tv.veg {vegdata}R Documentation

Tabulates vegetation tables from Turboveg database

Description

Tabulates vegetation tables from Turboveg resp. VegetWeb database, including taxonomic emendation and layer combination. Using various default parameters for the included functions. It is a wrapper for tv.obs, tv.taxval, tv.coverperc.

Usage

tv.veg(db, tv_home, tax = TRUE, convcode=TRUE, lc = c("layer", "mean", "max", "sum", "first"), pseudo = list(lc.1, "LAYER"), values='COVER_PERC', concept, names=c('short','long'), dec = 0, obs, refl, spc, site, RelScale, uncertain = NULL, sysPath = FALSE, ...)

Arguments

db Name of your Turboveg database. Directory name containing tvabund.dbf, tvhabita.dbf and tvwin.set. Please specify pathnames below (if you sorted your databases in subfolders) but not above Turbowin/Data.
tv_home Turbowin installation path.
tax Should taxonomic valuation (see tv.taxval) be performed?
convcode Should cover code be converted to percentage values?
lc Layer combination type. Possible values: layer (default), sum, mean or max, see details
pseudo List for layer combinations, see details
values Name of the variable which should be used for the vegetations matrix.
concept Name of alternative taxon concept list, see vignette(vegdata)
names Should species numbers be replaced by shortletters or real names?
dec Number of decimals for cover values in the resulting vegetation matrix.
obs Observations, optional
refl Taxonomic reference list, optional
spc If you want to pick a subset of species.
site Dataframe with site informations.
RelScale Vector with Cover Scale code per Releve.
uncertain List of length two, first the column name of uncertainty information, second a dataframe with uncertainty value and in column two one of 'delete','aggregate','preserve', see example.
sysPath Load system files instead of Turboveg files.
... additional arguments for included functions

Details

layer means, the different layers are combined assuming there independence (a species occuring in two layers with a cover of 50% will result in a overall cover of 75%. sum will sum up cover values of all layers

comb means, which layers should be combined?. Give a list of first the name of the combination data.frame and second the columns for combination, each as character vectors (see ?lc.0 and ?lc.1 for examples) Use for example comb = list('lc.1',c('LAYER')). For further details see also tv.coverperc and tv.taxval.

Value

Function returns an object of class matrix with (combined) cover values.

Author(s)

Florian Jansen jansen@uni-greifswald.de

Examples

## Not run: vignette("vegdata")
# If you have a local Turboveg installation try for a beginning tv.veg('your databasename').
veg <- tv.veg('taxatest', sysPath=TRUE)
names(veg)
tv.veg('taxatest', uncertain=list('DET_CERT', data.frame(0:2,c('pres','agg','del'))), sysPath=TRUE)

[Package vegdata version 0.1.1 Index]