September problem 3 part 2: 12 month hackathon Scenario 2 Q2a,c (Model extraction and simulation for SV2AIR3 full version)

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12 month hackathon, Scenario 2 ( Model extraction and simulation for SV2AIR3 full version)

Extend the model to incorporate multiple strains and 2 vaccine types, according to publication Fig. 1B and equations #2-12.
a. (TA 1 Model Extraction Workflow) Get the extended model by extracting it directly from the publication, and code at https://github.com/MehrshadSD/SARS-CoV-2-variants-of-concern-in-Ontario.
c. (TA3 Simulation Workflows/ Unit Tests) As in the paper, simulate the spread of Covid-19 in Ontario, over a 2 year period from January 1st, 2020 – December 31st, 2021, incorporating 2 vaccine types (Pfizer and AstraZeneca), and 3 Covid-19 variants/strains (including Wild Type, Alpha, and Delta, ignoring Omicron at the end of 2021). Set parameter values according to publication supplementary material. Use the 2019 population of Ontario, 14.57 million people. For initial conditions, assume the entire population was susceptible at the beginning of the simulation timeframe, except for 15 infected symptomatic individuals.

Reproduce Figs. 3a, b, d, and e.

	Problem 2a	Problem 2b	Problem 2c
Inputs	SV2AIR3 publication + accompanying code	Extracted model from Problem 1	Either model from 2a or 2b Parameters: as described in publication and supplementary material document
Task	Extract full SV2AIR3 model	Extend model to create full SV2AIR3 model	Run simulation for January 1st, 2020 – December 31st
Outputs	Extracted model	Extended model, compare against 2a	Reproduce Figs. 3a, b, d, and e.