refdb (version 0.1.2)

refdb_set_ncbitax: Replace the current taxonomy using the NCBI Taxonomy database

Description

Replace the current taxonomy using the NCBI Taxonomy database

Usage

refdb_set_ncbitax(
  x,
  min_level = "species",
  force_species_name = TRUE,
  verbose = TRUE
)

Value

The reference database with the NCBI taxonomy for the genus level and higher ranks. (the original taxonomy above the genus level is removed).

Arguments

x

a reference database (tibble) with one or several columns giving the taxonomy of each record and explicitly indicated in the field taxonomy. See refdb_set_fields.

min_level

minimum taxonomic level at which taxonomy should be replaced. Default is the finest level ("species").

force_species_name

if TRUE, species not found in NCBI Taxonomy will keep their original names instead of NAs.

verbose

print information in the console.

Examples

# \donttest{
lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
try(refdb_set_ncbitax(lib))
# }