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A multi-country analysis of differential mortality risks of PM2.5 components

DOI

R code and results attached to the publication:

Masselot P, Sera F, Schneider R, ..., Gasparrini A. Differential mortality risks associated to PM2.5 components: a multi-country multi-city study. Epidemiology. 2022;33(2):167-175 (https://doi.org/10.1097/ede.0000000000001455)

Data and Results

Data are not available currently due to restricted data sharing agreement between the collaborators of this study. Therefore, the code is not fully reproducible.

Data are normally included in a subfolder Data. It should contain:

  • Mortality and pollution data, stored in a list of city-specific data.frames. Also contains a descriptive data.frame with one line for each city.
  • PM2.5 components, stored in one csv files per year of data. Each csv file contains one line per city.
  • City-specific characteristics, stored as a data.frame with one line per city.

R code

The R code to reproduce the analysis is available. Scripts are meant to be executed in order:

  • 0_PrepData.R Loads and and links mortality, PM2.5, composition and city-specific characteristics. Performs city selection.
  • 1a_DataSummary.R Creates Table 1 providing descriptive statistics.
  • 1b_CompositionSummary.R Provides descriptive statistics of PM2.5 compositions. Produces Figure 2.
  • 2_FirstStage.R Runs the first-stage model on each selected city to produce city-level relative risks.
  • 3_SecondStage_MetaRegComposition.R Pools first-stage results in a meta analysis including city-specific compositions and socio-economic indicators. Produces Figures 1 and 3 as well as several eFigures.
  • 4_SupplementaryResults.R Produces several supplementary results and eFigures, including the PCA summary and residuals analysis.

Results

Figures and Tables generated for the publication (including supplemental ones) are available in the Results folder of this repository.

Acknowledgements

This work was supported by the Medical Research Council of UK (Grant ID: MR/M022625/1), the Natural Environment Research Council of UK (Grant ID: NE/R009384/1), and the European Union’s Horizon 2020 Project Exhaustion (Grant ID: 820655).