Type:	Package
Title:	Tools for Stable Isotope Geochemistry
Version:	1.1.1
Description:	This toolbox makes working with oxygen, carbon, and clumped isotope data reproducible and straightforward. Use it to quickly calculate isotope fractionation factors, and apply paleothermometry equations.
License:	GPL (≥ 3)
URL:	https://davidbajnai.github.io/isogeochem/
BugReports:	https://github.com/davidbajnai/isogeochem/issues
Encoding:	UTF-8
LazyData:	true
RoxygenNote:	7.2.3
Suggests:	shades, viridisLite, knitr, rmarkdown, devtools, spelling, testthat (≥ 3.0.0), covr
VignetteBuilder:	knitr
Imports:	stats, graphics, methods, grDevices
Depends:	R (≥ 3.1.0)
Language:	en-US
NeedsCompilation:	no
Packaged:	2023-03-15 14:34:45 UTC; bajnaidavid
Author:	David Bajnai [aut, cre], Julian Tödter [ctb]
Maintainer:	David Bajnai <david.bajnai@uni-goettingen.de>
Repository:	CRAN
Date/Publication:	2023-03-15 14:50:02 UTC

Isotope delta from fractionation factor

Description

A_from_a() calculates the isotope delta value of A from the isotope fractionation factor and the isotope delta value of B.

Usage

A_from_a(a, B)

Arguments

Value

Returns the isotope delta value of B (‰).

See Also

a_A_B() calculates the isotope fractionation factor between A and B.

B_from_a() calculates the isotope delta value of B.

Examples

A_from_a(a = 1.033, B = -10)

Isotope delta from fractionation factor

Description

B_from_a() calculates the isotope delta value of B from the isotope fractionation factor and the isotope delta value of A.

Usage

B_from_a(a, A)

Arguments

Value

Returns the Isotope delta value of B (‰).

See Also

a_A_B() calculates the isotope fractionation factor between A and B.

A_from_a() calculates the isotope delta value of A.

Examples

B_from_a(a = 1.033, A = 10)

Triple oxygen isotope value

Description

D17O() calculates the D17O value.

Usage

D17O(d18O, d17O, lambda = 0.528)

Arguments

Details

\Delta^{17}O_{VSMOW} = \delta'^{17}O_{VSMOW} - \lambda \times \delta'^{18}O_{VSMOW}

Value

Returns the D17O value (‰).

Examples

D17O(d18O = -10, d17O = -5, lambda = 0.528)

Equilibrium carbonate D47 value

Description

D47() calculates the equilibrium carbonate D47 value for a given temperature.

Usage

D47(temp, eq)

Arguments

Details

"Petersen19":

\Delta_{47, CDES90} = 0.0383 \times \frac{10^{6}}{T^{2}} + 0.170

"Anderson21":

\Delta_{47, I-CDES90} = 0.0391 \times \frac{10^{6}}{T^{2}} + 0.154

"Fiebig21":

\Delta_{47, CDES90} = 1.038 \times (-5.897 \times \frac{1}{T} - 3.521 \times \frac{10^{3}}{T^{2}} + 2.391 \times \frac{10^{7}}{T^{3}} - 3.541 \times \frac{10^{9}}{T^{4}}) + 0.1856

Value

Returns the carbonate D47 value expressed on the CDES90 scale (‰).

References

Petersen, S. V., Defliese, W. F., Saenger, C., Daëron, M., Huntington, K. W., John, C. M., et al. (2019). 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, 20(7), 3495-3519. doi:10.1029/2018GC008127

Anderson, N. T., Kelson, J. R., Kele, S., Daëron, M., Bonifacie, M., Horita, J., et al. (2021). A unified clumped isotope thermometer calibration (0.5-1100°C) using carbonate-based standardization. Geophysical Research Letters, 48(7), e2020GL092069. doi:10.1029/2020gl092069

Fiebig, J., Daëron, M., Bernecker, M., Guo, W., Schneider, G., Boch, R., et al. (2021). Calibration of the dual clumped isotope thermometer for carbonates. Geochimica et Cosmochimica Acta. doi:10.1016/j.gca.2021.07.012

See Also

temp_D47() calculates growth temperature from a D47 value.

