next_gen_flu

Reproducible flexible next-generation vaccine flu model. Takes some vaccine programs and epidemic data, and outputs weekly vaccination-status and age-specific influenza infections.

Based on https://github.com/lucy-gf/flu_model_LG

vacc_types.R

Contains functions to define vaccine programs for no vaccinations and 5 NGIVs (can be edited).

• Inputs: coverage level, targeted ages
• Outputs: VE, mean immunity length, coverage across model age groups

functions/demography.R

Calculates weekly age- and vaccination-status specific population over the relevant time period (can remove ageing if needed), for a given country and vaccine program, and contains the function to calculate contact matrices from a given country and age-specific population.

functions/transmission_model.R

Contains the ODE model builder, epidemic simulation function, a function to calculate vaccination status-specific demography.

functions/flu_sim.R

Contains:

• one_flu(), which runs an epidemic,
• many_flu(), which takes a data-table of epidemic data and combines many epidemics,
• dfn_vaccine_calendar(), which converts the vaccine program and epidemic dates into a vaccine calendar
• flu_doses(), which calculates how many vaccines were given (before wastage) in the same epidemics as many_flu()

flu_parallel.R

Sets vaccine programs, then runs many_flu() for some epidemic data, parallelised across each vaccine type.

flu_plots.R

Plots influenza incidence and cumulative infections.