Is network clustering detectable in transmission trees?

Viruses

Volumn 3, Issue 12, 2011, Pages 659-676

  Welch, David ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Clustering; Contact network; Epidemics; Network; Population structure; SEIR; Simulations; Transmission tree

Indexed keywords

ALGORITHM; ARTICLE; BERNOULLI NETWORK; BIOSTATISTICS; CLUSTER ANALYSIS; COMPUTER MODEL; CONTACT NETWORK; DISEASE TRANSMISSION; EPIDEMIC; POPULATION STRUCTURE; POWER LAW NETWORK; SIMULATION; SOCIAL NETWORK; STATISTICAL ANALYSIS; STATISTICAL DISTRIBUTION; STATISTICAL MODEL; STOCHASTIC MODEL; SUSCEPTIBLE EXPOSED INFECTIOUS REMOVED EPIDEMICS; TRANSMISSION TREE;

EID: 79959679150     PISSN: None     EISSN: 19994915     Source Type: Journal    
DOI: 10.3390/v3060659     Document Type: Article

References (37)

1. Goldenberg, A.; Zheng, A.; Fienberg, S.; Airoldi, E. A survey of statistical network models. Foundations and Trends in Machine Learning 2009, 2, 129-233.
2. Network Epidemiology: A Handbook for Survey Design and Data Collection; Morris, M., Ed.; Oxford University Press: Oxford, UK, 2004.
3. Newman, M.E.J. The Structure and Function of Complex Networks. SIAM Review 2003, 45, 167-256.
4. Britton, T.; O'Neill, P. Bayesian Inference for Stochastic Epidemics in Populations with Random Social Structure. Scand. J. Stat. 2002, 29, 375-390.
5. Groendyke, C.; Welch, D.; Hunter, D.R. Bayesian Inference for Contact Networks Given Epidemic Data. Scand. J. Stat. 2011, doi:10.1111/j.1467-9469.2010.00721.x.
6. Groendyke, C.; Welch, D.; Hunter, D.R. A Network-based Analysis of the 1861 Hagelloch Measles Data; Technical Report 11-03; Department of Statistics, Pennsylvania State University: University Park, PA, USA, 2011.
7. Lewis, F.; Hughes, G.J.; Rambaut, A.; Pozniak, A.; Brown, A.J.L. Episodic Sexual Transmission of HIV Revealed by Molecular Phylodynamics. PLoS Med. 2008, 5, e50.
8. Cottam, E.M.; Thebaud, G.; Wadsworth, J.; Gloster, J.; Mansley, L.; Paton, D.J.; King, D.P.; Haydon, D.T. Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus. Proc. Roy. Soc. B-Biol. Sci. 2008, 275, 887-895.
9. Welch, D.; Bansal, S.; Hunter, D.R. Statistical inference to advance network models in epidemiology. Epidemics 2011, 3, 38-45.
10. Wallinga, J.; Teunis, P. Different epidemic curves for severe acute respiratory syndrome reveal similar impacts of control measures. Am. J. Epidemiol. 2004, 160, 509-516.
11. Pybus, O.; Rambaut, A. Evolutionary analysis of the dynamics of viral infectious disease. Nat. Rev. Genet. 2009, 10, 540-560.
12. Watts, D.J.; Strogatz, S.H. Collective Dynamics of Small World Networks. Nature 1998, 393, 440-442.
13. Newman, M.E.J.; Park, J. Why social networks are different from other types of networks. Phys. Rev. E 2003, 68, 036122.
14. Newman, M.E.J. Properties of highly clustered networks. Phys. Rev. E 2003, 68.
15. Britton, T.; Deifen, M.; Lageras, A.N.; Lindholm, M. Epidemics on random graphs with tunable clustering. J. Appl. Probab. 2008, 45, 743-756.
16. Kiss, I.Z.; Green, D.M. Comment on "Properties of highly clustered networks". Phys. Rev. E 2008, 78, 048101.
17. Ball, F.; Sirl, D.; Trapman, P. Analysis of a stochastic SIR epidemic on a random network incorporating household structure. Math. Biosci. 2010, 224, 53-73.
