Format observed symptom onset data for use with stan

The package stan code (accessed using epict_model()) has more extensive documentation.

Usage

epict_onset_obs_as_list(obs, onsets = TRUE)

Arguments

obs

A data.frame with the following variables:

• id: An integer vector uniquely identifying eahc infection.

• test_id: An integer vector uniquely identiying each test

• ct_value: Numeric cycle threshold value.

• t: Relative (to a baseline) time of the test yielding a Ct value.

• t_rel_uncensored: Time of test relative to the first uncensored Ct value for that id.

• onset_t: Relative (to a baseline) time of onset for each infection

• onset_t_rel_uncensored: Time of onset relative to the first uncensored Ct value for that id. (optional). NA if unavailable/asymptomatic.

• censored: Logical, indicating if the Ct has been censored.

onsets

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

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_model_opts(), epict_obs_as_list(), epict_population_priors_as_list(), epict_posterior_as_prior(), piecewise_formula(), select_piecewise_parameters()

Author

Sam Abbott