23 Public function index

Every exported function and registered S3 method has a chapter assignment. An example link identifies an authored executable chunk. An example link shows that the function is exercised by executed code; it is not a claim that the chapter’s scientific claims have passed independent review.

Function or method	Planned chapter	Authored example
`[.Population()`	Maps, haplotypes, and founders	cross-f1, mating-composition, founders-subset, prediction-pedigree, selection-population
`a_matrix()`	Relationship matrices and prediction	prediction-amatrix
`additive()`	Additive phenotype models	first-model, additive-model, additive-effects, additive-phase, additive-fixed-qtn, additive-mice, nonadditive-orthogonal, nonadditive-degree, binary-model, complex-vqtl, complex-stack, complex-inputs
`additive_value()`	Trait values across generations	trait-fixed-scale, trait-genotypic, optimization-midparent, optimization-usefulness-check, markers-index, programs-progeny, prediction-trait, prediction-multitrait
`as_numeric()`	Genotype input and quality control	first-genotypes, input-toy-hapmap, input-reference, input-counted-column, input-coding, input-to-file, input-gds-error, input-human, input-classes
`as_population()`	Maps, haplotypes, and founders	cross-founders, mating-pools, founders-maize, founders-human, founders-mice-map, prediction-founders, selection-population
`breed_composition()`	Mating designs and crossbreeding	mating-composition
`bulk()`	Combining ability and breeding schemes	programs-schemes
`c.Population()`	Combining ability and breeding schemes	cross-families, mating-composition, programs-pool, prediction-pedigree
`coheritability()`	Pleiotropy, linkage, and multiple traits	multitrait-coheritability, multitrait-ar1, binary-two-traits, complex-correlation
`combining_ability()`	Combining ability and breeding schemes	programs-diallel, programs-diallel-check, programs-diallel-sim, programs-topcross
`complex_phenotypes()`	Complex phenotype architectures	complex-combine, complex-combine-options, complex-terminal
`cor_ar1()`	Pleiotropy, linkage, and multiple traits	multitrait-ar1
`create_phenotypes()`	Legacy interface and migration	legacy-single, legacy-pleiotropic, legacy-ld
`cross()`	Meiosis and crossing	cross-f1, cross-families, mating-composition
`cross_usefulness()`	Contributions and cross usefulness	optimization-usefulness, optimization-usefulness-check, optimization-selfcross
`crossbreed()`	Mating designs and crossbreeding	mating-crossbreed, mating-three-way
`dominance()`	Dominance and epistasis	nonadditive-dominance, nonadditive-dominance-separate
`dosages()`	Maps, haplotypes, and founders	cross-f1-het, cross-linkage, founders-haplotypes, founders-from-haplotypes, founders-coalescent-presets, markers-founders, programs-schemes-compare, prediction-gmatrix-options
`double_haploid()`	Meiosis and crossing	cross-dh, cross-interference, trait-genotypic, optimization-usefulness-check
`epistasis()`	Dominance and epistasis	nonadditive-epistasis, nonadditive-epistasis-types, complex-stack
`families()`	Meiosis and crossing	cross-families, mating-mate, selection-population
`filter_geno()`	Genotype input and quality control	input-filter-maf, input-filter-ld, input-filter-pairphase, input-filter-blocks, input-filter-population, optimization-inbred, legacy-pleiotropic-v2
`founders_coalescent()`	Maps, haplotypes, and founders	founders-coalescent, founders-coalescent-presets
`g_matrix()`	Relationship matrices and prediction	optimization-g, prediction-gmatrix, prediction-gmatrix-options, prediction-amatrix
`genetic_values()`	Additive phenotype models	first-tables, additive-var-explained, nonadditive-rebuild, multitrait-library, binary-liability, complex-classes, complex-inputs, complex-correlation, trait-fixed-scale, trait-replication, mediation-genetic-values, output-truth, output-vary-qtn, selection-trait, selection-progeny, selection-multitrait
`genotypic_value()`	Trait values across generations	trait-genotypic, programs-template-check
`gxe_value()`	Trait values across generations	trait-gxe
`haplotypes()`	Maps, haplotypes, and founders	founders-haplotypes, founders-human, founders-from-haplotypes
`heterosis()`	Mating designs and crossbreeding	mating-heterosis
`liability_threshold()`	Binary phenotypes with human genotypes	binary-model, binary-two-traits, binary-ordinal, binary-random, binary-replications
`mabc_select()`	Marker-assisted breeding	markers-mabc, markers-mabc-record
`marker_select()`	Marker-assisted breeding	markers-foreground, markers-pyramid, markers-staged, markers-index
`mate()`	Mating designs and crossbreeding	cross-selfing, trait-carry, mating-mate, prediction-pedigree, selection-population, selection-progeny
`mating_design()`	Mating designs and crossbreeding	mating-design, mating-mate, prediction-pedigree, selection-population, selection-progeny
`mediation_split()`	Expression-mediated phenotypes	mediation-split, mediation-genes, mediation-real, mediation-multitrait
`n_individuals()`	Maps, haplotypes, and founders	cross-founders, founders-maize, selection-mass, selection-intensity, selection-family, selection-per-family
