Data for niche overlap null models is a data frame where each row represents a different species in the assemblage being analyzed. Each column represents a different niche category. In the example data set, MacArthur’s Warblers (MacArthur and Levins 1967) provides an index of niche overlap.

MacArthur’s Warblers
Species X1T X1M X1B X2T X2M X2B X3T X3M X3B
Cape May warbler 49.9 13.2 0.0 20.6 8.3 0.0 4.0 0.5 0.0
Myrtle warbler 6.6 4.1 0.3 7.8 4.9 1.3 9.3 9.8 3.6
Black-throated green warbler 12.1 5.7 0.0 17.3 8.8 0.7 21.8 14.1 1.5
Blackburnian warbler 34.8 10.5 3.2 15.1 8.3 2.7 13.1 11.0 0.7
Bay-breasted warbler 3.5 1.9 1.4 6.5 8.0 5.9 11.4 19.1 13.1

Run the niche overlap model with the RA3 (Winemiller and Pianka 1990) algorithm and the Pianka (1973) index of overlap.

warbMod <- niche_null_model(dataMacWarb)
summary(warbMod)
## Time Stamp:  Tue Mar 31 22:24:23 2015 
## Reproducible:  FALSE 
## Number of Replications:  1000 
## Elapsed Time:  0.45 secs 
## Metric:  pianka 
## Algorithm:  ra3 
## Observed Index:  0.55514 
## Mean Of Simulated Index:  0.39179 
## Variance Of Simulated Index:  0.0026146 
## Lower 95% (1-tail):  0.31953 
## Upper 95% (1-tail):  0.47923 
## Lower 95% (2-tail):  0.30868 
## Upper 95% (2-tail):  0.51059 
## Lower-tail P =  0.992 
## Upper-tail P =  0.008 
## Observed metric > 992 simulated metrics 
## Observed metric < 8 simulated metrics 
## Observed metric = 0 simulated metrics 
## Standardized Effect Size (SES):  3.1946

Get a standard histogram plot of output.

plot(warbMod, type="hist")

Plot the resource utilization matrix.

plot(warbMod, type="niche")

References

MacArthur, R. and R. Levins. 1967. The limiting similarity, convergence, and divergence of coexisting species. The American Naturalist 101: 377-385.

Pianka, E.R. 1973. The structure of lizard communities. Annual Review of Ecology and Systematics 4: 53-74.

Winemiller, K.O. and E.R. Pianka. 1990. Organization in natural assemblages of desert lizards and tropical fishes. Ecological Monographs 60: 27-55.