2 Pre-Reading

We recommend reading the following papers before the course to ground our discussion on network-based epidemic models. For at least one paper, we also suggest reading the Supplementary Technical Appendix (there is substantial overlap between them).

2.1 Further Reading

You may also be interested in the statistical methods behind the course and applied research using these methods. All Statnet packages are open source and available on GitHub.

ERGM Statistical 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]
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, 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. 2017; 11(1): 427-455. [PubMed] [Paper]
Krivitsky PN, Hunter DR, Morris M, Klumb C. ergm 4: New Features for Analyzing Exponential-Family Random Graph Models. Journal of Statistical Software. 2023; 105(6): 1-44. [Paper]
Krivitsky PN, Hunter DR, Morris M, Klumb C. ergm 4: Computational Improvements. arXiv preprint 2203.08198. [Paper]

Applications of ERGMs

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]

Network Models of Epidemics using ERGMs (Pre-EpiModel)

Goodreau SM, Cassels S, Kasprzyk D, Montano 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. [PubMed]
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. [PubMed]
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. [PubMed]
Carnegie NB, Goodreau SM, Liu A, Vittinghoff E, Sanchez J, Lama JR, Buchbinder S. Targeting pre-exposure prophylaxis among men who have sex with men in the United States and Peru: partnership types, contact rates, and sexual role. J Acquir Immune Defic Syndr. 2015; 69(1): 119-125. [PubMed]

Applied Research using EpiModel

EpiModel and its extension packages have been used in many scientific journal articles across a wide array of fields. A full list is available on the EpiModel wiki. Selected examples of network modeling applications across disease areas:

Jenness SM, Goodreau SM, Rosenberg E, Beylerian EN, Hoover KW, Smith DK, Sullivan P. Impact of the Centers for Disease Control’s HIV Preexposure Prophylaxis Guidelines for Men Who Have Sex with Men in the United States. J Infect Dis. 2016; 214(12): 1800-1807. [PubMed]
Goldstein ND, Eppes SC, Mackley A, Tuttle D, Paul DA. A Network Model of Hand Hygiene: How Good Is Good Enough to Stop the Spread of MRSA? Infect Control Hosp Epidemiol. 2017; 38(8): 945-952. [PubMed]
Robinson SJ, Barbieri MM, Murphy S, Baker JD, Harting AL, Craft ME, Littnan CL. Model recommendations meet management reality: implementation and evaluation of a network-informed vaccination effort for endangered Hawaiian monk seals. Proc Biol Sci. 2018; 285(1870): 20171899. [PubMed]
Jenness SM, Johnson JA, Hoover KW, Smith DK, Delaney KP. Modeling an integrated HIV prevention and care continuum to achieve the Ending the HIV Epidemic goals. AIDS. 2020; 34(14): 2103-2113. [PubMed]
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; 35(9): 1479-1489. [PubMed]
Jenness SM, Le Guillou A, Chandra C, Mann LM, Sanchez T, Westreich D, Marcus JL. Projected HIV and Bacterial Sexually Transmitted Infection Incidence Following COVID-19-Related Sexual Distancing and Clinical Service Interruption. J Infect Dis. 2021; 223(6): 1019-1028. [PubMed]
Spicknall IH, Pollock ED, Clay PA, Oster AM, Charniga K, Masters N, Nakazawa YJ, Rainisch G, Gundlapalli AV, Gift TL. Modeling the Impact of Sexual Networks in the Transmission of Monkeypox virus Among Gay, Bisexual, and Other Men Who Have Sex with Men — United States, 2022. MMWR. 2022; 71(35): 1131-1135. [PubMed]
Jenness SM, Le Guillou A, Lyles C, Bernstein KT, Krupinsky K, Enns EA, Sullivan PS, Delaney KP. The Role of HIV Partner Services in the Modern Biomedical HIV Prevention Era: A Network Modeling Study. Sex Transm Dis. 2022; 49(12): 801-807. [PubMed]
Hamilton DT, Hoover KW, Delaney KP. Reducing HIV incidence in the Southern United States through routine opt-out HIV screening. AIDS. 2025; 39(11): 1632-1640. [PubMed]

