LEMHIVpack package and github repository contains all model functions, code modules and input data to run our dynamic compartmental simulation model for the localized HIV microepidemics in Atlanta, Baltimore, Los Angeles, Miami, NYC, Seattle. Please see this slide deck, the Articles section of this site, as well as the references below for more details.
devtools
install.packages("devtools")Open R Studio and load project file LEMHIVpack.Rproj from the main folder of the LEMHIVpack github repository.
Download and install LEMHIVpack package from GitHub using:
devtools::install_github("HERU-LEM/LEMHIVpack")The remaining R scripts to run the model and conduct the analysis are organized into three sections:
Setup contains R scripts for core modules. Users can modify these files as necessary (e.g. adjusting analysis time-horizon, intervention sustainment period, discount rate etc.), but do not need to run these scripts prior to running the model, as they will be called by modules in the next two steps.
Run model contains R scripts to run the model and produce raw outputs (costs, QALYs, HIV incidence) for single interventions and combinations (deterministic and PSA), which will be used in subsequent analyses.
Analysis contains R scripts to use raw model outputs generated in R/02_Run_model to conduct the primary analyses: cost-effectiveness analysis (CEA), HIV incidence reduction between different implementation scenarios and the status-quo, disaggregated cost breakdown by component (implementation, medical care, PrEP, ART, MOUD), determining optimal combination implementation strategy (OCIS), generating health production functions, and other visualizations of results.
For more detail on the evidence synthesis, model development, and analysis, please see the following manuscripts:
Krebs, E., Enns, B., Wang, L., Zang, X., Panagiotoglou, D., Del Rio, C., Dombrowski, J., Feaster, D. J., Golden, M., Granich, R., Marshall, B., Mehta, S. H., Metsch, L., Schackman, B. R., Strathdee, S. A., Nosyk, B., & localized HIV modeling study group (2019). “Developing a dynamic HIV transmission model for 6 U.S. cities: An evidence synthesis”. PloS one, 14(5), e0217559. https://doi.org/10.1371/journal.pone.0217559
Zang, X., Krebs, E., Min, J. E., Pandya, A., Marshall, B., Schackman, B. R., Behrends, C. N., Feaster, D. J., Nosyk, B., & Localized HIV Modeling Study Group (2020). “Development and Calibration of a Dynamic HIV Transmission Model for 6 US Cities”. Medical decision making : an international journal of the Society for Medical Decision Making, 40(1), 3–16. https://doi.org/10.1177/0272989X19889356
Krebs, E., Zang, X., Enns, B., Min, J. E., Behrends, C. N., Del Rio, C., Dombrowski, J. C., Feaster, D. J., Gebo, K. A., Golden, M., Marshall, B., Metsch, L. R., Schackman, B. R., Shoptaw, S., Strathdee, S. A., Nosyk, B., & Localized Economic Modeling Study Group (2020). “The impact of localized implementation: determining the cost-effectiveness of HIV prevention and care interventions across six United States cities”. AIDS (London, England), 34(3), 447–458. https://doi.org/10.1097/QAD.0000000000002455
Nosyk, B., Zang, X., Krebs, E., Enns, B., Min, J. E., Behrends, C. N., Del Rio, C., Dombrowski, J. C., Feaster, D. J., Golden, M., Marshall, B., Mehta, S. H., Metsch, L. R., Pandya, A., Schackman, B. R., Shoptaw, S., Strathdee, S. A., & Localized HIV Modeling Study Group (2020). “Ending the HIV epidemic in the USA: an economic modelling study in six cities”. The lancet. HIV, 7(7), e491–e503. https://doi.org/10.1016/S2352-3018(20)30033-3