HybridModelCOVID-19

MATLAB code contents

1. Italy parameter estimation ###

   Italy Days 1-22
    Used to generate parameter fitting results for Italy from Days 1-22 (February 20, 2020 - March 12, 2020)
  

2. BC parameter estimation ###

   BC Phase I
   Used to generate parameter fitting results for BC from Days 1-60 (January 30, 2020 - March 31, 2020)
  
   BC Phase II
   Used to generate parameter fitting results for BC from Days 60-109 (March 31, 2020 - May 19, 2020)
  

3. Hybrid stochastic model ###

   Hybrid Model
   The hybrid model calls both the NHP and SDE. Ensure all files in the folder are downloaded
   
   

How to run MultiStart

The main file name is COVIDMultiStart.m, which calls COVIDmodel.m. Fixed and fitted parameter values are specific to the version of the code included in each section. The fixed parameters are listed in COVID_model.m.
  

Inputs

    COVID_MultiStart(NoStartPoints, Tstart, Tend, place, testnumber)
    - NoStartPoints: The number of starting points you want MultiStart to use, the more you use the longer the code will take to run - Tstart: Day of data you want to start fitting the model to - Tend: Day of data you want to end fitting the model to - Place: Location you are fitting for ('BC' for British Columbia or 'IT' for Italy) - Testnumber: Test number recorded on all outputs to help you keep track of then number of runs
   
    Note: Ensure the corresponding excel data file is in the same folder as both COVIDMultiStart.m and COVIDmodel.m.
   

Outputs

• COVIDParameters: a matrix of all the possible local minimum parameter values, size will relate to the NoStartPoints
• fvalues: all the objective functional minimum values that correspond to the COVIDParameters
• ExitFlags: these values give insight into the convergence of fmincon. We want a 1, and will accept a 2. You will get one for each COVIDParameter and fvalues combo.
• Endpoints: The state variables values at Tend

    When you run the code, it will also save some files in the same folder labelled with the place and the testnumber: - An excel file with the COVIDParameters, values, and ExitFlags - An excel file with the endpoints - A figure file of the output trendline plotted on top of data - A figure of the ODE solution, outlining the number of individuals in S, E, A, I, R, respectively

    The command window will print out: - Case Minimization Value - Death Minimization Value - Total Minimization Value - R0
   
   

How to run hybrid stochastic model

The parameter values for the hybrid model are derived from parameter estimation. Change the values for r and CV to see the change in transmission dynamics associated with environmental variation. Update nsim to change the number of simulations you plan to run.