Code and data to accompany the article "Assessing the risk of diseases with epidemic and pandemic potential in a changing world"
Angela Fanelli (ORCID)
Alessandro Cescatti
Juan Carlos Ciscar
Gregoire Dubois
Dolores Ibarreta
Rachel Lowe (ORCID)
Nicola Riccetti (ORCID)
Marine Robuchon (ORCID)
Ilaria Capua (ORCID)
Wojtek Szewczyk
Emanuele Massaro (ORCID)
Cite as: Angela Fanelli et al. ,Assessing the risk of diseases with epidemic and pandemic potential in a changing world.Sci. Adv.11,eadw6363(2025).DOI:10.1126/sciadv.adw6363
Contact information: Angela.FANELLI@ec.europa.eu
This repository contains the data and code used to assess the risk of diseases with epidemic and pandemic potential, as described in the article Assessing the risk of diseases with epidemic and pandemic potential in a changing world.
The repository is divided as follows:
- Input
- Scripts
It assumes that the results will be saved in a folder called Output and relative subfolders.
The Scripts folder contains all R scripts, while the Input folder holds the data files sourced by these scripts. Please note that the scripts are applied to a simulated dataset, and the results will differ from those presented in the manuscript.
Important notes:
- Data availability: The outbreak data used in this analysis is the sole and exclusive property of GIDEON and is protected by copyright and other intellectual property laws. As such, we are not permitted to share the full dataset.
- Sample dataset: As agreed with GIDEON, in EXTRA_GIDEON.Rmd we show a sample dataset containing 10 records for illustrative purposes only.
- GIDEON Services: For more information about GIDEON and their services, please visit their website. You can also contact them directly to learn more about their datasets and services.
A detailed description is provided below.
Contains data used as input for the project.
Covariates and raster template for predictions.
aridityIndex.tif: Aridity index raster.covariates_30km_gridded.csv: Covariates data at 30km grid resolution.
Outbreak data and subsets.
GIDEONSample.csv: Sample outbreak data from GIDEON.Subsets: Directory for storing subsets of outbreak data.
Data related to zoonotic events and human-animal health interface.
IHRC3.dbf,IHRC3.prj,IHRC3.shp,IHRC3.shx: Shapefile components for IHR C3 data.IHR_C3_summary.csv: Summary of IHR C3 data.IHR_C3.xlsx: IHR C3 data downloaded from the Global Health Observatory.
Shapefile and ISO codes for world countries and regions.
ISO-3166-Countries-with-Regional-Codes.csv: ISO codes for countries and regions.World_union.dbf,World_union.prj,World_union.shp,World_union.shx: Shapefile components for world countries.
Contains R scripts for running the project.
00_Run_all.R: Script to run all other scripts in sequence.01_Load_packages.R: Script to load required R packages.02_Functions.R: Script containing custom functions.03_SimulateOutbreaks.R: Script to simulate outbreaks.04_Subsets_Outbreaks.R: Script to create subsets of outbreak data.05_Models.R: Script to run models.06_Models_correction.R: Script to correct models.07_Predictions.R: Script to make predictions.08_MarginalEffects.R: Script to calculate marginal effects.09_VisResults.R: Script to visualise the results.Extra_GIDEON.Rmd: Additional Rmd file to show GIDEON data.
Session info
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setting value
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