R/optNll.R

In seroincidence: Estimating Infection Rates from Serological Data

.optNll <- function(stratumData, antibodies, params, censorLimits, ivc = FALSE, m, par0, start)
{
  # Any column but "Stratum" incidence can not be calculated if there are zero observations.
  if (nrow(stratumData) == 0) {
    return(NULL)
  }

  # First, check if we find numeric results...
  res <- .nll(stratumData, antibodies, params, censorLimits, ivc, m, par0, start)
  if (is.na(res)) {
    return(NULL)
  }

  # Estimate log.lambda
  fit <- stats::optim(par = start, fn = .nll,
                      stratumData = stratumData, antibodies = antibodies, params = params,
                      censorLimits = censorLimits, ivc = ivc, m = 0, par0 = par0,
                      method = "L-BFGS-B", lower = -13, upper = 0, hessian = TRUE,
                      control = list(fnscale = 1))
  return(fit)
}