Format observations and model settings for use with stan

Format observations and model settings for use with stan

Usage

epict_convert_to_list(
  obs,
  piecewise_formula = epict::piecewise_formula(~1, obs),
  adjustment_formula = epict::adjustment_formula(~1, obs),
  priors = epict::epict_priors(),
  model_opts = epict::epict_model_opts(),
  inference_opts = epict::epict_inference_opts()
)

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.

piecewise_formula

A list describing the piecewise linear cycle threshold formula as described by piecewise_formula().

adjustment_formula

A list describing the cycle threshold linear adjustment formula (shift and scale) as described by adjustment_formula().

priors

A data.table of population-level priors as produced by epict_priors().

model_opts

A list of model options. See epict_model_opts() for details

inference_opts

A list of options to use for inference. See epict_inference_opts() for details.

Value

A list as required by stan.

See also

Functions used for modelling epict_inits(), epict_model(), epict_priors()

Author

Sam Abbott