Below are all the network data used for several papers (including MacKay et al, 2020; Johnson 2019; Johnson & Jones, 2017; Klaise & Johnson, 2017; and Johnson et al, 2014), although not all these networks were used for every paper.
The data set is a compilation of directed networks obtained from various sources. For each network we provide the adjacency matrix as a list of edges in a text file: the numbers in the first column are labels for the in-node and those in the second are the out-node (i.e. the entry "42 3" means there is a directed edge from node 3 to node 42). Directed edges have different meanings depending on the nature of the network. For example, in food webs the edges go from prey (resource species) to predator (consumer species). In many of the original data there was more information than we give here, such as node descriptions or edge weights. The 81 networks are provided in a zipped folder containing seven sub-folders, corresponding to food webs, gene regulatory networks, metabolic networks, language networks (i.e. word adjacency graphs), social networks, networks of international trade, and neural networks (connectomes).
For the original sources of these data and whom to cite when using them, please see the tables in the Supplementary Info of Looplessnes in networks is linked to trophic coherence (freely available on the arXiv). See also Wikipedia: Trophic Coherence.
You can find these data here. There is a zipped folder with seven sub-folders, each containing the adjacency matrices for a class of network, as described above.
The C++ code used for analysing these networks, as well as for simulating trophically coherent networks with the preferential preying model, can be found here. There is a brief description of how to compile and run the code in the first few lines. For more information on how to use it don't hesitate to get in touch.
Some other sites with network data or other resources:
Tiago Peixoto's website
R.M. Thompson and C.R. Townsend's Interaction Web Data Base
Uri Alon's website
The ENCODE Project: ENCyclopedia Of DNA Elements
CCNR - László Barabási
Mark Newman's website
Stanford Large Network Dataset Collection
Alex Arenas' website