R/get.isotope.standard.R

In gholtgrieve/HEEL: Miscellaneous Functions From HEEL Members

#' @title Helper function to access information in the isotope.standards dataframe
#'
#' @description This function is used to pull out isotope standard data from the isotope.standards dataframe
#' easily and efficiently.  The isotope.standards dataframe contains only raw isotope ratios,
#' so this function also will convert to delta value relative to the common international standard.
#'
#' @param std  Character vector with name(s) of the isotope standard of interest.
#'
#' @param isotope.system  Character vector of length one indicating the (single) isotope system of interest. Currently supported isotope systems are "C", "N", "S", "H", "O18", "O17".
#'
#' @return A list with the following elements.
#' \describe{
#'   \item{delta}{Numeric value of the standard in delta notation for the given isotope system. Uses the most common international standard for each isotope system.
#'                Specifically, VPDB for C, air for N, VCDT for S, and VSMOW for H, O18, and O17.}
#'   \item{std.R}{The ratio of heavy to light isotope of the standard for the given isotope system (e.g., 13C/12C)}
#'   \item{R}{The ratio of the standard relative to ratio of the common international standard for the given isotope system (i.e., R_std/R_VPDB)}
#'   \item{massPct}{The mass percent of the standard for the given isotope system.}
#'   }
#'
#' @author Gordon W. Holtgrieve
#'
#' @export

get.isotope.standard <- function(std, isotope.system){

 switch(isotope.system,
        C = {
          dataType_R <- "R_13C12C"
          dataType_mass <- "massPctC"
          reference.std.R <- 0.01118000  #Value for VPDB
        },
        N = {
          dataType_R <- "R_15N14N"
          dataType_mass <- "massPctN"
          reference.std.R <-0.00367600 #Value for air
        },
        S = {
          dataType_R <- "R_34S32S"
          dataType_mass <- "massPctS"
          reference.std.R <- 0.04416260  #Value for VCDT
        },
        H = {
          dataType_R <- "R_DH"
          dataType_mass <- "massPctH"
          reference.std.R <- 0.00015576  #Value for VSMOW
        },
        O18 = {
          dataType_R <- "R_18O16O"
          dataType_mass <- "massPctO"
          reference.std.R <- 0.00200520  #Value for VSMOW
        },
        O17 = {
          dataType_R <- "R_17O16O"
          dataType_mass <- "massPctO"
          reference.std.R <- 0.00037990  #Value for VSMOW
        },
        stop("Parameter isotope.system is missing or not one of the currently supported systems.")
        )

  #Check name given as standard against list of possible names and return the 'offical' name
  offical.standard.name <- check.isotope.standard.name(std)

  std.R <- isotope.standards$Value[isotope.standards$Name %in% offical.standard.name & isotope.standards$dataType == dataType_R]
  if(length(std.R)==0)  stop("No data available.  Try again.")

  R <- std.R/reference.std.R
  delta <- (R - 1) * 1000
  temp <- isotope.standards$Value[isotope.standards$Name %in% offical.standard.name & isotope.standards$dataType == dataType_mass]
  if(length(temp)==0){
    massPct <- NA
  } else {
    massPct = temp
  }

 return(list(std = offical.standard.name, isotope.system = isotope.system, delta = delta, std.R = std.R, R = R, massPct = massPct))
}