Prepare Breedbase phenotype data for multi-environment analysis — prepare_breedbase

This function standardizes Breedbase phenotype data into five columns: environment, genotype, replicate, block, and value.

Usage

prepare_breedbase_pheno(
  pheno_raw,
  trait_col,
  location_col = NULL,
  genotype_col = NULL,
  rep_col = NULL,
  block_col = NULL
)

Arguments

pheno_raw: A raw Breedbase phenotype data frame, usually read from a Breedbase Excel file.
trait_col: Name of the trait column to analyze.
location_col: Optional location/environment column name. If NULL, the function tries to guess it.
genotype_col: Optional genotype/accession column name. If NULL, the function tries to guess it.
rep_col: Optional replicate column name.
block_col: Optional block column name.

Value

A tibble with standardized phenotype data.

Examples

df <- data.frame(
  location = c("Loc1", "Loc1", "Loc2", "Loc2"),
  germplasmName = c("G1", "G2", "G1", "G2"),
  rep = c(1, 1, 1, 1),
  phenotype = c(10, 12, 15, 14)
)

prepare_breedbase_pheno(df, trait_col = "phenotype")
#> # A tibble: 4 × 5
#>   environment genotype replicate block value
#>   <fct>       <fct>    <fct>     <fct> <dbl>
#> 1 Loc1        G1       1         1        10
#> 2 Loc1        G2       1         1        12
#> 3 Loc2        G1       1         1        15
#> 4 Loc2        G2       1         1        14