Temperature-related mortality exposure-response functions for 854 cities in Europe

This repository contains data to reconstruct the exposure-response functions (ERF) of temperature-related mortality by five 5 age groups in 854 cities in Europe.

These ERFs have been derived in the study by Masselot et al. 2023, Excess mortality attributed to heat and cold: a health impact assessment study in 854 cities in Europe, The Lancet Planetary Health (https://doi.org/10.1016/S2542-5196(23)00023-2). An associated semi-replicable GitHub repository is available at https://github.com/PierreMasselot/Paper--2023--LancetPH--EUcityTRM to reproduce part of the analysis and the full results, as well as to provide technical details on the derivation of these ERFs.

Note: This updated version contains revised data after the correction of an error in the code related to the computation of the age-specific baseline mortality rates. Details about the error can be found in the GitHub repository linked above. This correction only affects the figures of excess mortality (found in the `results.zip` archive) while the ERFs are negligibly affected. The originally published results can be found in V1.0.0 of this repository.

Extraction of the ERFs

The ERFs are provided as coefficients of B-spline functions that can be used to reconstruct the ERFs, along with variance-covariance matrices and quantiles from location-specific temperature distributions. The parametrisation associated with these coefficients is a quadratic B-spline (degree 2), with knots located at the 10th, 75th and 90th percentiles of the temperature distribution. In R, the associated basis can be constructed using the dlnm package, with a temperature series x, as follows:

library(dlnm) 

basis <- onebasis(x, fun = "bs", degree = 2, knots = quantile(x, c(.1, .75, .9)))

The main files associated with ERFs are the following:

coefs.csv: The B-spline coefficients for each age group and city.

vcov.csv: The variance-covariance matrix of the coefficients in each city and age group. It is provided here as the lower triangular part of the matrix with names indicating the position of each value (v[row][column]). In R, assuming x is a row of this file, the matrix can be reconstructed using xpndMat(x) after loading the mixmeta package.

coef_simu.csv: 1000 simulations from the distribution of each city and age-specific coefficients. Useful to derive empirical confidence intervals for derived measures such as excess deaths or attributable fractions.

tmean_distribution.csv: The city-specific temperature percentiles representing the distribution of the data derived from the ERA5-Land dataset.

Health impact assessment results

results.zip: A summary of the results from the health impact assessment reported in the analysis. The dataset includes several impact measures provided in files representing different geographical levels, including city, country and regional level. Different files are also provided for age-group specific or all age results.

Additional data

We provide additional data that are useful to reproduce or extend the analysis. Please note that due to restrictive data-sharing agreements for the mortality series, only a part of the code is reproducible. See the associated GitHub repository for more details.

metadata.csv: City-specific metadata used to create the ERFs and perform the health impact assessment.

additional_data.zip: contains further data used to replicate the second stage of the analysis and the final health impact assessment. It includes the full city-level daily temperature series (era5series.csv), the detail of extracted metadata for available years (metacityyear.csv), a description of the city-level characteristics (metadesc.csv), and the first-stage ERF coefficients for all available city and age-groups (stage1res.csv). Additionally, the file meta-model.RData contains R object defining the second-stage model that can be used to predict new ERFs.