Taxonstand (version 2.4)

TPL: Standardize a list of plant names according to The Plant List.

Description

Connects to The Plant List (TPL) website and validates the names of a vector of plant taxa, replacing synonyms by accepted names and removing orthographical errors in plant names.

Usage

TPL(splist, genus = NULL, species = NULL, infrasp = NULL, 
infra = TRUE, corr = TRUE, diffchar = 2, max.distance = 1, 
version = "1.1", encoding = "UTF-8", author = TRUE, 
drop.lower.level = FALSE, file = "", silent = TRUE, repeats = 6)

Arguments

splist

A character vector specifying the input taxa, each element including genus and specific epithet and, potentially, author name and infraspecific abbreviation and epithet.

genus

A character vector containing the genera of plant taxon names.

species

A character vector containing the specific epithets of plant taxon names.

infrasp

A character vector containing the infraspecific epithets of plant taxon names.

infra

Logical. If TRUE (default), infraspecific epithets are used to match taxon names in TPL.

corr

Logical. If TRUE (default), spelling errors are corrected (only) in the specific and infraspecific epithets prior to taxonomic standardization.

diffchar

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

max.distance

A number indicating the maximum distance allowed for a match in agrep when performing corrections of spelling errors in specific epithets. Not used if corr = FALSE.

version

A character vector 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 from TPL website; defaults to "UTF-8" (see read.csv and Encoding).

author

Logical. If TRUE (default), the function tries to extract author names from the input taxon (see Details).

drop.lower.level

Logical. If TRUE, the variety is dropped from the input taxon if both subspecies and variety are given, and the forma is dropped from the input taxon if both subspecies or variety and forma are given. If specific and subspecific epithet are identical, the subspecies [variety] part is dropped instead, and variety [forma] is kept. Defaults to FALSE.

file

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

silent

Logical. If FALSE, the function prints the taxon name that is currently processed in the output. Defaults to TRUE.

repeats

A number indicating how many times TPLck should be called if no connection to TPL website can be established (temporarily).

Value

A data.frame with the following components:

$Taxon

Original taxon name as provided in input.

$Genus

Original genus name as provided in input.

$Hybrid.marker

Hybrid marker, if taxon is indicated as hybrid in the input.

$Species

Original specific epithet as provided in input.

$Abbrev

Original abbreviation other than infraspecific rank included in input taxon, including "cf.", "aff.", "agg.", "nom. cons.", "nom. cons. prop.", "nom. inval.", "s.l.", and "s.str." and their orthographic variants.

$Infraspecific.rank

Original infraspecific rank abbreviation as provided in input, including "subsp.", "var.", "f.", and their orthographic variants.

$Infraspecific

Original infraspecific epithet as provided in input. If infra = FALSE, this is not shown.

$Authority

Original author of taxon name as provided in input.

$ID

The Plant List record ID of the matched taxon before resolving synonyms.

$Plant.Name.Index

Logical. If TRUE the name is in TPL. If a taxon at infraspecific level is not in TPL, Plant.Name.Index equals FALSE, except for nominal infraspecies. Also compare Higher.level.

$TPL.version

Version of TPL used.

$Taxonomic.status

Taxonomic status of the matched taxon in TPL, either 'Accepted', 'Synonym', 'Unresolved', or 'Misapplied'.

$Family

Family name, extracted from TPL for the valid form of the taxon.

$New.Genus

Genus name, extracted from TPL for the valid form of the taxon.

$New.Hybrid.marker

Hybrid marker, extracted from TPL for the valid form of the taxon.

$New.Species

Specific epithet, extracted from TPL for the valid form of the taxon.

$New.Infraspecific.rank

Infraspecific rank abbreviation, extracted from TPL for the valid form of the taxon, including "subsp.", "var." and "f.".

$New.Infraspecific

Infraspecific epithet, extracted from TPL for the valid form of the taxon.

$New.Authority

Author of taxon name, extracted from TPL for the valid form of the taxon.

$New.ID

The Plant List record ID of the taxon, once synonyms have been replaced by valid names. For accepted and unresolved names, this field will be equivalent to ID.

$New.Taxonomic.status

Taxonomic status of the resolved taxon in TPL, once synonyms have been replaced by valid names. 'Accepted' or 'Unresolved'.

$Typo

Logical. If TRUE there was a spelling error in the specific or infraspecific 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 solution.

$Higher.level

Logical. If TRUE, the input taxon is at infraspecific level and does not occur in TPL, and the higher (species) level is provided in the output instead. Also see Plant.Name.Index.

$Date

Current date according to Sys.Date.

Details

The procedure used for taxonomic standardization is based on function TPLck. A progress bar indicates the proportion of taxon names processed so far. In case the TPL website cannot be reached temporarily, the function returns an error but repeats trying to match the given taxon multiple times (see repeats). If standardization is still not successful, the input taxon is returned in field 'Taxon' with NA in all other fields.

References

Cayuela, L., Granzow-de la Cerda, I., Albuquerque, F.S. and Golicher, J.D. 2012. Taxonstand: An R package for species names standardization 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

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
#----------------------------------
# Download all records available in GBIF of all species within genus
# Liriodendron (GBIF table; note that a list of species can be also
# downloaded from GBIF for a defined geographical area)
require(dismo)
liriodendron <- gbif("Liriodendron", "*", geo = TRUE)

# Perform taxonomic standardization on plant names (TPL table)
sp.check <- TPL(unique(liriodendron$scientificName), infra = TRUE, 
corr = TRUE)
head(sp.check)

# Join GBIF table with TPL table
require(dplyr)
liriodendron.check <- liriodendron %>%
left_join(., sp.check, by = c("scientificName" = "Taxon"))

# }