https://github.com/dkobak/excess-mortality
Raw File
Tip revision: f765cf8bb7d3246bed22f85c832a63b0cf58b904 authored by Dmitry Kobak on 06 July 2021, 09:27 UTC
Update README.md
Tip revision: f765cf8
README.md
# Excess mortality during the COVID-19 pandemic

**Preprint:** Karlinsky & Kobak 2021, The World Mortality Dataset: Tracking excess mortality across countries during the COVID-19 pandemic, https://www.medrxiv.org/content/10.1101/2021.01.27.21250604

Analysis code: [`all-countries.ipynb`](https://github.com/dkobak/excess-mortality/blob/main/all-countries.ipynb) (can be [run in Colab](https://colab.research.google.com/github/dkobak/excess-mortality/blob/main/all-countries.ipynb)).

The data are sourced from the [World Mortality Dataset](https://github.com/akarlinsky/world_mortality). Excess mortality is computed relative to the baseline obtained using linear extrapolation of the 2015–19 trend. In each subplot in the figure below, gray lines are 2015–19, black line is baseline for 2020, red line is 2020, blue line is 2021. Countries are sorted by the % increase over the baseline.

Red number: excess mortality starting from the first officially reported Covid-19 death.<br>
Gray number: excess mortality as a % of the annual baseline deaths.<br>
Black number: excess mortality per 100,000 population.<br>
Blue number: ratio to the daily reported Covid-19 deaths over the same period (sourced from WHO).

<p><a href="img/all-countries.png?raw=true"><img src="img/all-countries.png" width="800" title="Excess mortality all over the world"></a>
  
The same data but now represented as the number of deaths per 1000 people per year, and with countries sorted accordingly:
  
<p><a href="img/all-countries-per1000.png?raw=true"><img src="img/all-countries-per1000.png" width="800" title="Excess mortality all over the world, per 1000 population"></a>

Top-10 countries in the World Mortality Dataset according to different metrics (only countries with over 500,000 population are shown): 

<p><a href="img/leaderboard.png?raw=true"><img src="img/leaderboard.png" width="600" title="Top countries by excess mortality"></a>

See full table in CSV: [`excess-mortality.csv`](https://github.com/dkobak/excess-mortality/blob/main/excess-mortality.csv).

Compare with: [FT](https://www.ft.com/content/a2901ce8-5eb7-4633-b89c-cbdf5b386938), [NYT](https://www.nytimes.com/interactive/2020/04/21/world/coronavirus-missing-deaths.html), [The Economist](https://www.economist.com/graphic-detail/coronavirus-excess-deaths-tracker), [WSJ](https://www.wsj.com/articles/the-covid-19-death-toll-is-even-worse-than-it-looks-11610636840). 
  
Tracking of excess mortality and official Covid deaths:
  
<p><a href="img/tracking.png?raw=true"><img src="img/tracking.png" width="800" title="Excess mortality tracking Covid mortality"></a>


### Extrapolation until today
Daily reported Covid-19 mortality and estimated excess mortality across the countries with the most reported Covid-19 deaths. Note that in this figure the excess mortality in all countries is FORECASTED using the undercount coefficient and the LATEST daily reported number of deaths. So this corresponds to the gray markers in the figure above.

<p><a href="img/countries.png?raw=true"><img src="img/countries.png" width="600" title="Across countries"></a>


--------------------------

## Excess mortality in Russia

The code for my February 2021 paper in *Significance* [Excess mortality reveals Covid's true toll in Russia](https://rss.onlinelibrary.wiley.com/doi/10.1111/1740-9713.01486) is available in the `significance2021` folder, together with the frozen data and the final figures.

Figures below are updated every month. The up-to-date data can be found in the `russian-data` folder. Code: [`russia.ipynb`](https://github.com/dkobak/excess-mortality/blob/main/russia.ipynb)

<p><a href="img/allregions.png?raw=true"><img src="img/allregions.png" width="800" title="Excess mortality in Russian regions"></a>
  
<p>Note that around 10 thousand excess deaths in July in the Ural region and West Siberia could have been due to the heat wave.
  
<p>Animation (English):

<p><a href="img/animation-eng.gif?raw=true"><img src="img/animation-eng.gif" width="600" title="Excess mortality in Russia, animation"></a>

<p>Animation (Russian):

<p><a href="img/animation-rus.gif?raw=true"><img src="img/animation-rus.gif" width="600" title="Excess mortality in Russia, animation RUS"></a>
  
<p>Map (English):

<p><a href="img/map-eng.png?raw=true"><img src="img/map-eng.png" width="600" title="Excess mortality in Russian regions"></a>

<p>Map (Russian):

<p><a href="img/map-rus.png?raw=true"><img src="img/map-rus.png" width="600" title="Excess mortality in Russian regions"></a>

<p>Without regions:

<p><a href="img/russia.png?raw=true"><img src="img/russia.png" width="400" title="Excess mortality in Russia"></a>
 
<p>Yearly deaths:

<p><a href="img/yearly.png?raw=true"><img src="img/yearly.png" width="400" title="Yearly deaths in Russia"></a>
<p style="font-size: 80%">Back in 2019 Rosttat made <a href="https://rosstat.gov.ru/folder/12781">forecast for 2020</a> (<a href="https://rosstat.gov.ru/storage/mediabank/progn5.xls">xls</a>): 1.7890 million deaths (1.7413--1.8304). The actual number in 2019 was 1,800,683. The actual number in 2020 was 2,124,479. The excess compared to their forecast is 335 thousand. For reference, my linear forecast is 1.7660.</p>

<p>Detailed statistics in regions with the most excess deaths:

<p><a href="img/regions.png?raw=true"><img src="img/regions.png" width="600" title="Regions"></a>
 

### Some technical figures

<p>Extrapolation of the linear trend:

<p><a href="img/average-monthly.png?raw=true"><img src="img/average-monthly.png" width="400" title="Monthly deviations"></a>

<p>Seasonal variation:

<p><a href="img/monthly-deviations.png?raw=true"><img src="img/monthly-deviations.png" width="400" title="Monthly deviations"></a>

<p>Evolution of the undercount coefficient:

<p><a href="img/undercount.png?raw=true"><img src="img/undercount.png" width="400" title="Excess mortality in Russia"></a>
back to top