R/enpls.ad.R

In enpls: Ensemble Partial Least Squares Regression

#' Ensemble Partial Least Squares for Model Applicability Domain Evaluation
#'
#' Model applicability domain evaluation with ensemble partial least squares.
#'
#' @param x Predictor matrix of the training set.
#' @param y Response vector of the training set.
#' @param xtest List, with the i-th component being the i-th test set's
#' predictor matrix (see example code below).
#' @param ytest List, with the i-th component being the i-th test set's
#' response vector (see example code below).
#' @param maxcomp Maximum number of components included within each model.
#' If not specified, will use the maximum number possible (considering
#' cross-validation and special cases where n is smaller than p).
#' @param cvfolds Number of cross-validation folds used in each model
#' for automatic parameter selection, default is \code{5}.
#' @param space Space in which to apply the resampling method.
#' Can be the sample space (\code{"sample"}) or
#' the variable space (\code{"variable"}).
#' @param method Resampling method. \code{"mc"} (Monte-Carlo resampling)
#' or \code{"boot"} (bootstrapping). Default is \code{"mc"}.
#' @param reptimes Number of models to build with Monte-Carlo resampling
#' or bootstrapping.
#' @param ratio Sampling ratio used when \code{method = "mc"}.
#' @param parallel Integer. Number of CPU cores to use.
#' Default is \code{1} (not parallelized).
#'
#' @note Note that for \code{space = "variable"}, \code{method} could
#' only be \code{"mc"}, since bootstrapping in the variable space
#' will create duplicated variables, and that could cause problems.
#'
#' @return A list containing:
#' \itemize{
#' \item \code{tr.error.mean} -
#' absolute mean prediction error for training set
#' \item \code{tr.error.median} -
#' absolute median prediction error for training set
#' \item \code{tr.error.sd} -
#' prediction error sd for training set
#' \item \code{tr.error.matrix} -
#' raw prediction error matrix for training set
#' \item \code{te.error.mean} -
#' list of absolute mean prediction error for test set(s)
#' \item \code{te.error.median} -
#' list of absolute median prediction error for test set(s)
#' \item \code{te.error.sd} -
#' list of prediction error sd for test set(s)
#' \item \code{te.error.matrix} -
#' list of raw prediction error matrix for test set(s)
#' }
#'
#' @author Nan Xiao <\url{https://nanx.me}>
#'
#' @export enpls.ad
#'
#' @importFrom doParallel registerDoParallel
#' @importFrom foreach foreach "%dopar%"
#'
#' @examples
#' data("alkanes")
#' x <- alkanes$x
#' y <- alkanes$y
#'
#' # training set
#' x.tr <- x[1:100, ]
#' y.tr <- y[1:100]
#'
#' # two test sets
#' x.te <- list(
#'   "test.1" = x[101:150, ],
#'   "test.2" = x[151:207, ]
#' )
#' y.te <- list(
#'   "test.1" = y[101:150],
#'   "test.2" = y[151:207]
#' )
#'
#' set.seed(42)
#' ad <- enpls.ad(
#'   x.tr, y.tr, x.te, y.te,
#'   space = "variable", method = "mc",
#'   ratio = 0.9, reptimes = 50
#' )
#' print(ad)
#' plot(ad)
#' # the interactive plot requires a HTML viewer
#' \dontrun{
#' plot(ad, type = "interactive")
#' }
enpls.ad <- function(
  x, y,
  xtest, ytest,
  maxcomp = NULL,
  cvfolds = 5L,
  space = c("sample", "variable"),
  method = c("mc", "boot"),
  reptimes = 500L,
  ratio = 0.8,
  parallel = 1L) {
  if (missing(x) | missing(y) | missing(xtest) | missing(ytest)) {
    stop("Please specify x, y, xtest, and ytest")
  }

  if (!all(sapply(xtest, ncol) == ncol(x))) {
    stop("All test sets must have identical # of variables as the training set")
  }

  space <- match.arg(space)
  method <- match.arg(method)

