null.breadth.focal: null.breadth.focal

In ordiBreadth: Ordinated Diet Breadth

Description

This function calculates the null expectation of ordinated host breadth for each herbivore individually. The ordination for each herbivore is based on PCoA where the focal herbivore is not included.

Usage

null.breadth.focal(dat, dis.method = "jaccard", reps = 100)

Arguments

dat	A matrix of diet associations. Rows are herbivores and columns are diet items.
dis.method	Dissimilarity index passed on to vegdist in the vegan package.
reps	The number of permutations to generate a null distribution.

Details

In situations where the focal herbivore is the only species using a particular diet item, that diet item is not included in the ordination. This is the modified plant richness.

Value

A list containing the following:

species

Name of herbivore species (row name of dat

)

observed.breadth	Ordinated diet breadth
scale.factor	Ordinated diet breadth of most extreme generalist herbivore based on ordination
observed.breadth.scaled	Scaled ordinated diet breadth
totalplantrichness	Taxonomic diet richness of focal species
modplantrichness	Modified taxonomic diet richness of focal species (see details)
null	A vector of null ordinated diet values

Author(s)

James Fordyce

References

Fordyce, J.A., C.C. Nice, C.A. Hamm, & M.L. Forister. Quantifying diet breadth through ordination of host association. Ecology

Examples

testdata<-	
	c(		
			0,0,0,0,1,0,0,0,0,0,#1
			0,0,0,0,0,0,1,1,0,0,#2
			1,1,1,0,0,0,0,0,0,0,#3
			0,0,0,0,1,1,0,1,0,1,#4
			1,1,1,0,0,0,1,0,0,0,#4
			1,1,0,0,1,0,1,0,0,0,#4
			0,0,0,1,0,0,1,0,1,1,#4
			1,0,1,0,1,1,0,0,0,1, #5
			1,1,0,0,1,0,0,1,1,1,#6
			1,1,1,0,1,1,0,1,1,1) #8


dat<-array(dim=c(10,10),data=testdata)
dat<-t(dat)
colnames(dat)<-paste("",LETTERS[1:10],sep="")
rownames(dat)<-paste("bug",1:10,sep="")

null.breadth.focal(dat)

ordiBreadth documentation built on May 2, 2019, 9:41 a.m.