Skip to main content

Data from: Ecological network inference from long-term presence-absence data

Cite this dataset

Sander, Elizabeth L.; Wootton, J. Timothy; Allesina, Stefano (2018). Data from: Ecological network inference from long-term presence-absence data [Dataset]. Dryad.


Ecological communities are characterized by complex networks of trophic and nontrophic interactions, which shape the dy-namics of the community. Machine learning and correlational methods are increasingly popular for inferring networks from co-occurrence and time series data, particularly in microbial systems. In this study, we test the suitability of these methods for inferring ecological interactions by constructing networks using Dynamic Bayesian Networks, Lasso regression, and Pear-son’s correlation coefficient, then comparing the model networks to empirical trophic and nontrophic webs in two ecological systems. We find that although each model significantly replicates the structure of at least one empirical network, no model significantly predicts network structure in both systems, and no model is clearly superior to the others. We also find that networks inferred for the Tatoosh intertidal match the nontrophic network much more closely than the trophic one, possibly due to the challenges of identifying trophic interactions from presence-absence data. Our findings suggest that although these methods hold some promise for ecological network inference, presence-absence data does not provide enough signal for models to consistently identify interactions, and networks inferred from these data should be interpreted with caution.

Usage notes


National Science Foundation, Award: DEB 1148867, OCE 9711802, OCE 0117801, OCE 0452687, DEB 0919420, OCE 0928232, DEB 1148867, DEB 1556874


Tatoosh Island