List the statistic terms of Breedbase (SGNSTAT ontology)

Breedbase saves analysis results as a trait combined with a statistic term of its statistics ontology (SGNSTAT), e.g. "Adjusted Means from Spatial Correction using SpATS R". Breedbase loads these terms from the file ontology/cxgn_statistics.obo of its source code, which breedtools includes (system.file("extdata", "cxgn_statistics.obo", package = "breedtools")), so the terms can be listed and checked without a server. With a connection, the terms of that Breedbase are listed and compared with the ontology file.

Usage

breedbase_statistics(con = NULL, pattern = "")

Arguments

con

Optional connection from breedbase_login(). Without it, the terms of the ontology file are listed.

pattern

Optional text the term must contain (any case).

Value

A tibble with statistic (the name), accession (e.g. "SGNSTAT:0000054") and definition (from the ontology file); with a connection also db_id (the server's id) and in_ontology (TRUE when name and accession match the ontology file).

Examples

if (FALSE) { # \dontrun{
con <- breedbase_login("https://cassavabase.org", "jdoe")
breedbase_statistics(con)
breedbase_statistics(con, "BLUE")
} # }
breedbase_statistics(pattern = "spatial")      # from the ontology file
#> # A tibble: 5 × 3
#>   statistic                                                 accession definition
#>   <chr>                                                     <chr>     <chr>     
#> 1 Adjusted Means from Spatial Correction using SpATS R      SGNSTAT:… Values of…
#> 2 Multivariate linear mixed model 2D spline spatial BLUPs … SGNSTAT:… NA        
#> 3 Multivariate linear mixed model genetic BLUPs using gene… SGNSTAT:… NA        
#> 4 Multivariate linear mixed model residual using genetic r… SGNSTAT:… NA        
#> 5 Univariate linear mixed model spatial BLUPs using geneti… SGNSTAT:… NA