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.
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.
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.
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.
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.
Goodreau SM, Rosenberg ES, Jenness SM, Luisi N, Stansfield SE, Millett G, Sullivan P. Sources of Racial Disparities in HIV Prevalence among Men Who Have Sex with Men in Atlanta, GA: A Modeling Study. Lancet HIV. Epub ahead of print. DOI: 10.1016/ S2352-3018(17)30067. [PubMed] [Paper] [Appendix]
Jenness SM, Goodreau SM, Rosenberg E, Beylerian EN, Hoover KW, Smith DK, Sullivan P. Impact of CDC’s HIV Preexposure Prophylaxis Guidelines among MSM in the United States. Journal of Infectious Diseases. 2016; 214(12): 1800-1807. [PubMed] [Paper] [Appendix]
Jenness SM, Goodreau SM and Morris M. EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks. Journal of Statistical Software. 2018; 84(8): 1-47. [PubMed] [Paper]
You may be also interested in reading papers on the statistical methods featured in this course and/or applications using these methods.
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. [PubMed] [Paper]
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. [PubMed] [Paper (PMC)]
Krivitsky PN, Handcock MS. A separable model for dynamic networks. J R Stat Soc Series B Stat Methodol. 2014;76(1):29–46. [PubMed] [Paper]
Krivitsky PN and Morris M. Inference for social network models from egocentrically sampled data, with application to understanding persistent racial disparities in hiv prevalence in the US. Ann Appl Stat. 11(1), 427–455. [PubMed] [Paper]
Krivitsky PN, Hunter DR, Morris M, Klumb C. ergm 4.0: New features and improvements. arXiv preprint 2021; 2106.04997. [Paper]
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. [PubMed] [Paper]
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. [PubMed] [Paper]
Carnegie NB, Morris M. Size matters: concurrency and the epidemic potential of HIV in small networks. PloS One. 2012;7(8):e43048. [PubMed] [Paper]
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]
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]
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]
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]
EpiModel and its extension packages have been used in many scientific journal articles, in a wide array of fields. A list of these articles can be accessed in a wiki page or on Zotero.
A good current example is:
Jenness SM, Knowlton G, Smith DK, Marcus JL, Anderson EJ, Siegler AJ, Jones J, Sullivan PS, Enns E. A decision analytics model to optimize investment in interventions targeting the HIV preexposure prophylaxis cascade of care. AIDS. 2021 Jul 15;35(9):1479-1489. [PubMed] [Preprint]
Last updated: 2022-07-07