epict_convert_to_list: Format observations and model settings for use with stan

In seabbs/epict: Flexible Cycle Threshold Modelling

Format observations and model settings for use with stan

Description

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.

Author(s)

Sam Abbott

See Also

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

seabbs/epict documentation built on July 3, 2023, 6:42 a.m.