## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----eval=FALSE---------------------------------------------------------------
# # function that checks data for internal consistency and returns a preprocessed table
# df <- bistablehistory::preprocess_data(br_single_subject,
#                                        state="State",
#                                        duration="Duration",
#                                        run="Block")
# 
# # data for Stan model
# stan_data <- list(
#   # complete time-series
#   rowsN = nrow(df),
#   duration = df$duration,
#   istate = df$istate,
#   is_used = df$is_used,
#   run_start = df$run_start,
#   session_tmean = df$session_tmean,
# 
#   # only valid clear percepts
#   clearN = sum(df$is_used),
#   clear_duration = df$duration[df$is_used == 1],
# 
#   # history parameters, all fixed to default values
#   history_starting_values = c(0, 0),
#   mixed_state = 0.5
# )

## ----eval=FALSE---------------------------------------------------------------
# # compile the model
# model <- cmdstanr::cmdstan_model("example.stan")
# 
# # sample model
# fit <- model$sample(data=stan_data, chains=1)
# 
# # extract posterior samples for tau parameter
# tau <- fit$draws(variables = "tau")