Other equilibrium_carbonate: D48(), d17O_c(), d18O_c()

Examples

D47(temp = 33.7, eq = "Petersen19") # Returns 0.577
D47(temp = 33.7, eq = "Fiebig21") # Returns 0.571

Equilibrium carbonate D47 value

Description

D48() calculates the equilibrium carbonate D48 value for a given temperature.

Usage

D48(temp, eq)

Arguments

Details

"Fiebig21":

\Delta_{48, CDES90} = 1.028 \times (6.002 \times \frac{1}{T} - 1.299 \times \frac{10^{4}}{T^{2}} + 8.996 \times \frac{10^{6}}{T^{3}} - 7.423 \times \frac{10^{8}}{T^{4}}) + 0.1245

"Swart21":

\Delta_{48, CDES90} = 0.0142 \times \frac{10^{6}}{T^{2}} + 0.088

Value

Returns the carbonate equilibrium D48 value expressed on the CDES90 scale (‰).

References

Bajnai, D., Guo, W., Spötl, C., Coplen, T. B., Methner, K., Löffler, N., et al. (2020). Dual clumped isotope thermometry resolves kinetic biases in carbonate formation temperatures. Nature Communications, 11, 4005. doi:10.1038/s41467-020-17501-0

Fiebig, J., Daëron, M., Bernecker, M., Guo, W., Schneider, G., Boch, R., et al. (2021). Calibration of the dual clumped isotope thermometer for carbonates. Geochimica et Cosmochimica Acta. doi:10.1016/j.gca.2021.07.012

Swart, P. K., Lu, C., Moore, E., Smith, M., Murray, S. T., & Staudigel, P. T. (2021). A calibration equation between D48 values of carbonate and temperature. Rapid Communications in Mass Spectrometry, 35(17), e9147. doi:10.1002/rcm.9147

See Also

Other equilibrium_carbonate: D47(), d17O_c(), d18O_c()

Examples

D48(temp = 33.7, eq = "Fiebig21") # Returns 0.237
D48(temp = 33.7, eq = "Swart21") # Returns 0.239

Oxygen isotope stratigraphy from the Geologic Time Scale 2020: macrofossils

Description

A dataset containing a compilation of d18O and d13C values of various macrofossils (bivalves, gastropods, belemnites, ammonites) together with information on their age, shell mineralogy, and the climate zone they represent. This dataset is a condensed version of the entire dataset presented in the Geologic Time Scale 2020. Specifically, the full dataset was filtered for those "select" d18O and d13C values that also have age information.

Usage

GTS2020

Format

A data frame with 9676 rows and 8 variables:

age

Age of the sample expressed as millions of years before present (Ma).

d18O_VPDB

Carbonate d18O value expressed on the VPDB scale (‰).

d13C_VPDB

Carbonate d13C value expressed on the VPDB scale (‰).

mineralogy

The mineralogy of the carbonate hard part.

group

Taxonomic group of the sample (bivalve, gastropod, belemnite, ammonite).

clim_zone

The climate zone the sample represents.

Source

https://download.pangaea.de/dataset/930093/files/GTS2020-App_10.2A.xlsx

References

Grossman, E. L., & Joachimski, M. M. (2020). Oxygen isotope stratigraphy. In F. M. Gradstein, J. G. Ogg, M. D. Schmitz, & G. M. Ogg (Eds.), Geologic Time Scale 2020: Volume 1 (pp. 279-307): Elsevier. doi:10.1016/B978-0-12-824360-2.00010-3

See Also

Other "datasets": LR04, devilshole, meteoric_water

A Pliocene-Pleistocene benthic foraminifera d18O stack

Description

A dataset containing the LR04 benthic d18O stack.

Usage

LR04

Format

A data frame with 2115 rows and 3 variables:

age

Age of the sample expressed as thousands of years before present (ka).

d18O_VPDB

Carbonate d18O value expressed on the VPDB scale (‰).

d18O_error

Standard error on the d18O value.

Source

https://lorraine-lisiecki.com/stack.html

References

Lisiecki, L. E., & Raymo, M. E. (2005). A Pliocene-Pleistocene stack of 57 globally distributed benthic d18O records. Paleoceanography, 20(1), PA1003. doi:10.1029/2004pa001071

See Also

Other "datasets": GTS2020, devilshole, meteoric_water

Dissolved inorganic carbon species

Description

X_DIC() calculates the relative abundance of the DIC species as a function of solution temperature, pH, and salinity.

