vegdata (version 0.9.8)

isc: Indicate site conditions with community weighted mean values of traits or with mode of gradient classes (sum of species amplitudes).

Description

Calculates community weighted mean trait values, like mean Ellenberg indicator values. Alternatively (method = 'mode') environmental conditions can be calculated according to the concept of sums of amplitudes of species along ecological gradients.

Usage

isc(veg, refl, trait.db = 'ecodbase.dbf', ivname, keyname = 'LETTERCODE', 
method = c('mean', 'mode'), weight, db, ...)
showindiplot(veg, trait.db, plotid, weight, keyname = 'LETTERCODE')

Arguments

veg

Vegetation matrix with plots in rows and species in columns

refl

Name of Turboveg taxonomic reference list

trait.db

data frame with species trait values

ivname

Name of the trait in trait.db to be used

keyname

Name of the column in trait dataframe to join with colnames of veg table

method

mean (weighted value of single traits, or mode (maximum) of trait classes)

weight

additional weight, e.g niche breath of species

db

name of Turboveg database

plotid

number or id of the plot to show

…

additional arguments

Value

Vector with the ecological classification of sites. Either mean trait values or mode of gradient classes.

Details

Zero trait values will be handled as NA values.

Examples

# NOT RUN {
db <- 'elbaue'
veg <- tv.veg(db, cover.transform='sqrt', check.critical = FALSE)
site <- tv.site(db, verbose = FALSE)
# Exclude plots with very high water level fluctuation
veg <- veg[site$SDGL < 60,]
veg <- veg[,colSums(veg) > 0]
site <- site[site$SDGL < 60,]
# Load species trait value database
traits <- tv.traits(db)

# Mean indicator values of Ellenberg F values
mEIV_F <- isc(veg, trait.db = traits, ivname = 'OEK_F', method = 'mean')
plot(site$MGL, mEIV_F, xlab = 'Mean groundwater level')

# Mode (most frequent level) of Ellenberg F values
library(reshape)
traitmat <- cast(traits, LETTERCODE ~ OEK_F)
traitmat <- traitmat[,-14]
ilevel <- isc(veg, trait.db = traitmat, ivname = as.character(1:11), method = 'mode')
boxplot(site$MGL ~ ordered(ilevel, levels = levels(ilevel)[c(2,4,3,5,6:10,1)]))
# }