Handling of taxonomy in vegetation data.

Description

Performs taxonomic valuation of species names according to synonomy, taxonomic level, unambiguity of biotic content etc. Necessary prerequisite is information about taxonomic status (synonomy) and hierarchy (next higher aggregat). Until now only applicable for reference list 'GermanSL' (>= vers. 1.1, see References Section), which is valid in Germany and adjacent countries.

Usage

taxval(obs, refl, db,
ag = c('conflict', 'adapt', 'preserve'), 
rank, mono = c('species', 'higher', 'lower', 'preserve'), monolist = "monotypic-D", 
maxtaxlevel = 'ROOT', check.critical = TRUE, interactive = FALSE, ...)
comb.species(x, sel, newname, refl)

Arguments

Details

Working with vegetation datasets, especially from different sources needs taxonomic valuation. The function tries to automate this process. Therefore the German taxonomic reference list (GermanSL, http://geobot.botanik.uni-greifswald.de/reflist/ ) contains additional taxon attributes (tax.dbf) and monotypic taxa of Germany (monotypic.dbf). Without an appropriate species list (see tax) the function will not work.

Possible values for adapting the taxonomic hierarchy within the dataset (child/parent taxa) are: preserve: Leave everything untouched. conflict: Dissolve only in case of conflicts, e.g. if a subspecies occurrs also at the species level within the same dataset. In this case the subspecies will be aggregated to the higher level. adapt: Dissolve all nested taxa to e.g. species level for option ag. For this option also option rank, specifying the rank to which the taxa shall be adapted, must be given.

Monotypic taxa, e.g. a species which occur only with 1 subspecies in the survey area. They have to be combined, since otherwise two different (valid) taxa would denominate the same entity. If lower the higher taxon (e.g. species rank) is replaced by the lower level (subspecies rank). If neither lower nor higher monotypic species are preserved. Since the list of monotypic species strongly depends on the considered area you have to choose, which area is covered by your database and create an appropriate list of monotypic taxa. Within the package "monotypic-D.dbf" is provided as a compilation of monotypic species within the GermanSL list (see tv.mono.

Option maxtaxlevel determines the maximum taxonomic level within the given names, which should be used. All higher taxon observations are deleted. If you have a single field observation determined as Asteraceae spec. all your obervations of taxa from that family will be aggregated to the family level, if you choose ag=conflict.

Interactive If you want to manually adapt the taxonomic harmonization interactive=TRUE will create a table with all original names and NewTaxonID's according to the chosen rules. The table will be saved as taxvalDecisionTable.csv in your actual working directory. You can manipulate the column NewTaxonID. If you run taxval again (e.g. through function tv.veg) and a file with this name exist in your working directory, it will be used.

Value

Functions return the input dataframe of observations with harmonised taxon numbers.

Author(s)

Florian Jansen jansen@uni-greifswald.de

References

Jansen, F. and Dengler, J. (2008) GermanSL - eine universelle taxonomische Referenzliste f"ur Vegetationsdatenbanken. Tuexenia, 28, 239-253. Jansen, F. and Dengler, J. (2010) Plant names in vegetation databases - a neglected source of bias. Journal of Vegetation Science, 21, 1179-1186.

See Also

tv.veg, tv.obs

Examples

## Not run: 
# Turboveg installation needed
obs <- taxval(db='taxatest')
## For explanations see vignette('vegdata').

veg <- tv.veg('taxatest')
veg <- comb.species(veg, c('ARMEM-E','ARMEM-H'))

## End(Not run)

Results