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A SEIR Model For The COVID-19 Epidemic

This document outlines a simulation project for a COVID-19 SEIR model. Students are asked to: 1) Develop a SEIR model based on two referenced works, reducing the governing equations from one to match the other. 2) Create their own model implementation including predictions for deaths. 3) Validate their model by reproducing figures from the references. 4) Fit early case data from a country/state to identify the reproduction number, R0. 5) Simulate two scenarios - one with strict measures reducing R0 by half, and one with no measures. The report must be at least 7 pages discussing the problem, methods, results and figures. Code and parameters are

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Zain Ul Abidin
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22 views

A SEIR Model For The COVID-19 Epidemic

This document outlines a simulation project for a COVID-19 SEIR model. Students are asked to: 1) Develop a SEIR model based on two referenced works, reducing the governing equations from one to match the other. 2) Create their own model implementation including predictions for deaths. 3) Validate their model by reproducing figures from the references. 4) Fit early case data from a country/state to identify the reproduction number, R0. 5) Simulate two scenarios - one with strict measures reducing R0 by half, and one with no measures. The report must be at least 7 pages discussing the problem, methods, results and figures. Code and parameters are

Uploaded by

Zain Ul Abidin
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as DOC, PDF, TXT or read online on Scribd
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BME 2740 Spring 2021

BME Simulaiton Project


A SEIR model for the COVID-19 epidemic

Due on April 16th

Develop a SEIR (Susceptible-Exposed-Infectious-Removed) epidemiology model for COVID-19. Base


your model on the following works:
1) Carcione et al. A Simulation of a COVID-19 Epidemic Based on a Deterministic SEIR Model, Front.
Public Health (28), 2020. [https://doi.org/10.3389/fpubh.2020.00230)].
2) The online epidemic calculator by Gabriel Goh: https://gabgoh.github.io/COVID/index.html

Your report must be at least 7 complete double spaced pages, not including figures and tables.
Therefore, there must be at least 7 pages of text. Use ¾ -inch margin at top, bottom, right and left. In
the Introduction section briefly define the overall problem being examined. In the Methods section
define the system and model assumptions, equations, parameters, and numerical methods employed for
the solution. In the Results section describe what changes are being made to the model, what results are
expected, and how the results might accurately reflect (or not) the real systems. Don’t simply state what
is in the figures but interpret and explain the results. Refer to each figure in the result section so that it is
clear that you understand what the output is and how it reflects that changes in the model. In the result
section print your output (plots) label all figures with figure #s and legends and refer to each figure in
you result section of your report (i.e. Fig. #). Put your response and output for each question asked in a
separate subsection of the results section numbered and with a short descriptive title. Give a print out of
your code and/or set of parameter values in the Appendix.
You will be graded on originality in results and implementation, on your description of the
simulations, writing style and presentation, the critical review of the results and the amount of effort
made on the assignment. Assign specific targets to each group member. Each member of the group
should be ready to give a 5 min power point presentation of the Methods and Results the last day of
classes. If there is evidence that groups worked together they will not receive credit for the assignment.

Mandatory Tasks:
1) Show how the governing equations (1) in Carcione et al. can be reduced to the Transmission
Dynamics component of the Goh calculator. State the assumptions needed and the relationship between
parameters in the two models.
2) Use similar assumptions as Goh to create your own model implementation and include also prediction
for deaths (SEIDR model). [For example by adding Equation 3 from Carcione et al.]
3) Reproduce Fig. 2 in Carcione et al. and the default simulation in Goh’s calculator to validate your
model.
4) Find and Download stats for confirmed cases in the early days of the pandemic for a country or state
of your choice. Use data for 60 days after confirmed cases exceeded 50 and fit them with your model to
identify the Reproduction Number, R0, in your region of interest. Use values for the rest of the
parameters from the two cited studies or any other published study of your choice.
5) Simulate two extreme alternative scenarios of how the disease could have progressed over the next
three months (after the 60 days). In scenario A, assume that strict lockdowns and mask mandates
reduced the Reproduction Number, to half the original value (Rt=R0/2). In scenario B, assume that no
measures are taken and the disease progressed with the same Reproduction Number (Rt=R0).
This is an open ended project. Think of additional simulations of interest that can be performed.
Alternative ways to program and present the model (MATLAB livescript, web app). Literature studies
that provide parameters and their dependence with time or human activity and government policies.

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