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For code specific questions reach out to:

Ariel Shurygin (uva5) or Ben Kok Toh (tjk3) or Michael Batista(upi8)

For implementation questions reach out to Tom Hladish (utx5)

Table of Contents:

​​Anticipated Applications

High Level Summary

Model Structure, Moving Parts, and Customizable Elements

• Model Structure
• Compartments
• Immunity
• Compartment Strata
• Limitations: The Not-So-Easily Changed Bits
  • Compartments: SEIP*C
  • Dimensionality: Age, Immune History, Vaccination, Waning, and Infected by

Vaccination

Waning

Introduction of New Strains and External Populations

Modifying Beta

Contact Matrices

Model Epochs and Strain Combination

Inference and MCMC

Plotting Capabilities

Configuration Scripts and Scenario/Epoch specific Configs

Appendix

• Appendix A: Data Sources
• Appendix B: Basic Examples
• Appendix C: Model Priors
• Appendix D: Example Figures ​