Convert an agricolae field book for saving to Breedbase

Adapts a design generated by the CRAN package agricolae to save_breedbase() and phenotype_template(). The randomization is kept; no design is generated or randomized by this function. Conversion is entirely offline and does not require agricolae to be installed. To also record the trial name, location, breeding program and year for a later save, use prepare_breedbase_trial().

Usage

as_breedbase_design(
  design,
  accession = NULL,
  checks = NULL,
  design_type = NULL,
  plot = NULL,
  block = NULL,
  rep = NULL,
  row = NULL,
  col = NULL
)

Arguments

design

An agricolae design (a list with book and parameters), or its field-book data frame, including the result of agricolae::zigzag().

accession

Name of the field-book column containing Breedbase accession names. Inferred only when exactly one non-structural column is present. For factorial, split-plot, strip-plot and Graeco-Latin designs, explicitly select the genotype column; combinations of treatment factors are not turned into accession names.

checks

Character vector of check accession names. By default, uses parameters$trt1 for an agricolae augmented block design (design.dau()), and no checks for other designs. Use character(0) to explicitly mark no checks.

design_type

Breedbase design type. Inferred for crd ("CRD"), rcbd ("RCBD"), alpha ("Alpha"), lattice ("Lattice"), dau ("Augmented"), split ("splitplot") and strip ("stripplot"); factorial designs use their underlying CRD or RCBD. Required for a bare field book or a design without a direct Breedbase type, such as Latin squares, Youden, BIB and cyclic designs. Select a compatible type accepted by your Breedbase installation; the original agricolae type remains in the returned object's parameters.

plot, block, rep, row, col

Optional field-book column names. Defaults detect plots, block, a replicate column (replication, replicate, rep or r), and the pair row, col. Missing block or replicate columns are set to 1; in RCBD, block also supplies replicate. Augmented blocks are not treated as replicates. Coordinates are used only when both columns are available, and are never inferred from plot numbers or the sketch. Mapped numeric columns must contain positive integers.

Value

A breedbase_design list with the standardized plot table (design), Breedbase design_type, original book and parameters. Pass the whole object to save_breedbase() or phenotype_template().

Details

Plot numbers, accessions, blocks, replicates and any explicit coordinates retain their field-book values. Alpha designs' cols column describes positions within blocks and is not assumed to be a field coordinate. For split plots, where plots is repeated across subplots, sequential unique plot numbers are assigned in field-book row order. An explicit plot mapping must always identify each row uniquely.

The original field book and generation parameters are retained as book and parameters. Saving uploads one plot per row, with accession, block, replicate, check status and optional coordinates. Other treatment factors and the main-plot/subplot hierarchy are retained locally, but are not uploaded by save_breedbase(). In particular, this conversion does not create treatment records or an analysis model for factorial designs.

Accession names must already exist in Breedbase. Supply the new trial's name, year, location, description and breeding program to save_breedbase(); use dry_run = TRUE to inspect or check before saving.

See also

save_breedbase(), phenotype_template()

Examples

if (requireNamespace("agricolae", quietly = TRUE)) {
  accessions <- c("G1", "G2", "G3", "CHECK_A")
  randomized <- agricolae::design.rcbd(accessions, r = 3, seed = 2026)
  converted <- as_breedbase_design(randomized, checks = "CHECK_A")
  payload <- save_breedbase(converted, trial_name = "RCBD_2026",
    year = 2026, location = "Ibadan", description = "RCBD from agricolae",
    dry_run = TRUE)
  sheet <- phenotype_template(converted, "RCBD_2026", traits = "yield")
}
#> Dry run without a connection: returning the data that would be sent.