  n.testset <- length(xtest)
  nsamp.tr <- nrow(x)
  nsamp.te <- sapply(xtest, nrow)

  errorlist.tr <- vector("list", reptimes)
  errorlist.te <- vector("list", n.testset)
  for (i in 1L:n.testset) errorlist.te[[i]] <- vector("list", reptimes)

  if (space == "sample") {
    idx.row <- vector("list", reptimes)

    if (method == "boot") {

      # 1. space = "sample" & method = "boot"
      for (i in 1L:reptimes) {
        idx.row[[i]] <-
          sample(1L:nsamp.tr, nsamp.tr, replace = TRUE)
      }
    } else {

      # 2. space = "sample" & method = "mc"
      n.samp <- round(nsamp.tr * ratio)
      for (i in 1L:reptimes) {
        idx.row[[i]] <-
          sample(1L:nsamp.tr, n.samp, replace = FALSE)
      }
    }

    if (parallel < 1.5) {
      for (i in 1L:reptimes) {
        plsdf.tr <- as.data.frame(cbind(x[idx.row[[i]], ],
                                        "y" = y[idx.row[[i]]]
        ))
        fit <- suppressWarnings(enpls.ad.core.fit(plsdf.tr, maxcomp, cvfolds))
        errorlist.tr[[i]] <- suppressWarnings(enpls.ad.core.pred(
          fit, as.data.frame(cbind(x, "y" = y))
        ))
        for (j in 1L:n.testset) {
          errorlist.te[[j]][[i]] <-
            suppressWarnings(enpls.ad.core.pred(
              fit, as.data.frame(cbind(xtest[[j]], "y" = ytest[[j]]))
            ))
        }
      }
    } else {
      registerDoParallel(parallel)
      fit.list <- foreach(i = 1L:reptimes) %dopar% {
        plsdf.tr <- as.data.frame(cbind(x[idx.row[[i]], ], "y" = y[idx.row[[i]]]))
        enpls.ad.core.fit(plsdf.tr, maxcomp, cvfolds)
      }

      for (i in 1L:reptimes) {
        errorlist.tr[[i]] <- suppressWarnings(enpls.ad.core.pred(
          fit.list[[i]], as.data.frame(cbind(x, "y" = y))
        ))
        for (j in 1L:n.testset) {
          errorlist.te[[j]][[i]] <-
            suppressWarnings(enpls.ad.core.pred(
              fit.list[[i]], as.data.frame(cbind(xtest[[j]], "y" = ytest[[j]]))
            ))
        }
      }
    }
  } else {
    if (method == "boot") {

      # 3. space = "variable" & method = "boot"
      stop('method cannot be "boot" when space = "variable"')
    } else {

      # 4. space = "variable" & method = "mc"
      x.col <- ncol(x)
      idx.col <- vector("list", reptimes)

      n.var <- round(x.col * ratio)
      for (i in 1L:reptimes) {
        idx.col[[i]] <-
          sample(1L:x.col, n.var, replace = FALSE)
      }

      if (parallel < 1.5) {
        for (i in 1L:reptimes) {
          plsdf.tr <- as.data.frame(cbind(x[, idx.col[[i]]], "y" = y))
          fit <- suppressWarnings(enpls.ad.core.fit(plsdf.tr, maxcomp, cvfolds))
          errorlist.tr[[i]] <- suppressWarnings(enpls.ad.core.pred(fit, plsdf.tr))
          for (j in 1L:n.testset) {
            errorlist.te[[j]][[i]] <-
              suppressWarnings(enpls.ad.core.pred(
                fit, as.data.frame(cbind(xtest[[j]][, idx.col[[i]]], "y" = ytest[[j]]))
              ))
          }
        }
      } else {
        registerDoParallel(parallel)
        fit.list <- foreach(i = 1L:reptimes) %dopar% {
          plsdf.tr <- as.data.frame(cbind(x[, idx.col[[i]]], "y" = y))
          enpls.ad.core.fit(plsdf.tr, maxcomp, cvfolds)
        }

