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, 
simplify = FALSE, quiet = FALSE, reflist.type = 'Turboveg', ...)
child(x, refl = tv.refl(), gen = 4, quiet = FALSE, syn = FALSE, ...)
parent(x, refl = tv.refl(), rank, quiet = FALSE, ...)
syn(x, refl = tv.refl(), quiet = FALSE, ...)
taxname.abbr(x, hybrid = c('remove', 'retain'), 
species = FALSE, cf = FALSE, ...)
taxname.simplify(x, genus=TRUE, epithet=TRUE,  hybrid = c("remove", "retain"), 
        rank = c("remove", "retain"), concept.status = c("remove", "retain"), ...)
parse.taxa(x, epis)
taxname.removeAuthors(x)

Arguments

Species number, lettercode or species name(s)

refl

Taxonomic reference list

detailed

In old Turboveg versions detailed taxonomic information could only be given in an extra file which was called tax.dbf in GermanSL. Compatibility mode.

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

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 lists are supported in the official package.

rank

Taxonomical level of taxa to find

hybrid

remove hybrid markers for comparisons

species

use spec., sp., or species for genus level taxa

remove 'in doubt' marker

genus

simplify genus name part

epithet

simplify epithet(s)

concept.status

remove s. str. s. l.

epis

vector of rank marker strings, if missing: 'subsp.', 'var.', 'v.'

...

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 huge 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.

taxname.simplify: Before string comparison with reference list names it will eliminate diacritic marks, double consonants, "th", "y" versus "i(i)" and other frequent differences in writing style. If genus = TRUE (non stable) endings of genus names will be ignored, epithet = TRUE will eliminate endings for the epithet part.

taxname.abbr: standardisation of rank names

parse.taxa: parse genus and epitheta from name strings.

taxname.removeAuthors Remove name authors from full scientific name strings.

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 {
taxname.abbr('Achillea millefolium s. millefolium')
taxname.simplify('Vicia sylvatica') == taxname.simplify('Vicia silvaticum')


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