vegdata (version 0.3.2)

tv.veg: 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, taxval = TRUE, convcode=TRUE, lc = c("layer", "mean", "max", "sum", "first"), pseudo = list(lc.1, "LAYER"), values='COVER_PERC', concept, spcnames=c('short','long','numbers'), dec = 0, cover.transform = c('no', 'pa', 'sqrt'), obs, refl, spc, site, RelScale, 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.

taxval

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)

spcnames

Should species numbers be replaced by shortletters or real names?

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-absnece or 'squareroot' for the dec rounded square root.

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.

sysPath

Load system files instead of Turboveg files.

...

additional arguments for included functions

Value

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

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

With option pseudo you can decide, which layers should be combined. Give a list with a combination data.frame (see lc and second the name of the column for combination. For an example see pseudo = list(lc.1,c('LAYER')). Option pseudo=NULL will prevent any layer aggregation. For further details see also tv.coverperc and tv.taxval.

Examples

vignette("vegdata")
# If you have Turboveg installed on your computer try for a beginning tv.veg('databasename', tax=FALSE).
args(tv.veg)
args(tv.taxval)

veg <- tv.veg('taxatest', sysPath=TRUE)
names(veg)
tv.veg('taxatest', uncertain=list('DET_CERT', data.frame(0:2,c('pres','agg','agg'))), pseudo=list(lc.0,'LAYER'), genus = 'delete', sysPath=TRUE)