Published August 8, 2024
| Version v1
Dataset
Open
Ecology and environment predict spatially stratified risk of highly pathogenic avian influenza in wild birds across Europe
-
1.
University of Liverpool
-
2.
University of Manchester
-
3.
University of Oxford
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4.
University of Glasgow
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 |
Files
anatinae_rast.tif
Files
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Additional details
Related works
- Is supplement to
- Preprint: 10.1101/2024.07.17.603912 (DOI)
Software
- Repository URL
- https://github.com/sarahhayes/avian_flu_sdm/
- Programming language
- R