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H5N1-Within-DairyFarm

Purpose

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"

Contents

  • 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

Contact

Brinkley Bellotti: bbellott@wakehealth.edu