In bbolker/McMasterPandemic: Pandemic Model

Goal

Simulate an age-structured version of the MacPan model with vaccination to explore various (age-structured) vaccine roll-out strategies.

What we have

• contact matricies to adjust $\beta_0$ for each pair of age groups

What we need

• to verify scaling/normalization of contact matricies (more testing)
• to be able to specify age-specific parameters for hospitalization, ICU admission, death
• age-specific vaccination

Required updates

Methods

• summary.params_pansim?
• update get_r, get_R0, get_Gbar to perform the relevant calculations for the age-specific model
• make_state
• run_sim_range to actually run the simulation (and nlist?)
• summary.pansim that is age-specific?
• plot.pansim

Other

• Demo param file with age-specific params
• Stochastic simulations

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General to do

• what are the implied parameter units on the entires of the contact matrix?
• read refactor.Rmd
• read Mistry et al to figure out how others are modelling age structure/scaling their matrices
• make param table with units
• add FOI to ageified sim result
• figure out scaling of contact matrix
• try running ageify with non-homogenous parameters across age classes (e.g. delta
• try running ageify with non-homogenous initial state of susceptibles

make sure to run devtools::check() on the package before pushing changes

bbolker/McMasterPandemic documentation built on Aug. 25, 2024, 6:35 p.m.