taxval: 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

obs

data.frame of observations in TURBOVEG format, for example loaded with tv.obs

refl

Name of taxonomic reference list

a name of a Turboveg database directory containing tvabund.dbf, tvhabita.dbf and twin.set

Treatment of childs and parents within the dataset, see details

rank

If ag='adapt', rank specifies the taxonomic rank to which taxa should be coarsened to. All higher taxa in this taxonomic tree will be deleted, see maxtaxlevel.

mono

Should monotypic taxa be combined at subspecies = or species level =

monolist

Name of monotypic species list, must be in dbase format and in the same directory as the reference list, e.g. "monotypic-D" for the area of germany.

maxtaxlevel

Maximum taxonomic levels to be used. See details.

check.critical

Check for critical names in your dataset and give warnings.'

interactive

Do you want to adapt the list of changes.

Dataframe of class 'veg'. See tv.veg

sel

Vector of species (column names) to be combined.

newname

Name of the combined taxon.

...

Other parameters passed to functions.

Value

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

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.

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.

Examples

Run this code

# 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'))

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