These materials will be useful in preparation for the NME workshop. We require at the least a working knowledge of the R programming language. If you are inclined, feel free to also browse through the Statnet tutorials and literature listed on this page.

Installation

Please read the EpiModel installation instructions below to have the software ready before the workshop. This includes installing R and Rstudio.

R Tutorials

The NME workshop will depend on a good working knowledge of the R statistical software language, which is the basis of the statnet software for the analysis of network data. A good place to start is our R tutorial below.

Statnet Tutorials

We encourage you to explore and practice your R skills with the tutorials for the statnet suite of software for the analysis of networks. You can find these tutorials HERE.

Readings

To guide discussion on the use of our network-based models, we recommend that you read the following two papers in Lancet HIV and the Journal of Infectious Diseases before the course. Because many of the methods are not included in the main papers, we suggest that you peruse the Supplementary Technical Appendices of at least one of the papers (you will see there is a good deal of overlap in the appendices between the two papers). In addition, you may be interested in reading through other related network analysis and modeling literature referenced below.

Other Literature

ERGM Statistical Methods

  1. Hunter DR, Handcock MS, Butts CT, Goodreau SM, Morris M. ergm: A Package to Fit, Simulate and Diagnose Exponential-Family Models for Networks. J Stat Softw. 2008;24(3):nihpa54860. LINK

  2. Krivitsky PN, Handcock MS, Morris M. Adjusting for network size and composition effects in exponential-family random graph models. Stat Methodol. 2011;8(4):319–339. LINK

  3. Krivitsky PN, Handcock MS. A separable model for dynamic networks. J R Stat Soc Series B Stat Methodol. 2014;76(1):29–46. LINK

Applications of ERGMs to Social Science

  1. Morris M, Kurth AE, Hamilton DT, Moody J, Wakefield S. Concurrent Partnerships and HIV Prevalence Disparities by Race: Linking Science and Public Health Practice. Am J Public Health. 2009;99(6):1023–1031. LINK

  2. Goodreau SM, Kitts JA, Morris M. Birds of a feather, or friend of a friend? Using exponential random graph models to investigate adolescent social networks. Demography. 2009;46(1):103–126. LINK

  3. Carnegie NB, Morris M. Size matters: concurrency and the epidemic potential of HIV in small networks. PloS One. 2012;7(8):e43048. LINK

Applied HIV/STI Models with EpiModel

  1. Jenness SM, Goodreau SM, Morris M, Cassels S. Effectiveness of Combination Packages for HIV-1 Prevention in Sub-Saharan Africa Depends on Partnership Network Structure. Sexually Transmitted Infections. 2016; 92(8): 619-624. LINK

  2. Jenness SM, Sharma A, Goodreau SM, Rosenberg ES, Weiss KM, Hoover KW, Smith DK, Sullivan P. Individual HIV Risk versus Population Impact of Risk Compensation after HIV Preexposure Prophylaxis Initiation among Men Who Have Sex with Men. PLoS One. 2017; 12(1): e0169484. LINK

  3. Jenness SM, Weiss KM, Goodreau SM, Rosenberg E, Gift T, Chesson H, Hoover KW, Smith DK, Liu AY, Sullivan P. Incidence of Gonorrhea and Chlamydia Following HIV Preexposure Prophylaxis among Men Who Have Sex with Men: A Modeling Study. Clinical Infectious Diseases. Epub ahead of print. DOI: 10.1093/cid/cix439. LINK

Applied HIV/STI using ERGMs (Same Methods, Pre-EpiModel)

  1. Goodreau SM, Cassels S, Kasprzyk D, Montaño DE, Greek A, Morris M. Concurrent Partnerships, Acute Infection and HIV Epidemic Dynamics Among Young Adults in Zimbabwe. AIDS Behav. 2010;16(2):312–322. LINK

  2. Eaton JW, Hallett TB, Garnett GP. Concurrent sexual partnerships and primary HIV infection: a critical interaction. AIDS Behav. 2011;15(4):687–692. LINK

  3. Goodreau SM, Carnegie NB, Vittinghoff E, Lama JR, Sanchez J, Grinsztejn B, Koblin BA, Mayer KH, Buchbinder SP. What drives the US and Peruvian HIV epidemics in men who have sex with men (MSM)? PloS One. 2012;7(11):e50522. LINK

  4. Goodreau SM, Carnegie NB, Vittinghoff E, Lama JR, Fuchs JD, Sanchez J, Buchbinder SP. Can male circumcision have an impact on the HIV epidemic in men who have sex with men? PLoS One. 2014;9(7):e102960. LINK

  5. Carnegie NB, Goodreau SM, Liu A, Vittinghoff E, Sanchez J, Lama JR, Buchbinder S. Carnegie NB1, Goodreau SM, Liu A, Vittinghoff E, Sanchez J, Lama JR, Buchbinder S. J Acquir Immune Defic Syndr. 2015;69(1):119–25. LINK



Last updated: 2017-08-10