This is reproducible code and data for our PNAS Brief Report, Dynamics of racial disparities in all-cause mortality during the COVID-19 pandemic, which uses the CDC WONDER provisional data to estimate monthly age-standardized mortality rates and rate ratios. We use the NCI Joinpoint Regression Program to fit segmented regressions (joinpoint models) to summarize trends in the monthly rate ratios. The full citation is:
Aschmann, Hélène E., Alicia R. Riley, Ruijia Chen, Yea-Hung Chen, Kirsten Bibbins-Domingo, Andrew C. Stokes, M. Maria Glymour, and Mathew V. Kiang. 2022. “Dynamics of Racial Disparities in All-Cause Mortality during the COVID-19 Pandemic.” Proceedings of the National Academy of Sciences 119(40):e2210941119. doi: 10.1073/pnas.2210941119.
As research documenting disparate impacts of COVID-19 by race and ethnicity grows, little attention has been given to dynamics in mortality disparities during the pandemic and whether changes in disparities persist. We estimate age-standardized monthly all-cause mortality in the United States from January 2018 through February 2022 for seven racial/ethnic populations. Using joinpoint regression, we quantify trends in race-specific rate ratios relative to non-Hispanic White mortality to examine the magnitude of pandemic-related shifts in mortality disparities. Prepandemic disparities were stable from January 2018 through February 2020. With the start of the pandemic, relative mortality disadvantages increased for American Indian or Alaska Native (AIAN), Native Hawaiian or other Pacific Islander (NHOPI), and Black individuals, and relative mortality advantages decreased for Asian and Hispanic groups. Rate ratios generally increased during COVID-19 surges, with different patterns in the summer 2021 and winter 2021/2022 surges, when disparities approached prepandemic levels for Asian and Black individuals. However, two populations below age 65 fared worse than White individuals during these surges. For AIAN people, the observed rate ratio reached 2.25 (95% CI = 2.14, 2.37) in October 2021 vs. a prepandemic mean of 1.74 (95% CI = 1.62, 1.86), and for NHOPI people, the observed rate ratio reached 2.12 (95% CI = 1.92, 2.33) in August 2021 vs. a prepandemic mean of 1.31 (95% CI = 1.13, 1.49). Our results highlight the dynamic nature of racial/ethnic disparities in mortality and raise alarm about the exacerbation of mortality inequities for Indigenous groups due to the pandemic.
All analyses are conducted using R, which can be downloaded via
CRAN. We also recommend the use of
RStudio when
running R, which will allow users to take advantage of
renv for dependency
management. If not using renv, we provide session information at the
end of this file to ensure packages are the correct version. Note that
for the joinpoint analyses, you must use an external program, Joinpoint
Regression Program which
can be downloaded from the National Cancer Institute website.
We use publicly available data — the README.md file in data_raw has
links to our CDC WONDER query and each query file has the dates of data
access.
The code files (in code) are designed to be run in order. Files 01
to 04 manipulate the raw data into files that can be run in the
Joinpoint regression program. After running these files, one must run
joinpoint analyses in Joinpoint Regression Program. For convenience, we
have provided our saved analysis settings (files ending in .jps) as
well as our model results (files ending in .jpo). Once files have been
exported out of the Joinpoint Regression Program, one can run code files
05 and higher to gather the results and create plots.
The numeric representations of the figures in our paper are available in
output.
- Hélène Aschmann
(
: heleneaschmann | (
: @LnAschmann)
- Kirsten
Bibbins-Domingo
(
- Ruijia Chen
(
- Yea-Hung Chen
(
- Maria Glymour
(
- Mathew Kiang
(
- Alicia Riley
(
- Andrew Stokes
(
> sessioninfo::session_info()
─ Session info ─────────────────────────────────────────────────────────
setting value
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language (EN)
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pandoc 2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown)
─ Packages ─────────────────────────────────────────────────────────────
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[1] /Users/mvk/Library/CloudStorage/Dropbox/Projects_Active/dynamic_inequality/renv/library/R-4.1/x86_64-apple-darwin17.0
[2] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
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