18. Eames, K. Modelling disease spread through random and regular contacts in clustered populations. Theor. Popul. Biol. 2008, 73, 104-111.
19. Keeling, M. The implications of network structure for epidemic dynamics. Theor. Pop. Biol. 2005, 67, 1-8.
20. Serrano, M.A.; Bogu ̃n ́a, M. Percolation and Epidemic Thresholds in Clustered Networks. Phys. Rev. Lett. 2006, 97, 088701.
21. Miller, J.C. Spread of infectious disease through clustered populations. J. R. Soc. Interface 2009, 6, 1121-1134.
22. Miller, J.C. Percolation and epidemics in random clustered networks. Phys. Rev. E 2009, 80, 020901.
23. Badham, J.; Stocker, R. The impact of network clustering and assortativity on epidemic behaviour. Theor. Popul. Biol. 2010, 77, 71-75.
24. Moslonka-Lefebvre, M.; Pautasso, M.; Jeger, M.J. Disease spread in small-size directed networks: Epidemic threshold, correlation between links to and from nodes, and clustering. J. Theor. Biol. 2009, 260, 402-411.
25. Melnik, S.; Hackett, A.; Porter, M.A.; Mucha, P.J.; Gleeson, J.P. The unreasonable effectiveness of tree-based theory for networks with clustering. arXiv 2011, arXiv:1001.1439.
26. Erdos, P.; Renyi, A. On random graphs. Publ. Math. Debrecen 1959, 6, 290-297.
27. Albert, R.; Barab ́asi, A.L. Statistical mechanics of complex networks. Rev. Mod. Phys. 2002, 74, 47-97.
28. Molloy, M.; Reed, B. A Critical Point for Random Graphs with a Given Degree Sequence. Random Struct. Algorithm. 1995, 6, 161-180.
29. Handcock, M.S.; Hunter, D.R.; Butts, C.T.; Goodreau, S.M.; Morris, M.; Krivitsky, P. Ergm: A Package to Fit, Simulate and Diagnose Exponential-Family Models for Networks, Version 2.2-2. Available online: http://statnetproject.org (accessed on 1 February 2011).
30. R Development Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing: Vienna, Austria, 2009. ISBN 3-900051-07-0.
31. Bansal, S.; Khandelwal, S.; Meyers, L. Exploring biological network structure with clustered random networks. BMC Bioinformatics 2009, 10, 405.
32. Hunter, D.R.; Handcock, M.S.; Butts, C.T.; Goodreau, S.M.; Morris, M. ergm: A Package to Fit, Simulate and Diagnose Exponential-Family Models for Networks. J. Stat. Software 2008, 24, 1-29.
33. Mckenzie, A.; Steel, M. Distributions of cherries for two models of trees. Math. Biosci. 2000, 164, 81-92.
34. Salath́e, M.; Kazandjieva, M.; Lee, J.W.; Levis, P.; Feldman, M.W.; Jones, J.H. A high-resolution human contact network for infectious disease transmission. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 22020-22025.
35. Wallinga, J.; Teunis, P.; Kretzschmar, M. Using Data on Social Contacts to Estimate Age-specific Transmission Parameters for Respiratory-spread Infectious Agents. Am. J. Epidemiol. 2006, 164, 936-944.
36. Mossong, J.; Hens, N.; Jit, M.; Beutels, P.; Auranen, K.; Mikolajczyk, R.; Massari, M.; Salmaso, S.; Tomba, G.S.; Wallinga, J.; Heijne, J.; Sadkowska-Todys, M.; Rosinska, M.; Edmunds, W.J. Social Contacts and Mixing Patterns Relevant to the Spread of Infectious Diseases. PLoS Med. 2008, 5, e74.
37. Goudie, R. What does a tree tell us about a network? Master's thesis, Oxford University, Oxford, UK, September 2008.