Usage

X_DIC(temp, pH, S)

Arguments

Value

Returns a data frame with the relative abundance of the DIC species:

• Relative abundance of dissolved CO2 (%).

• Relative abundance of bicarbonate ion (%).

• Relative abundance of carbonate ion (%).

References

Harned, H. S., and Scholes, S. R. (1941). The ionization constant of HCO3- from 0 to 50°. J. Am. Chem. Soc., 63(6), 1706-1709. doi:10.1021/ja01851a058

Harned, H. S., and Davis, R. (1943). The ionization constant of carbonic acid in water and the solubility of carbon dioxide in water and aqueous salt solutions from 0 to 50°. J. Am. Chem. Soc., 65(10), 2030-2037. doi:10.1021/ja01250a059

Millero, F. J., Graham, T. B., Huang, F., Bustos-Serrano, H., et al. (2006). Dissociation constants of carbonic acid in seawater as a function of salinity and temperature. Mar. Chem., 100(1-2), 80-94. doi:10.1016/j.marchem.2005.12.001

Examples

X_DIC(temp = 25, pH = 7, S = 30)

Relative rates of CO2 absorption reactions

Description

X_absorption() calculates the relative abundance of the DIC species as a function of solution temperature, pH, and salinity.

Usage

X_absorption(temp, pH, S)

Arguments

Details

X_hydration = ((kCO2 / (kCO2 + kOHxKw / aH)) * 100), where

• kCO2 is the rate constant for CO2 hydration from Johnson (1982)

• kOHxKw is the rate constant for CO2 hydroxylation x Kw from Schulz et al. (2006).

• aH is 10^(-pH)

Value

Returns a data frame with the relative rates of CO2 absorption reactions:

• Relative rate of CO2 hydration (%).

• Relative rate of CO2 hydroxylation (%).

References

Johnson, K. S. (1982). Carbon dioxide hydration and dehydration kinetics in seawater. Limnology and Oceanography, 27(5), 894-855. doi:10.4319/lo.1982.27.5.0849

Schulz, K. G., Riebesell, U., Rost, B., Thoms, S., & Zeebe, R. E. (2006). Determination of the rate constants for the carbon dioxide to bicarbonate inter-conversion in pH-buffered seawater systems. Marine Chemistry, 100(1-2), 53-65. doi:10.1016/j.marchem.2005.11.001

Examples

X_absorption(temp = 25, pH = 7, S = 30)

13C/12C fractionation factor between CO2(g) and CO2(aq)

Description

a13_CO2g_CO2aq() calculates the 13C/12C fractionation factor between gaseous and dissolved CO2.

Usage

a13_CO2g_CO2aq(temp)

Arguments

Details

\alpha^{13}_{CO2(g)/CO2(aq)} = (\frac{-1.18 + 0.0041 \times (T - 273.15)}{1000} + 1)^{-1}

Value

Returns the 13C/12C fractionation factor.

References

Vogel, J. C., Grootes, P. M., & Mook, W. G. (1970). Isotopic fractionation between gaseous and dissolved carbon dioxide. Zeitschrift für Physik A: Hadrons and Nuclei, 230(3), 225-238. doi:10.1007/Bf01394688

See Also

Other fractionation_factors: a18_CO2acid_c(), a18_CO2aq_H2O(), a18_CO2g_H2O(), a18_CO3_H2O(), a18_H2O_OH(), a18_HCO3_H2O(), a18_c_H2O(), a_A_B()

18O/16O acid fractionation factor

Description

a18_CO2acid_c() calculates the 18O/16O fractionation factor between CO2 produced from acid digestion and carbonate.

Usage

a18_CO2acid_c(temp, min)

Arguments

Details

calcite (Kim et al. 2015):

\alpha^{18}_{CO2acid/calcite} = e^{(3.48 \times \frac{1}{T} - 0.00147)}

aragonite (Kim et al. 2007):

\alpha^{18}_{CO2acid/aragonite} = e^{(3.39 \times \frac{1}{T} - 0.00083)}

dolomite (Rosenbaum & Sheppard 1986):

\alpha^{18}_{CO2acid/dolomite} = e^{(665 \times \frac{1}{T^{2}} + 0.00423)}

Value

Returns the 18O/16O fractionation factor.

