| ecospat.nichePOSNB {ecospat} | R Documentation |
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)
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. |
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.
Value
The function returns a matrix containing the average niche position and niche breadth of each taxa along each environmental axi.
Author(s)
Lucie Malard lucie.malard@unil.ch and Olivier Broennimann olivier.broennimann@unil.ch
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))