Here, we provide code used to duplicate the results from the MMWR "Modeling the impact of sexual networks in the transmission of Monkeypox virus between gay, bisexual, and other men who have sex with men".
To duplicate these results, run the file run_network_models_mmwr.R. This code will load in mpx_network_object.rda, which contains target statisticts for a sexual network of Gay, Bisexual, and other men who have sex with men (E.g., the proportion of individuals in the model that should have long term sexual partners). The code will additionally load in functions contained in network_modules.R. These functions will control the dynamics of our simulations (e.g., individuals initiating and ending sexual contact, individuals contracting and recovering from Monkeypox). Finally, the code will run simulations for all scenarios presented in the MMWR.
The code will create and save 12 files-
mmwr_nobehavechange_hightrans.Rdata : Raw data for higher transmission scenario where individuals do not reduce the rate of acquiring one time sexual contacts. mmwr_behavechange_hightrans.Rdata : Raw data for higher transmission scenario where individuals reduce the rate of acquiring one time sexual contacts. mmwr_nobehavechange_lowtrans.Rdata : Raw data for lower transmission scenario where individuals do not reduce the rate of acquiring one time sexual contacts. mmwr_behavechange_lowtrans.Rdata : Raw data for lower transmission scenario where individuals reduce the rate of acquiring one time sexual contacts.
mmwr_nobehavechange_hightrans_noextinct_means.csv : Means for results of higher transmission scenario where individuals do not reduce the rate of acquiring one time sexual contacts mmwr_behavechange_hightrans_noextinct_means.csv : Means for results of higher transmission scenario where individuals reduce the rate of acquiring one time sexual contacts mmwr_nobehavechange_lowtrans_noextinct_means.csv : Means for results of lower transmission scenario where individuals do not reduce the rate of acquiring one time sexual contacts mmwr_behavechange_lowtrans_noextinct_means.csv : Means for results of lower transmission scenario where individuals reduce the rate of acquiring one time sexual contacts
mmwr_nobehavechange_hightrans_noextinct_medians.csv : Medians and interquartile ranges for results of higher transmission scenario where individuals do not reduce the rate of acquiring one time sexual contacts mmwr_behavechange_hightrans_noextinct_medians.csv : Medians and interquartile ranges for results of higher transmission scenario where individuals reduce the rate of acquiring one time sexual contacts mmwr_nobehavechange_lowtrans_noextinct_medians.csv : Medians and interquartile ranges for results of lower transmission scenario where individuals do not reduce the rate of acquiring one time sexual contacts mmwr_behavechange_lowtrans_noextinct_medians.csv : Medians and interquartile ranges for results of lower transmission scenario where individuals reduce the rate of acquiring one time sexual contacts
CSV files of mean values for scenarios with no behavior change can be used to recreate figure 1 by using the se.flow.main.mean, se.flow.pers.mean, and se.flow.ot.mean variables, which are the average per day number of individuals who contracted monkeypox via "main" partnerships, "casual" partnerships, and "one time" partnerships respectively.
CSV files of median and IQR values for all scenarios can be used to recreate figure 2 by using the cuml.infs.med, cuml.infs.iqr1, and cuml.infs.iqr3 variables, which are the median, first quartile, and third quartile of the cumulative number of individuals who have contracted monkeypox over time.