cwm: Indicate site conditions with community weighted mean values...

In vegdata: Access Vegetation Databases and Treat Taxonomy

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

cwm(veg, refl, trait.db = 'ecodbase.dbf', ivname, keyname = 'LETTERCODE',
      method, weight, db, ...)

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
...	additional arguments

Details

Trait values of 0 will be handled as NA values because Turboveg dBase can not handle NA values properly.

Value

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

Author(s)

Florian Jansen [e-mail]

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)]))
  
## End(Not run)

vegdata documentation built on Dec. 28, 2022, 2:39 a.m.