References

Sharma, T., and Clayton, R. N. (1965). Measurement of ratios of total oxygen of carbonates. Geochimica et Cosmochimica Acta, 29(12), 1347-1353. doi:10.1016/0016-7037(65)90011-6

Rosenbaum, J. and Sheppard, S.M.F. (1986). An isotopic study of siderites, dolomites and ankerites at high temperatures. Geochimica et Cosmochimica Acta, 50, 1147-1150. doi:10.1016/0016-7037(86)90396-0

Kim, S.-T., Mucci, A., and Taylor, B. E. (2007). Phosphoric acid fractionation factors for calcite and aragonite between 25 and 75 °C: Revisited. Chemical Geology, 246(3-4), 135-146. doi:10.1016/j.chemgeo.2007.08.005

Kim, S.-T., Coplen, T. B., and Horita, J. (2015). Normalization of stable isotope data for carbonate minerals: Implementation of IUPAC guidelines. Geochimica et Cosmochimica Acta, 158, 276-289. doi:10.1016/j.gca.2015.02.011

See Also

Other fractionation_factors: a13_CO2g_CO2aq(), a18_CO2aq_H2O(), a18_CO2g_H2O(), a18_CO3_H2O(), a18_H2O_OH(), a18_HCO3_H2O(), a18_c_H2O(), a_A_B()

Examples

a18_CO2acid_c(temp = 90, min = "calcite")
a18_CO2acid_c(temp = 72, min = "aragonite")

18O/16O fractionation factor between CO2(aq) and H2O(l)

Description

a18_CO2_H2O() calculates the 18O/16O fractionation factor between dissolved CO2 and liquid water.

Usage

a18_CO2aq_H2O(temp)

Arguments

Details

\alpha^{18}_{CO2(aq)/H2O(l)} = e^{2.52 \times \frac{1000}{T^{2}} + 0.01212}

Value

Returns the 18O/16O fractionation factor.

References

Beck, W. C., Grossman, E. L., & Morse, J. W. (2005). Experimental studies of oxygen isotope fractionation in the carbonic acid system at 15°, 25°, and 40°C. Geochimica et Cosmochimica Acta, 69(14), 3493-3503. doi:10.1016/j.gca.2005.02.003

See Also

Other fractionation_factors: a13_CO2g_CO2aq(), a18_CO2acid_c(), a18_CO2g_H2O(), a18_CO3_H2O(), a18_H2O_OH(), a18_HCO3_H2O(), a18_c_H2O(), a_A_B()

18O/16O fractionation factor between CO2(g) and H2O(l)

Description

a18_CO2_H2O() calculates the 18O/16O fractionation factor between gaseous CO2 and liquid water.

Usage

a18_CO2g_H2O(temp)

Arguments

Details

\alpha^{18}_{CO2(g)/H2O(l)} = (17.604 \times \frac{1}{T} - 0.01793) + 1

Value

Returns the 18O/16O fractionation factor.

References

Brenninkmeijer, C. A. M., Kraft, P., & Mook, W. G. (1983). Oxygen isotope fractionation between CO2 and H2O. Chemical Geology, 41, 181-190. doi:10.1016/S0009-2541(83)80015-1

See Also

Other fractionation_factors: a13_CO2g_CO2aq(), a18_CO2acid_c(), a18_CO2aq_H2O(), a18_CO3_H2O(), a18_H2O_OH(), a18_HCO3_H2O(), a18_c_H2O(), a_A_B()

18O/16O fractionation factor between CO3(2-) and H2O

Description

a18_CO3_H2O() calculates the 18O/16O fractionation factor between carbonate ion CO3(2-) and water.

Usage

a18_CO3_H2O(temp)

Arguments

Details

\alpha^{18}_{CO3(2-)/H2O} = e^{2.39 \times \frac{1000}{T^{2}} - 0.00270}

The equation above and in the function is the uncorrected equation in Beck et al. (2005). They experimentally determined the fractionation factor using BaCO3 precipitation experiments. However, they applied the acid fractionation factor of calcite during the data processing and not that of BaCO3. The acid fractionation factor of BaCO3 is not known accurately, which may result in a bias of up to 1‰ in the calculated 1000lna values.

Value

Returns the 18O/16O fractionation factor.

