Species Interaction Networks

The SpeciesInteractionNetworks package enables analyses of species interaction networks in Julia. The list of implemented measures (and more broadly, the design of the package) closely follows the recommendations in Delmas et al. (2019).

Organisation of the package

The measures in the documentation are organized by level of organisation, following a simple convention.

Micro-level measures return information at the level of the node. Typically, these will return a value for each species in the network. When called on an entire network, these will return a dictionary mapping the species to their value; when called on a network and a species, these will return the value of the species.

Meso-level measures return information about more than one species, but not about the entire network. Examples are shortest paths, motif enumeration, etc. The type of returned objects for these functions is more diverse and domain-specific.

Macro-level measures are summaries of the entire network, and typically return one value for the entire network.

Finally, meta-level measures are intended to be applied to a collection of networks; network dissimilarity measures are one example.

Why a new package?

TL;DR: technical bankruptcy.

The very first lines of EcologicalNetworks were written for Julia 0.4 (or 0.5?), and the language has changed immensely since then. By working with the package consistently over the years, it became apparent that we were often working around design decisions. A lot of code was also awkward to maintain, in part because it dated from before changes in the langage.

It wasn't broken, but it wasn't boss. Think of this package as a re-telling of the same story. It does the same thing (it does more things, even!), often in ways that are a little different, because we have written thousands of line of code using EcologicalNetworks and that gave us a really good understanding of how not to write this package. So this is the second attempt.