match_species_id.Rd
Parses species codes in input data and matches them with the BETY species ID.
match_species_id(input_codes, format_name = "custom", bety = NULL, translation_table = NULL, ...)
input_codes | Character vector of species codes |
---|---|
format_name | Species code format name (see details) |
bety |
|
translation_table | Data frame with custom translation table (see details). |
data.frame
containing the following columns:
input_code
Character provided as input
bety_species_id
Big integer species ID, unique and specific to BETY
genus
Genus part of Latin name, from BETY
species
Species part of Latin name, from BETY
format_name
can be one of the following:
usda
USDA Plants database symbol (e.g. QURU, TSCA)
fia
FIA species code
latin_name
Scientific name, as "Genus species"; must match exactly and unambiguously to scientificname
field in BETY
custom
A data frame matching BETY IDs (column name bety_species_id
) to input codes (column name input_code
). This data frame must be passed via the translation_table
argument.
# NOT RUN { bety <- dplyr::src_postgres(dbname = 'bety', user = 'bety', password = 'bety', host = 'localhost') input_codes <- c('ACRU', 'PIMA', 'TSCA') format_name <- 'usda' match_species_id(input_codes = input_codes, format_name = format_name, bety = bety) # }