R/normalize_totalSpectrum.R

In CVUA-RRW/tidySpectR: An R package for tidy chemometrics

#' Normalizes spectra to their integrals
#'
#' Sums up the signal over the whole spectrum and use it as a 
#'   normalization factor. This assumes that the total signal 
#'   varies proportionally to the sample concentration
#'
#' @aliases normalize_totalSpectrum normalize_totalSpectrum.collection
#' @export
normalize_totalSpectrum <- function(x, ...)
    UseMethod("normalize_totalSpectrum")

#' @rdname normalize_totalSpectrum
#' @param x A`collection` object
#' @param skip Skip the creation of of processor step. If TRUE, this step will not be added to
#'   the list of processing steps. Typically reserved for nested function calls.
#' @param ... further arguments passed to or from other methods(not
#'   currenctly used).
#' @return An updated version of `collection`.
#' @importFrom dplyr group_by summarise
#' @export
#' @examples
#' library(tidySpectR)
#' 
#' normalize_totalSpectrum(fa_nmr)
normalize_totalSpectrum.collection <- function(x, skip = FALSE, ...){
    factors <- x$data %>%
                group_by(id) %>%
                summarise(factors = 1 / sum(values))
                
    new_obj <- normalize_factor(x, factors, skip = TRUE)
    
    # Add processing step 
    if (!skip){
        new_obj$processor <- new_obj$processor %>%
                             new_step(normalize_factor, 
                                      list(factors = factors), 
                                      name = "totalSpectrum_normalization")
    }
    
    return(new_obj)
}