#' Control parameters for train
#' 
#' Control the computational nuances of the \code{\link{train}} function
#' 
#' When setting the seeds manually, the number of models being evaluated is
#' required. This may not be obvious as \code{train} does some optimizations
#' for certain models. For example, when tuning over PLS model, the only model
#' that is fit is the one with the largest number of components. So if the
#' model is being tuned over \code{comp in 1:10}, the only model fit is
#' \code{ncomp = 10}. However, if the vector of integers used in the
#' \code{seeds} arguments is longer than actually needed, no error is thrown.
#' 
#' Using \code{method = "none"} and specifying more than one model in
#' \code{\link{train}}'s \code{tuneGrid} or \code{tuneLength} arguments will
#' result in an error.
#' 
#' Using adaptive resampling when \code{method} is either \code{"adaptive_cv"},
#' \code{"adaptive_boot"} or \code{"adaptive_LGOCV"}, the full set of resamples
#' is not run for each model. As resampling continues, a futility analysis is
#' conducted and models with a low probability of being optimal are removed.
#' These features are experimental. See Kuhn (2014) for more details. The
#' options for this procedure are:
#' 
#' \itemize{ \item \code{min}: the minimum number of resamples used before
#' models are removed \item \code{alpha}: the confidence level of the one-sided
#' intervals used to measure futility \item \code{method}: either generalized
#' least squares (\code{method = "gls"}) or a Bradley-Terry model (\code{method
#' = "BT"}) \item \code{complete}: if a single parameter value is found before
#' the end of resampling, should the full set of resamples be computed for that
#' parameter. ) }
#' 
#' The option \code{search = "grid"} uses the default grid search routine. When
#' \code{search = "random"}, a random search procedure is used (Bergstra and
#' Bengio, 2012). See \url{http://topepo.github.io/caret/random-hyperparameter-search.html} for
#' details and an example.
#' 
#' The supported bootstrap methods are:
#' 
#' \itemize{
#'   \item \code{"boot"}: the usual bootstrap.
#'   \item \code{"boot632"}: the 0.632 bootstrap estimator (Efron, 1983).
#'   \item \code{"optimism_boot"}: the optimism bootstrap estimator.
#'     (Efron and Tibshirani, 1994).
#'   \item \code{"boot_all"}: all of the above (for efficiency, 
#'     but "boot" will be used for calculations).
#' }
#' 
#' The \code{"boot632"} method should not to be confused with the 0.632+ 
#' estimator proposed later by the same author.
#' 
#' Note that if \code{index} or \code{indexOut} are specified, the label shown by \code{train} may not be accurate since these arguments supersede the \code{method} argument.
#' 
#' @param method The resampling method: \code{"boot"}, \code{"boot632"},
#' \code{"optimism_boot"}, \code{"boot_all"},
#' \code{"cv"}, \code{"repeatedcv"}, \code{"LOOCV"}, \code{"LGOCV"} (for
#' repeated training/test splits), \code{"none"} (only fits one model to the
#' entire training set), \code{"oob"} (only for random forest, bagged trees,
#' bagged earth, bagged flexible discriminant analysis, or conditional tree
#' forest models), \code{timeslice}, \code{"adaptive_cv"}, \code{"adaptive_boot"} or
#' \code{"adaptive_LGOCV"}
#' @param number Either the number of folds or number of resampling iterations
#' @param repeats For repeated k-fold cross-validation only: the number of
#' complete sets of folds to compute
#' @param verboseIter A logical for printing a training log.
#' @param returnData A logical for saving the data
#' @param returnResamp A character string indicating how much of the resampled
#' summary metrics should be saved. Values can be \code{"final"}, \code{"all"}
#' or \code{"none"}
#' @param savePredictions an indicator of how much of the hold-out predictions
#' for each resample should be saved. Values can be either \code{"all"},
#' \code{"final"}, or \code{"none"}. A logical value can also be used that
#' convert to \code{"all"} (for true) or \code{"none"} (for false).
#' \code{"final"} saves the predictions for the optimal tuning parameters.
#' @param p For leave-group out cross-validation: the training percentage
#' @param search Either \code{"grid"} or \code{"random"}, describing how the
#' tuning parameter grid is determined. See details below.
#' @param initialWindow,horizon,fixedWindow,skip possible arguments to
#' \code{\link{createTimeSlices}} when method is \code{timeslice}.
#' @param classProbs a logical; should class probabilities be computed for
#' classification models (along with predicted values) in each resample?
