epict: Model Cycle Thresholds

In seabbs/epict: Flexible Cycle Threshold Modelling

Model Cycle Thresholds

Description

Provides a user friendly interface around package functionality to model cycle thresholds, and symptom onsets from observed preprocessed data, a piecewise linear model, and a linear adjustment model.

Usage

epict(
  obs,
  model = epict_model(),
  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(),
  convert_to_list = epict_convert_to_list,
  inits = epict_inits,
  ...
)

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.
model	A compiled cmdstanr model object. By default this uses epict_model().
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.
convert_to_list	Convert observations and model settings into a list for use in stan. Defaults to using epict_convert_to_list().
inits	A function that combined with a list of data returns sample initial conditions for use during model fitting based on model priors. Defaults to epict_inits()
...	Additional arguments passed to cmdstanr.

Value

A cmdstanr model fit containing posterior samples

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