ecospat (version 3.3)

ecospat.nichePOSNB: Niche position and niche breadth)

Description

ecospat.nichePOSNB calculates the niche breadth and niche position of taxa along environmental gradients from abundance data.

Usage

ecospat.nichePOSNB (df,colvar,colfreq)

Value

The function returns a matrix containing the average niche position and niche breadth of each taxa along each environmental axi.

Arguments

df

dataframe with (relative) abundance data. Each row correspond to an abundance.

colvar

The column(s) in df corresponding to environmental axe(s).

colfreq

The columns in df corresponding to taxa frequencies.

Author

Lucie Malard and Olivier Broennimann

Details

The function calculates niche position and niche breadth of taxa along one or multiple environmental axes. Niche position is calculated as the mean of the variable, weighted by the relative abundance of the species. Niche breadth is calculated as the standard deviation of each variable, weighted by the relative abundance of the species at each sampling site.

References

L.A. Malard, H.K. Mod, N. Guex, O. Broennimann, E. Yashiro, E. Lara, E.D.A. Mitchell, H. Niculita-Hirzel & A. Guisan. The ecological niche of soil bacterial, archaeal, fungal and protist communities along environmental gradients in the Alps. 2021. Accepted in Soil Biology and Biochemistry.

Examples

data(ecospat.testNichePOSNB)
df<-ecospat.testNichePOSNB

# 1 axes
POSNB<-ecospat.nichePOSNB(df,colvar=c(2),colfreq = 6:17) 

# 2 axes
POSNB<-ecospat.nichePOSNB(df,colvar=c(2:3),colfreq = 6:17) 
ecospat.nicheNBmean(POSNB,w=c(2,1))

# 4 axes
POSNB<-ecospat.nichePOSNB(df,colvar=c(2:5),colfreq = 6:17) 
ecospat.nicheNBmean(POSNB,w=c(1,0.8,0.2,0.1))