TPLck: Connects to The Plant List (TPL) website and check for the validity of a plant name

Description

Connects to TPL and validates the name of a single plant species name, replacing synonyms for accepted names and removing orthographical errors in plant names

Usage

TPLck(sp, corr = TRUE, diffchar = 2, max.distance = 1, 
infra = TRUE, abbrev = TRUE, version = "1.1",
encoding = "UTF-8")

Arguments

A character specifying the genus and specific epithet and, additionally, the infraspecific epithet.

corr

Logical. If 'TRUE' (default), then removal of spelling errors is performed (only) on the specific and infraspecific epithets prior to taxonomic standardization.

diffchar

A number indicating the maximum difference between number of characters in corrected and original species names. Not used if corr=FALSE.

max.distance

Maximum distance allowed for a match in agrep function when performing corrections of spelling errors in specific epithets. Not used if corr=FALSE.

infra

Logical. If 'TRUE' (default) then infraspecific epithets are used to validate the taxonomic status of species names in TPL.

abbrev

Logical. If 'TRUE' (default), abbreviations (aff., cf., subsp., var.) and their variants are removed prior to taxonomic standardization.

version

A character indicating whether to connect to the newest version of TPL (1.1) or to the older one (1.0). Defaults to "1.1".

encoding

Encoding to be assumed for input strings. It is used to mark character strings as known to be in Latin-1 or UTF-8 (see 'Encoding'). It is not used to re-encode the input, but allows R to handle encoded strings in their native encoding (if one of those two). Defaults to "UTF-8" but it can be changed to "unknown" or "Latin-1".

Value

$Genus: Original genus of species provided as input for taxonomic standardization.
$Species: Original specific epithet of species provided as input for taxonomic standardization.
$Abbrev: Standard annotation used in species epithet, including "cf.", "aff.", "s.l.", and "s.str." and their orthographic variants.
$Infraspecific: Original intraspecific epithet of species provided as input for taxonomic standardization. If 'infra=FALSE', this is not shown.
$ID: The Plant List record 'id'.
$Plant.Name.Index: Logical. If 'TRUE' the name is in TPL.
$Taxonomic.status: Taxonomic status as in TPL, either 'Accepted', 'Synonym', 'Unresolved', or 'Misapplied'.
$TPL_version: Version of TPL used.
$Family: Family name, extracted from TPL for the valid form of the name.
$New.Genus: Genus, extracted from TPL for the valid form of the name.
$New.Hybrid.marker: Hybrid marker, extracted from TPL for the valid form of the name.
$New.Species: Specific epithet, extracted from TPL for the valid form of the name.
$New.Infraspecific: Infraspecific epithet, extracted from TPL for the valid form of the name.
$Authority: A field designating the scientist(s) who first published the name, extracted from TPL for the valid form of the name.
$New.ID: The Plant List record 'id' for the species name, once synonyms have been replaced by accepted names. In all other cases, this field will be equivalent to 'ID'.
$Typo: Logical. If 'TRUE' there was a spelling error in the specific epithet that has been corrected.
$WFormat: Logical. If 'TRUE', fields in TPL had the wrong format for information to be automatically extracted as they were not properly tabulated or, alternatively, there was not a unique solutions (see 'note').

Details

The procedure searches for a species name in The Plant List (TPL) and provides its taxonomic status. If the status is either 'Accepted' or 'Unresolved' (i.e. names for which the contributing data sources did not contain sufficient evidence to decide whether they were 'Accepted' or 'Synonyms'), the function returns the species name unchanged. In those cases where the species name provided as input is recognised as a "Synonym", it is replaced with the current accepted name. Some data sets which contributed to The Plant List record not only how plant names should be used but also where in the published literature a given name may previously have been used inappropriately (to refer erroneously to another species). In those cases, the function returns the accepted name of the species to which this name has been previously and erroneously applied. Orthographic errors can be corrected only in specific epithets. By increasing arguments 'diffchar' and 'max.distance', larger differences can be detected in typos, but this also increases false positives (i.e. replacement of some names for others that do not really match), so some caution is recommended here. If 'infra=FALSE', then infraspecific epithets are neither considered for species name validation in TPL, nor returned in the output. A new version of TPL was released in September 2013. Version 1.1 replaces Version 1.0, which still remains accessible. Version 1.1 includes new data sets, updated versions of the original data sets and improved algorithms to resolve logical conflicts between those data sets.

References

Cayuela, L., Granzow-de la Cerda, I., Albuquerque, F.S. and Golicher, J.D. 2012. Taxonstand: An R package for species names standardisation in vegetation databases. Methods in Ecology and Evolution, 3(6): 1078-1083.

Kalwij, J.M. 2012. Review of 'The Plant List, a working list of all plant species'. Journal of Vegetation Science, 23(5): 998-1002.

Examples

Run this code

  ## Not run: 
# # An accepted name
# sp1 <- TPLck("Amblystegium serpens juratzkanum")
# sp1
# # An unresolved name
# sp2 <- TPLck("Bryum capillare cenomanicum")
# sp2
# # A synonym
# sp3 <- TPLck("Pottia acutidentata")
# sp3
# # A misapplied name
# sp4 <- TPLck("Colutea istria")
# sp4
# # A spelling error in specific epithet
# sp5 <- TPLck("Pohlia longicola", corr=TRUE)
# sp5
# # A spelling error that is not corrected ('max.distance' defaults to 1)
# sp6 <- TPLck("Microbryum curvicollum", corr=TRUE)
# sp6
# # If increasing 'max.distance', the spelling error is accounted for
# sp7 <- TPLck("Microbryum curvicollum", corr=TRUE, max.distance=3)
# sp7
# ## End(Not run)

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