A polynomial regression model for excess mortality in Mexico 2020-2022 due to the COVID-19 pandemic

Authors: Andreu Comas-García & Arturo Erdely

Preprint: arXiv

Instructions for reproducibility

Download and install the Julia programming language.
Download and unzip the data from the following Google Drive link in a working directory of your election.
Open the Julia terminal and change to the working directory where you unzipped the files. You may do this by defining a string variable path with the path to the files directory and then execute in the terminal cd(path). For example, in the operating system Windows it may look something like:
```
path = "D:/MyFiles/rawdata2022mx"
cd(path)
readdir()
```
Download the code files clicking in the green button <> Code of this GitHub repository and DownloadZIP. Unzip the downloaded file and move the following files into the same working directory as the downloaded data in the previous step: 0auxfunctions.jl, 1packages.jl, 2deaths.jl, 3population.jl, 4figures.jl, 5tables.jl, and 6other.jl
Install the required packages by executing the following command in the Julia terminal. This may take a while:
```
include("1packages.jl")
```
Process deaths data. This will take several hours (4 approx) and will generate several new .csv data files:
```
include("2deaths.jl")
```
Process population data. This is quite fast and will generate several new .csv data files:
```
include("3population.jl")
```
Create 4 figures as .png image files:
```
include("4figures.jl")
```
- Figure1.png: % of non-illnes deaths & observed illness-related deaths 1998-2019
- Figure2.png: illness-related excess mortality 2020 | 2021 | 2022
- Figure3.png: % illness-related excess of mortality 2020-2022 males vs females
- Figure4.png: illness-related excess mortality 2020-2022 by sex and age groups
Create 6 tables in .csv file format:
```
include("5tables.jl")
```
- Table1.csv: Excess mortality in Mexico 2020
- Table2.csv: Excess mortality in Mexico 2021
- Table3.csv: Excess mortality in Mexico 2022
- Table4.csv: Excess mortality in Mexico 2020-2022
- Table5.csv: Excess mortality in Mexico 2020-2022 (males)
- Table6.csv: Excess mortality in Mexico 2020-2022 (females)
Generate supplementary figures and calculations:
```
include("6other.jl")
```
- FigureExtra1.png: illness-related deaths evolution of fitted parameters
- FigureExtra2.png: adjusted R-squared and Anderson-Darling test for normality of residuals
- FigureExtra3.png: some examples of the fitted model

aerdely/excessmortmx

A polynomial regression model for excess mortality in Mexico 2020-2022 due to the COVID-19 pandemic

Instructions for reproducibility