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Save analysis results to Breedbase as an analysis

Source: R/breedbase_analysis.R
save_breedbase_analysis.Rd

Saves analysis results as a Breedbase analysis (a project of type analysis), through the same upload as the "Upload analysis" form of Breedbase:

level = "accession"

"Analysis of: accessions": one value per genotype, e.g. second-stage adjusted means from second_stage_values().

level = "plot"

"Analysis of: plots": one value per field plot, e.g. first-stage values from first_stage_values(). Breedbase finds the field trial(s) of the plots and gives the analysis one plot per field plot (named "<analysis_name>_<field plot name>"), with the same accession, rep, block, row and column.

Each trait is saved together with a statistic term, as Breedbase does for every analysis. The analysis then appears on the Analyses page and can be used in later analyses. Every name (analysis, accessions or plots, traits, statistic) is checked first, and all problems are listed before anything is written. The field trials do not change.

Usage

save_breedbase_analysis(
  data,
  con = NULL,
  analysis_name,
  program,
  description,
  year = format(Sys.Date(), "%Y"),
  level = c("accession", "plot"),
  traits = NULL,
  accession = "accession",
  plot = "plot_name",
  estimate = NULL,
  statistic = NULL,
  protocol = NULL,
  time_terms = NULL,
  upload_file = NULL,
  dry_run = FALSE,
  confirm = interactive(),
  folder = NULL,
  create_folder = FALSE
)

Arguments

data

A data frame with one row per accession (level = "accession") or per plot (level = "plot") and one numeric column per trait.

con

A connection from breedbase_login(); NULL with dry_run = TRUE returns the file that would be uploaded.

analysis_name

Name of the new analysis (must not exist yet). Spaces and special characters are replaced with "_" (only letters, digits, _, - and . are kept).

program

Breeding program of the analysis.

description

Description of the analysis (required).

year

Year of the analysis (default: this year).

level

"accession" or "plot" (Breedbase's "Analysis of").

traits

Trait columns (default: all except the name and design columns). Their names are the Breedbase trait names.

accession, plot

Names of the accession and plot-name columns.

estimate

For the default statistic: "blue" or "blup" (adjusted means of that kind), or "spatial" (spatial correction, the default for level = "plot"). By default taken from the data (second_stage_values(), first_stage_values()).

statistic

Optional statistic term: its name, "name|SGNSTAT:id" or the id, as listed by breedbase_statistics(). It must be a term of the Breedbase statistics ontology (checked against the ontology file, with suggestions for misspelled names, and then on the server). By default chosen by estimate.

protocol

The model, e.g. a formula: "SpATS(yield ~ genotype + PSANOVA(col, row))". Default: the description.

time_terms

Optional time terms per trait, as in the form's "Compose Trait Info With Time Term", e.g. c("fresh root yield|CO_334:0000013" = "day 300|TIME:0000300").

upload_file

Where to write the upload file when the site's web pages are closed by a web password (see Details). Default: the analysis name + "_upload.csv" in the working folder.

dry_run

Logical. Check everything but write nothing.

confirm

Logical. Ask before writing (default in interactive sessions).

folder

Optional folder of the program to put the analysis in, e.g. the folder of its trials. Without a folder (the default, NULL) the analysis is in the breeding program itself. An existing folder is used as it is; a new one (special characters replaced with "_") is created when create_folder = TRUE.

create_folder

Logical. Create folder when it does not exist.

Value

Invisibly, a tibble with the analysis name and id, the number of rows (accessions or plots) sent and read back, and the analysis page; or, when the web pages are closed, a list with the upload file and the form values.

Details

The form's fields map to the arguments: Analysis Name (analysis_name, unique), Analysis Description (description), Analysis Protocol (protocol), Analysis Of (level), Breeding Program (program), Statistical Ontology Term (statistic) and the optional time terms (time_terms). The model type is Breedbase's own one for uploaded results (uploaded_generic_analysis_model).

Sites with a web password

Breedbase creates analyses through its web pages; BrAPI cannot create an analysis project. Test sites such as cassava-test.sgn.cornell.edu close their web pages with an extra web password. With it (see breedbase_login()), the analysis is uploaded directly. Without it, everything is checked through BrAPI and the file of the "Upload analysis" form is written, with the value of every form field printed: upload it in the browser and Breedbase creates the same analysis project.

Examples

prep <- augmented_prep_design(paste0("E", 1:60), locations = c("North", "South"), seed = 1)
d <- prep$design
set.seed(1)
d$yield <- rnorm(nrow(d), 25, 3)
fit <- analyze_augmented_prep_two_stage(d, "yield")
means <- second_stage_values(fit, trait = "fresh root yield")
sent <- save_breedbase_analysis(means, analysis_name = "PREP_2026_stage2", program = "IITA",
                                description = "Two-stage analysis, weighted", dry_run = TRUE)
#> Dry run without a connection: returning the upload that would be sent (trait names and the statistic are completed from Breedbase when connected).
head(sent$file)
#>   stock_names fresh root yield
#> 1         E50 30.0238650149583
#> 2         E45 29.8904456685267
#> 3         E39 28.5504753824033
#> 4         E11 27.8069635554438
#> 5          E2 27.5851896298825
#> 6         E28 27.4592783525858

if (FALSE) { # \dontrun{
con <- breedbase_login("https://cassavabase.org", "jdoe")
# Second stage: one value per accession.
save_breedbase_analysis(means, con, analysis_name = "PREP_2026_stage2", program = "IITA",
                        description = "Two-stage analysis, weighted")
# First stage: one value per field plot ("Analysis of: plots").
stage1 <- first_stage_values(fit, prep, "PREP_2026", trait = "fresh root yield")
save_breedbase_analysis(stage1, con, analysis_name = "PREP_2026_stage1", program = "IITA",
                        description = "SpATS per location", level = "plot")
} # }