Load location coordinates — read_locations • breedtools

Loads location metadata from a .xlsx, .xls, or .csv file, or from an already loaded data frame. The returned table has standardized columns: location, latitude, and longitude.

Usage

read_locations(
  file,
  location_col = NULL,
  latitude_col = NULL,
  longitude_col = NULL,
  phenotype_data = NULL,
  phenotype_location_col = NULL,
  match_by = "location",
  reference_locations = NULL,
  ignore_case = FALSE,
  sheet = NULL,
  ...
)

Arguments

file: Path to a location file, or an already loaded data frame.
location_col: Optional location name column.
latitude_col: Optional latitude column.
longitude_col: Optional longitude column.
phenotype_data: Optional raw phenotype data frame, prepared phenotype data frame, or result from run_environment_stratification(). If supplied, location names are extracted and checked against the location file.
phenotype_location_col: Optional location column in phenotype_data.
match_by: Column to extract when phenotype_data is a stratification result. Use "location", "environment", or "environment_label".
reference_locations: Optional character vector of expected location names. If supplied, every reference location must be present in file.
ignore_case: Logical. If TRUE, location matching ignores case.
sheet: Optional Excel sheet name or number passed to read_breedbase_file().
...: Additional arguments passed to read_breedbase_file().

Value

A tibble with location, latitude, and longitude.

Examples

locations <- data.frame(
  location = c("Loc1", "Loc2"),
  latitude = c(35.1, 36.2),
  longitude = c(-78.9, -79.4)
)

read_locations(locations)
#> # A tibble: 2 × 3
#>   location latitude longitude
#>   <chr>       <dbl>     <dbl>
#> 1 Loc1         35.1     -78.9
#> 2 Loc2         36.2     -79.4

# Breedbase-style location file, checked against the phenotype locations
loc_file <- system.file("extdata", "breedbase_locations.csv", package = "breedtools")
pheno <- read_breedbase_file(
  system.file("extdata", "breedbase_pheno.csv", package = "breedtools")
)
read_locations(loc_file, phenotype_data = pheno)
#> # A tibble: 4 × 3
#>   location latitude longitude
#>   <chr>       <dbl>     <dbl>
#> 1 Ithaca      42.4     -76.5 
#> 2 Geneva      42.9     -77.0 
#> 3 Ibadan       7.38      3.95
#> 4 Ubiaja       6.66      6.39