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

## ----high level showcase, eval=FALSE------------------------------------------
# options(
#   crmpack_extensions = function() {
#     # ..... user code .....
#   }
# )

## ----LogisticNormalTruncPrior Definition, eval = FALSE------------------------
# library(crmPack)
# 
# my_own_extension <- function() {
#   # Attach the package checkmate with library(checkmate) here, to avoid usage of
#   # the :: operator in the code below.
# 
#   # LogisticNormalTruncPrior ----
# 
#   ## class ----
# 
#   #' `LogisticNormalTruncPrior`
#   #'
#   #' @description `r lifecycle::badge("experimental")`
#   #'
#   #' [`LogisticNormalTruncPrior`] is the class for the usual logistic regression
#   #'  model with bivariate normal prior on the intercept and slope.
#   #'
#   #' @aliases LogisticNormalTruncPrior
#   #' @export
#   #'
#   #' @slot mean1 the mean of the intercept
#   #' @slot mean2 the mean of the slope
#   #' @slot var1 the variance of the intercept
#   #' @slot var2 the variance of the slope
#   #'
#   .LogisticNormalTruncPrior <- setClass(
#     Class = "LogisticNormalTruncPrior",
#     contains = "GeneralModel",
#     slots = c(
#       mean1 = "numeric",
#       mean2 = "numeric",
#       var1 = "numeric",
#       var2 = "numeric"
#     )
#   )
# 
#   ## constructor ----
# 
#   #' @rdname LogisticNormalTruncPrior-class
# 
#   #' Initialization function for the `LogisticNormalTruncPrior` class
#   #'
#   #' @param mean1 the mean of the intercept
#   #' @param mean2 the mean of the slope
#   #' @param var1 the variance of the intercept
#   #' @param var2 the variance of the slope
#   #' @return the \code{\linkS4class{LogisticNormalTruncPrior}} object
#   #'
#   #' @export
#   #' @keywords methods
#   LogisticNormalTruncPrior <<- function(mean1, mean2, var1, var2) {
#     .LogisticNormalTruncPrior(
#       mean1 = mean1,
#       mean2 = mean2,
#       var1 = var1,
#       var2 = var2,
#       datamodel = function() {
#         for (i in 1:nObs) {
#           y[i] ~ dbern(mean[i])
#           logit(mean[i]) <- alpha0 + alpha1 * x[i]
#         }
#       },
#       priormodel = function() {
#         alpha0 ~ dnorm(mean1, 1 / var1)
#         alpha1 ~ dnorm(mean2, 1 / var2) %_% I(0, )
#       },
#       datanames = c("nObs", "y", "x"),
#       modelspecs = function() {
#         list(
#           mean1 = mean1,
#           mean2 = mean2,
#           var1 = var1,
#           var2 = var2
#         )
#       },
#       init = function() {
#         list(alpha0 = mean1, alpha1 = mean2)
#       },
#       sample = c("alpha0", "alpha1")
#     )
#   }
# 
#   ## dose ----
# 
#   #' @describeIn dose compute the dose level reaching a specific toxicity
#   #'   probability.
#   #'
#   #' @aliases dose-LogisticNormalTruncPrior
#   #' @export
#   #'
#   setMethod(
#     f = "dose",
#     signature = signature(
#       x = "numeric",
#       model = "LogisticNormalTruncPrior",
#       samples = "Samples"
#     ),
#     definition = function(x, model, samples) {
#       checkmate::assert_probabilities(x)
#       checkmate::assert_subset(c("alpha0", "alpha1"), names(samples))
#       assert_length(x, len = size(samples))
# 
#       alpha0 <- samples@data$alpha0
#       alpha1 <- samples@data$alpha1
#       (logit(x) - alpha0) / alpha1
#     }
#   )
# 
#   ## prob ----
# 
#   #' @describeIn prob compute the toxicity probability of a specific dose.
#   #'
#   #' @aliases prob-LogisticNormalTruncPrior
#   #' @export
#   #'
#   setMethod(
#     f = "prob",
#     signature = signature(
#       dose = "numeric",
#       model = "LogisticNormalTruncPrior",
#       samples = "Samples"
#     ),
#     definition = function(dose, model, samples) {
#       checkmate::assert_numeric(
#         dose,
#         lower = 0L, any.missing = FALSE, min.len = 1
#       )
#       checkmate::assert_subset(c("alpha0", "alpha1"), names(samples))
#       assert_length(dose, len = size(samples))
# 
#       alpha0 <- samples@data$alpha0
#       alpha1 <- samples@data$alpha1
#       1 / (1 + exp(-alpha0 - alpha1 * dose))
#     }
#   )
# }

## ----eval = FALSE-------------------------------------------------------------
# # Store the function into the global option crmpack_extensions.
# options(crmpack_extensions = my_own_extension)

## ----make user written code available, eval = FALSE---------------------------
# # Execute the user written extensions.
# getOption("crmpack_extensions")()

