COVID-19 is an infectious disease caused by the SARS-Cov-2 virus that was first identified in Wuhan, China in 2019. The virus spreads primarily via airborne mechanisms. In COVID-19, “CO” stands for corona, “VI” for virus, “D” for disease, and \(19\) for \(2019\), the first year the virus was identified in humans. According to the World Health Organization, COVID-19 has become a world pandemic with more than \(767\) million confirmed infections and almost \(7\) million confirmed deaths in virtually every country of the world by June 6, 2023.
Here we focus on mortality data collected in the US before and during the pandemic. The COVID-19 data used in this book can be downloaded here. The data used in this book can also be loaded using the following lines of code.
library(refund)
data(COVID19)str(COVID19)## List of 12
## $ US_weekly_mort : num [1:207] 61114 59454 58176 58537 59175 ...
## $ US_weekly_mort_dates : Date[1:207], format: "2017-01-14" "2017-01-21" ...
## $ US_weekly_mort_CV19 : num [1:52] 0 0 3 1 0 2 0 5 9 37 ...
## $ US_weekly_mort_CV19_dates : chr [1:52] "01/04/2020" "01/11/2020" "01/18/2020" "01/25/2020" ...
## $ US_weekly_excess_mort_2020 : num [1:52] 1698 2222 1011 1111 535 ...
## $ US_weekly_excess_mort_2020_dates : Date[1:52], format: "2020-01-04" "2020-01-11" ...
## $ US_states_names : chr [1:52] "Alabama" "Alaska" "Arizona" "Arkansas" ...
## $ US_states_population : num [1:52] 4921532 731158 7421401 3030522 39368078 ...
## $ States_excess_mortality : num [1:52, 1:52] 4 -4 -52 -20 196 18 1 14 2 121 ...
## $ States_excess_mortality_per_million: num [1:52, 1:52] 0.813 -5.471 -7.007 -6.6 4.979 ...
## $ States_CV19_mortality : num [1:52, 1:52] 0 0 0 0 0 0 0 0 0 0 ...
## $ States_CV19_mortality_per_million : num [1:52, 1:52] 0 0 0 0 0 0 0 0 0 0 ...The all-cause mortality data is weekly mortality (week ending on 2017-01-14 to week ending on 2021-04-10) for a total of \(222\) weeks. Data are made available by the National Center for Health Statistics. More precisely, the dataset link is called National and State Estimates of Excess Deaths. It can be accessed from this website. A direct link to the file can be accessed here.
The COVID-19 mortality data is weekly mortality with COVID-19 as cause of death (week ending on 2020-01-04 to week ending on 2021-04-17) for a total of \(68\) weeks. Data are made available by the National Center for Health Statistics. More precisely, the dataset link is called National and State Estimates of Excess Deaths. It can be accessed from this website. A direct link to the file can be accessed here.
A third data set contains the estimated population size for all US states and teritories as of 2020-07-01. The source for these data is Wikipedia.