R/SAVE.R

Defines functions SAVE

Documented in SAVE

#'SAVE
#'
#' @inheritParams SYS
#'
#' @return list of reduced data, projection matrix, 
#'          group variable, discrimination function, 
#'          m matrix.
#' @export
#'
SAVE <- function(x, svdMethod = svd, ...){
  
  matrix_ls <- x

  prior <- prior(matrix_ls)
  xbar <- lapply(matrix_ls, colMeans)
  B <- S_B(prior, xbar)
  S <- S_W(prior, matrix_ls)
  covs <- lapply(matrix_ls, cov)

  S_hatGamma <- (1 / length(covs)) *
    Reduce(`+`,
           lapply(covs, function(x){
             (x - S) %*%
               solve(B + S) %*%
               (x - S)
           })
    )

  rootGammaInv <- matInvSqrt(B + S)

  M <- (rootGammaInv %*% B %*% rootGammaInv) %*%
    (rootGammaInv %*% B %*% rootGammaInv) +
    (rootGammaInv %*% S_hatGamma %*% rootGammaInv)

  projection <- t(rootGammaInv %*% do.call(svdMethod, list(M))$u)

  projectedData <- lapply(matrix_ls, FUN = projection_func, proj = projection)
  
  object <- list(projectedData = projectedData,
                 projectionMatrix = projection,
                 M = M,
                 method = SAVE)
  object
}
BenBarnard/slidR documentation built on March 21, 2018, 2:26 p.m.