Contagion - Free Software for Network Analysis & Generation, and Disease Simulation

What is it?

Contagion is a C library for analysing and generating networks, and for simulating diseases processes upon them. It is free software, licenced under the GNU GPL, version 2. It has been tested on Mac OS X, Linux, and Solaris 9, but should work on any platform with a recent C99 compiler.

What does it do?

• Different ways of representing a network in memory, with an object-oriented abstraction layer:
  • integer matrix
  • bit-field matrix
  • array of adjacency lists
• A range of network analysis functions:
  • shortest-path and mean shortest path
  • Betweenness centrality
  • Clustering coefficient
  • Degree distribution
  • Dyad and triad census
  • Strong and weak component counting
• Disease simulation upon networks, using a stochastic discrete-time SIR model.
• Network generation, by several different methods:
  • Poisson networks
  • Preferential-attachment model (for generating "scale-free" networks)
  • Two-dimensional degree-distribution matched networks (with optional dyad-census rewiring)

Why use it?

• Contagion is free software—you are free to use it, share it with colleagues, examine its workings, and enhance it for your own purposes. Free software is (or at least ought to be!) the gold standard for scientific applications.
• Contagion is lightweight, and fast. Wherever possible, the best available algorithms are deployed; the overhead from the library's abstraction layers is minimal.
• Contagion is portable—you can compile and use it on just about any machine with a modern operating system.
• Contagion is relatively straightforward to use and extend. Much of the complexity of the library can be hidden from the user, and new functions can be written without detailed knowledge of the underlying library structure.

Citing Contagion

If you use Contagion in any published work, you are encouraged to cite it, as follows:

Vernon, M. C. (2007). Contagion: Free Software for Network Analysis & Generation, and Disease Simulation. http://contagion.principate.org/

The following BibTeX fragment might be useful:

@misc{Contagion,
author ={Matthew Christopher Vernon},
title ={Contagion: Free Software for Network Analysis \& Generation, and Disease Simulation},
howpublished={\texttt{http://contagion.principate.org/}},
year=2007}

Downloading

You can download the version 1.0 here. The documentation is available online as a PDF document; it's an excerpt from my thesis, which is why the layout is a little unusual for software documentation.

Issues with version 1.0

As per the documentation, the header files in version 1.0 use the development name of this software, gsalgs. The next release will rename the header files and soname to fit the new name, Contagion.

Forthcoming features

The next release version will incorporate dynamic networks, and a range of static network models based upon dynamic networks. The simulation model will also be slightly updated. An HTML version of the documentation is also in the works.

There will be a python module with the next release, as well, enabling the library structures and routines to be used direct from python code.

The features described above are mostly implemented in the author's code-base; if you have a particular need for them, please get in touch. They are not generally available yet, to avoid making it too easy for my current research to be replicated before I've published it!