These materials will be useful in preparation for the 2020 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.

Software Installation

Please read the installation instructions linked below and have the software loaded before the workshop. This includes installing R and Rstudio.

It’s a good idea to have the most recent versions of all software installed – the course instructors will all be using current versions, and the code scripts provided in the course for you to run will assume this as well. This is especially true for the packages EpiModel and statnetWeb.

For 2020 NME, you must install the latest version of the EpiModel and statnetWeb packages; if you have earlier versions installed on your computer, update your packages accordingly.

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 skimming our primary methods paper on EpiModel in the Journal of Statistical Software.

Other Literature

You may be also interested in reading papers on the statistical methods featured in this course and/or applications using these methods.

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 Infectious Disease Models 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]

Applied Research using EpiModel

EpiModel and its extension packages have been used in the following scientific journal articles. A list of these articles can be accessed in a wiki page or on Zotero.



Last updated: 2020-08-13