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sir-parameter-estimation-in-matlab-with-fmincon-multistart-parallelization

Base code to do Parameter Estimation for an SIR ODE model in MATLAB using fmincon MultiStart Parallelization

https://github.com/cedholm/sir-parameter-estimation-in-matlab-with-fmincon-multistart-parallelization

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Base code to do Parameter Estimation for an SIR ODE model in MATLAB using fmincon MultiStart Parallelization

Basic Info
  • Host: GitHub
  • Owner: cedholm
  • Language: MATLAB
  • Default Branch: main
  • Size: 354 KB
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Created over 2 years ago · Last pushed about 1 year ago
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Readme Citation

README.md

SIR-Parameter-Estimation-in-MATLAB-with-fmincon-MultiStart-Parallelization

Base code to do Parameter Estimation for a SIR ODE model in MATLAB using fmincon MultiStart Parallelization

SIRMultiStart.m calls SIRModel.m to run parameter estimation analysis for an Ordinary Differential Equation (ODE) model, using fmincon to find a local minimum and MultiStart to do multiple runs of fmincon in the given parameter ranges. The code is currently set up to use parallelization for computation with MultiStart.

You can edit:

NoStartPoints - how many interactions of fmincon will be run in the parameter ranges using MultiStart

LowerBounds/UpperBounds - changes the parameter range, here for just beta

This code outputs for each run: the parameters, minimized difference function value, and the exit flags on convergence. The code also plots the "best fit".

SIR_Model.m is a base ODE model for a Susceptible Infected Recovered (SIR) system.

$$\begin{align} \frac{dS}{dt} &= -\beta S I\ \frac{dI}{dt} &= \beta S I - \gamma I\ \frac{dR}{dt} &= \gamma I\, \end{align}$$

We add an additional state equation to keep track of cumulative infections (CI):

$$\begin{align} \frac{dCI}{dt} &= \beta S I \end{align}$$

The Math185 Class Scripps College Spring 2024 with Christina Edholm.pdf are class slides for Prof. Edholm's Math 185 (Methods in Modern Modeling) course which includes using the code here, class activity, and associated worksheet/homework problems in the To Do.

There is an addtional SIRMultiStartSave.m which mirrors SIR_MultiStart.m, but saves the estmiation outputs in an excel and also the resulting best fit plots. This code also has the output value to minimized now normalized by the data.

Owner

  • Name: Christina Edholm
  • Login: cedholm
  • Kind: user
  • Location: Claremont, CA
  • Company: Scripps College

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Edholm
    given-names: Christina
title: "SIR Parameter Estimation in MATLAB with Fmincon MultiStart Parallelization"
date-released: 2024-2-25
url: "https://github.com/cedholm/SIR-Parameter-Estimation-in-MATLAB-with-fmincon-MultiStart-Parallelization"

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