R/getVarExplained.R

In ChemoSpecUtils: Functions Supporting Packages ChemoSpec and ChemoSpec2D

#'
#' Compute the Variance Explained from PCA or Other Reduction Methods
#'
#' *Internal function*.
#'
#' @param so A object returned by a data reduction method.
#' 
#' @return A vector giving the variance explained by each successive component.
#'
#' @author `r .writeDoc_Authors("BH")`
#' @export
#' @keywords internal
#'
.getVarExplained <- function(so) {
  found <- FALSE

  # sparse pca via arrayspc objects
  if ("pev" %in% names(so)) {
    return(so$pev * 100)
  }

  # prcomp-based objects
  if ("sdev" %in% names(so)) {
    eigensum <- sum(so$sdev * so$sdev)
    return(100 * (so$sdev * so$sdev / eigensum))
  }

  # mia objects
  if ("lc" %in% names(so)) {
    return(100 * (so$lc / sum(so$lc)))
  }

  if (!found) stop("Could not compute variance from data provided")
}