multiannual: Multi-annual model of infection and vaccination (version 2)

In kylieainslie/MoreVac: Modelling Repeat Vaccination

Multi-annual model of infection and vaccination (version 2)

Description

This function initializes the population before running the model.

Usage

multiannual(
  n = 30000,
  years = 1918:2028,
  max_age = 80,
  start_vac_year = 2000,
  vac_coverage = 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,
  drift_rate = 1,
  drift_off = FALSE,
  epsilon = 0,
  seed = NULL
)

Arguments

n	number of individuals to be simulated
years	vector of years to run simulation over (YYYY format)
max_age	maximum age of an individual (removed from population after max_age)
start_vac_year	year that vaccination starts (YYYY)
vac_coverage	vaccination coverage
betas	vector of force of infection parameters for every year
vac_protect	protective effect of vaccine
vac_strategy	Integer value indicating frequency of vaccination (1 = annual, 2 = biannual, 3 =triannual,...)
rho	correlation of vaccination
wane	amount of protection of vaccine due to waning (0, 1) (inclusive)
take	percentage of vaccine take (0, 1) (inclusive)
drift_rate	rate of exponential drift: exp(drift_rate) used to calculate amount of drift each year
drift_off	logical. if TRUE there is no antigenic drift
epsilon	exposure penalty. Takes values between 0 and 1.
seed	set random seed

Value

list with two elements: 1) a list of infection histories and attack rates and 2) a plot of annual attack rates by vaccination scenario

kylieainslie/MoreVac documentation built on March 22, 2022, 8:49 a.m.