R/std_nmr.R

In SOMnmR: Analysis of Soil Organic Matter using Nuclear Magnetic Resonance

#' Create a data frame of standard NMR areas
#'
#' The function creates a data frame with all standards of the selected ecosystem (Terrestrial or Aquatic).
#' @param ecosys Standards from the ecosystem to be fitted. "Terr_Nelson" or "Terr_Baldock" for terrestrial, "Aqua_Nelson" or "Aqua_Baldock" for aquatic.
#' @returns A data frame with all standards of the selected ecosystem ("Terr_Nelson" or "Terr_Baldock" for terrestrial, "Aqua_Nelson" or "Aqua_Baldock" for aquatic).
#' @keywords standards
#' @export
#' @examples
#' std_table <- std_nmr(ecosys="Terr_Nelson")


std_nmr <- function (ecosys=NULL) {

  ## create dummy vectors for standard spectra and names
  if (is.null(ecosys)) {

    stop("Please choose an ecosystem model composition by typic 'Terr' for Terrestrial or 'Aqua' for Aquatic")

  } else if (ecosys == "Terr_Nelson") {

    ## Area composition
    MMM <- list(data.frame("Protein" = c(0.32, 39.6, 21.9, 2.1, 0.0, 7.5, 2.5, 26.4, 1.0, 0.32, 1.59, 0.37), "Carbohydrates" = c(0.0, 0.0, 4.3, 79.0, 15.7, 1.0, 0.0, 0.0, 1.0, 0.0, 1.67, 0.83),
                           "Lignin" = c(0.0, 10.5, 13.8, 12.5, 8.6, 30.6, 19.5, 4.6, 1.0, 0.0, 1.24, 0.43), "Lipid" =c(0.0, 75.6, 4.5, 9.0, 0.0, 3.6, 0.7, 6.6, 1.0, 0.0, 1.94, 0.24),
                           "Carbonyl" = c(0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 100.00, 1.0, 0.0, 1.0, 2.0), "Char" = c(0.0, 0.0, 0.0, 0.0, 4.3, 73.9, 16.1, 5.6, 1.0, 0.0, 0.45, 0.41)))

  } else if (ecosys == "Terr_Baldock") {

    MMM <- list(data.frame("Protein" = c(0.275, 35.4, 22.6, 3.5, 0.0, 8.9, 1.3, 28.3, 1.0, 0.275, 1.10, 0.16), "Carbohydrates" = c(0.0, 0.0, 0.0, 83.3, 16.7, 0.0, 0.0, 0.0, 1.0, 0.0, 1.67, 0.83),
               "Lignin" = c(0.0, 10.5, 13.8, 12.5, 8.6, 30.6, 19.5, 4.6, 1.0, 0.0, 1.24, 0.43), "Lipid" =c(0.0, 75.6, 4.5, 9.0, 0.0, 3.6, 0.7, 6.6, 1.0, 0.0, 1.94, 0.24),
               "Carbonyl" = c(0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 100.00, 1.0, 0.0, 1.0, 2.0), "Char" = c(0.0, 0.0, 1.7, 1.8, 5.3, 72.1, 15.2, 3.9, 1.0, 0.0, 0.5, 0.4)))

  } else if (ecosys == "Aqua_Nelson") {

    ## Area composition
    MMM <- list(data.frame("Protein" = c(0.266, 36.6, 24.7, 2.9, 0.0, 4.5, 1.0, 30.4, 1.0, 0.266, 1.17, 0.12),"Carbohydrates" = c(0.0, 0.0, 0.0, 83.3, 16.7, 0.0, 0.0, 0.0, 1.0, 0.0, 1.67, 0.83),
                "Lignin" = c(0.0, 10.5, 13.8, 12.5, 8.6, 30.6, 19.5, 4.6, 1.0, 0.0, 1.24, 0.43), "Lipid" =c(0.0, 94.4, 0.0, 0.0, 0.0, 0.0, 0.0, 5.6, 1.0, 0.0, 1.98, 0.13),
                "Carbonyl" = c(0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 100.00, 1.0, 0.0, 1.0, 2.0), "Char" = c(0.0, 0.0, 0.0, 0.0, 4.3, 73.9, 16.1, 5.6, 1.0, 0.0, 0.45, 0.41)))

  } else if (ecosys == "Aqua_Baldock") {

    ## Area composition
    MMM <- list(data.frame("Protein" = c(0.27, 40.4, 21.0, 2.3, 0.0, 9.1, 1.4, 25.7, 1, 0.27, 1.17, 0.12),"Carbohydrates" = c(0.0, 0.0, 0.0, 83.3, 16.7, 0.0, 0.0, 0.0, 1.0, 0.0, 1.67, 0.83),
                           "Lignin" = c(0.0, 10.5, 13.8, 12.5, 8.6, 30.6, 19.5, 4.6, 1.0, 0.0, 1.24, 0.43), "Lipid" =c(0.0, 94.4, 0.0, 0.0, 0.0, 0.0, 0.0, 5.6, 1.0, 0.0, 1.98, 0.13),
                           "Carbonyl" = c(0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 100.00, 1.0, 0.0, 1.0, 2.0), "Char" = c(0.0, 0.0, 1.7, 1.8, 5.3, 72.1, 15.2, 3.9, 1.0, 0.0, 0.5, 0.4)))

  }
  ## transform results to data frame and change its column names
  ## return resulting data frame
  return(MMM)
  ## close function
}