View source: R/resolve_sci_taxa.R
Resolve taxa to preferred authorities and get associated IDs.
resolve_sci_taxa(x = NULL, data.sources, path = NULL)
(character) A vector of taxa names.
(numeric) An ordered vector of authority IDs to be queried (
(character) Path to directory containing taxa_map.csv. This tracks
provenance throughout the data cleaning process. Create this file with
(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
a data frame of taxa_map.csv to the R environment.
## Not run: # 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()) ## End(Not run)
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