DOI: 10.5281/zenodo.13273108
title: Ecology and environment predict spatially stratified risk of highly pathogenic avian influenza in wild birds across Europe

description: The data in this repository were used to conduct the analysis outlined in the following bioRxiv preprint:



Sarah Hayes, Joe Hilton, Joaquin Mould-Quevedo, Christl Donnelly, Matthew Baylis, Liam Brierley (2024) "Ecology and environment predict spatially stratified risk of highly pathogenic avian influenza in wild birds across Europe." bioRxiv doi:10.1101/2024.07.17.603912


The codes used for the analyses are available at https://github.com/sarahhayes/avian_flu_sdm/ 

The following lookup table can be used to cross-reference between the variable descriptions in Tables 1 and 2 of the preprint and the files in this repository:

 






 Variable description 



 Filename 



 Minimum elevation (metres above sea level)  
 elevation_min_10kres.tif 


 Maximum elevation (metres above sea level)  
 elevation_max_10kres.tif 


 Difference between minimum and maximum elevation   
 elevation_diff_10kres.tif 


 Modal elevation (metres above sea level)  
 elevation_mode_10kres.tif 


 Normalised Difference Vegetation Index (NDVI)  
 ndvi_*_quart_2022_10kres.tif 


 Land cover 
 landcover_output_full_2022_10kres.tif 


 Distance to coast 
 dist_to_coast_10kres.csv 


 Distance to inland water 
 dist_to_water_output_10kres.csv 


 Relative humidity 
 mean_relative_humidity_q*_10kres.tif 


 Mean of the difference in the minimum monthly temperature and maximum monthly temperature for each month within the quarter (degrees centigrade)    
 mean_diff_*_quart_10kres.tif  


 Quarterly mean of monthly mean temperatures (degrees centigrade)  (Mean monthly temperature for each month calculated using: Mean temperature = Minimum temperature + diurnal range/2)   
 mean_temp_q*_10kres.tif  


 Quarterly temperature variation (degrees centigrade)  (Difference between the maximum of the 3 monthly maximum temperatures within the quarter and the minimum of the 3 minimum monthly temperatures within the quarter)   
 variation_in_quarterly_mean_temp_q*_10kres.tif 


 Precipitation  
 mean_prec_*_quart_10kres.tif  


 Quarterly mean of the mean monthly zero-degree isotherm (metres)  
 isotherm_mean_q*.tif 


 Number of days the zerodegree isotherm was below 1 metre at midday at Coordinated Universal Time (UTC)  
 isotherm_midday_days_below1_q*.tif 


 Chicken density 
 chicken_density_2010_10kres.tif 


 Duck density 
 duck_density_2010_10kres.tif 


 Anatinae (dabbling ducks) 
 anatinae_rast.tif 


 Anserinae (swans and geese) 
 anserinae_rast.tif 


 Ardeidae (herons)  
 ardeidae_rast.tif 


 Arenaria/Calidris (turnstones and sandpipers) 
 arenaria_calidris_rast.tif 


 Aythyini (diving ducks)
 or pochards)  


 Laridae (gulls) 
 laridae_rast.tif 


 Percentage time spent feeding within 2m of water surface 
 around_surf_rast.tif 


 Percentage time spent feeding >2m below water surface 
 below_surf_rast.tif 


 Percentage diet plants 
 plant_rast.tif 


 Percentage diet scavenging 
 scav_rast.tif 


 Percentage diet endothermic vertebrates 
 vend_rast.tif 


 Congregative 
 cong_rast.tif 


 Migratory 
 migr_rast.tif 


 Below threshold phylogenetic distance to known host species  
 host_dist_rast.tif 


 Species richness 
  species_richness_rast.tif