This function corrects typos for a given taxonomic name using the Taxonomic Name Resolution Service (TNRS).

Usage

correctTaxo(
  genus,
  species = NULL,
  score = 0.5,
  useCache = FALSE,
  verbose = TRUE,
  accepted = FALSE
)

Arguments

genus: Vector of genera to be checked. Alternatively, the whole species name (genus + species) or (genus + species + author) may be given (see example).
species: (optional) Vector of species to be checked (same size as the genus vector).
score: Score of the matching ( see https://tnrs.biendata.org/instructions ) below which corrections are discarded.
useCache: logical. Whether or not use a cache to reduce online search of taxa names (NULL means use cache but clear it first)
verbose: logical. If TRUE various messages are displayed during process
accepted: logical. If TRUE accepted names will be returned instead of matched names. Cache will not be used as synonymy changes over time.

Value

The function returns a dataframe with the corrected (or not) genera and species.

Details

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).

Localisation

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

References

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

Author

Ariane TANGUY, Arthur PERE, Maxime REJOU-MECHAIN, Guillaume CORNU

Examples

# \donttest{
correctTaxo(genus = "Astrocarium", species = "standleanum")
#> Using useCache=TRUE is recommended to reduce online search time for the next query
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
#> Source iplant_tnrs:1
#> Corrections TRUE:1
#>   genusCorrected speciesCorrected nameModified
#> 1    Astrocaryum     standleyanum         TRUE
correctTaxo(genus = "Astrocarium standleanum")
#> Using useCache=TRUE is recommended to reduce online search time for the next query
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
#> Source iplant_tnrs:1
#> Corrections TRUE:1
#>   genusCorrected speciesCorrected nameModified
#> 1    Astrocaryum     standleyanum         TRUE
# }