tax: Query of Turboveg 2 taxonomic reference lists including (if available) concept synonomy and taxonomic hierarchy.

Description

Input is either species number (integer), shortletter (7 characters) or full (exact!) species name.

Usage

# S3 method for default
tax(x, refl, detailed = FALSE, syn = TRUE, concept = NULL, strict = FALSE, 
vernacular = FALSE, simplify = FALSE, quiet = FALSE, reflist.type = 'Turboveg', ...)
child(x, refl = tv.refl(), gen = 4, tree = FALSE, quiet = FALSE, syn = FALSE, ...)
parent(x, refl = tv.refl(), rank, quiet = FALSE, ...)
syn(x, refl = tv.refl(), quiet = FALSE, ...)

Arguments

Species number, lettercode or species name

refl

Taxonomic reference list

detailed

Load tax.dbf with additional taxonomic information (e.g. Secundum) instead of species.dbf

syn

Return also synonym names

concept

Name of the file with an alternative taxon view stored in the reference list directory, see details.

strict

Exact match or partial matching with grep

vernacular

Search in vernacular names instead of scientific names.

simplify

Will simplify species names for matching.

gen

Number of child generations to return

quiet

Hide screen messages

reflist.type

Type of taxonomic reference list to use. Until now only Turboveg lsits are suppported in the official package.

tree

Opens a gWidgets window with interactive taxonomic tree view. Requires package gWidgets

rank

Taxonomical level of parentship to find

...

additional attributes

Details

concept: GermanSL is a list with a single taxon view according to the standard lists of the different taxon groups (e.g Wisskirchen and Haeupler for higher plants, see). Nevertheless a hugh number of synonyms is included which allows in many cases the transformation into different concepts. For illustration the concept of Armeria maritima from Korneck 1996 is included, which accepts e.g. Armeria maritima ssp. bottendorfensis. simplify: Before string comparison with reference list names it will eliminate diacritic marks, double consonants, "th", "y" and others. If genus=TRUE critical, i.e. non stable endings of genus names will be ignored, epithet = TRUE will eliminate specific endings for the last epithet.

References

Jansen, F. and Dengler, J. (2008) GermanSL - eine universelle taxonomische Referenzliste f\"ur Vegetationsdatenbanken. Tuexenia, 28, 239-253.

Examples

Run this code

# NOT RUN {
## GermanSL in Turboveg installation path needed
tax(27)
tax('Achillea millefolium')
tax('ACHIMILL')
# }
# NOT RUN {
childs(0, gen=1)
childs(94419, tree=TRUE)
# }