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      The dual-Barab\'asi-Albert model

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          Abstract

          The ability to sample random networks that can accurately represent real social contact networks is essential to the study of viral epidemics. The Barab\'asi-Albert model and its extensions attempt to capture reality by generating networks with power-law degree distributions, but properties of the resulting distributions (e.g. minimum, average, and maximum degree) are often unrealistic of the social contacts the models attempt to capture. I propose a novel extension of the Barab\'asi-Albert model, which I call the "dual-Barab\'asi-Albert" (DBA) model, that attempts to better capture these properties of real networks of social contact.

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          Mean-field theory for scale-free random networks

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            FAVITES: simultaneous simulation of transmission networks, phylogenetic trees, and sequences

            Motivation: The ability to simulate epidemics as a function of model parameters allows for the gain of insights unobtainable from real datasets. Further, reconstructing transmission networks for fast-evolving viruses like HIV may have the potential to greatly enhance epidemic intervention, but transmission network reconstruction methods have been inadequately studied, largely because it is difficult to obtain "truth" sets on which to test them and properly measure their performance. Results: We introduce FAVITES, a robust framework for simulating realistic datasets for epidemics that are caused by fast-evolving pathogens like HIV. FAVITES creates a generative model that produces many items relevant to an epidemic, such as contact networks, transmission networks, phylogenetic trees, and error-prone sequence datasets. FAVITES is designed to be flexible and extensible by dividing the generative model into modules, each of which is expressed as a fixed API that can be implemented using various sub-models. We use FAVITES to simulate HIV datasets resembling the San Diego epidemic and show that the simulated datasets are realistic. We then use the simulated data to make inferences about the epidemic and how it is impacted by increased treatment efforts. We also study two transmission network reconstruction methods and their effectiveness in detecting fast-growing clusters. Availability and implementation: FAVITES is available at https://github.com/niemasd/FAVITES, and a Docker image can be found on DockerHub (https://hub.docker.com/r/niemasd/favites).
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              Author and article information

              Journal
              24 October 2018
              Article
              1810.10538
              ddc66b64-d51c-4a36-a01b-36641c9fb71d

              http://creativecommons.org/licenses/by/4.0/

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              Custom metadata
              3 pages, no figures
              physics.soc-ph

              General physics
              General physics

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