        for (i in 1L:reptimes) {
          errorlist.tr[[i]] <- suppressWarnings(enpls.ad.core.pred(
            fit.list[[i]], as.data.frame(cbind(x[, idx.col[[i]]], "y" = y))
          ))
          for (j in 1L:n.testset) {
            errorlist.te[[j]][[i]] <-
              suppressWarnings(enpls.ad.core.pred(
                fit.list[[i]], as.data.frame(cbind(xtest[[j]][, idx.col[[i]]], "y" = ytest[[j]]))
              ))
          }
        }
      }
    }
  }

  errormat.tr <- matrix(NA, ncol = nsamp.tr, nrow = reptimes)
  errormat.te <- vector("list", n.testset)
  for (i in 1L:n.testset) {
    errormat.te[[i]] <-
      matrix(NA, ncol = nsamp.te[i], nrow = reptimes)
  }

  for (i in 1L:reptimes) errormat.tr[i, ] <- errorlist.tr[[i]]
  for (i in 1L:reptimes) {
    for (j in 1L:n.testset) {
      errormat.te[[j]][i, ] <- errorlist.te[[j]][[i]]
    }
  }

  tiny.mean <- function(x) abs(colMeans(x, na.rm = TRUE))
  tiny.median <- function(x) abs(apply(x, 2L, median, na.rm = TRUE))
  tiny.sd <- function(x) apply(x, 2L, sd, na.rm = TRUE)

  tr.error.mean <- tiny.mean(errormat.tr)
  tr.error.median <- tiny.mean(errormat.tr)
  tr.error.sd <- tiny.sd(errormat.tr)

  te.error.mean <- lapply(errormat.te, tiny.mean)
  te.error.median <- lapply(errormat.te, tiny.median)
  te.error.sd <- lapply(errormat.te, tiny.sd)

  res <- list(
    "tr.error.mean" = tr.error.mean,
    "tr.error.median" = tr.error.median,
    "tr.error.sd" = tr.error.sd,
    "tr.error.matrix" = errormat.tr,
    "te.error.mean" = te.error.mean,
    "te.error.median" = te.error.median,
    "te.error.sd" = te.error.sd,
    "te.error.matrix" = errormat.te
  )
  class(res) <- "enpls.ad"

  res
}

#' core fitting function for enpls.ad
#'
#' select the best ncomp with cross-validation and
#' use it to fit the complete training set. scale = TRUE
#'
#' @return the fitted plsr object
#'
#' @keywords internal

enpls.ad.core.fit <- function(trainingset, maxcomp, cvfolds) {
  if (is.null(maxcomp)) {
    plsr.cvfit <- plsr(
      y ~ .,
      data = trainingset,
      scale = TRUE,
      method = "simpls",
      validation = "CV",
      segments = cvfolds
    )
  } else {
    plsr.cvfit <- plsr(
      y ~ .,
      data = trainingset,
      ncomp = maxcomp,
      scale = TRUE,
      method = "simpls",
      validation = "CV",
      segments = cvfolds
    )
  }

  # select best component number using adjusted CV
  cv.bestcomp <- which.min(RMSEP(plsr.cvfit)[["val"]][2L, 1L, -1L])

  plsr.fit <- plsr(
    y ~ .,
    data = trainingset,
    ncomp = cv.bestcomp,
    scale = TRUE,
    method = "simpls",
    validation = "none"
  )

  list("plsr.fit" = plsr.fit, "cv.bestcomp" = cv.bestcomp)
}

#' core prediction function for enpls.ad
#'
#' @return the error vector between predicted and real response
#'
#' @keywords internal

enpls.ad.core.pred <- function(model, testset) {
  pred <- predict(
    model$"plsr.fit",
    ncomp = model$"cv.bestcomp",
    newdata = testset[, !(colnames(testset) %in% c("y"))]
  )[, 1L, 1L]

  errorvec <- testset[, "y"] - pred
  names(errorvec) <- NULL

  errorvec
}