status: Looking for the taxonomic status of species

In helixcn/plantlist: Looking Up the Status of Plant Scientific Names based on The Plant List Database, Searching the Chinese Names and Making checklists of plants

Looking for the taxonomic status of species

Description

Looking for the taxonomic status of a scientific name for a plant based on the database from The Plant List Website.

Usage

status(species = NA, exact = TRUE, spell_error_max = NULL, detail = FALSE)

Arguments

species	A vector of character strings representing the scientific names of species
exact	Logical, Wheter the exactly matching search will be applied.
spell_error_max	Integer, represents the number of spelling errors. Only effective when exact = FALSE.
detail	Logical, implicate whether detailed version of the results will be displayed, including ID for the names being searched.

Details

The scientific names will be formatted before being processed, including: The first letter of the scientific name will be changed to upper case while the rest will be in lower case; multiple whites paces will be replaced by one, and the white space at the beginning or the end will be removed. The scientific name will then be parsed to GENUS, SPECIES, AUTHOR_OF_SPECIES, INFRASPECIFIC_RANK, INFRASPECIFIC_EPITHET, AUTHOR_OF_INFRASPECIFIC_RANK, respectively. However, only GENUS, SPECIES, INFRASPECIFIC_RANK, INFRASPECIFIC_EPITHET will be used for searching against the embedded TPL database. Please note the authorship will not be used in searching, therefore the same scientific name with different authorship should result in multiple entries.

Since 'f.' is also used in the authorship,please do not provide the author name for the species when it is a form.Eg. the name "Hypoxishirsuta (L.) Coville f. vollosissima Fernald". should be provided as "Hypoxis hirsuta f. vollosissima Fernald" or "Hypoxis hirsuta f. vollosissima".

if exact = TRUE, the function only show the species that perfectly matching the "keywords". If exact = FALSE, the function use the general expression(function grep()) and will return all the species containting the "keywords".

The function also allows Approximate String Matching (Fuzzy Matching) using agrep(), when exact = FALSE and spell_error_max > 0. But it will be much more slower.

Value

The function will reture a data frame containing the following columns

SCIENTIFIC_NAME	The scientifc name matched
AUTHOR	the authorship for SCIENTIFIC_NAME
STATUS	status of this matched scientific name
FAMILY	The family provided by the plantlist website
ACCEPTED_ID	the accepted ID for the matched scientific name
ACCEPTED_SPECIES	The accepted species
ACCEPTED_AUTHOR	The authorship for the accepted species

Author(s)

Jinlong Zhang [e-mail]

References

The Plantlist Website http://www.theplantlist.org/

The embedded database is available at http://pan.baidu.com/s/1hqHrW9I

See Also

See Also TPL for family of each genus

Examples

sp <- c( "Elaeocarpus decipiens",
"Syzygium buxifolium",
"Daphniphyllum oldhamii",
"Loropetalum chinense",
"Rhododendron latoucheae",
"Rhododendron ovatum",
"Vaccinium carlesii",
"Schima superba")

status(sp)
status(sp, detail = TRUE)
status("Myrica rubra")
status(c("Myrica rubra", "Adinandra millettii", 
         "Machilus thunbergii", "Ranunculus japonicus", 
         "Cyclobalanopsis neglecta" ))
status("Adinandra millettii")
status("cyclobalanopsis neglecta")
status("Lirianthe henryi")

helixcn/plantlist documentation built on Aug. 4, 2022, 1:22 p.m.