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Save first-stage results to Breedbase as a trait of the field plots

Source: R/breedbase_analysis.R
save_breedbase_first_stage.Rd

Saves plot-level first-stage results (from first_stage_values()) on the plots of the field trial, as values of a trait made for adjusted values, so raw and adjusted values stay apart. By default that trait is the measured trait composed with a statistic, e.g. "fresh root yield|Adjusted Means from Spatial Correction using SpATS R": it is found, or created (after you confirm) when it does not exist yet; see breedbase_adjusted_trait(). Or name your own traits with as_trait. The values are saved through BrAPI, like save_breedbase_phenotypes().

Usage

save_breedbase_first_stage(
  values,
  con = NULL,
  as_trait = NULL,
  statistic = NULL,
  create_trait = TRUE,
  dry_run = FALSE,
  confirm = interactive()
)

Arguments

values

A table from first_stage_values() (or any table with a plot_name column and one numeric column per trait).

con

A connection from breedbase_login(); NULL with dry_run = TRUE returns what would be sent.

as_trait

Optional named vector: for each trait column of values, an existing Breedbase trait to save it under, e.g. c("fresh root yield" = "fresh root yield adjusted|COMP:0000123").

statistic

The statistic composed with each trait when as_trait is not given. By default chosen from this Breedbase's own statistics (the spatial correction term); see breedbase_statistics().

create_trait

Logical. Create the composed traits that do not exist yet (you are asked first when confirm = TRUE).

dry_run, confirm

As in save_breedbase_phenotypes().

Value

As save_breedbase_phenotypes(): one row per trait with the values sent and found.

Slow servers

Accessions are searched 25 names at a time, because Breedbase looks up the pedigree of each one. If the server times out (HTTP 504, 502, 503 or 429), the batch is split in half and tried again, so a busy server is slower but still works. A line is printed after each batch with the names done and the time. Accessions found are remembered until R is restarted, so save_breedbase() after breedbase_check() does not search them again.

When creating the folder, the trial or its plots times out, the save does not stop: the server may still finish the job, so it checks for the result every 20 seconds for 3 minutes, and tries once more if it is not there (Breedbase refuses names that already exist, so this cannot make duplicates). If a save is cut off anyway, run save_breedbase() again: an existing folder is used, and a trial left without plots gets its plots. Settings: options(breedtools.write_wait = 30, breedtools.write_checks = 10). Settings: options(breedtools.germplasm_batch = 10) for smaller batches, options(breedtools.breedbase_timeout = 600) to wait longer (seconds) for each answer.

Examples

rc <- augmented_row_column_design(paste0("G", 1:108), paste0("C", 1:4),
                                  12, 12, 4, 4, n_candidates = 5, seed = 1)
d <- rc$design
set.seed(1)
d$yield <- 25 + 0.4 * d$row + rnorm(nrow(d), sd = 2)
fit <- analyze_augmented_row_column_design(d, "yield")
values <- first_stage_values(fit, rc, "AYT_2026_Ibadan", trait = "fresh root yield")
obs <- save_breedbase_first_stage(values, dry_run = TRUE)
#> Dry run without a connection: returning the observations that would be sent.
head(obs)
#> # A tibble: 6 × 4
#>   plot_name               trait                                  value timestamp
#>   <chr>                   <chr>                                  <chr> <chr>    
#> 1 AYT_2026_Ibadan_G51_1_1 fresh root yield|Adjusted Means from … 28.7… NA       
#> 2 AYT_2026_Ibadan_G64_1_1 fresh root yield|Adjusted Means from … 29.9… NA       
#> 3 AYT_2026_Ibadan_G97_1_1 fresh root yield|Adjusted Means from … 29.8… NA       
#> 4 AYT_2026_Ibadan_C3_1_1  fresh root yield|Adjusted Means from … 27.3… NA       
#> 5 AYT_2026_Ibadan_G8_2_1  fresh root yield|Adjusted Means from … 28.2… NA       
#> 6 AYT_2026_Ibadan_C2_2_2  fresh root yield|Adjusted Means from … 28.0… NA       

if (FALSE) { # \dontrun{
con <- breedbase_login("https://cassavabase.org", "jdoe")
save_breedbase_first_stage(values, con, dry_run = TRUE)   # check; shows the trait to create
save_breedbase_first_stage(values, con)                   # creates the trait if needed, saves
} # }