simulatetsir function

simulatetsir

This function just simulates the forward prediction given the data and a parms list generated from estpars or mcmcestpars.

simulatetsir(
  data,
  nsim = 100,
  IP = 2,
  parms,
  method = "deterministic",
  epidemics = "cont",
  pred = "forward",
  threshold = 1,
  inits.fit = FALSE,
  add.noise.sd = 0,
  mul.noise.sd = 0
)

Arguments

• data: The data frame containing cases and interpolated births and populations.
• nsim: The number of simulations to do. Defaults to 100.
• IP: The infectious period. Defaults to 2.
• parms: Either the parameters estimated by estpars or mcmcestpars, or a list containing beta, rho, Z, sbar, alpha, X, Y, Yhat, contact, alphalow, alphahigh, loglik, pop vectors.
• method: The type of next step prediction used. Options are 'negbin' for negative binomial, 'pois' for poisson distribution, and 'deterministic'. Defaults to 'deterministic'.
• epidemics: The type of data splitting. Options are 'cont' which doesn't split the data up at all, and 'break' which breaks the epidemics up if there are a lot of zeros. Defaults to 'cont'.
• pred: The type of prediction used. Options are 'forward' and 'step-ahead'. Defaults to 'forward'.
• threshold: The cut off for a new epidemic if epidemics = 'break'. Defaults to 1.
• inits.fit: Whether or not to fit initial conditions using simple least squares as well. Defaults to FALSE. This parameter is more necessary in more chaotic locations.
• add.noise.sd: The sd for additive noise, defaults to zero.
• mul.noise.sd: The sd for multiplicative noise, defaults to zero.