run_sim_2: Run simulations of multiannual() model of infection and...

In kylieainslie/MoreVac: Modelling Repeat Vaccination

Run simulations of multiannual() model of infection and vaccination

Description

Run simulations of multiannual() model of infection and vaccination

Usage

run_sim_2(
  sim = 100,
  n = 10000,
  years = 1820:2019,
  max_age = 80,
  start_vac_year = 2000,
  vac_cov = c(rep(0.5, 80)),
  betas = c(0.4, rep(0.2, 199)),
  vac_protect = 0.7,
  vac_strategy = 1,
  rho = 0.9,
  wane = 0,
  take = 1,
  epsilon = 0.03,
  drift_off = FALSE,
  file.out = FALSE,
  tag = "",
  trim_age_mat = NULL,
  length_study = 19,
  seed = NULL
)

Arguments

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

Value

list of infection histories, vaccination histories, and age matrices for each simulation

kylieainslie/MoreVac documentation built on Oct. 9, 2024, 1:53 p.m.