#' @param summaryFunction a function to compute performance metrics across
#' resamples. The arguments to the function should be the same as those in
#' \code{\link{defaultSummary}}. Note that if \code{method = "oob"} is used, 
#' this option is ignored and a warning is issued. 
#' @param selectionFunction the function used to select the optimal tuning
#' parameter. This can be a name of the function or the function itself. See
#' \code{\link{best}} for details and other options.
#' @param preProcOptions A list of options to pass to \code{\link{preProcess}}.
#' The type of pre-processing (e.g. center, scaling etc) is passed in via the
#' \code{preProc} option in \code{\link{train}}.
#' @param sampling a single character value describing the type of additional
#' sampling that is conducted after resampling (usually to resolve class
#' imbalances). Values are \code{"none"}, \code{"down"}, \code{"up"},
#' \code{"smote"}, or \code{"rose"}. The latter two values require the
#' \pkg{DMwR} and \pkg{ROSE} packages, respectively. This argument can also be
#' a list to facilitate custom sampling and these details can be found on the
#' \pkg{caret} package website for sampling (link below).
#' @param index a list with elements for each resampling iteration. Each list
#' element is a vector of integers corresponding to the rows used for training
#' at that iteration.
#' @param indexOut a list (the same length as \code{index}) that dictates which
#' data are held-out for each resample (as integers). If \code{NULL}, then the
#' unique set of samples not contained in \code{index} is used.
#' @param indexFinal an optional vector of integers indicating which samples
#' are used to fit the final model after resampling. If \code{NULL}, then
#' entire data set is used.
#' @param timingSamps the number of training set samples that will be used to
#' measure the time for predicting samples (zero indicates that the prediction
#' time should not be estimated.
#' @param predictionBounds a logical or numeric vector of length 2 (regression
#' only). If logical, the predictions can be constrained to be within the limit
#' of the training set outcomes. For example, a value of \code{c(TRUE, FALSE)}
#' would only constrain the lower end of predictions. If numeric, specific
#' bounds can be used. For example, if \code{c(10, NA)}, values below 10 would
#' be predicted as 10 (with no constraint in the upper side).
#' @param seeds an optional set of integers that will be used to set the seed
#' at each resampling iteration. This is useful when the models are run in
#' parallel. A value of \code{NA} will stop the seed from being set within the
#' worker processes while a value of \code{NULL} will set the seeds using a
#' random set of integers. Alternatively, a list can be used. The list should
#' have \code{B+1} elements where \code{B} is the number of resamples, unless
#' \code{method} is \code{"boot632"} in which case \code{B} is the number of
#' resamples plus 1. The first \code{B} elements of the list should be vectors
#' of integers of length \code{M} where \code{M} is the number of models being
#' evaluated. The last element of the list only needs to be a single integer
#' (for the final model). See the Examples section below and the Details
#' section.
#' @param adaptive a list used when \code{method} is \code{"adaptive_cv"},
#' \code{"adaptive_boot"} or \code{"adaptive_LGOCV"}. See Details below.
#' @param trim a logical. If \code{TRUE} the final model in
#' \code{object\$finalModel} may have some components of the object removed so
#' reduce the size of the saved object. The \code{predict} method will still
#' work, but some other features of the model may not work. \code{trim}ing will
#' occur only for models where this feature has been implemented.
#' @param allowParallel if a parallel backend is loaded and available, should
#' the function use it?
#' @return An echo of the parameters specified
#' @author Max Kuhn
#' @references Efron (1983). ``Estimating the error rate of a prediction rule:
#' improvement on cross-validation''. Journal of the American Statistical
#' Association, 78(382):316-331
#' 
#' Efron, B., & Tibshirani, R. J. (1994). ``An introduction to the bootstrap'',
#' pages 249-252. CRC press.
#' 
#' Bergstra and Bengio (2012), ``Random Search for Hyper-Parameter
#' Optimization'', Journal of Machine Learning Research, 13(Feb):281-305
#' 
#' Kuhn (2014), ``Futility Analysis in the Cross-Validation of Machine Learning
#' Models'' \url{http://arxiv.org/abs/1405.6974},
#' 
#' Package website for subsampling:
#' \url{https://topepo.github.io/caret/subsampling-for-class-imbalances.html}
#' @keywords utilities
#' @examples
#' 
#' \dontrun{
#' 
#' ## Do 5 repeats of 10-Fold CV for the iris data. We will fit
#' ## a KNN model that evaluates 12 values of k and set the seed
#' ## at each iteration.
