Analysis of the effect of punctuated vs continual evolution on projections

[saraloo]

Project aims are to compare the effect of punctuated variant emergence vs our continuous immune ladder evolution structure on projections.

Overall plan

• Refit Round 17 phases with all the fixed boundary issues etc that were possibly there during when we ran it
• Run variant structure for calibration period and projection period
• Run variant structure until after omicron, then run immune ladder structure

Generate configs

Note: some changes from Round 17 runs - phase 2 continuation resume from phase 1 so we can use the good fit of phase 1, rather than refit (gets worse)

• [x] Phase 1: wild type only, no vaccination 2020
• [x] Phase 2: from mid 2020 to Omicron 2022-03-27 (Wild, alpha, delta, omicron), with all vaccination.
• [ ] Phase 3-variant: from the end of Omicron to 2022-03-27 to Round 17 end 2023 April.
• [x] Phase 3-immune ladder: config built already, as in Round 17
• [ ] Phase 4-variant: add seeding of new variants ~6 month cadence
• [x] Phase 4-immune ladder: config built already, as in Round 17

Work is in: https://github.com/HopkinsIDD/COVID19_USA/tree/evol-projection

[saraloo]

As of 20/11/2023 configs are all built, just need to think about how to seed new variants when source type (Sunvaccinated*) are 0.