269 (fixed add branch); same pattern :123-125 (indirect add), :976-983, :1467-1473 |
| V1 | v1-pleio-effects | Additive genetic value | genetic_effect |
R/legacy_genetic_effect.R:111–57 |
| V1 | v1-pleio-effects | Geometric effect series | check_in |
R/legacy_check_in.R:905–837 |
| V1 | v1-pleio-effects | Dominance genetic value | genetic_effect |
R/legacy_genetic_effect.R:120–77; R/legacy_check_in.R:274 |
| V1 | v1-pleio-effects | Epistatic genetic value | genetic_effect |
R/legacy_genetic_effect.R:151–91 |
| V1 | v1-pleio-effects | Total genetic value | genetic_effect |
R/legacy_genetic_effect.R:186–96 |
| V1 | v1-pleio-effects | Component variances | genetic_effect |
R/legacy_genetic_effect.R:115,59,69,76,87,90 |
| V1 | v1-pleio-effects | MAF of a QTN | qtn_pleiotropic, qtn_partially_pleiotropic, constraint |
R/legacy_QTN_pleiotropic.R:205–165; …partially….R:165–169; R/legacy_constraint.R:47–43 |
| V1 | v1-pleio-effects | QTN sampling seeds (pleiotropic) | qtn_pleiotropic |
R/legacy_QTN_pleiotropic.R:174,318,408,485 |
| V1 | v1-pleio-effects | QTN sampling seeds (partially) | qtn_partially_pleiotropic |
…partially….R:125,153,446,475,621,637 |
| V1 | v1-pleio-effects | Het re-sample loop | both QTN samplers | R/legacy_QTN_pleiotropic.R:180–145,324–333; …partially….R:131–140,160–170,452–461,481–493 |
| V1 | v1-pleio-effects | Whitening | base_line_multi_traits |
R/legacy_Base_line_multi_traits.R:151–109,178–184 |
| V1 | v1-pleio-effects | Colouring & rescale | base_line_multi_traits |
…multi_traits.R:160–120,185–194 |
| V1 | v1-pleio-effects | PD repair | make_pd |
R/legacy_make_pd.R:61–21 |
| V1 | v1-pleio-effects | Residual variance (context) | phenotypes |
R/legacy_Phenotypes.R:216,239,650 |
| V1 | v1-pleio-effects | vQTL residual scale | vQTL |
R/legacy_vQTL.R:89,62–71,76–89 |
| V1 | v1-pleio-effects | vQTL sample heritability | vQTL |
R/legacy_vQTL.R:251–193 |
| V1 | v1-pleio-effects | Numeric normalisation | genotypes/numeric_df |
R/legacy_Genotypes.R:79–62 |
| V1 | v1-pleio-effects | maf_cutoff filter |
genotypes |
R/legacy_Genotypes.R:163–111 |
| V1 | v1-pleio-effects (codex) | Fully pleiotropic QTN-set construction | qtn_pleiotropic |
R/legacy_QTN_pleiotropic.R:169-201 (add), 313-345 (dom), 403-423 (var), 480-500 (epi) |
| V1 | v1-pleio-effects (codex) | Partial-pleiotropy locus construction | qtn_partially_pleiotropic |
R/legacy_QTN_partially_pleiotropic.R:165-233 (add+dom-loop), 294-360 (add only), 441-533 (dom), 616-684 (epi) |
| V1 | v1-pleio-effects (codex) | Epistatic physical-marker demand | qtn_pleiotropic, qtn_partially_pleiotropic |
R/legacy_QTN_pleiotropic.R:524-532; R/legacy_QTN_partially_pleiotropic.R:586-611 (also :654) |