DOI: 10.5061/dryad.6hdr7sr8x
title: Data from: Utilising citizen science data to rapidly assess changing associations between wild birds and avian influenza outbreaks in poultry

description: High pathogenicity avian influenza virus (HPAIV) is a rapidly evolving
 virus causing significant economic and environmental harm. Wild birds are
 a key reservoir of AIVs and an important source of viral incursions into
 many animal populations, including poultry. However, we lack thorough
 understanding of which species drive incursions and whether this changes
 over time. We explored associations between abundances of 152 avian
 species and cases of HPAI in poultry premises across Great Britain between
 October-2021 and January-2023. Spatial generalised additive models were
 used, with species abundance distributions sourced from eBird.
 Associations were investigated at the species-specific level and across
 species aggregations. During autumn/winter, associations were generally
 strongest with waterbirds such as ducks and geese; however, we also found
 significant associations in groups such as non-native gamebirds, and rapid
 change in species-specific associations over time. Our results demonstrate
 the value of citizen science to rapidly explore which wild species could
 be potential facilitators of disease incursions into well-monitored
 populations, especially in regions where viral surveillance in wild
 species is limited. This can be a critical step towards prioritising
 targeted surveillance that could inform species-specific biosecurity
 measures; particularly for HPAIV, which has undergone sudden shifts in
 host-range and continues to rapidly evolve.
description: # Utilising citizen science data to rapidly assess changing associations
 between wild birds and avian influenza outbreaks in poultry.
 [https://doi.org/10.5061/dryad.6hdr7sr8x](https://doi.org/10.5061/dryad.6hdr7sr8x) ## Description of the data and file structure Manuscript_code.R * Code to run all analyses and production of manuscript figures model_coefs.xlsx * Coefficients from species-specific generalised additive models. * Each tab provides coefficients for a variable within the species-specific models. Tab 1 details the intercept coefficients, tab 2 details the beta coefficients for the species abundance variable, and tab 3 details the beta coefficients for the Total poultry stock variable. * Each tab has the following columns: * Estimate – model beta coefficient. Variables were scaled and cantered prior to model fitting. Prior to centring and scaling, species abundance and total poultry stock were integer counts. * Std..Error – standard error of the beta coefficient. * z.value – z values for the variable. * Pr...z.. – P-value for the variable. * dev.expl – deviance explained for the variable. * Species – the 6 character species code used by eBird for the species modelled. * Coefficient – the name of the coefficient. * common_name – the common name of the species modelled. * Outbreak – the epidemic period analysed by the model. * Grouping_1 – which species grouping the species belongs to, high coarseness. * Grouping_2 – which species grouping the species belongs to, medium coarseness. * Grouping_3 – which species grouping the species belongs to, low coarseness. RAD_correlations.xlsx * Correlation coefficients between species abundance layers. Separate tabs provides coefficients for a distinct epidemic period (1–3). Species codes used are those used by eBird, and corresponding full species name can be found within the ebirdst R package. ### Sharing/Access information Primary data from the Great British Poultry Register and on poultry premise outbreaks cannot be provided due to data sharing constraints as a result of identifiable information and potential for reputational risk. It is not possible to provide processed data used within models as individual farms can remain identifiable. These data can be requested directly from APHA, and require active data sharing agreements to possess. Avian abundance data used in models must be obtained from eBird directly and cannot be hosted by a third-party. Instructions to obtain this data are provided with the manuscript code and are publicly available. Data was derived from the following sources: * eBird * The Great British Poultry Register * Animal and Plant Health Agency * Empress-i ### Code/Software Code compiled April– 2024 on R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing. Platform: x86_64-apple-darwin17.0 (64-bit). Required additional packages within R are given within the code file.