Ecology and environment predict spatially stratified risk of highly pathogenic avian influenza in wild birds across Europe

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

本仓库中的数据用于开展下述bioRxiv预印本中所述的分析：

Sarah Hayes、Joe Hilton、Joaquin Mould-Quevedo、Christl Donnelly、Matthew Baylis、Liam Brierley（2024）《欧洲野生鸟类高致病性禽流感空间分层风险的生态与环境预测因子》，bioRxiv，doi:10.1101/2024.07.17.603912

本分析所用代码已公开于 https://github.com/sarahhayes/avian_flu_sdm/

下述对照表可用于关联该预印本表1、表2中的变量描述与本仓库中的对应文件：

| 变量描述 | 文件名 |
| --- | --- |
| 最小海拔（米，相对于海平面） | elevation_min_10kres.tif |
| 最大海拔（米，相对于海平面） | elevation_max_10kres.tif |
| 最大海拔与最小海拔的差值 | elevation_diff_10kres.tif |
| 众数海拔（米，相对于海平面） | elevation_mode_10kres.tif |
| 归一化差分植被指数（Normalised Difference Vegetation Index，NDVI） | ndvi_*_quart_2022_10kres.tif |
| 土地覆盖 | landcover_output_full_2022_10kres.tif |
| 到海岸的距离 | dist_to_coast_10kres.csv |
| 到内陆水体的距离 | dist_to_water_output_10kres.csv |
| 相对湿度 | mean_relative_humidity_q*_10kres.tif |
| 季度内各月的月最低气温与月最高气温差值的平均值（摄氏度） | mean_diff_*_quart_10kres.tif |
| 季度月均气温平均值（摄氏度）（月均气温计算方式：月均气温 = 最低气温 + 日温差/2） | mean_temp_q*_10kres.tif |
| 季度气温波动值（摄氏度）（季度内3个月月最高气温的最大值与3个月月最低气温的最小值之差） | variation_in_quarterly_mean_temp_q*_10kres.tif |
| 降水量 | mean_prec_*_quart_10kres.tif |
| 季度月均零度等温线平均值（米） | isotherm_mean_q*.tif |
| 协调世界时（UTC）正午时分零度等温线低于1米的天数 | isotherm_midday_days_below1_q*.tif |
| 鸡养殖密度 | chicken_density_2010_10kres.tif |
| 鸭养殖密度 | duck_density_2010_10kres.tif |
| 鸭亚科（Anatinae，钻水鸭） | anatinae_rast.tif |
| 雁亚科（Anserinae，雁与天鹅） | anserinae_rast.tif |
| 鹭科（Ardeidae，鹭类） | ardeidae_rast.tif |
| 滨鹬属/滨鹬类（Arenaria/Calidris，翻石鹬与滨鹬） | arenaria_calidris_rast.tif |
| 潜鸭族（Aythyini，潜鸭或斑背潜鸭） | |
| 鸥科（Laridae，鸥类） | laridae_rast.tif |
| 水面2米范围内觅食时长占比 | around_surf_rast.tif |
| 水面2米以下觅食时长占比 | below_surf_rast.tif |
| 植物性食物占日粮比例 | plant_rast.tif |
| 食腐食物占日粮比例 | scav_rast.tif |
| 内温脊椎动物食物占日粮比例 | vend_rast.tif |
| 集群性 | cong_rast.tif |
| 迁徙性 | migr_rast.tif |
| 与已知宿主物种的系统发育距离低于阈值 | host_dist_rast.tif |
| 物种丰富度 | species_richness_rast.tif