🚀 Code at the time of publication

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+.DS_Store

Data/README.md

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+# Data  
+
+Information on sources of data for calculations are found in this folder. For description of the methods, please see the [Methods Supplement](https://read.dukeupress.edu/demography/article/doi/10.1215/00703370-10575276/343372/Research-Note-COVID-19-Is-Not-an-Independent-Cause#supplementary-data)
+
+For information about data sources for the Brazil analysis, please see the data folder in the [repository](https://github.com/mcastrolab/Brazil-Covid19-e0-change/tree/main/data) for our 2021 Nature paper, [Reduction in life expectancy in Brazil after COVID-19](https://www.nature.com/articles/s41591-021-01437-z) 
+
+Information on data for the U.S. analysis, please see below:
+
+## I. Raw data
+
+  01. 2020 Provisional US Life Expectancy: 
+      - Source: [NVSS, Vital Statistic Rapid Release, No 015. Provisional Life Expectancy Estimates](https://stacks.cdc.gov/view/cdc/107201) 
+      - Analysis Sheet name: *Appendix 4b. 2020 LT NCHS_raw*
+
+  02. 2019 US Life Table. 
+      -Source: [NCHS, National Vital Statistics System Mortality](https://www.cdc.gov/nchs/data/nvsr/nvsr70/nvsr70-19.pdf)
+      - Analysis Sheet name: *Appendix 5b 2019 LT NCHS*
+
+  03. 2020 All-cause and COVID-19 Death Data by age-group and sex: 
+      - Source: [CDC WONDER](https://wonder.cdc.gov/ucd-icd10-expanded.html) (Downloaded 1/23/2022) 
+      - Analysis Sheet name: *Appendix 2a. Deaths 2020*
+
+  04. 2019 All-cause Death Data by age-group and sex: 
+      - Source: [CDC WONDER](https://wonder.cdc.gov/ucd-icd10-expanded.html) (Downloaded 1/23/2022)
+      - Analysis Sheet name: *Appendix 2b. Deaths 2019*
+
+
+## II. Processed data:
+
+ 01. Person-years 2020 by age group and sex
+      - Sources: Calculated from US Population and US Deaths
+      - Anaysis Sheet name: *Appendix 1a. Person-years 2020*
+
+ 02. Person-years 2019 by age group and sex
+      - Sources: Calculated from US Population and US Deaths
+      - Anaysis Sheet name: *Appendix 1b. Person-years 2019*
+
+  03. 2020 Abridged Life Table
+      - Description: Life table abridged from NCHS (Appendix 4b) to match the 10 year age-groups used in the analysis.  
+      - Analysis Sheet name: *Appendix 4a. 2020 LT NCHS_abridged*  
+
+  04. 2019 Abridged Life Table
+      - Description: Life table abridged fro NCHS (Appendix 5b) to match the 10 year age-groups used in the analysis.  
+      - Analysis Sheet name: *Appendix 5a. 2019 LT_NCHS_abridged*  
+
+  05. 2020 Constructed Life Table
+      - Description: Life Table constructed by authors from published mortality data (Appendix 2a) and estimated person-years lived (Appendix 1a) to estimate ex in 2020.  
+      - Analysis Sheet name: *Appendix 3a. 2020 LT_construct*  
+
+  06. 2019 Constructed Life Table
+      - Description: Life Table constructed by authors from published mortality data (Appendix 2b) and estimated person-years lived (Appendix 1b) to estimate ex in 2019.  
+      - Analysis Sheet name: *Appendix 3b. 2019 LT_construct*  
+
+## III Analysis Sheets:
+  DT19 - Analysis sheet for the DT19 methods
+
+  DT20 - Analysis sheet for the DT20 methods
+
+  Summary: Final Table and Appendix Table for DT19, DT20 and LT19-LT20 for ex0, ex15 and ex65
+
+      
+      
+      
+
+
+## License
+The data collected and presented is licensed under the [Creative Commons Attribution 4.0 license](https://creativecommons.org/licenses/by/4.0/), and the underlying code used to format, analyze and display that content is licensed under the [MIT license](http://opensource.org/licenses/mit-license.php). 
+
+