References

Beck, W. C., Grossman, E. L., & Morse, J. W. (2005). Experimental studies of oxygen isotope fractionation in the carbonic acid system at 15°, 25°, and 40°C. Geochimica et Cosmochimica Acta, 69(14), 3493-3503. doi:10.1016/j.gca.2005.02.003

See Also

Other fractionation_factors: a13_CO2g_CO2aq(), a18_CO2acid_c(), a18_CO2aq_H2O(), a18_CO2g_H2O(), a18_H2O_OH(), a18_HCO3_H2O(), a18_c_H2O(), a_A_B()

18O/16O fractionation factor between water and hydroxide ion

Description

a18_H2O_OH() calculates the 18O/16O fractionation factor between water and aqueous hydroxide ion.

Usage

a18_H2O_OH(temp, eq)

Arguments

Value

Returns the 18O/16O fractionation factor.

References

Zeebe, R. E. (2020). Oxygen isotope fractionation between water and the aqueous hydroxide ion. Geochimica et Cosmochimica Acta, 289, 182-195. doi:10.1016/j.gca.2020.08.025

See Also

Other fractionation_factors: a13_CO2g_CO2aq(), a18_CO2acid_c(), a18_CO2aq_H2O(), a18_CO2g_H2O(), a18_CO3_H2O(), a18_HCO3_H2O(), a18_c_H2O(), a_A_B()

Examples

a18_H2O_OH(temp = 90, eq = "Z20-X3LYP")

18O/16O fractionation factor between HCO3(-) and H2O

Description

a18_HCO3_H2O() calculates the 18O/16O fractionation factor between bicarbonate ion HCO3(-) and water.

Usage

a18_HCO3_H2O(temp)

Arguments

Details

\alpha^{18}_{HCO3(-)/H2O} = e^{2.59 \times \frac{1000}{T^{2}} + 0.00189}

The equation above and in the function is the uncorrected equation in Beck et al. (2005). They experimentally determined the fractionation factor using BaCO3 precipitation experiments. However, they applied the acid fractionation factor of calcite during the data processing and not that of BaCO3. The acid fractionation factor of BaCO3 is not known accurately, which may result in a bias of up to 1‰ in the calculated 1000lna values.

Value

Returns the 18O/16O fractionation factor.

References

Beck, W. C., Grossman, E. L., & Morse, J. W. (2005). Experimental studies of oxygen isotope fractionation in the carbonic acid system at 15°, 25°, and 40°C. Geochimica et Cosmochimica Acta, 69(14), 3493-3503. doi:10.1016/j.gca.2005.02.003

See Also

Other fractionation_factors: a13_CO2g_CO2aq(), a18_CO2acid_c(), a18_CO2aq_H2O(), a18_CO2g_H2O(), a18_CO3_H2O(), a18_H2O_OH(), a18_c_H2O(), a_A_B()

18O/16O fractionation factor between carbonate and water

Description

a18_c_H2O() calculates the 18O/16O fractionation factor between carbonate and water.

Usage

a18_c_H2O(temp, min, eq)

Arguments

Details

Options for eq if min = "calcite":

"ONeil69": O'Neil et al. (1969), modified by Friedman and O'Neil (1977):

\alpha^{18}_{calcite/water} = e^{(2.78 \times \frac{1000}{T^{2}} - 0.00289)}

"KO97-orig": Kim and O'Neil (1997):

\alpha^{18}_{calcite/water} = e^{(18.03 \times \frac{1}{T} - 0.03242)}

NOTE: The "KO97-orig" equation should only be applied to data that considers a CO2(acid)/calcite AFF as in Kim & O'Neil (1997), i.e., 10.44 at 25 °C.

"KO97": Kim and O'Neil (1997), reprocessed here to match the IUPAC-recommended AFF as in Kim et al. (2007, 2015):

\alpha^{18}_{calcite/water} = e^{(18.04 \times \frac{1}{T} - 0.03218)}

"Coplen07": Coplen (2007):

\alpha^{18}_{calcite/water} = e^{(17.4 \times \frac{1}{T} - 0.0286)}

"Tremaine11": Tremaine et al. (2011):

\alpha^{18}_{calcite/water} = e^{(16.1 \times \frac{1}{T} - 0.0246)}

"Watkins13": Watkins et al. (2013):

\alpha^{18}_{calcite/water} = e^{(17.747 \times \frac{1}{T} - 0.029777)}

"Daeron19": Daëron et al. (2019):

\alpha^{18}_{calcite/water} = e^{(17.57 \times \frac{1}{T} - 0.02913)}

Options for eq if min = "aragonite":

"GK86": Grossman and Ku (1986), modified by Dettman et al. (1999):

\alpha^{18}_{aragonite/water} = e^{(2.559 \times \frac{1000}{T^{2}} + 0.000715)}

"Kim07": Kim et al. (2007):

\alpha^{18}_{aragonite/water} = e^{(17.88 \times \frac{1}{T} - 0.03114)}

Options for eq if min = "apatite". Apatite refers to apatite-bound carbonate.

