run_sim_2 | R Documentation |
Run simulations of multiannual() model of infection and vaccination
run_sim_2( sim = 100, n = 30000, years = 1918:2028, max_age = 80, start_vac_year = 2000, vac_cov = c(rep(0.5, 80)), betas = c(0.4, rep(0.2, 110)), vac_protect = 0.7, vac_strategy = 1, rho = 0.9, wane = 0, take = 1, epsilon = 0.03, drift_off = FALSE, trim_age_mat = NULL, length_study = 19, seed = NULL )
sim |
number of simulations to run |
n |
number of individuals to be simulated |
years |
vector of years in YYYY format |
max_age |
maimum age of an individual before they are removed from the population |
start_vac_year |
year to start vaccinating (YYYY format) |
vac_cov |
vector of vaccination coverages for each age group (should be of length max_age) |
betas |
vector of force of infetion for each year (should be same length as years) |
vac_protect |
vaccine efficacy |
vac_strategy |
integer indicating which vaccination strategy to use (0 = no vaccination, 1 = annual, 2 = biennial) |
rho |
correlation of repeat vaccination in individuals (between 0 and 1 (inclusive)) |
wane |
amount of vaccine waning |
take |
proportion of individuals who receive the vaccine and are protected |
epsilon |
exposure penalty |
drift_off |
logical. if TRUE there will be no antigenic drift |
trim_age_mat |
year before which age matrix is subsetted. If the year 2000 is used, then age matrix will only contain ages for year 2000 and beyond. |
length_study |
length of time to follow cohorts |
seed |
seed for simulations |
list of infection histories, vaccination histories, and age matrices for each simulation
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