# Pre-Reading We recommend reading the following papers before the course to ground our discussion on network-based epidemic models. For at least one paper, we also suggest reading the Supplementary Technical Appendix (there is substantial overlap between them). ::: {.callout-note title="Recommended Reading"} 1. Goodreau SM, Rosenberg ES, Jenness SM, et al. Sources of Racial Disparities in HIV Prevalence among Men Who Have Sex with Men in Atlanta, GA: A Modeling Study. *Lancet HIV.* 2017; 4(7): e311-e320. [[PubMed]](https://www.ncbi.nlm.nih.gov/pubmed/28431923) [[Paper]](pdf/Goodreau-LancetHIV-RacialDisparities.pdf) [[Appendix]](pdf/Goodreau-LancetHIV-RacialDisparities-App.pdf) 2. Jenness SM, Willebrand KS, Malik AA, Lopman BA, Omer S. Dynamic Network Strategies for SARS-CoV-2 Control on a Cruise Ship. *Epidemics.* 2021; 37: 100488. [[PubMed]](https://pubmed.ncbi.nlm.nih.gov/34438256/) [[Paper]](pdf/Jenness-Epidemics-COVIDCruise.pdf) [[Appendix]](pdf/Jenness-Epidemics-COVIDCruise-App.pdf) 3. Jenness SM, Goodreau SM, Morris M. EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks. *Journal of Statistical Software.* 2018; 84(8): 1-47. [[PubMed]](https://www.ncbi.nlm.nih.gov/pubmed/29731699) [[Paper]](https://www.jstatsoft.org/index.php/jss/article/view/v084i08/v84i08.pdf) ::: ## Further Reading You may also be interested in the statistical methods behind the course and applied research using these methods. All Statnet packages are open source and available on [GitHub](https://github.com/statnet). ::: {.callout-tip title="ERGM Statistical Methods" collapse="true"} 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. [[PubMed]](http://www.ncbi.nlm.nih.gov/pubmed/19756229) [[Paper]](https://www.jstatsoft.org/article/view/v024i03) 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. [[PubMed]](http://www.ncbi.nlm.nih.gov/pubmed/21691424) [[Paper]](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117581/) 3. Krivitsky PN, Handcock MS. A separable model for dynamic networks. *J R Stat Soc Series B Stat Methodol.* 2014; 76(1): 29-46. [[PubMed]](http://www.ncbi.nlm.nih.gov/pubmed/24443639) [[Paper]](https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12014) 4. Krivitsky PN, 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.* 2017; 11(1): 427-455. [[PubMed]](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737754/) [[Paper]](https://doi.org/10.1214/16-AOAS1010) 5. Krivitsky PN, Hunter DR, Morris M, Klumb C. ergm 4: New Features for Analyzing Exponential-Family Random Graph Models. *Journal of Statistical Software.* 2023; 105(6): 1-44. [[Paper]](https://doi.org/10.18637/jss.v105.i06) 6. Krivitsky PN, Hunter DR, Morris M, Klumb C. ergm 4: Computational Improvements. arXiv preprint 2203.08198. [[Paper]](https://arxiv.org/pdf/2203.08198) ::: ::: {.callout-tip title="Applications of ERGMs" collapse="true"} 1. 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]](http://www.ncbi.nlm.nih.gov/pubmed/19348111) [[Paper]](https://read.dukeupress.edu/demography/article/46/1/103/169916/Birds-of-a-feather-or-friend-of-a-friend-using) 2. 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]](http://www.ncbi.nlm.nih.gov/pubmed/19372508) [[Paper]](https://ajph.aphapublications.org/doi/10.2105/AJPH.2008.147835) 3. Carnegie NB, Morris M. Size matters: concurrency and the epidemic potential of HIV in small networks. *PLoS One.* 2012; 7(8): e43048. [[PubMed]](http://www.ncbi.nlm.nih.gov/pubmed/22937011) [[Paper]](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043048) ::: ::: {.callout-tip title="Network Models of Epidemics using ERGMs (Pre-EpiModel)" collapse="true"} 1. Goodreau SM, Cassels S, Kasprzyk D, Montano 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. [[PubMed]](http://www.ncbi.nlm.nih.gov/pubmed/21190074) 2. 