Example data for OptiDesign — OptiDesign_example

Synthetic example data shipped with OptiDesign for illustrating and testing the main design constructors, relationship-matrix workflows, optional dispersion optimisation, and efficiency evaluation across both design families.

Format

A named list with the following components:

OptiDesign_lines: A data frame with columns Treatment and Family representing a synthetic pool of line identifiers and their family labels. Used as a starting point for constructing both prep_famoptg() and alpha_rc_stream() treatment vectors.
OptiDesign_id_map: A data frame with columns Treatment and LineID used to map treatment labels to the rownames and colnames of relationship matrices when those names differ from the treatment identifiers. Relevant for cluster_source %in% c("GRM", "A") and for prediction_type %in% c("GBLUP", "PBLUP").
OptiDesign_GRM: A synthetic genomic relationship matrix with rownames and colnames corresponding to line IDs. Can be used for matrix-based grouping (cluster_source = "GRM"), dispersion optimisation (dispersion_source = "GRM"), or as a K matrix for GBLUP efficiency evaluation.
OptiDesign_A: A synthetic pedigree-style relationship matrix with rownames and colnames corresponding to line IDs. Can be used for pedigree-based grouping (cluster_source = "A"), dispersion optimisation (dispersion_source = "A"), or as a K matrix for PBLUP efficiency evaluation.
OptiDesign_K: A synthetic genomic kernel matrix with rownames and colnames corresponding to line IDs. Intended for workflows that supply a K matrix directly, such as prediction_type = "GBLUP" in evaluate_famoptg_efficiency() or evaluate_alpha_efficiency(), CDmean computation in optimize_famoptg() or optimize_alpha_rc(), and dispersion optimisation with dispersion_source = "K".
OptiDesign_famoptg_example: A named list containing the core treatment vectors and field dimensions needed to call prep_famoptg(). Includes check treatments, p-rep treatments with replication counts, unreplicated treatments, family labels for all treatment classes, number of blocks, and field dimensions (n_rows, n_cols). Combine with one of OptiDesign_famoptg_args_family or OptiDesign_famoptg_args_grm to form a complete argument list.
OptiDesign_alpha_example: A named list containing the core treatment vectors and field dimensions needed to call alpha_rc_stream(). Includes check treatments, entry treatments, family labels, number of replicates, and field dimensions (n_rows, n_cols). Combine with one of OptiDesign_alpha_args_family or OptiDesign_alpha_args_grm to form a complete argument list.
OptiDesign_famoptg_args_family: A named list of supplementary arguments for a family-based call to prep_famoptg(). Specifies cluster_source = "Family", field traversal settings, block placement options, and does not include efficiency evaluation arguments (those are now passed to evaluate_famoptg_efficiency() separately).
OptiDesign_famoptg_args_grm: A named list of supplementary arguments for a GRM-based call to prep_famoptg(). Specifies cluster_source = "GRM", includes GRM and id_map references, and illustrates matrix-based grouping and optional dispersion settings. Efficiency evaluation arguments are passed to evaluate_famoptg_efficiency() separately.
OptiDesign_alpha_args_family: A named list of supplementary arguments for a family-based call to alpha_rc_stream(). Specifies cluster_source = "Family", field traversal settings, and block size constraints. Efficiency evaluation arguments are passed to evaluate_alpha_efficiency() separately.
OptiDesign_alpha_args_grm: A named list of supplementary arguments for a GRM-based call to alpha_rc_stream(). Specifies cluster_source = "GRM", includes GRM and id_map references, and illustrates matrix-based grouping and optional dispersion settings. Efficiency evaluation arguments are passed to evaluate_alpha_efficiency() separately.

Source

Generated internally by data-raw/generate_example_data.R.

Details

The objects in this dataset are fully synthetic and are intended for:

package examples and vignettes,
unit tests,
workflow demonstrations,
and user exploration of argument combinations.

The dataset covers both design families in the package and is structured so that OptiDesign_famoptg_example and OptiDesign_alpha_example provide the treatment and field inputs, while the *_args_* lists provide the algorithmic and model settings. This separation mirrors the construct-then-evaluate architecture of the package.

Illustrative workflows

Repeated-check block design (family-based):

x <- OptiDesign_example_data

design <- do.call(prep_famoptg,
  c(x$OptiDesign_famoptg_example, x$OptiDesign_famoptg_args_family)
)

eff <- evaluate_famoptg_efficiency(
  field_book       = design$field_book,
  n_rows           = x$OptiDesign_famoptg_example$n_rows,
  n_cols           = x$OptiDesign_famoptg_example$n_cols,
  check_treatments = x$OptiDesign_famoptg_example$check_treatments,
  treatment_effect = "fixed"
)

Alpha row-column stream design (GRM-based):

x <- OptiDesign_example_data

design <- do.call(alpha_rc_stream,
  c(x$OptiDesign_alpha_example, x$OptiDesign_alpha_args_grm)
)

eff <- evaluate_alpha_efficiency(
  field_book       = design$field_book,
  n_rows           = x$OptiDesign_alpha_example$n_rows,
  n_cols           = x$OptiDesign_alpha_example$n_cols,
  check_treatments = x$OptiDesign_alpha_example$check_treatments,
  treatment_effect = "fixed"
)

Optimised repeated-check block design:

x <- OptiDesign_example_data

opt <- do.call(optimize_famoptg,
  c(
    x$OptiDesign_famoptg_example,
    x$OptiDesign_famoptg_args_family,
    list(
      treatment_effect = "fixed",
      criterion        = "A",
      n_restarts       = 20
    )
  )
)
opt$optimization$best_score

Optimised alpha row-column stream design:

x <- OptiDesign_example_data

opt <- do.call(optimize_alpha_rc,
  c(
    x$OptiDesign_alpha_example,
    x$OptiDesign_alpha_args_family,
    list(
      treatment_effect = "fixed",
      method           = "RS",
      criterion        = "A",
      n_restarts       = 20
    )
  )
)
opt$optimization$best_score