maxthreshold function

maxthreshold

A function used to optimize the threshold parameter to give the best fit to the data. Optimizes the fit based on R squared.

maxthreshold(
  data,
  nsim = 2,
  IP = 2,
  method = "deterministic",
  inits.fit = FALSE,
  parms,
  thresholdmin = 2,
  thresholdmax = 20,
  printon = FALSE
)

Arguments

• data: The time, cases, births, pop data frame.
• nsim: The number of simulations to do.
• IP: The infectious period, which should the time step of the data.
• method: The forward simulation method used, i.e. deterministic, negbin, pois.
• inits.fit: Whether or not to fit initial conditions as well. Defaults to FALSE here. This parameter is more necessary in more chaotic locations.
• parms: The estimated parameters from estpars or mcmcestpars.
• thresholdmin: The minimum number of cases to be considered an outbreak.
• thresholdmax: The max number of cases to be considered an outbreak.
• printon: A T/F statement to print the progress.

Examples

require(kernlab)
Mold <- twentymeas[["Mold"]]
plotdata(Mold)
## Not run:

parms <- estpars(data=Mold,alpha=0.97)
tau <- maxthreshold(data=Mold,parms=parms,
thresholdmin=8,thresholdmax=12,inits.fit=FALSE)
res <- simulatetsir(data=Mold,parms=parms,
epidemics='break',threshold=tau,method='negbin',inits.fit=FALSE)
plotres(res)
## End(Not run)