Skip to main content Accesibility Help
×
×
Home

Using R to Build and Assess Network Models in Biology

  • G. Hartvigsen
Abstract

In this paper we build and analyze networks using the statistical and programming environment R and the igraph package. We investigate random, small-world, and scale-free networks and test a standard problem of connectivity on a random graph. We then develop a method to study how vaccination can alter the structure of a disease transmission network. We also discuss a variety of other uses for networks in biology.

Copyright
Corresponding author
Corresponding author. E-mail: hartvig@geneseo.edu
References
Hide All
[1] Albert, R., Barabási, A.-L.. Statistical mechanics of complex networks. Reviews of Modern Physics, 74 (2002), 4797.
[2] G. Chartrand. Introductory graph theory. Dover Publications, 1985.
[3] M. Crawley. The R book. John Wiley & Sons, 2007.
[4] P. Dalgaard. Introductory Statistics with R, 2/e. Springer, 2008.
[5] Erdös, P., Rényi, A.. On Random Graphs. I. Publicationes Mathematicae, 6 (1959), 290-297.
[6] Euler, L.. Solutio problematis ad geometriam situs pertinentis. Commentarii academiae scientiarum Petropolitanae, 8 (1741), 128-140.
[7] Hartvigsen, G., Dresch, J.M., Zielinski, A.L., Macula, A.J., Leary, C.C.. Network structure and vaccination strategy and effort interact to affect the dynamics of influenza epidemics. Journal of Theoretical Biology, 246, Vol. 2, (2007), 205213.
[8] Kermack, W.O., McKendrick, A.G.. A Contribution to the mathematical theory of epidemics. Proceedings of the Royal Society of London A, 115 (1927), 700721.
[9] M.E. Newman, A.-L. Barabási, D.J. Watts. The Structure and Dynamics of Networks. Princeton University Press, 2006.
[10] M.E. Newman. Networks: an Introduction. Oxford University Press, 2010.
[11] R Development Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing (2010), Vienna, Austria. URL http://www.R-project.org/.
[12] Solomonoff, R., Rapoport, A.. Connectivity of random nets. Bulletin of Mathematical Biophysics, 13 (1951), 107.
[13] Watts, D.J., Strogatz, S.H.. Collective dynamics of "small-world" networks. Nature, 393 (1998), 440442.
[14] A.F. Zuur, E.N. Ieno, E.H.W.G. Meesters. A Beginner’s Guide to R, Springer, 2009.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Mathematical Modelling of Natural Phenomena
  • ISSN: 0973-5348
  • EISSN: 1760-6101
  • URL: /core/journals/mathematical-modelling-of-natural-phenomena
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×

Keywords

Metrics

Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed