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Choose which mapping-file columns are compared with GEOME, GBIF, and NCBI

Source: R/specimen_reconcile.R
set_metadata_columns.Rd

RiboPilot compares specimen details (coordinates, collection date, country, locality, voucher, collector, sex, and life stage) between your mapping file, GEOME, GBIF, and NCBI, and flags disagreements. It finds the mapping-file columns by name; use this function when a column has a name it does not recognize, or to stop comparing one. The Taxon column is always compared.

Usage

set_metadata_columns(path = ".", ...)

Arguments

path

Path to the project directory (default = current working directory)

...

Named concept = column pairs. Concepts: coordinates, collection_date, country, locality, voucher, collector, sex, dev_stage. coordinates takes one combined column or two columns (latitude, then longitude). NA returns a concept to automatic detection; "" stops comparing it.

Value

Invisibly, a data frame of each concept and the column(s) now used (NA when none).