`observe_counts()`	Transcriptome simulation and counts	expression-counts, expression-library-size
`optimum_contribution()`	Contributions and cross usefulness	optimization-ocs, optimization-ocs-check, optimization-frontier, optimization-target
`parentage()`	Meiosis and crossing	cross-parentage, cross-selfing, programs-pool, prediction-pedigree, prediction-amatrix, selection-population
`pedigree()`	Combining ability and breeding schemes	programs-schemes, programs-population-trait
`phenotype_value()`	Trait values across generations	trait-var-e, trait-gxe, prediction-trait, prediction-design, prediction-multitrait
`phenotypes_long()`	Inspecting and exporting results	first-tables, binary-tables, binary-replications, complex-classes, output-long-wide, output-counts
`phenotypes_wide()`	Inspecting and exporting results	first-tables, binary-two-traits, mediation-reconstruct, output-long-wide, output-wide-cor, selection-trait, selection-progeny
`plot.phenotype_sim()`	Inspecting and exporting results	first-plot, additive-plot, multitrait-plot, output-plot
`population_from_haplotypes()`	Maps, haplotypes, and founders	founders-from-haplotypes
`population_trait()`	Trait values across generations	trait-none, trait-carry, programs-population-trait, selection-progeny
`predict.transcriptome_sim()`	Transcriptome simulation and counts	expression-predict, expression-predict-reference
`predict_ebv()`	Relationship matrices and prediction	prediction-ebv, prediction-design, prediction-multitrait, prediction-custom-k
`prediction_accuracy()`	Relationship matrices and prediction	prediction-accuracy, prediction-design, prediction-multitrait
`print.Population()`	Maps, haplotypes, and founders	cross-founders, cross-f1, mating-pools, mating-mate, founders-maize, founders-subset, founders-coalescent, prediction-founders, selection-population, selection-mass
`print.combining_ability()`	Combining ability and breeding schemes	programs-diallel, programs-diallel-sim
`print.ocs()`	Contributions and cross usefulness	optimization-ocs, optimization-target
`print.phenotype_sim()`	Inspecting and exporting results	first-model, additive-model, nonadditive-dominance, binary-model, complex-vqtl, complex-combine, output-print
`print.transcriptome_sim()`	Transcriptome simulation and counts	expression-simulate
`progeny_test()`	Combining ability and breeding schemes	programs-progeny
`qtn_table()`	Additive phenotype models	first-tables, additive-model, additive-reps, additive-var-explained, nonadditive-rebuild, multitrait-ld, complex-vqtl-table, complex-shared, complex-terminal, trait-fixed-scale, mediation-qtn, output-truth, output-vary-qtn
`recurrent_parent_recovery()`	Marker-assisted breeding	markers-mabc, markers-foreground, markers-drag, markers-weights
`recurrent_selection()`	Combining ability and breeding schemes	programs-recurrent, programs-recurrent-cycles
`sample_parents()`	Contributions and cross usefulness	optimization-parents, optimization-parents-coancestry
`select_ind()`	Individual, family, and multivariate selection	trait-carry, selection-mass, selection-intensity, selection-response, selection-criteria, selection-random, selection-progeny, selection-family, selection-per-family, selection-multitrait, selection-culling, selection-bqp
`selection_methods()`	Individual, family, and multivariate selection	selection-manifest
`selfcross()`	Meiosis and crossing	cross-f2, cross-selfing, trait-base
`simulate_phenotype()`	Additive phenotype models	first-model, first-random-residuals, additive-model, additive-one-call, additive-reps, additive-mean-subset, multitrait-independent, multitrait-pleiotropy, multitrait-ld, binary-model, binary-replications, binary-random, binary-two-traits, complex-vqtl, complex-replications, complex-random, complex-inputs, trait-base, trait-inherit, trait-replication, mediation-model, mediation-real, mediation-genotype-free, output-vary-qtn, legacy-single-v2, legacy-ld-v2, selection-trait, selection-progeny, selection-multitrait
`simulate_transcriptome()`	Transcriptome simulation and counts	expression-simulate, expression-fixed-h2, expression-coexpression, expression-epistasis, expression-mimic
`single_seed_descent()`	Combining ability and breeding schemes	programs-schemes, programs-pool
`synthetic_map()`	Maps, haplotypes, and founders	founders-human, founders-mice-map, founders-map-shape, founders-map-options, prediction-founders
`template_effects()`	Combining ability and breeding schemes	optimization-midparent, programs-trait, programs-schemes-compare, programs-recurrent
`transcriptome()`	Expression-mediated phenotypes	mediation-model, mediation-genes, mediation-real, mediation-genotype-free, mediation-multitrait
`vqtl()`	Complex phenotype architectures	complex-vqtl, complex-replications, complex-random, complex-shared, complex-stack
`write_phenotypes()`	Inspecting and exporting results	first-export, output-write, output-roundtrip, output-split, output-split-json
`write_qtn_table()`	Inspecting and exporting results	first-export, output-write-qtn

23.1 Method option coverage

This initial checklist is seeded from selection, prediction, mating, and architecture options. It will expand with each methods chapter; it is not yet an exhaustive option inventory.

