Published code to accompany the manuscript "Challenges and lessons learned from preliminary modelling of with-in herd transmission of highly pathogenic avian influenza H5N1 in dairy cattle"
- data-raw subfolder: contains saved case data from USDA H5N1 dashboard
- figures subfolder: contains figures generated in code
- BackgroundFigures_maps.r: generates map figures included in the manuscript
- H5N1_Model: specifies set of ODEs, generates model results, and visualizes model
- Parameterization: Stochastic version of model with parameter estimation
- Sensitivity_analysis: sensitivity analysis exploring affect of proportion of herd susceptible, observed FFI on R0 estimation
Brinkley Bellotti: [email protected]