Description Usage Arguments Details Value Localisation Author(s) References Examples
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()
).
1 2 | correctTaxo(genus, species = NULL, score = 0.5, useCache = TRUE,
verbose = TRUE)
|
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 |
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.
The function returns a dataframe with the corrected (or not) genera and species.
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()
Ariane TANGUY, Arthur PERE, Maxime REJOU-MECHAIN, Guillaume CORNU
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.
1 2 3 4 5 | ## Not run:
correctTaxo(genus = "Astrocarium", species = "standleanum")
correctTaxo(genus = "Astrocarium standleanum")
## End(Not run)
|
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