nllik_seas: Evaluate the approximate negative log-likelihood of a...

In jbracher/hhh4underreporting: Fitting endemic-epidemic models to underreported data

Description

The likelihood approximation is based on an approximation of the process by a second-order equivalent process with complete reporting.

Usage

nllik_seas(
  observed,
  alpha_nu,
  gamma_nu,
  delta_nu,
  alpha_phi,
  gamma_phi = 0,
  delta_phi = 0,
  alpha_kappa,
  psi,
  q,
  L,
  max_lag = 5,
  return_contributions = FALSE
)

Arguments

observed	a time series of counts (numeric vector)
alpha_nu, gamma_nu, delta_nu	the endemic model parameters (scalar)
alpha_phi, gamma_phi, delta_phi, alpha_kappa	the autoregressive model parameters (scalars)
psi	overdispersion parameter (scalar)
q	the assumed reporting probability
L	the period length (integer; e.g. 52 for weekly data and yearly seasonality)
max_lag	in evaluation of likelihood only lags up to max_lag are taken into account
return_contributions	shall the log-likelihood contributions of each time point be returned (as vector)?

Value

The negative log-likelihood as scalar or (if return_contributions == TRUE) the vector of negative log-likelihood contributions.

jbracher/hhh4underreporting documentation built on July 21, 2020, 2:08 p.m.