Taxonstand (version 1.8)

TPL: Connection to The Plant List (TPL) website to check for the validity of a list of plant names

Description

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

Usage

TPL(splist, genus = NULL, species = NULL, infrasp = NULL, 
infra = TRUE, abbrev = TRUE, corr = TRUE, diffchar = 2, 
max.distance = 1, version = "1.1", encoding = "UTF-8",
file = "")

Arguments

splist

A vector of plant names, each element including the genus and specific epithet and, additionally, the infraspecific epithet.

genus

A vector containing the genera for plant species names.

species

A vector containing the specific epithets for plant species names.

infrasp

A vector containing the infraspecific epithets for plant species names (i.e. varieties and subspecies).

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.

corr

Logical. If 'TRUE' (default), then removal of orthographical errors is performed (only) on 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 orthographical errors in specific epithets. Not used if corr=FALSE.

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".

file

Either a character string naming a file or a connection open for writing. "" (default) indicates output to the console.

Value

The function return an object of class data.frame with the following components:

$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 used for taxonomic standardization is based on function TPLck. If 'infra=FALSE', then infraspecific epithets are neither considered for species name validation in TPL, nor returned in the output.

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.

See Also

See also TPLck.

Examples

  ## Not run: 
# data(bryophytes)
# 
# # Species names in full
# r1 <- TPL(bryophytes$Full.name[1:20], corr=TRUE)
# str(r1)
# 
# # A separate specification for genera, specific, and infraspecific
# # epithets 
# r2 <- TPL(genus = bryophytes$Genus, species = bryophytes$Species, 
# infrasp = bryophytes$Intraspecific, corr=TRUE)
# str(r2)
# 
# ####################################
# ### An example using data from GBIF
# ####################################
# require(dismo)
# # Download data containing all records available in GBIF of all species 
# # within genus Oreopanax (GBIF table)
# oreopanax <- gbif("Oreopanax", "*", geo=T)
# # But a list of species can be also downloaded from GBIF for a defined
# # geographical area
# 
# # Names downloaded from GBIF often include the authority
# # The column names need to be split using the spaces as the split 
# # This will result in multiple columns. We essentially only need the
# # first two columns
# sp.list <- do.call("rbind", strsplit(oreopanax$species, split=" "))
# sp.list <- as.factor(paste(sp.list[,1], sp.list[,2]))
# 
# # Perform taxonomic standardisation on plant names list (TPL table)
# sp.check <- TPL(levels(sp.list), infra=FALSE, corr=TRUE)
# head(sp.check)
# 
# # Bind GBIF table with TPL table
# oreopanax$id <- as.numeric(sp.list)
# sp.check$id <- 1:dim(sp.check)[1]
# oreopanax.check <- merge(oreopanax, sp.check, by="id", all=T)
# ## End(Not run)