Get Observation Function Based on User Configuration

This helper function allows users to specify key options such as time resolution, age group, inclusion of prevalence, and whether to model SMC as a covariate using beta_1.

Usage

get_observation_function(
  month = TRUE,
  age_for_inf = "u5",
  incidence_df,
  include_prev = TRUE,
  use_SMC_as_covariate = FALSE
)

Arguments

month

Logical. TRUE for monthly data, FALSE for weekly.

age_for_inf

Character. One of: "total", "sep_ages", "u5", "o5", "all_ages".

incidence_df

A data frame of observed incidence and prevalence values.

include_prev

Logical. If TRUE, includes prevalence likelihood.

use_SMC_as_covariate

Logical. If TRUE, uses beta_1 covariate effect on incidence.

Value

A likelihood function that takes (state, observed, pars) as arguments.