Associate columns to fields — refdb_set

Associate columns to fields so they are recognized and appropriately treated by refdb functions.

refdb_set_fields(
  x,
  source = NA,
  id = NA,
  organism = NA,
  taxonomy = NA,
  sequence = NA,
  marker = NA,
  latitude = NA,
  longitude = NA,
  reference = NA,
  config_yaml = NULL
)

Arguments

x: a reference database (tibble).
source: name of the column which contains the data source.
id: name of the column which contains the record IDs.
organism: name of the column which contains the names of the organisms.
taxonomy: a vector of column names.
sequence: name of the column which contains the sequences.
marker: name of the column which contains marker names.
latitude: name of the column which contains latitudes (WGS 84)
longitude: name of the column which contains longitudes (WGS 84).
reference: a vector of column names.
config_yaml: a file path to a YAML file

Value

The function returns x with updated attributes.

Details

Taxonomy reordering. NA to ignore, NULL to delete. Fields set using config_yaml always overwrite those set by arguments

Examples

lib <- read.csv(system.file("extdata", "ephem.csv", package = "refdb"))
lib <- refdb_set_fields(lib,
                        taxonomy = c(family = "family_name",
                            genus = "genus_name",
                            species = "species_name"),
                        sequence = "DNA_seq",
                        marker = "marker")