Co-Occurrence quickstart

Data for co-occurrence null models should be a species by site matrix of incidence data.

West Indian Finch Data
Species Cuba Hispaniola Jamaica Puerto_Rico Guadeloupe Martinique Dominica St_Lucia Barbados
Carduelis_dominicensis 0 1 0 0 0 0 0 0 0
Loxia_leucoptera 0 1 0 0 0 0 0 0 0
Volatinia_jacarina 0 0 0 0 0 0 0 0 0
Sporophila_nigricollis 0 0 0 0 0 0 0 0 0
Melopyrrha_nigra 1 0 0 0 0 0 0 0 0

EcoSimR provides an easy way to plot and summarize output. We’ll use the SIM9 algorithm (See table 2 Gotelli 2000) and the C-Score metric (Stone and Roberts 1990).

finchMod <- cooc_null_model(dataWiFinches, algo="sim9",nReps=10000,burn_in = 500)
## Summary and plot info
summary(finchMod)
## Time Stamp:  Tue Mar 31 23:19:27 2015 
## Reproducible:  
## Number of Replications:  
## Elapsed Time:  1.7 secs 
## Metric:  c_score 
## Algorithm:  sim9 
## Observed Index:  3.7941 
## Mean Of Simulated Index:  2.7487 
## Variance Of Simulated Index:  0.027411 
## Lower 95% (1-tail):  2.5221 
## Upper 95% (1-tail):  3.0368 
## Lower 95% (2-tail):  2.4926 
## Upper 95% (2-tail):  3.1546 
## Lower-tail P >  0.9999 
## Upper-tail P <  1e-04 
## Observed metric > 10000 simulated metrics 
## Observed metric < 0 simulated metrics 
## Observed metric = 0 simulated metrics 
## Standardized Effect Size (SES):  6.3145
plot(finchMod,type="hist")

See a plot of the actual matrix compared to a single simulated matrix

plot(finchMod,type="cooc")

References

Gotelli, N.J. 2000. Null model analysis of species co-occurrence patterns. Ecology 81: 2606-2621

Stone, Lewis and Roberts, Alan 1990. The checkerboard score and species distributions. Oecologia 85 (1): 74–79.