Format formula data for use with stan

Format formula data for use with stan

Usage

epict_model_opts(
  onsets = TRUE,
  switch = FALSE,
  latent_infections = TRUE,
  variation = "correlated"
)

Arguments

onsets

Logical, defaults to TRUE. Should symptom onsets observations be included in the model if available.

switch

Logical, default to FALSE. Should a secondary breakpoint be included in the piecewise linear Cycle threshold model.

latent_infections

Logical, defaults to TRUE. Should latent time of infection be modelled and used to adjust time from first positive test.

variation

A character string indicating the type of individual level variation to include. Defaults to "correlated" (a random effect with modelled correlation structure). Other options include "uncorrelated" ( a random effect with no modelled correlation structure), and "none" (for no individual level variation).

Value

A list as required by stan.

See also

Functions used to design and setup models adjustment_formula(), epict_formula_as_list(), epict_individual_priors_as_list(), epict_inference_opts(), epict_obs_as_list(), epict_onset_obs_as_list(), epict_population_priors_as_list(), epict_posterior_as_prior(), piecewise_formula(), select_piecewise_parameters()

Author

Sam Abbott

Examples

# Default options
epict_model_opts()
#> $switch
#> [1] 0
#> 
#> $onsets
#> [1] 1
#> 
#> $latent_inf
#> [1] 1
#> 
#> $ind_var_m
#> [1] 1
#> 
#> $ind_corr
#> [1] 1
#> 
#> $K
#> [1] 3
#> 

# No variation and use the piecewise switch
epict_model_opts(switch = TRUE, variation = "none")
#> $switch
#> [1] 1
#> 
#> $onsets
#> [1] 1
#> 
#> $latent_inf
#> [1] 1
#> 
#> $ind_var_m
#> [1] 0
#> 
#> $ind_corr
#> [1] 0
#> 
#> $K
#> [1] 5
#>