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Correct trees taxonomy

Source: R/correctTaxo.R
correctTaxo.Rd

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

  1. BIOMASS.cache option set to an existing folder

  2. 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

  3. 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

if (FALSE) { # \dontrun{
correctTaxo(genus = "Astrocarium", species = "standleanum")
correctTaxo(genus = "Astrocarium standleanum")
} # }