"Lecuyer10": Lécuyer et al. (2010):

\alpha^{18}_{apatite/water} = e^{(25.19 \times \frac{1}{T} - 0.05647)}

Options for eq if min = "siderite":

"vanDijk18": van Dijk et al. (2018):

\alpha^{18}_{siderite/water} = e^{(19.67 \times \frac{1}{T} - 0.03627)}

Options for eq if min = "dolomite":

"Vasconcelos05": Vasconcelos et al. (2005):

\alpha^{18}_{dolomite/water} = e^{(2.73 \times \frac{1000}{T^{2}} + 0.00026)}

"Muller19": Müller et al. (2019):

\alpha^{18}_{dolomite/water} = e^{(2.9923 \times \frac{1000}{T^{2}} + 0.0023592)}

Value

Returns the 18O/16O fractionation factor.

References

O'Neil, J. R., Clayton, R. N., & Mayeda, T. K. (1969). Oxygen isotope fractionation in divalent metal carbonates. The Journal of Chemical Physics, 51(12), 5547-5558. doi:10.1063/1.1671982

Grossman, E. L., & Ku, T. L. (1986). Oxygen and carbon isotope fractionation in biogenic aragonite: Temperature effects. Chemical Geology, 59(1), 59-74. doi:10.1016/0009-2541(86)90044-6

Kim, S.-T., & O'Neil, J. R. (1997). Equilibrium and nonequilibrium oxygen isotope effects in synthetic carbonates. Geochimica et Cosmochimica Acta, 61(16), 3461-3475. doi:10.1016/S0016-7037(97)00169-5

Dettman, D. L., Reische, A. K., & Lohmann, K. C. (1999). Controls on the stable isotope composition of seasonal growth bands in aragonitic fresh-water bivalves (unionidae). Geochimica et Cosmochimica Acta, 63(7-8), 1049-1057. doi:10.1016/s0016-7037(99)00020-4

Vasconcelos, C., McKenzie, J. A., Warthmann, R., & Bernasconi, S. M. (2005). Calibration of the d18O paleothermometer for dolomite precipitated in microbial cultures and natural environments. Geology, 33(4), 317-320. doi:10.1130/g20992.1

Kim, S.-T., Mucci, A., & Taylor, B. E. (2007). Phosphoric acid fractionation factors for calcite and aragonite between 25 and 75 °C: Revisited. Chemical Geology, 246(3-4), 135-146. doi:10.1016/j.chemgeo.2007.08.005

Coplen, T. B. (2007). Calibration of the calcite-water oxygen-isotope geothermometer at Devils Hole, Nevada, a natural laboratory. Geochimica et Cosmochimica Acta, 71(16), 3948-3957. doi:10.1016/j.gca.2007.05.028

Lécuyer, C., Balter, V., Martineau, F., Fourel, F., Bernard, A., Amiot, R., et al. (2010). Oxygen isotope fractionation between apatite-bound carbonate and water determined from controlled experiments with synthetic apatites precipitated at 10-37°C. Geochimica et Cosmochimica Acta, 74(7), 2072-2081. doi:10.1016/j.gca.2009.12.024

Tremaine, D. M., Froelich, P. N., & Wang, Y. (2011). Speleothem calcite farmed in situ: Modern calibration of d18O and d13C paleoclimate proxies in a continuously-monitored natural cave system. Geochimica et Cosmochimica Acta, 75(17), 4929-4950. doi:10.1016/j.gca.2011.06.005