README.md

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+# COVID-19 is not an Independent Cause of Death
+
+Here we provide the data and pipeline for: [COVID-19 is not an Independent Cause of Death](https://doi.org/10.1215/00703370-10575276)
+
+### Citation
+
+Marcia C Castro, Susie Gurzenda, Cassio M Turra, Sun Kim, Theresa Andrasfay, Noreen Goldman. COVID-19 is not an Independent Cause of Death. *Demography* 2023; 10575276. doi: [https://doi.org/10.1215/00703370-10575276](https://doi.org/10.1215/00703370-10575276)
+
+
+## Abstract
+
+The COVID-19 pandemic has had overwhelming global impacts with deleterious social, economic, and health consequences. To assess the COVID-19 death toll, researchers have estimated declines in 2020 life expectancy at birth (*e0*). When data are available only for COVID-19 deaths, but not for deaths from other causes, the risks of dying from COVID-19 are typically assumed to be independent of those from other causes. In this research note, we explore the soundness of this assumption using data from the United States and Brazil, the countries with the largest number of reported COVID-19 deaths. We use three methods: one estimates the difference between 2019 and 2020 life tables and therefore does not require the assumption of independence, and the other two assume independence to simulate scenarios in which COVID-19 mortality is added to 2019 death rates or is eliminated from 2020 rates. Our results reveal that COVID-19 is not independent of other causes of death. The assumption of independence can lead to either an overestimate (Brazil) or an underestimate (United States) of the decline in *e0*, depending on how the number of other reported causes of death changed in 2020.
+
+
+![Figure 1](Figures/Figure1.png "Figure 1")
+
+
+__Fig 1__ Percent change in age-specific death rates in the United States and Brazil, by sex. 
+Panel a: between 2019 and 2020 for all non-COVID-19 causes combined. 
+Panel b: heat map of the percentage change between 2018-2019 and 2019-2020, for major categories of cause of death, ages 45+.
+
+
+## Organization
+For additional information see the `README.md` files in each folder: 
+- `data` — Excel files for calculations for change in life expectancy associated with COVID-19, including data used as inputs for the life expectancy calculations  
+- `figures` - All figure and Appendix figure from the publication
+
+## Correspondence
+For any issues with anonymization or major issues with the functionality of the script please [create an issue](https://github.com/mcastrolab/Covid-19_competing_risk/issues).
+
+### License
+The data collected and presented is licensed under the [Creative Commons Attribution 4.0 license](https://creativecommons.org/licenses/by/4.0/), and the underlying code used to format, analyze and display that content is licensed under the [MIT license](http://opensource.org/licenses/mit-license.php). 
+
+
+
+# Authors
+
+
+- __Marcia C Castro__: Department of Global Health and Population, Harvard TH Chan School of Public Health | ![Twitter](http://i.imgur.com/wWzX9uB.png): [\@marciacastrorj](https://twitter.com/marciacastrorj)
+- __Susie Gurzenda__: The Cecil G. Sheps Center for Health Services Research, The University of North Carolina at Chapel Hill | ![Twitter](http://i.imgur.com/wWzX9uB.png): [\@susiegurzenda](https://twitter.com/susiegurzenda)
+- __Cassio M Turra__: Demography Department, Cedeplar, Universidade Federal de Minas Gerais | ![Twitter](http://i.imgur.com/wWzX9uB.png): [\@CassioMTurra](https://twitter.com/CassioMTurra)
+- __Sun Kim__: Department of Global Health and Population, Harvard TH Chan School of Public Health | ![Twitter](http://i.imgur.com/wWzX9uB.png): [\@SunKim0710](https://twitter.com/SunKim0710) 
+- __Theresa Andrasfay__: Leonard Davis School of Gerontology, University of Southern California
+- __Noreen Goldman__: Office of Population Research and Princeton School of Public and International Affairs, Princeton University