## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", fig.width = 7, fig.height = 4.5)

## -----------------------------------------------------------------------------
library(gp3bayes)
sim <- simulate_advanced_pupil_timecourse(
  n_participants = 10,
  trials_per_participant = 4,
  time_points = 31,
  missing_fraction = 0.08,
  measurement_error_sd = 0.02,
  seed = 3030
)

## -----------------------------------------------------------------------------
measurement <- create_pupil_measurement_model(
  baseline_error = "baseline_se",
  luminance_error = "luminance_se",
  response_error = "pupil_se"
)

missingness <- create_pupil_missingness_spec(
  response = "model",
  predictors = character(),
  assumptions = "MAR"
)

spec <- specify_advanced_pupil_timecourse_model(
  sim$data,
  temporal_structure = "smooth",
  family = "gaussian",
  autocorrelation = "none",
  covariates = c("baseline_pupil", "luminance"),
  measurement_model = measurement,
  missingness_model = missingness
)

## -----------------------------------------------------------------------------
measurement_audit <- audit_pupil_measurement_model(spec)
measurement_audit
plot_pupil_measurement_uncertainty(measurement_audit)

missing_audit <- audit_pupil_missingness(spec)
missing_audit
plot_pupil_missingness(missing_audit)

## ----eval=FALSE---------------------------------------------------------------
# translated <- translate_advanced_pupil_model_to_brms(spec)
# translated
# fit <- fit_advanced_pupil_model_backend(spec, backend = "cmdstanr")