simulatetsir {tsiR}

simulatetsir

Description

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

Usage

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.