Associate columns to fields

Source: R/fields.R

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

TODO taxonomy reordering

NA to ignore, NULL to delete

fields set using config_yaml always overwrite those set by arguments