R/scale.R

In r-hyperspec/hyperSpec: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

# Function -------------------------------------------------------------------

.scale <- function(x, center = TRUE, scale = TRUE) {
  validObject(x)

  if (!is.logical(center)) center <- as.matrix(center)
  if (!is.logical(scale)) scale <- as.matrix(scale)

  x@data$spc <- scale(x@data$spc, center, scale)

  x
}

#' Center and scale `hyperSpec` object
#'
#' Scales the spectra matrix. `scale(x, scale = FALSE)` centers the data.
#'
#' Package \pkg{scale} provides a fast alternative for [base::scale()]
#'
#' @name scale,hyperSpec-method
#' @rdname scale
#' @aliases scale scale-methods scale,hyperSpec-method
#' @docType methods
#'
#' @param x the `hyperSpec` object
#' @param center if `TRUE`, the data is centered to `colMeans(x)`, `FALSE`
#' suppresses centering. Alternatively, an object that can be converted to numeric of length
#' `nwl(x)` by [base::as.matrix()] (e.g. hyperSpec object containing 1 spectrum) can
#' specify the center spectrum.
#' @param scale if `TRUE`, the data is scaled to have unit variance at each wavelength,
#' `FALSE` suppresses scaling. Alternatively, an object that can be converted to numeric of
#' length `nwl(x)` by [base::as.matrix()] (e.g. hyperSpec object containing 1 spectrum)
#' can specify the center spectrum.
#'
#'
#' @return the centered & scaled `hyperSpec` object
#' @author C. Beleites
#' @seealso [base::scale()]
#'
#' package scale.
#'
#' @export
#'
#' @keywords methods
#' @concept manipulation
#' @concept preprocessing
#'
#' @examples
#'
#' ## mean center & variance scale
#' tmp <- scale(faux_cell)
#' plot(tmp, "spcmeansd")
#' plot(sample(tmp, 5), add = TRUE, col = 2)
#'
#' ## mean center only
#' tmp <- scale(faux_cell, scale = FALSE)
#' plot(tmp, "spcmeansd")
#' plot(sample(tmp, 5), add = TRUE, col = 2)
#'
#' ## custom center
#' tmp <- sweep(faux_cell, 1, mean, `/`)
#' plot(tmp, "spcmeansd")
#' tmp <- scale(tmp, center = quantile(tmp, .05), scale = FALSE)
setMethod("scale", signature = signature(x = "hyperSpec"), .scale)


# Unit tests -----------------------------------------------------------------

hySpc.testthat::test(.scale) <- function() {
  context("scale")

  # Perform tests
  test_that("scale() returnts output silently", {
    expect_silent(spc_1 <- scale(flu))
    expect_silent(spc_2 <- scale(flu, scale = FALSE))
    expect_silent(spc_3 <- scale(flu, center = FALSE))
    expect_silent(spc_4 <- scale(flu, center = rep(0, 181), scale = rep(1, 181)))
  })

  # FIXME (tests): add tests to check the correctness of the output!!!
}