correctTaxo: Checking typos in names

In ArthurPERE/biomass: Estimating Aboveground Biomass and Its Uncertainty in Tropical Forests

Description

This function corrects typos for a given taxonomic name using the Taxonomic Name Resolution Service (TNRS) via the Taxosaurus interface. This function has been adapted from the tnrs function from the taxize package (taxize::tnrs()).

Usage

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

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 http://tnrs.iplantcollaborative.org/instructions.html#match) 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

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 servor requests.

By default, names are queried in batches of 50, with a 0.5s delay between each query. These values can be modified using options: options(BIOMASS.batch_size=50) for batch size, options(BIOMASS.wait_delay=0.5) for delay.

Value

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

Localisation

The localisation of the folder is :

• On Linux : ~/.local/share/BIOMASS

• On Mac OS X : ~/Library/Application Support/BIOMASS

• On Windows 7 up to 10 : C:\Users\<username>\AppData\Local\BIOMASS\BIOMASS

• On Windows XP : C:\Documents and Settings\<username>\Data\BIOMASS\BIOMASS

See this function for more information : rappdirs::user_data_dir()

Author(s)

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

References

Boyle, B. et al. (2013). The taxonomic name resolution service: An online tool for automated standardization of plant names. BMC bioinformatics, 14, 1.

Chamberlain, S. A. and Szocs, E. (2013). taxize: taxonomic search and retrieval in R. F1000Research, 2.

Examples

## Not run: 
correctTaxo(genus = "Astrocarium", species = "standleanum")
correctTaxo(genus = "Astrocarium standleanum")

## End(Not run)

ArthurPERE/biomass documentation built on May 18, 2019, 2:33 a.m.