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. [[PubMed]](http://www.ncbi.nlm.nih.gov/pubmed/23209768) 3. 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. [[PubMed]](http://www.ncbi.nlm.nih.gov/pubmed/25076493) 4. Carnegie NB, Goodreau SM, Liu A, Vittinghoff E, Sanchez J, Lama JR, Buchbinder S. Targeting pre-exposure prophylaxis among men who have sex with men in the United States and Peru: partnership types, contact rates, and sexual role. *J Acquir Immune Defic Syndr.* 2015; 69(1): 119-125. [[PubMed]](http://www.ncbi.nlm.nih.gov/pubmed/25942463) ::: ::: {.callout-tip title="Applied Research using EpiModel" collapse="true"} EpiModel and its [extension packages](https://github.com/statnet/EpiModelHIV) have been used in many scientific journal articles across a wide array of fields. A full list is available on the [EpiModel wiki](https://github.com/statnet/EpiModel/wiki/EpiModel-in-the-Scientific-Literature). Selected examples of network modeling applications across disease areas: 1. Jenness SM, Goodreau SM, Rosenberg E, Beylerian EN, Hoover KW, Smith DK, Sullivan P. Impact of the Centers for Disease Control's HIV Preexposure Prophylaxis Guidelines for Men Who Have Sex with Men in the United States. *J Infect Dis.* 2016; 214(12): 1800-1807. [[PubMed]](https://pubmed.ncbi.nlm.nih.gov/27418048/) 2. Goldstein ND, Eppes SC, Mackley A, Tuttle D, Paul DA. A Network Model of Hand Hygiene: How Good Is Good Enough to Stop the Spread of MRSA? *Infect Control Hosp Epidemiol.* 2017; 38(8): 945-952. [[PubMed]](https://pubmed.ncbi.nlm.nih.gov/28656884/) 3. Robinson SJ, Barbieri MM, Murphy S, Baker JD, Harting AL, Craft ME, Littnan CL. Model recommendations meet management reality: implementation and evaluation of a network-informed vaccination effort for endangered Hawaiian monk seals. *Proc Biol Sci.* 2018; 285(1870): 20171899. [[PubMed]](https://pubmed.ncbi.nlm.nih.gov/29321294/) 4. Jenness SM, Johnson JA, Hoover KW, Smith DK, Delaney KP. Modeling an integrated HIV prevention and care continuum to achieve the Ending the HIV Epidemic goals. *AIDS.* 2020; 34(14): 2103-2113. [[PubMed]](https://pubmed.ncbi.nlm.nih.gov/32910062/) 5. 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; 35(9): 1479-1489. [[PubMed]](https://pubmed.ncbi.nlm.nih.gov/33831910/) 6. Jenness SM, Le Guillou A, Chandra C, Mann LM, Sanchez T, Westreich D, Marcus JL. Projected HIV and Bacterial Sexually Transmitted Infection Incidence Following COVID-19-Related Sexual Distancing and Clinical Service Interruption. *J Infect Dis.* 2021; 223(6): 1019-1028. [[PubMed]](https://pubmed.ncbi.nlm.nih.gov/33507308/) 7. Spicknall IH, Pollock ED, Clay PA, Oster AM, Charniga K, Masters N, Nakazawa YJ, Rainisch G, Gundlapalli AV, Gift TL. Modeling the Impact of Sexual Networks in the Transmission of Monkeypox virus Among Gay, Bisexual, and Other Men Who Have Sex with Men — United States, 2022. *MMWR.* 2022; 71(35): 1131-1135. [[PubMed]](https://pubmed.ncbi.nlm.nih.gov/36048619/) 8. Jenness SM, Le Guillou A, Lyles C, Bernstein KT, Krupinsky K, Enns EA, Sullivan PS, Delaney KP. The Role of HIV Partner Services in the Modern Biomedical HIV Prevention Era: A Network Modeling Study. *Sex Transm Dis.* 2022; 49(12): 801-807. [[PubMed]](https://pubmed.ncbi.nlm.nih.gov/36194831/) 9. Hamilton DT, Hoover KW, Delaney KP. Reducing HIV incidence in the Southern United States through routine opt-out HIV screening. *AIDS.* 2025; 39(11): 1632-1640. [[PubMed]](https://pubmed.ncbi.nlm.nih.gov/40372031/) :::