Data from: Utilising citizen science data to rapidly assess changing associations between wild birds and avian influenza outbreaks in poultry
Data files
Aug 20, 2024 version files 1.08 MB
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model_coefs.xlsx
146.12 KB
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RAD_correlations.xlsx
935.06 KB
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README.md
3.02 KB
Abstract
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.
README: 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
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.