#' 
#' set.seed(123)
#' seeds <- vector(mode = "list", length = 51)
#' for(i in 1:50) seeds[[i]] <- sample.int(1000, 22)
#' 
#' ## For the last model:
#' seeds[[51]] <- sample.int(1000, 1)
#' 
#' ctrl <- trainControl(method = "repeatedcv",
#'                      repeats = 5,
#'                      seeds = seeds)
#' 
#' set.seed(1)
#' mod <- train(Species ~ ., data = iris,
#'              method = "knn",
#'              tuneLength = 12,
#'              trControl = ctrl)
#' 
#' 
#' ctrl2 <- trainControl(method = "adaptive_cv",
#'                       repeats = 5,
#'                       verboseIter = TRUE,
#'                       seeds = seeds)
#' 
#' set.seed(1)
#' mod2 <- train(Species ~ ., data = iris,
#'               method = "knn",
#'               tuneLength = 12,
#'               trControl = ctrl2)
#' 
#' }
#' 
#' @export trainControl
trainControl <- function(method = "boot",
                         number = ifelse(grepl("cv", method), 10, 25),
                         repeats = ifelse(grepl("[d_]cv$", method), 1, NA),
                         p = .75,
                         search = "grid",
                         initialWindow = NULL,
                         horizon = 1,
                         fixedWindow = TRUE,
                         skip = 0,
                         verboseIter = FALSE,
                         returnData = TRUE,
                         returnResamp = "final",
                         savePredictions = FALSE,
                         classProbs = FALSE,
                         summaryFunction = defaultSummary,
                         selectionFunction = "best",
                         preProcOptions = list(thresh = 0.95, ICAcomp = 3, k = 5, 
                                               freqCut = 95/5, uniqueCut = 10,
                                               cutoff = 0.9),
                         sampling = NULL,
                         index = NULL,
                         indexOut = NULL,
                         indexFinal = NULL,
                         timingSamps = 0,
                         predictionBounds = rep(FALSE, 2),
                         seeds = NA,
                         adaptive = list(min = 5, alpha = 0.05, method = "gls", complete = TRUE),
                         trim = FALSE,
                         allowParallel = TRUE)
{
  if(is.null(selectionFunction)) stop("null selectionFunction values not allowed")
  if(!(returnResamp %in% c("all", "final", "none"))) stop("incorrect value of returnResamp")
  if(length(predictionBounds) > 0 && length(predictionBounds) != 2) stop("'predictionBounds' should be a logical or numeric vector of length 2")
  if(any(names(preProcOptions) == "method")) stop("'method' cannot be specified here")
  if(any(names(preProcOptions) == "x")) stop("'x' cannot be specified here")
  if(!is.na(repeats) & !(method %in% c("repeatedcv", "adaptive_cv")))
    warning("`repeats` has no meaning for this resampling method.", call. = FALSE)
  
  if(!(adaptive$method %in% c("gls", "BT"))) stop("incorrect value of adaptive$method")
  if(adaptive$alpha < .0000001 | adaptive$alpha > 1) stop("incorrect value of adaptive$alpha")
  if(grepl("adapt", method)) {
    num <- if(method == "adaptive_cv") number*repeats else number
    if(adaptive$min >= num) stop(paste("adaptive$min should be less than", num))
    if(adaptive$min <= 1) stop("adaptive$min should be greater than 1")
  }
  if(!(search %in% c("grid", "random")))
    stop("`search` should be either 'grid' or 'random'")
  if(method == "oob" & any(names(match.call()) == "summaryFunction")) {
    warning("Custom summary measures cannot be computed for out-of-baf resampling. ",
            "This value of `summaryFunction` will be ignored.", 
            call. = FALSE)
  }
  
  list(method = method,
       number = number,
       repeats = repeats,
       search = search,
       p = p,
       initialWindow = initialWindow,
       horizon = horizon,
       fixedWindow = fixedWindow,
       skip = skip,
       verboseIter = verboseIter,
       returnData = returnData,
       returnResamp = returnResamp,
       savePredictions = savePredictions,
       classProbs = classProbs,
       summaryFunction = summaryFunction,
       selectionFunction = selectionFunction,
       preProcOptions = preProcOptions,
       sampling = sampling,
       index = index,
       indexOut = indexOut,
       indexFinal = indexFinal,
       timingSamps = timingSamps,
       predictionBounds = predictionBounds,
       seeds = seeds,
       adaptive = adaptive,
       trim = trim,
       allowParallel = allowParallel)
}
