This function corrects typos for a given taxonomic name using the Taxonomic Name Resolution Service (TNRS).
correctTaxo(
genus,
species = NULL,
score = 0.5,
useCache = FALSE,
verbose = TRUE,
accepted = FALSE
)
The function returns a dataframe with the corrected (or not) genera and species.
Vector of genera to be checked. Alternatively, the whole species name (genus + species) or (genus + species + author) may be given (see example).
(optional) Vector of species to be checked (same size as the genus vector).
Score of the matching ( see https://tnrs.biendata.org/instructions ) below which corrections are discarded.
logical. Whether or not use a cache to reduce online search of taxa names (NULL means use cache but clear it first)
logical. If TRUE various messages are displayed during process
logical. If TRUE accepted names will be returned instead of matched names. Cache will not be used as synonymy changes over time.
Cache path discovery protocol
BIOMASS.cache option set to an existing folder
existing user data folder rappdirs::user_data_dir()
On Linux : ~/.local/share/R/BIOMASS
On Mac OS X : ~/Library/Application Support/R/BIOMASS
On Windows 7 up to 10 : C:\\Users\\<username>\\AppData\\Local\\R\\BIOMASS
On Windows XP : C:\\Documents and Settings\\<username>\\Data\\R\\BIOMASS
fallback to R session tempdir
Ariane TANGUY, Arthur PERE, Maxime REJOU-MECHAIN, Guillaume CORNU
This function create a file named correctTaxo.log (see Localisation), this file have the memory of all the previous requests, as to avoid the replication of time-consuming server requests.
By default, names are queried in batches of 500, with a 0.5s delay between each query. These values can be modified using options:
options(BIOMASS.batch_size=500)
for batch size (max 1000), options(BIOMASS.wait_delay=0.5)
for delay (in seconds).
Boyle, B. et al. (2013). The taxonomic name resolution service: An online tool for automated standardization of plant names. BMC bioinformatics, 14, 1. doi:10.1186/1471-2105-14-16
# \donttest{
correctTaxo(genus = "Astrocarium", species = "standleanum")
correctTaxo(genus = "Astrocarium standleanum")
# }
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