Function	Method or configuration	Example status
`select_ind()`	`mass`	Authored: trait-carry, selection-mass
`select_ind()`	`within_family`	Authored: selection-family, selection-per-family
`select_ind()`	`among_family`	Authored: selection-family
`select_ind()`	`combined`	Authored: selection-family
`select_ind()`	`index`	Authored: selection-multitrait
`select_ind()`	`quadratic_index`	Authored: selection-multitrait
`select_ind()`	`random`	Authored: selection-random
`select_ind()`	`culling`	Authored: selection-culling
`select_ind()`	`bqp`	Authored: selection-bqp
`predict_ebv()`	`gblup, single trait`	Authored: prediction-ebv
`predict_ebv()`	`pedigree, single trait`	Authored: prediction-ebv
`predict_ebv()`	`gblup, multiple traits`	Authored: prediction-multitrait
`predict_ebv()`	`pedigree, multiple traits`	Authored: prediction-multitrait
`simulate_phenotype()`	`independent`	Authored: multitrait-independent, binary-model, complex-vqtl
`simulate_phenotype()`	`pleiotropy`	Authored: multitrait-pleiotropy, binary-two-traits, complex-inputs, legacy-pleiotropic-v2
`simulate_phenotype()`	`ld`	Authored: multitrait-ld, legacy-ld-v2
`sample_parents()`	`allocate`	Authored: optimization-parents
`sample_parents()`	`multinomial`	Authored: optimization-parents-coancestry
`combining_ability()`	`expected`	Authored: programs-diallel
`combining_ability()`	`simulated`	Authored: programs-diallel-sim
`mating_design()`	`random`	Authored: prediction-pedigree
`mating_design()`	`factorial`	Planned
`mating_design()`	`nested`	Planned
`mating_design()`	`diallel`	Planned
`mating_design()`	`half_diallel`	Planned
`combining_ability()`	`topcross`	Authored: programs-topcross
`combining_ability()`	`factorial`	Authored: programs-topcross
`combining_ability()`	`diallel`	Authored: programs-diallel
`simulate_phenotype()`	`residual_mode = fixed / random`	Authored: first-random-residuals
`simulate_phenotype()`	`distinct_chr = TRUE`	Authored: multitrait-distinct-chr
`simulate_phenotype()`	`pi (partial pleiotropy)`	Authored: multitrait-partial
`simulate_phenotype()`	`n_pleio_major, prop_var_major`	Authored: multitrait-major
`simulate_phenotype()`	`resid_cor`	Authored: multitrait-resid-cor
`simulate_phenotype()`	`ld_phase coded/coupling/repulsion`	Authored: multitrait-ld-phase
`simulate_phenotype()`	`vary_qtn`	Authored: additive-reps
`simulate_phenotype()`	`reps (entry means)`	Authored: additive-mean-subset
`simulate_phenotype()`	`model = "AD"`	Authored: nonadditive-model-ad
`additive()`	`orthogonal = TRUE`	Authored: nonadditive-orthogonal
`additive()`	`phase = "repulsion"`	Authored: additive-phase
`dominance()`	`same_as_add = FALSE`	Authored: nonadditive-dominance-separate
`epistasis()`	`interaction_type a/d, interaction = 3`	Authored: nonadditive-epistasis-types
`simulate_phenotype()`	`residual_mode`	Authored: binary-random, complex-random, complex-combine-options
`liability_threshold()`	`prop, two categories`	Authored: binary-model
`liability_threshold()`	`prop, more than two categories`	Authored: binary-ordinal
`liability_threshold()`	`trait = subset of traits`	Authored: binary-two-traits
`vqtl()`	`same_as_add = TRUE`	Authored: complex-shared
`vqtl()`	`qtn = fixed locus`	Authored: complex-vqtl
`complex_phenotypes()`	`reps, resid_cor, residual_mode`	Authored: complex-combine-options
`simulate_phenotype()`	`n_reps`	Authored: binary-replications, complex-replications
`mating_design()`	`random, factorial, nested, diallel, half_diallel`	Authored: mating-design
`cross()`	`interference = "poisson" vs gamma default`	Authored: cross-interference
`crossbreed()`	`two_way, backcross, rotational`	Authored: mating-crossbreed
`crossbreed()`	`three_way, terminal`	Authored: mating-three-way
