Resolve scientific names to an authority — resolve_sci

Resolve taxa to preferred authorities and get associated IDs.

resolve_sci_taxa(x = NULL, data.sources, path = NULL)

Arguments

x: (character) A vector of taxa names.
data.sources: (numeric) An ordered vector of authority IDs to be queried ( view_taxa_authorities() lists currently supported authorities). Taxa are resolved to authorities in the order listed. If an authority and ID match cannot be made, then the next will be queried.
path: (character) Path to directory containing taxa_map.csv. This tracks provenance throughout the data cleaning process. Create this file with create_taxa_map().

Value

(data frame; taxa_map.csv) If using x, then a data frame containing the input taxa, accepted taxa name, rank, authority, authority ID, and score are returned. If using path, then an updated version of taxa_map.csv will be returned to path and a data frame of taxa_map.csv to the R environment.

Examples

if (FALSE) {
  # Input a list of taxa

  r <- resolve_sci_taxa(
    x = c("Cupressus macrocarpa", "Oncorhynchus tshawytscha", "Poa pratensis"),
    data.sources = c(3,11))
  r

  # Input taxa_map.csv

  data <- data.table::fread(file = system.file('example_data.txt', package = 'taxonomyCleanr'))
  tm <- create_taxa_map(path = tempdir(), x = data, col = "Species")
  r <- resolve_sci_taxa(data.sources = 3, path = tempdir())
  tm <- read_taxa_map(path = tempdir())
}