Abstract
Nestedness is a property of interaction networks widely observed in natural mutualistic communities, among other systems. A perfectly nested network is characterized by the peculiarity that the interactions of any node form a subset of the interactions of all nodes with higher degree. Despite a widespread interest on this pattern, no general consensus exists on how to measure it. Instead, several nestedness metrics, based on different but not necessarily independent properties of the networks, coexist in the literature, blurring the comparison between ecosystems. In this work, we present a detailed critical study of the behavior of six nestedness metrics and the variants of two of them. In order to evaluate their performance, we compare the obtained values of the nestedness of a large set of real networks among them and against a maximum-entropy and maximum-likelihood null model. We also analyze the dependencies of each metrics on different network parameters, as size, fill, and eccentricity. Our results point out, first, that the metrics do not rank networks universally in terms of their degree of nestedness. Furthermore, several metrics show significant dependencies on the network properties considered. The study of these dependencies allows us to understand some of the observed systematic shifts against the null model. Altogether, this paper intends to provide readers with a critical guide on how to measure nestedness patterns, by explaining the functioning of several metrics and disclosing their qualities and flaws. Besides, we also aim to extend the application of null models based on maximum entropy to the scarcely explored area of ecological networks. Finally, we provide a fully documented repository that allows constructing the null model and calculating the studied nestedness indexes. In addition, it provides the probability matrices to build the null model for a large dataset of more than 200 bipartite networks.