Parameter setup — parameter

Set up parameters to input into model

Usage

parameter_setup(
  FOI_spillover = c(),
  R0 = c(),
  vacc_data = list(),
  pop_data = list(),
  years_data = c(),
  year0 = 1940,
  vaccine_efficacy = 1,
  time_inc = 1,
  mode_start = 0,
  start_SEIRV = list(),
  mode_time = 0
)

Arguments

FOI_spillover: Vector of values of force of infection due to spillover from sylvatic reservoir (size depends on mode_time)
R0: Vector of values of basic reproduction number for urban spread of infection (size depends on mode_time)
vacc_data: Projected vaccination-based immunity (assuming vaccine_efficacy = 1) by age group and year
pop_data: Population by age group and year
years_data: Incremental vector of years denoting years for which to save data
year0: First year in population/vaccination data
vaccine_efficacy: Proportional vaccine efficacy
time_inc: Time increment in days to use in model (should be 1.0, 2.5 or 5.0 days)
mode_start: Flag indicating how to set initial population immunity level in addition to vaccination
If mode_start = 0, only vaccinated individuals
If mode_start = 1, shift some non-vaccinated individuals into recovered to give herd immunity (stratified by age)
If mode_start = 2, use SEIRV input in list from previous run(s)
start_SEIRV: SEIRV data from end of a previous run to use as input
mode_time: Type of time dependence of FOI_spillover and R0 to be used:
If mode_time = 0, no time variation (constant values)
If mode_time = 1, FOI/R0 vary annually without seasonality (number of values = number of years to consider)
If mode_time = 2, FOI/R0 vary with monthly seasonality without inter - annual variation (number of values = 12)
If mode_time = 3, FOI/R0 vary with daily seasonality without inter - annual variation (number of values = 365/dt)
If mode_time = 4, FOI/R0 vary annually with monthly seasonality (number of values = 12*number of years to consider)
If mode_time = 5, FOI/R0 vary annually with daily seasonality (number of values = (365/dt)*number of years to consider) '

Details

Takes in multiple inputs, outputs list for use by odin SEIRV model.