Tammy Elliott

Schefferville transitions

Co-occurence of congeners

April 12, 2016

R. 3.1

Co-occurrence probabilities calculated with co-occur package in R

Comparison of probabilities of co-occurrence for congeners

#dev.new(width=8, height=6)
par(mfrow=c(1,2), mar=c(4.5,4,1.5,2))
hist(lt, col="grey45", ylim=c(0,20), main="", xlab="Co-occurrence probability \nless than observed", cex.lab=1.15, cex.axis=0.9)
hist(gt, col="grey45",ylim=c(0,20), main="", xlab="Co-occurrence probability \ngreater than observed", cex.lab=1.15, cex.axis=0.9)

Mean co-occurrence probability less than observed

(mean(lt))

## [1] 0.5804989

---

Mean co-occurrence probability more than observed

(mean(gt))

## [1] 0.5107995

---

Calculate C-score

    #A higher c-score indicates a lower randomness, i.e. a greater likelihood that the distribution of one 
        #species has been directly affected by the presence of other species.
    # Not very informative
#make dataframe for large transects; with plot number, Habitat.description, latitude, longitude

(abd.sp.allsp.cscore<-C.score(abd.sp.allsp, normalise=TRUE, FUN=mean))

## [1] 0.6216141

# I didn't find this very informative, so a tried a different co-occurrence approach