EIDC
Konzen, E.; Delahay, R.J.; Hodgson, D.J.; McDonald, R.A.; Brooks Pollock, E.; Spencer, S.; McKinley, T.J.

R code for fitting a transmission model of bovine tuberculosis to a population of wild badgers

https://doi.org/10.5285/fe0f6bd7-ffd2-4e21-8c84-493cf4f3080d Cite this model code
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This resource provides code to fit a transmission model of bovine tuberculosis spread to a population of wild badgers in Woodchester Park in the UK. The code produces Markov chain Monte Carlo samples from a model fitted to individual-level badger data from Woodchester Park. The badger data came from and can be requested from the Animal and Plant Health Agency. Example outputs are provided in the Supporting Information. This code was developed as part of a Natural Environment Research Council funded grant (number NE/V000616/1).
Publication date: 2024-03-25

Format

text

Spatial information

Study area
Spatial representation type

Provenance & quality

The code was developed and tested in R over a two-year project. Careful checks on the fitted model outputs against the observed data were done in order to assess the efficacy of the code and the models developed. These are all shown in the Supporting Information.

Supplemental information

Detecting superspreaders in wildlife reservoirs of disease. Evandro Konzen, Richard J. Delahay, Dave J. Hodgson, Robbie A. McDonald, Ellen Brooks Pollock, Simon E. F. Spencer, Trevelyan J. McKinley bioRxiv 2024.01.26.576600
https://doi.org/10.1101/2024.01.26.576600

Correspondence/contact details

McKinley, T.J.
University of Exeter
 t.mckinley@exeter.ac.uk

Authors

Konzen, E.
University of Warwick
Delahay, R.J.
Animal and Plant Health Agency / University of Exeter
Hodgson, D.J.
University of Exeter
McDonald, R.A.
University of Exeter
Brooks Pollock, E.
University of Bristol
Spencer, S.
University of Warwick
McKinley, T.J.
University of Exeter

Other contacts

Rights holder
University of Exeter
Custodian
NERC EDS Environmental Information Data Centre
 info@eidc.ac.uk
Publisher
NERC EDS Environmental Information Data Centre
 info@eidc.ac.uk

Additional metadata

Topic categories
biota
INSPIRE theme
Environmental Monitoring Facilities
Keywords
Animal behaviour , badgers , Bovine tuberculosis , individual forward filtering backward sampling algorithm , Woodchester Park
Funding
Natural Environment Research Council Award: NE/V000616/1
Last updated
26 March 2024 10:16

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This model code is under embargo and will be made available by 12 February 2026 at the latest   Find out more »

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CITE AS: Konzen, E.; Delahay, R.J.; Hodgson, D.J.; McDonald, R.A.; Brooks Pollock, E.; Spencer, S.; McKinley, T.J. (2024). R code for fitting a transmission model of bovine tuberculosis to a population of wild badgers. NERC EDS Environmental Information Data Centre. https://doi.org/10.5285/fe0f6bd7-ffd2-4e21-8c84-493cf4f3080d