R/data_transformation.R

In sq77/PCA7:

#' A data transformation Function
#'
#' This function allows you to do data transformation.
#' @keywords transformation
#' @examples
#' data_transformation()

data_transformation <- function(D,variants){
  # Assertion: stop if D is not a matrix
  stopifnot(is.matrix(D))
  # Store number of columns, number of rows
  NC = dim(D)[2];NR = dim(D)[1];NRC = NC*NR
  GM = mean(D)
  AR = rowMeans(D);AC = colMeans(D)
  SDR = apply(D,1,sd);SDC = apply(D,2,sd)
  C = D
  if(variants == 1){C = D-GM}
  if(variants == 2){C = t(t(D)-AC)}
  if(variants == 3){C = D-AR}
  if(variants == 4){C = t(t(D)-AC)-AR+GM}
  if(variants == 5){C = t(t(t(t(D)-AC))/SDC)}
  if(variants == 6){C = (D-AR)/SDR}
  if(variants == 7){C = D}
  
  # ANOVA
  # Compute sum of squares for rows and columns
  DSSR = NC*sum((AR - GM)^2);DSSC = NR*sum((AC - GM)^2);DSST = sum((D-GM)^2)
  ## Sum of squares for RxC interactions
  DSSRXC = DSST-DSSC-DSSR
  ## Degrees of freedom
  DDFT = NRC - 1;DDFR = NR - 1;DDFC = NC - 1;DDFRXC = (NR-1)*(NC-1)
  
  return(list(C = C,DSST=DSST,DSSR=DSSR,DSSC=DSSC,DDFT=DDFT,DDFR=DDFR,DDFC=DDFC, 
              DSSRXC=DSSRXC,DDFRXC=DDFRXC))
}