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Prepare an agricolae design and trial information for Breedbase

Source: R/prepare_breedbase_trial.R
prepare_breedbase_trial.Rd

Converts an existing agricolae design and records the information needed to save it as a new Breedbase trial. For example, generate an RCBD (randomized complete block design) with agricolae::design.rcbd(), prepare it here, then call save_breedbase(trial, con). Preparation is offline; the randomized allocation, plot numbers and block assignments are kept.

Usage

prepare_breedbase_trial(
  design,
  trial_name = NULL,
  year = NULL,
  location = NULL,
  program = NULL,
  description = NULL,
  folder = NULL,
  checks = NULL,
  accession = NULL,
  design_type = NULL,
  trial_type = "phenotyping_trial",
  prompt = interactive(),
  ...
)

Arguments

design

An agricolae design, its field-book data frame, or a design already converted with as_breedbase_design().

trial_name

Name of the new trial.

year

Year of the trial, as an integer or integer-valued string.

location

Exact Breedbase location name, for one trial.

program

Exact Breedbase breeding program name.

description

Description of the trial's purpose, material and season.

folder

Optional Breedbase folder name. NULL saves directly in the breeding program. Use create_folder = TRUE in save_breedbase() if a new folder should be created.

checks, accession, design_type

As in as_breedbase_design(). Supply these when converting a raw agricolae design or field book.

trial_type

Breedbase trial type; defaults to "phenotyping_trial".

prompt

Logical. Ask for missing required trial information in the R console. Defaults to TRUE in an interactive session and FALSE in scripts. With FALSE, all missing fields are reported in one error.

...

Additional column mappings for as_breedbase_design(), such as plot, block, rep, row and col.

Value

A breedbase_trial object extending breedbase_design, with converted design, original book and parameters, design_type and the recorded trial information. Pass the whole object to save_breedbase() or phenotype_template().

Details

Required trial information is trial_name, year, location, program and description. Provide it as named arguments for a reproducible script. In RStudio, prepare_breedbase_trial(design) asks for these fields when they are missing.

Inspect trial$trial for the trial information and trial$design for the converted plot table. phenotype_template(trial) uses the recorded trial name to make a field sheet with the plot names that will be saved. save_breedbase(trial, dry_run = TRUE) previews the trial and plot payload without a connection. With a connection, it checks the breeding program, location, accessions and uniqueness of the new trial and plot names. save_breedbase(trial, con) then saves through the existing BrAPI workflow. Explicit arguments to the save function override recorded information, for example trial_name = "Another_trial".

No database names or accessions are created during preparation. Physical row and column coordinates are optional for saving; include them in the input field book when known, especially for later spatial analyses. They are not inferred from agricolae plot codes.

See also

as_breedbase_design(), save_breedbase(), phenotype_template()

Examples

if (requireNamespace("agricolae", quietly = TRUE)) {
  entries <- c("G1", "G2", "G3", "CHECK_A")
  rcbd <- agricolae::design.rcbd(entries, r = 3, seed = 2026)
  trial <- prepare_breedbase_trial(rcbd,
    trial_name = "RCBD_2026_Ibadan", year = 2026, location = "Ibadan",
    program = "IITA", description = "RCBD with three replicates",
    checks = "CHECK_A", prompt = FALSE)
  trial$trial
  head(trial$design)
  payload <- save_breedbase(trial, dry_run = TRUE)
  sheet <- phenotype_template(trial, traits = "fresh root yield")
}
#> Dry run without a connection: returning the data that would be sent.
if (FALSE) { # \dontrun{
con <- breedbase_login("https://your-breedbase.org", "your_username")
save_breedbase(trial, con, dry_run = TRUE)  # check names in the database
save_breedbase(trial, con)                  # save the new trial
} # }