A multi-country analysis of differential PM2.5-related mortality risks by pollutant mixture complexity
R code and intermediary data performing the analysis from the paper Air pollution mixture complexity and its effect on PM2.5-related mortality: a multi-country time-series study in 264 cities published in Environmental Epidemiology (https://doi.org/10.1097/EE9.0000000000000342).
Due to a restrictive data sharing agreement between MCC members on daily mortality and air pollutants, the original data cannot be shared publicly. We instead share city-level aggregated data as well as the log relative risks of PM2.5-related mortality estimated in the first-stage of the analysis. The city-level data can be found in the data folder, along with a codebook describing all variables.
The file analysis.R is the master file running the full analysis. It calls functions from the R files in the scripts folder.
Due to the restrictions mentioned above, the first-stage of the analysis is not reproducible. Instead, we saved the estimated city-specific log(RR) along with city-specific characteristic and any useful information in the data folder. The second-stage of the analysis is thus reproducible using the saved first-stage results. The script analysis.R automatically skips the first-stage of the analysis and load the saved results in data, unless the use has access to the original data, which would be stored in a original folder.
Note that the script used to perform the first stage is available and can therefore be checked and copied by any interested reader of the study.