tv.veg {vegdata} | R Documentation |
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
.
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, ...)
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 |
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
.
Function returns an object of class matrix with (combined) cover values.
Florian Jansen jansen@uni-greifswald.de
## 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)