Convenience wrapper that runs [hbr_fit_models()] followed by [hbr_cross_design()] and returns the combined `hgsi_advanced` object. See the two component functions for the full argument descriptions.
Usage
hbr_advanced_decision(
pipeline_result = NULL,
pipeline_results = NULL,
trait_dirs = NULL,
output_dir = NULL,
phenotypes = NULL,
phenotype_id_col = "ID",
gate_params = NULL,
min_concordance = 0.6,
plink_prefix = NULL,
weights = NULL,
top_parents = 25L,
n_cores = 1L,
seed = 1L,
verbose = TRUE,
cv_repeats = 10L,
cv_folds = 5L,
top_frac = 0.1,
min_count = 5L,
strata = NULL,
n_strata = 3L,
strict = TRUE,
final_model = c("auto", "gblup", "two_kernel"),
boot = 2000L,
cM_per_Mb = NULL,
genetic_map = NULL,
bin_cM = 1,
top_crosses = 20L,
relatedness_max = 0.3,
mating = c("DH", "RIL"),
sel_frac = 0.1,
h_sel = 1,
cross_rank = c("uc", "blocks", "balanced"),
haploblock_method = c("recomb", "ld", "fourgamete", "gabriel", "recomb+gabriel",
"recomb+fourgamete"),
haploblock_rmax = 0.01,
haploblock_r2 = 0.5,
haploblock_ld_max_cM = 3,
haploblock_max_span_cM = 5,
haploblock_flank_cM = 1,
haploblock_max_snps = 400L,
haploblock_min_gamete = 0.01,
run_set_selection = TRUE,
set_size = 8L,
n_candidates = 60L,
block_cM = 5
)Arguments
- pipeline_result
A single [haplobreed_analysis()] result.
- pipeline_results
Named list of results; takes precedence over `pipeline_result`.
- trait_dirs
Named character vector of pipeline output directories for traits without an in-memory result.
- output_dir
Directory for `hgsi_fit.rds` and the CV CSVs. `NULL` or `NA` writes nothing.
- phenotypes
Optional wide data.frame (ID + one column per trait, plus PC columns if the pipeline used PCs).
- phenotype_id_col
ID column of `phenotypes`.
- gate_params
Optional gate override list, per trait or shared.
- min_concordance
Minimum Jaccard overlap for the replay to count as faithful.
- plink_prefix
PLINK prefix; default `pipeline_summary$PLINK_Prefix`.
- weights
Named non-negative emphasis per genetic SD.
- top_parents
Number of parents reported.
- n_cores
Workers for the GRM.
- seed
Random seed.
- verbose
Print progress.
- cv_repeats, cv_folds
Cross-validation settings.
- top_frac
Fraction selected for realised gain.
- min_count
Minimum training carriers per haplotype indicator.
- strata, n_strata
Fold strata, or number of genotype clusters.
- strict
Recompute GRM allele frequencies inside each training fold.
- final_model
`"auto"`, `"gblup"` or `"two_kernel"`.
- boot
Bootstrap resamples for the CV comparison.
- cM_per_Mb, genetic_map, bin_cM
Genetic map. See [hbr_advanced_decision()].
- top_crosses
Number of crosses reported.
Maximum relatedness between parents of a cross.
- mating
`"DH"` or `"RIL"`.
- sel_frac, h_sel
Selection intensity and heritability for usefulness.
- cross_rank
How crosses are ordered: `"uc"`, `"blocks"` or `"balanced"`.
- haploblock_method
See [hbr_advanced_decision()].
- haploblock_rmax, haploblock_r2, haploblock_ld_max_cM, haploblock_max_span_cM
Map-based / LD block thresholds.
- haploblock_flank_cM, haploblock_max_snps, haploblock_min_gamete
SNP-level method settings.
- run_set_selection, set_size, n_candidates, block_cM
Set-selection settings.
Examples
toy <- system.file("extdata", "hgsi_toy", package = "HaploBreedR")
td <- file.path(toy, "trait_YLD")
fit <- try(hbr_advanced_decision(
trait_dirs = c(YLD = td),
plink_prefix = file.path(toy, "geno_toy"),
output_dir = tempdir(),
cv_repeats = 1L, cv_folds = 2L, strict = FALSE,
run_set_selection = FALSE,
save_plot = FALSE,
verbose = FALSE))
#> Error in hbr_advanced_decision(trait_dirs = c(YLD = td), plink_prefix = file.path(toy, :
#> unused argument (save_plot = FALSE)