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Specify the cycle threshold adjustment model formula

Source: R/model-tools.R
piecewise_formula.Rd

Specify the cycle threshold adjustment model formula

Usage

piecewise_formula(formula = ~1, obs, beta_default = c(0, 0.1), params = "all")

Arguments

formula

A model formula defaulting to ~1.

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.

beta_default

A vector of length two containing the default mean and standard deviation to use as the prior for all covariate effect sizes.

params

A character string indicating the paramters to adjust in the piecewise model. Defaults to "all". Options are: the time at peak ("t_p"), time at switch ("t_p"), time at clearance ("t_clear"), Cycle threshold (Ct) at peak ("c_p"), Ct at switch ("c_s"), incubation period mean ("inc_mean"), and incubation period standard deviation ("inc_sd").

Value

A named list including the design matrix ("design") and a data.table of priors for covariate effects ("beta").

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_onset_obs_as_list(), epict_population_priors_as_list(), epict_posterior_as_prior(), select_piecewise_parameters()

Author

Sam Abbott