tpoisot
commented
11 years ago It's undeniable that "neutral" (density-dependent) effects are important for ecological networks. However, as pointed out in several places in the manuscript, the goal of this measure is to be as broad as possible. The neutral effects are highly field-specific, and I feel that building null models specifically around them would decrease the perceived generality of the metric.
I nonetheless added a paragraph mentionning why networks might vary in interaction strength.
Replied to in 1d183de
The typically log-normal abundance of species in nature will introduce apparent structure into networks, even if the links simply reflect probabilistic interactions (i.e. any species interacts more with a common than a rare species). Thus, without a null model correcting for number of species, for their abundance and for the possibility of random networks also being modular, any index may report only spurious, artefactual results. Poisot uses a null model, but because his example data are binary networks (containing no information about the strength of a link), the best he (or anyone) can do is to use a null model based on degrees, which is only a very poor reflection of the actual abundance. Given that often more than a third of the species in a network are singletons, I believe that their contributions to modularity are overemphasized by any binary measure.