tv.veg: Tabulates vegetation tables from Turboveg database

In vegdata: Access Vegetation Databases and Treat Taxonomy

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*, *taxval*, *tv.coverperc* and creating a vegetation matrix

Usage

tv.veg(db, taxval=TRUE,tv_home,convcode=TRUE,
lc = c("layer","mean","max","sum","first"),
pseudo, values='COVER_PERC', spcnames=c('shortletters','ScientificNames','Numbers'),
dec = 0, cover.transform = c('no', 'pa', 'sqrt'), obs, site, refl, RelScale, ...)

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.
taxval	Should taxonomic valuation (see taxval) be performed?
tv_home	Turbowin installation path.
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 used for layer combinations, see details
values	Name of the variable which should be used for the vegetations matrix.
spcnames	Should species numbers be replaced by shortletters or ScientificNames? Layer information is appended with dot.
dec	Number of decimals for cover values in the resulting vegetation matrix.
cover.transform	If you want to transform the abundancce values within your samples you can choose 'pa' for presence-absence or 'sqrt' for the dec rounded square root.
obs	Observations, optional
site	plot header data, see tv.site
refl	Taxonomic reference list, optional
RelScale	Vector with Cover Scale code per Releve.
...	additional arguments for included functions

Details

layer means, the different layers are combined assuming there independence (a species occurring 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 With option pseudo you can decide, which layers should be combined. Give a list with a combination data.frame and second the name of the column for combination. The default is pseudo = list(lc.1, c('LAYER')), where lc.1 is a data.frame data(lc.1), which will combine all tree layers, all shrub layers and all layers below shrubs. An alternative would be data(lc.all), combining all layers. With option pseudo=NULL there will be no layer aggregation.

Value

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

Author(s)

Florian Jansen [e-mail]

See Also

taxval, tv.coverperc, tv.obs, tv.site

Examples

  ## Not run: 
    vignette("vegdata")
    #' If you have Turboveg installed on your computer try for a beginning
    #' tv.veg('databasename', tax=FALSE).
    args(tv.veg)
    help('taxval')

    veg <- tv.veg('taxatest')
    names(veg)
    tv.veg('taxatest', uncertain=list('DET_CERT', data.frame(0:2,c('pres','agg','agg'))),
           pseudo=list(lc.0,'LAYER'), genus = 'delete')
  
## End(Not run)

vegdata documentation built on May 29, 2024, 4:19 a.m.