11/16/2020 Benjamin Seligman, MD, PhD Boston VA Health Care System / Harvard Medical School This is the readme to guide you on replicating the simulation of COVID-19 deaths in the United States using the 2017-18 NHANES sample, as described in Seligman, Ferranna, and Bloom PLoS Medicine 2020. To begin, we assume the following file structure: COVID-19 COVID-19/Code - NHANES_Data 2020-11-16 FINAL.r - Params and Sim 2020-11-16 FINAL.r - Analysis - 2020-11-16 FINAL.r COVID-19/NHANES - NHANES 2017-18 files obtainable from: https://wwwn.cdc.gov/nchs/nhanes/continuousnhanes/default.aspx?BeginYear=2017 - We use: ALB_CR_J.XPT BIOPRO_J.XPT BPQ_J.XPT BPX_J.XPT DEMO_J.XPT DIQ_J.XPT GHB_J.XPT KIQ_U_J.XPT MCQ_J.XPT To run the simulation, run the R files in the following order: 1) NHANES_Data 2020-11-16 FINAL.r 2) Params and Sim 2020-11-16 FINAL.r 3) Analysis - 2020-11-16 FINAL.r They are meant to be run consecutively in the same R session Depending on your computer's performance, anticipate 30-120 minutes for step 2 to run. UPDATE 12/29/2021 Benjamin Seligman, MD, PhD Greater Los Angeles VA Health Care System / UCLA David Geffen School of Medicine We have updated the Analysis - 2020-11-15 FINAL.r file on lines 305 and 306 so that income categories are treated treated as the midpoints of each category, or the minimum value for top-coded category. The updated file is Analysis - 2021-12-29 FINAL.r and should be used in place of the original file.