R/T_from_d18O_d18Ow.R

In nielsjdewinter/ShellChron: Builds Chronologies from Oxygen Isotope Profiles in Shells

#' Function BLATANTLY STOLEN FROM SHELLCHRON PACKAGE to convert d18O data to SST
#'
#' Takes a matrix of d18Os data (in permille VPDB) against distance measures (in any unit), information
#' about the d18O value (in permille VSMOW) of the water and how it changes
#' from one value to another, and the transfer function used for of the record (e.g.
#' Kim and O'Neil, 1997 or Grossman and Ku, 1986). Converts the d18O data to SST
#' data (in degrees Celsius) using the supplied empirical transfer function.
#'
#' @param d18Oc Matrix with a distance column (values in any unit) and an d18Oc column
#' (values in permille VPDB)
#' @param d18Ow Either a single value (constant d18Ow) or a vector of length
#' equal to the number of d18O values
#' Defaults to constant d18Ow of 0 permille VSMOW
#' (the modern mean ocean value)
#' @param transfer_function String containing the name of the transfer function
#' (for example: \code{"KimONeil97"} or \code{"GrossmanKu86"}). Defaults to
#' Kim and O'Neil (1997).
#' @return A vector containing SST values for each d18Os value in \code{"d18Oc"}
#' @references Grossman, E.L., Ku, T., Oxygen and carbon isotope fractionation in biogenic
#' aragonite: temperature effects, _Chemical Geology_ **1986**, _59.1_, 59-74.
#'     \doi{10.1016/0168-9622(86)90057-6}
#' Kim, S., O'Niel, J.R., Equilibrium and nonequilibrium oxygen
#' isotope effects in synthetic carbonates, _Geochimica et Cosmochimica Acta_
#' **1997**, _61.16_, 3461-3475.
#'     \doi{10.1016/S0016-7037(97)00169-5}
#' Dettman, D.L., Reische, A.K., Lohmann, K.C., Controls on the stable isotope
#' composition of seasonal growth bands in aragonitic fresh-water bivalves
#' (Unionidae), _Geochimica et Cosmochimica Acta_ **1999**, _63.7-8_, 1049-1057.
#'     \doi{10.1016/S0016-7037(99)00020-4}
#' Brand, W.A., Coplen, T.B., Vogl, J., Rosner, M., Prohaska, T., Assessment of
#' international reference materials for isotope-ratio analysis (IUPAC Technical
#' Report), _Pure and Applied Chemistry_ **2014**, _86.3_, 425-467.
#'     \doi{10.1515/pac-2013-1023}
#' @examples
#' # Create dummy d18Os data
#' dist <- seq(1, 40, 1) #distance
#' val <- sin((0.5 * pi * (dist)) / 5)+1 # d18Os
#' d18O <- cbind(dist, val)
#' # Run SST model function
#' SST <- SST_model(d18O, 0, "KimONeil97")
#' @export
T_from_d18O_d18Ow <- function(d18Oc, # Function that converts d18Os values into SST
                       d18Ow = 0, # Information on the d18O of seawater (d18Ow), should be either one single number (constant) or a vector of length identical to the length of d18Os values.
                       transfer_function = "KimONeil97" # Supply transfer function. Current options are: Kim and O'Neil (calcite calibration; 1997; "KimONeil97") or Grossman and Ku (aragonite calibration; 1986; "GrossmanKu86")
){

  if(!is.numeric(d18Ow)){
    d18Ow <- rep(0, length(d18Oc[, 1])) # Set default d18Ow vector to constant at d18Ow = 0
  }else if(length(d18Ow) == 1){
    d18Ow <- rep(d18Ow, length(d18Oc[, 1])) # Create constant d18Ow vector if only one number is given
  }else{
    d18Ow <- c(0, rep(d18Ow, length(d18Oc[, 1])/length(d18Ow))) # If d18Ow is a vector with more than one value, multiply it to reach the same length of SST (multiply by "years")
  }
  if(transfer_function == "KimONeil97"){
    SST <- cbind(d18Oc[, 1], (18.03 * 1000) / (log((d18Oc / 1000 + 1) / (((d18Ow - 30.92) / 1.03092) / 1000 + 1)) * 1000 + 32.42) - 273.15)
  }else if(transfer_function == "GrossmanKu86"){
    SST <- cbind(d18Oc[, 1], -4.34 * d18Oc[, 2] + 4.34 * d18Ow + 21.468) # Use Grossmann and Ku (1986) modified by Dettmann et al. (1999)
  }else{
    return("ERROR: Supplied transfer function is not recognized")
  }
  return(SST)
}