In this repository can be found all of the work related to the paper:
Satorra, P., Tebé, C. Bayesian spatio-temporal analysis of the COVID-19 pandemic in Catalonia. Sci Rep 14, 4220 (2024). https://doi.org/10.1038/s41598-024-53527-w
- MakingData.R: import and clean the data from the official open data catalogue of the Government of Catalonia (https://analisi.transparenciacatalunya.cat/en/).
- SAE.R: estimation of the models with INLA.
All of the code is done using R software version 4.3.0. Mainly, the R packages dplyr and purrr have been used for data management and R-INLA for estimating the models with INLA.
- Analysis_Spatial_Temporal: contains the description of the variables of the study and presents the results of the spatial and the spatio-temporal models, including also the ABS characteristics in the modely.
- Analysis_Spatial_Temporal_Vaccination: contains the description of the vaccination data and the results of the estimated spatio-temporal model including the vaccination effect.
For each notebook, the R-markdown file with the code for elaborating the notebook is included together with the resulting html notebook in the Reports/ folder.
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dat.Rda: contains the evolution of the observed, expected, rate and standardised incidence ratios (SIR) of cases/hospitalisation/vaccination, for each ABS and week. It also has the information about the ABS characteristics. It is created in SAE.R and it contains all the information needed to run the different spatio-temporal models.
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shapefileT.R: contains the geography of the basic health areas (ABS) of Catalonia
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0_Raw/: this folder contains the external data needed, other than the data that is read through an API from the opendata portal of the Government of Catalonia.
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1_Processed/: this folder contains the processed data from MakingData.R
To have the data that would be inside the 2_Analysed/ folder, SAE.R has to be compiled. We have not uploaded them because of the big size of the files.
In the COVIDCAT_Evo/ folder we can find all of the code for developing the R shiny application (https://brui.shinyapps.io/covidcat_evo/), which visualizes the results of the study.