## ----initial study setup, eval = FALSE----------------------------------------
# # Create the dose grid.
# emptydata <- Data(
#   doseGrid = c(
#     10, 15, 20, 30, 40, 60, 80, 120, 160, 240, 320,
#     480, 640, 960, 1280, 1920, 2400, 3000, 4000
#   ),
#   placebo = FALSE
# )
# 
# # Create data for basic testing of the setup.
# my_data <- Data(
#   x = c(10, 20, 40, 80, 80, 160, 160),
#   y = c(0, 0, 0, 0, 0, 1, 1),
#   cohort = c(1, 2, 3, 4, 4, 5, 5),
#   ID = 1:7,
#   doseGrid = emptydata@doseGrid
# )
# 
# # Setup the model.
# my_model <- LogisticNormalTruncPrior(
#   mean1 = -3,
#   mean2 = 0.00075,
#   var1 = 1,
#   var2 = 0.000009
# )
# 
# # Options used for simulations.
# my_options <- McmcOptions(
#   burnin = 100,
#   step = 2,
#   samples = 100,
#   rng_kind = "Mersenne-Twister",
#   rng_seed = 94
# )
# 
# # Create mcmc samples.
# my_samples <- mcmc(my_data, my_model, my_options)
# 
# # Plot the dose toxicity curve.
# plot(my_samples, my_model, my_data)
# 
# # Specify increments.
# my_increments <- IncrementsRelativeDLT(
#   intervals = c(0, 1),
#   increments = c(1, 0.5)
# )
# 
# # Maximum dose.
# this_max_dose <- maxDose(my_increments, my_data)
# 
# # Next best dose.
# my_next_best <- NextBestMinDist(target = 0.3)
# this_next_dose <- nextBest(
#   my_next_best, this_max_dose, my_samples, my_model, my_data
# )$value
# 
# # Stopping rule.
# my_stopping <- StoppingPatientsNearDose(nPatients = 9, percentage = 0)
# 
# # Stop trial based on criteria and observed data.
# stopTrial(my_stopping, this_next_dose, my_samples, my_model, my_data)
# 
# # Cohorts size.
# my_size <- CohortSizeDLT(
#   intervals = c(0, 1),
#   cohort_size = c(1, 3)
# )
# 
# # Design.
# my_design <- Design(
#   model = my_model,
#   nextBest = my_next_best,
#   stopping = my_stopping,
#   increments = my_increments,
#   cohort_size = my_size,
#   data = emptydata,
#   startingDose = 10
# )

## ----examine the design, eval = FALSE-----------------------------------------
# # Examine the design.
# examine(my_design, my_options)

## ----perform study simulations, eval = FALSE----------------------------------
# # Set up scenarios
# scenario_setup <- function(intercept, mtd_prob, mtd_dose) {
#   probFunction(
#     my_model,
#     alpha0 = logit(intercept),
#     alpha1 = (logit(mtd_prob) - logit(intercept)) / mtd_dose
#   )
# }
# 
# safe_scenario <- scenario_setup(0.05, 0.3, 20000)
# late_scenario <- scenario_setup(0.05, 0.3, 2000)
# early_scenario <- scenario_setup(0.05, 0.3, 700)
# toxic_scenario <- scenario_setup(0.6, 0.3, -300)
# peak_scenario <- function(
#     dose,
#     scenario = cbind(emptydata@doseGrid, c(rep(0.05, 11), rep(0.80, 8)))) {
#   scenario[match(dose, scenario[, 1]), 2]
# }
# 
# # Helper function that outputs the elapsed time.
# report_time <- function(report_text) {
#   cat(
#     format(Sys.time(), usetz = TRUE),
#     report_text,
#     "done - elapsed time from start:",
#     round(difftime(Sys.time(), start_time, units = "mins"), digits = 1),
#     "\n"
#   )
# }
# 
# # Helper function that simulates a specific truth.
# get_oc <- function(truth) {
#   simulate(
#     my_design,
#     args = NULL,
#     truth = truth,
#     nsim = my_nsim,
#     mcmcOptions = my_options,
#     parallel = do_parallel,
#     nCores = parallelly::availableCores()
#   )
# }
# 
# # get operation characteristics without utilizing parallel computing for
# # selected truth (to reduce the run time).
# time_no_parallel <- system.time({
#   start_time <- Sys.time()
#   cat(format(Sys.time(), usetz = TRUE), "start", "\n")
# 
#   my_nsim <- 10
#   do_parallel <- FALSE
# 
#   safe <- get_oc(safe_scenario)
# 
#   report_time("safe (single core processing)")
# 
#   late <- get_oc(late_scenario)
# 
#   report_time("late (single core processing)")
# })

## ----perform study simulations multiple cores, eval = FALSE-------------------
# # Get full operation characteristics utilizing parallel computing.
# time <- system.time({
#   start_time <- Sys.time()
#   cat(format(Sys.time(), usetz = TRUE), "start", "\n")
# 
#   my_nsim <- 10
#   do_parallel <- TRUE
# 
#   safe <- get_oc(safe_scenario)
# 
#   report_time("safe")
# 
#   late <- get_oc(late_scenario)
# 
#   report_time("late")
# 
#   early <- get_oc(early_scenario)
# 
#   report_time("early")
# 
#   toxic <- get_oc(toxic_scenario)
# 
#   report_time("toxic")
# 
#   peak <- get_oc(peak_scenario)
# 
#   report_time("peak")
# })

## ----user code stored in external file----------------------------------------
if (FALSE) {
  # Store code example form above in external file and
  # remove the wrapper function structure.
  dump("my_own_extension", file = "user_extension.R")
  file_con <- file("user_extension.R")
  tmp <- readLines(file_con)[-c(1:3, 135)]
  tmp <- gsub("<<-", "<-", tmp)
  writeLines(tmp, file_con)

  # Source the stored file in the wrapper function.
  my_own_extension2 <- function() {
    source("user_extension.R")
  }

  options(crmpack_extensions = my_own_extension2)
  getOption("crmpack_extensions")()

  # Run the rest of the code from above example
}