carbmodel: Function that produces δ18O and Δ47 records

In seasonalclumped: Toolbox for Clumped Isotope Seasonality Reconstructions

Description

Takes vectors of time, temperature, growth rate and δ18O of the fluid and converts them into a δ18O and Δ47 record. The δ18O and Δ47 values are calculated for every depth value provided in the D vector. By default, the empirical transfer function by Kim and O'Neil (1997) is used to produce the δ18O record, but other transfer functions (e.g. Grossman and Ku, 1986) are also supported. The default transfer function for converting temperature data to Δ47 data is based on Bernasconi et al. (2018), but other transfer functions (e.g. Jautzy et al., 2020) are also supported.

Usage

carbmodel(
  time,
  SST,
  GR,
  d18Ow,
  D,
  d18O_fun = "KimONeil97",
  D47_fun = "Bernasconi18",
  AV = FALSE,
  plot = FALSE
)

Arguments

time	Time vector (values in years)
SST	A vector containing temperature data (values in degrees C; length must be equal to that of time)
GR	Growth rate vector (values in same time unit as time (years); length must be equal to that of time)
d18Ow	A vector containing data on the δ18O value of the precipitation fluid (values in permille VSMOW; length must be equal to that of time)
D	Depth vector (values in same depth unit as GR)
d18O_fun	String containing the name of the transfer function used to convert temperature and δ18Ow to δ18Oc data (for example: "KimONeil97" or "GrossmanKu86"). Defaults to Kim and O'Neil (1997).
D47_fun	String containing the name of the transfer function used to convert temperature to Δ47 data (for example: "Bernasconi18" or "Jautzy20"). Defaults to Bernasconi et al., 2018).
AV	Should the subsampling take into account the mean value within the sample interval? TRUE/FALSE If FALSE, the interpolated value corresponding to the exact position is used instead of the mean of the interval
plot	Should the result be plotted? TRUE/FALSE

Value

A matrix containing subsampled time, depth, δ18Oc and Δ47 values: "Tnew"): New time vector after subsampling "D"): New depth vector after subsampling "d18Oc"): Vector listing δ18Oc values for each sample "D47"): Vector listing Δ47 values for each sample

References

package dependencies: ggplot2, gridExtra function dependencies: subsample, subsample_mean Grossman, E.L., Ku, T., Oxygen and carbon isotope fractionation in biogenic aragonite: temperature effects, Chemical Geology 1986, 59.1, 59–74. https://doi.org/bvpzws

Kim, S., O'Niel, J.R., Equilibrium and nonequilibrium oxygen isotope effects in synthetic carbonates, Geochimica et Cosmochimica Acta 1997, 61.16, 3461–3475. https://doi.org/c7bwbp

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. https://doi.org/cbb7zc

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. https://doi.org/fpc2

Kele, S., Breitenbach, S. F., Capezzuoli, E., Meckler, A. N., Ziegler, M., Millan, I. M., Kluge, T., Deák, J., Hanselmann, K. and John, C. M., Temperature dependence of oxygen– and clumped isotope fractionation in carbonates: a study of travertines and tufas in the 6–95 C temperature range, Geochimica et Cosmochimica Acta 2015, 168, 172–192. https://doi.org/f7sgn6

Bernasconi, S.M., Müller, I.A., Bergmann, K.D., Breitenbach, S.F., Fernandez, A., Hodell, D.A., Jaggi, M., Meckler, A.N., Millan, I. and Ziegler, M., Reducing uncertainties in carbonate–clumped isotope analysis through consistent carbonate based standardization. Geochemistry, Geophysics, Geosystems 2018, 19–9, 2895–2914. https://doi.org/gfmjrw

Petersen, S. V., Defliese, W. F., Saenger, C., Daëron, M., Huntington, K. W., John, C. M., Kelson, J. R., Bernasconi, S. M., Colman, A. S., Kluge, T., Olack, G. A., Schauer, A. J., Bajnai, D., Bonifacie, M., Breitenbach, S. F. M., Fiebig, J., Fernandez, A. B., Henkes, G. A., Hodell, D., Katz, A., Kele, S., Lohmann, K. C., Passey, B. H., Peral, M. Y., Petrizzo, D. A., Rosenheim, B. E., Tripati, A., Venturelli, R., Young, E. D. and Winkelstern, I. Z., Effects of Improved 17O Correction on Interlaboratory Agreement in Clumped Isotope Calibrations, Estimates of Mineral–Specific Offsets, and Temperature Dependence of Acid Digestion Fractionation, Geochemistry, Geophysics, Geosystems *2019, 20–7, 3495–3519. https://doi.org/ggrc39

Jautzy, J. J., Savard, M. M., Dhillon, R. S., Bernasconi, S. M. and Smirnoff, A., Clumped isotope temperature calibration for calcite: Bridging theory and experimentation, Geochemical Perspectives Letters 2020, 14, 36–41. https://doi.org/fpc3

Examples

# Create test data (= ideal case)
# Set boundary conditions
Td <- seq(1, 12 * 365, 1) # Create timeline of 12 years in days
Ty <- Td / 365 # Convert to years
MAT <- 20 # Set mean annual temperature
Amp <- 10 # Set seasonal amplitude
Sext <- 2 * Amp # Calculate extent of seasonal variability
TSD <- 1.5 # Set the degree of random non–seasonal noise on the SST curve
# ("weather")
SST <- rnorm(length(Ty), MAT + Amp * sin(2 * pi * Ty), TSD) # Create virtual
# daily SST data
GR <- rep(10 / 365, length(Ty)) # Set growth rate to 10 mm/yr and create daily
# GR vector
DSD <- 0.6 # Set the degree of random non–seasonal noise on the d18Osw curve
# ("salinity fluctuations")
d18Osw<-rnorm(length(Ty), rep(0, length(Ty)), DSD) # Set d18Osw to 0 permille
# VSMOW, create daily d18Osw vector
SR <- 0.75 # Set sampling resolution to 0.75 mm
# Create vector for all samples along entire shell length by applying constant
# sampling resolution
D <- seq(SR, sum(GR), SR)
# Calculate virtual data
newdata <- carbmodel(Ty, SST, GR, d18Osw, D, AV = TRUE)

seasonalclumped documentation built on Jan. 16, 2021, 5:26 p.m.