README.md

In njhenry/covidemr: Tools for Mapping COVID Excess Mortality

Local variation in COVID excess mortality across Italy

This is a project being developed by Nat Henry, [e-mail]

Downloading Data

Mortality data, population data, and census-based covariates were downloaded from IStat, the Italian Statistical Authority.

Mortality

IStat has periodically released detailed tabulations of all-cause mortality by municipality to help explore the effects of COVID on mortality. I accessed the COVID mortality web page on November 4, 2020 and downloaded the "Dataset con i decessi giornalieri" (Dataset with daily deaths) which had last been updated on October 22, 2020. Direct link to the mortality dataset as of November 4, 2020, with full accounting of deaths for all Italian municipalities through August 31: https://www.istat.it/it/files//2020/03/Dataset-decessi-comunali-giornalieri-e-tracciato-record_22ottobre2020.zip

Population

Population data was downloaded from the IStat Data Portal under the header "Population and Households > Population > Resident Population on 1st January > All municipalities". I created a free account for the download and interacted with the Italian-language version of the website. I then used the following settings to download tabulated population data:

• Layout:
• Filters: Demographic variable, sex, year, marriage status
• Vertical dimensions: Territory (country/province/municipality), Age

• Horizontal dimensions: (None)

• Filters: I downloaded separate datasets for each sex (male/female) and each year (2015/2016/2017/2018/2019/2020) available in the COVID excess mortality data.

• Export: I exported to a CSV, using "custom format" export options:

• Included both codes and labels by field
• English language
• Comma separated

Covariates:

IStat Covariates

Covariates were downloaded by province for all available years since 2015: - Total fertility rate (2015-2018), by province - Proportion of targeted families receiving at-home social services (2015-2017), by province - Annual unemployment by sex, ages 15 and above (2015-2019), by province - Proportion of households with taxable income under 10k Euros (2015-2018), by commune (aggregated to province) - Average taxable income across all households (2015-2018), by commune (aggregated to province)

Elevation

I downloaded a digital elevation map at 15 arc-second resolution from the US Geological Survey Earth Explorer portal:

1. Create a free web account with the USGS EROS portal
2. Navigate to the USGS EarthExplorer: https://earthexplorer.usgs.gov/
3. Create a bounding box containing Italy: I used the coordinates bounded by [6.5 deg E, 35 deg N] and [20 deg E, 48 deg N]
4. From the "Data Sets" tab, select the "Digital Elevation > GMTED2010" product. This searches only for the USGS Global Multi-Resolution Terrain Elevation Data 2010 product.
5. Download and unzip TIFF file.

Healthcare access

I downloaded a gridded dataset showing travel time to the nearest health facility by motor vehicle (see Weiss et al 2020) using a direct download from the Malaria Atlas Project Data Explorer.

Weekly temperature

I downloaded point estimates of daily temperature from the three most populous pixels in each province using the Meteostat API. This required signing up for a free API key Because temperature data was not available for all time periods and locations, I used the following process to fill temperatures:

1. Find average weekly temperature across all observed days by year, week, and observed location.
2. Interpolate by week: in cases where 3 weeks or fewer were missing between observed data, interpolate temperature from neighboring weeks in a given observation location.
3. For each province, year, and week, average available observations across the three sampled sites
4. In cases where all observations for a province were missing for a given province-year-week, fill using temperature observations from neighboring provinces with a similar elevation and level of solar exposure.

Shapefile

A commune-level shapefile was downloaded from the IStat website. Direct link to 2020 shapefile as of August 18, 2020: - Most detailed (for analysis): http://www.istat.it/storage/cartografia/confini_amministrativi/non_generalizzati/Limiti01012020.zip - Less detailed (for mapping): http://www.istat.it/storage/cartografia/confini_amministrativi/generalizzati/Limiti01012020_g.zip

License

This repository operates under the GNU General Public License version 3.0. For more details, see the LICENSE file in this repository.

njhenry/covidemr documentation built on Feb. 2, 2022, 2:31 a.m.