cwm | R Documentation |
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.
cwm(veg, refl, trait.db = 'ecodbase.dbf', ivname, keyname = 'LETTERCODE',
method, weight, db, ...)
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 |
... |
additional arguments |
Trait values of 0 will be handled as NA values because Turboveg dBase can not handle NA values properly.
Vector with the ecological classification of sites. Either mean trait values or mode of gradient classes.
Florian Jansen florian.jansen@uni-rostock.de
## 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 <- cwm(veg, trait.db = traits, ivname = 'OEK_F', method = 'mean')
plot(site$MGL, mEIV_F, xlab = 'Mean groundwater level')
#' Mode (most frequent level) of Ellenberg F values
ilevel <- cwm(veg, trait.db = traitmat, ivname = as.character(1:11), method = 'mode')
mode <- as.numeric(cwm(veg, trait.db = traits, ivname = 'OEK_F', method = 'mode'))
boxplot(site$MGL ~ mode)
## End(Not run)
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