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Code for model of HIV SPVL evolution for F. Blanquart's analysis of Rakai SPVL

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Blanquart.2016

This is code used for a modeling sub-analysis in Francois Blanquart's analysis of set point viral load in Rakai, Uganda.

Very brief explanation

This is a stochastic, agent-based simulation of HIV epidemiology and evolution. To run, source the "Run.new.Oct2016.R" from within an R session. This R wrapper calls the .C file. To visualize key output, source the "Plots.R" script. The ".. .alpha ... .c" files incorporate different values of an evolutionary parameter that can be edited on line 810 of each file. Make sure the .R wrapper script calls the correct .c source (line 163 of the .R script).

References

This model has been used for the following studies, and is described in more detail within each manuscript:

An HIV Epidemic Model Based on Viral Load Dynamics: Value in Assessing Empirical Trends in HIV Virulence and Community Viral Load

Joshua T. Herbeck, John E. Mittler, Geoffrey S. Gottlieb, James I. Mullins

Published: 19 June 2014 http://dx.doi.org/10.1371/journal.pcbi.1003673 http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003673

Evolution of HIV virulence in response to widespread scale up of antiretroviral therapy: a modeling study

Joshua T. Herbeck, John E. Mittler, Geoffrey S. Gottlieb, Steven M. Goodreau, James T. Murphy, Anne Cori, Michael Pickles, Christophe Fraser

Published: 3 October 2016 http://dx.doi.org/10.1093/ve/vew028 http://ve.oxfordjournals.org/content/2/2/vew028

Contact

Questions can be sent to Josh Herbeck, herbeck@uw.edu.

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Code for model of HIV SPVL evolution for F. Blanquart's analysis of Rakai SPVL

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