Model_Run2 — Model

Run SEIRV model for multiple regions as one odin2 run

Usage

Model_Run2(
  FOI_spillover = 0,
  R0 = 1,
  vacc_data = list(),
  pop_data = list(),
  years_data = c(1940:1941),
  year0 = 1940,
  vaccine_efficacy = 1,
  time_inc = 1,
  output_type = "full",
  mode_start = 0,
  start_SEIRV = list(),
  mode_time = 0,
  n_particles = 1,
  n_threads = 1,
  deterministic = FALSE,
  seed = NULL
)

Arguments

FOI_spillover: Matrix of values of force of infection due to spillover from sylvatic reservoir (size depends on mode_time)
R0: Matrix 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 region. age group and year
pop_data: Population by region, 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)
output_type: Type of data to output:
"full" = SEIRVC + FOI for all steps and ages
"infs" = annual total new infections (C) summed across all ages
"sero" = TBA
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) (TBD)
start_SEIRV: SEIRV data from end of a previous run to use as input (if mode_start = 2)
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/time_inc)
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/time_inc)*number of years to consider)
n_particles: number of particles to use
n_threads: number of threads to use
deterministic: TRUE/FALSE - set model to run in deterministic mode if TRUE
seed: Random seed (set to NULL if not to be used) '

Details

TBA