`families()`	`full_sib, maternal_half_sib, selfed`	Authored: cross-families
`parentage()`	`ancestors = TRUE`	Authored: cross-parentage
`simulate_phenotype()`	`n_reps vs reps`	Authored: trait-replication
`simulate_phenotype()`	`refit = FALSE (carried trait)`	Authored: trait-inherit
`phenotype_value()`	`h2 / var_e / ref`	Authored: trait-var-e
`phenotype_value()`	`gxe, env`	Authored: trait-gxe
`mating_design()`	`allow_self = TRUE`	Authored: mating-design
`simulate_transcriptome()`	`h2 = "beta" vs numeric`	Authored: expression-simulate, expression-fixed-h2
`simulate_transcriptome()`	`geno = NULL, n_ind (genotype-free)`	Authored: expression-coexpression
`simulate_transcriptome()`	`epistasis > 0`	Authored: expression-epistasis
`simulate_transcriptome()`	`mimic`	Authored: expression-mimic
`observe_counts()`	`dispersion = 0 (Poisson) vs > 0`	Authored: expression-counts
`simulate_phenotype()`	`transcriptome = (derived) vs expression = (real) vs genotype-free`	Authored: mediation-model, mediation-real, mediation-genotype-free
`transcriptome()`	`n_genes vs explicit genes + slopes`	Authored: mediation-model, mediation-genes
`as_numeric()`	`method = "frequency" / "reference"`	Authored: input-reference
`as_numeric()`	`code_as = "012"`	Authored: input-coding
`as_numeric()`	`impute`	Authored: input-coding, input-human
`as_numeric()`	`counted_column = TRUE`	Authored: input-counted-column
`as_numeric()`	`to_file = TRUE`	Authored: input-to-file
`as_numeric()`	`GDS input`	Authored: input-human
`filter_geno()`	`maf_above`	Authored: input-filter-maf
`filter_geno()`	`hets = "include"`	Authored: input-filter-maf
`filter_geno()`	`indep_pairwise, window_unit = "kb"`	Authored: input-filter-ld
`filter_geno()`	`indep (VIF)`	Authored: input-filter-ld
`filter_geno()`	`indep_pairphase`	Authored: input-filter-pairphase
`filter_geno()`	`blocks = TRUE`	Authored: input-filter-blocks
`filter_geno()`	`Population input`	Authored: input-filter-population
`founders_coalescent()`	`species = "MAIZE", inbred = TRUE, split`	Authored: founders-coalescent-presets
`synthetic_map()`	`suppression = 0, total_cm`	Authored: founders-map-shape, founders-map-options
`optimum_contribution()`	`lambda`	Authored: optimization-frontier
`optimum_contribution()`	`target_coancestry`	Authored: optimization-target
`cross_usefulness()`	`scheme = dh`	Authored: optimization-usefulness
`cross_usefulness()`	`scheme = selfcross`	Authored: optimization-selfcross
`mabc_select()`	`flanking_markers, exclude_interval`	Authored: markers-mabc
`marker_select()`	`requirement carrier/homozygote`	Authored: markers-pyramid
`marker_select()`	`min_markers (staged)`	Authored: markers-staged
`marker_select()`	`rank_on`	Authored: markers-index
`recurrent_parent_recovery()`	`weights = "interval"`	Authored: markers-weights
`write_phenotypes()`	`format = long/wide, sep`	Authored: output-write
`write_phenotypes()`	`file_type = json`	Authored: output-write, output-split-json
`write_phenotypes()`	`split_markers, markers_files, rep = "all"`	Authored: output-split, output-split-json
`write_qtn_table()`	`rep = "all"`	Authored: output-write-qtn
`simulate_phenotype()`	`vary_qtn = TRUE`	Authored: output-vary-qtn
`create_phenotypes()`	`architecture = pleiotropic, model = AD, QTN_variance`	Authored: legacy-pleiotropic
`create_phenotypes()`	`architecture = LD, type_of_ld = indirect`	Authored: legacy-ld
`plot.phenotype_sim()`	`which panels`	Authored: output-plot
`predict_ebv()`	`K supplied`	Authored: prediction-custom-k
`g_matrix()`	`ridge, base_freq`	Authored: prediction-gmatrix-options
`select_ind()`	`intensity argument`	Authored: selection-intensity
`select_ind()`	`on = gv / bv, direction = low`	Authored: selection-criteria