Watkins, J. M., Nielsen, L. C., Ryerson, F. J., & DePaolo, D. J. (2013). The influence of kinetics on the oxygen isotope composition of calcium carbonate. Earth and Planetary Science Letters, 375, 349-360. doi:10.1016/j.epsl.2013.05.054

van Dijk, J., Fernandez, A., Müller, I. A., Lever, M., & Bernasconi, S. M. (2018). Oxygen isotope fractionation in the siderite-water system between 8.5 and 62 °C. Geochimica et Cosmochimica Acta, 220, 535-551. doi:10.1016/j.gca.2017.10.009

Daëron, M., Drysdale, R. N., Peral, M., Huyghe, D., Blamart, D., Coplen, T. B., et al. (2019). Most Earth-surface calcites precipitate out of isotopic equilibrium. Nature Communications, 10, 429. doi:10.1038/s41467-019-08336-5

Müller, I.A., Rodriguez-Blanco, J.D., Storck, J.-C., do Nascimento, G.S., Bontognali, T.R.R., Vasconcelos, C., Benning, L.G. & Bernasconi, S.M. (2019). Calibration of the oxygen and clumped isotope thermometers for (proto-)dolomite based on synthetic and natural carbonates. Chemical Geology, 525, 1-17. doi:10.1016/j.chemgeo.2019.07.014

See Also

Other fractionation_factors: a13_CO2g_CO2aq(), a18_CO2acid_c(), a18_CO2aq_H2O(), a18_CO2g_H2O(), a18_CO3_H2O(), a18_H2O_OH(), a18_HCO3_H2O(), a_A_B()

Examples

a18_c_H2O(temp = 25, min = "calcite", eq = "Coplen07")
a18_c_H2O(temp = 25, min = "aragonite", eq = "GK86")

Isotope fractionation factor between A and B

Description

a_A_B() calculates the isotope fractionation factor.

Usage

a_A_B(A, B)

Arguments

Details

\alpha^{i}E_{A/B} = \frac{\delta^{i}E_{A} + 1}{\delta^{i}E_{B} + 1}

Value

Returns the isotope fractionation factor.

See Also

A_from_a() calculates the isotope delta value of A.

B_from_a() calculates the isotope delta value of B.

Other fractionation_factors: a13_CO2g_CO2aq(), a18_CO2acid_c(), a18_CO2aq_H2O(), a18_CO2g_H2O(), a18_CO3_H2O(), a18_H2O_OH(), a18_HCO3_H2O(), a18_c_H2O()

Examples

a_A_B(A = 10, B = 12)

Triple oxygen isotope values of carbonates

Description

d17O_c() calculates the equilibrium d18O, d17O, and D17O values of a calcite grown at a given temperature.

Usage

d17O_c(
  temp,
  d18O_H2O_VSMOW,
  D17O_H2O = 0,
  min = "calcite",
  eq17 = "Wostbrock20",
  eq18 = "Daeron19",
  lambda = 0.528
)

Arguments

Details

\theta_{A/B} = \frac{\alpha^{17}_{A/B}}{\alpha^{18}_{A/B}}

\delta'^{17}O_{H2O,VSMOW} = \beta \times \delta'^{18}O_{H2O,VSMOW} + \gamma \textrm{ , where } \beta=0.528 \textrm{ and } \gamma = 0

\Delta^{17}O_{CaCO3,VSMOW} = \delta'^{17}O_{CaCO3,VSMOW} - \lambda \times \delta'^{18}O_{CaCO3,VSMOW}

"Wostbrock20": Wostbrock et al. (2020):

\theta_{aragonite/water} = \frac{-1.53}{T} + 0.5305

\theta_{calcite/water} = \frac{-1.39}{T} + 0.5305

"GZ19": Guo and Zhou (2019):

\theta_{aragonite/water} = \frac{78.1173}{T^{2}} - \frac{1.5152}{T} + 0.5299

\theta_{calcite/water} = \frac{59.1047}{T^{2}} - \frac{1.4089}{T} + 0.5297

Value

Returns a data frame:

1. d18O value of the carbonate expressed on the VSMOW scale (‰).

2. d17O value of the carbonate expressed on the VSMOW scale (‰).

3. D17O value of the carbonate expressed on the VSMOW scale (‰).

References

Wostbrock, J.A.G., Brand, U., Coplen, T.B., Swart, P.K., Carlson, S.J., Brearley, A.J., and Sharp, Z.D. (2020). Calibration of carbonate-water triple oxygen isotope fractionation: Seeing through diagenesis in ancient carbonates. Geochimica et Cosmochimica Acta, 288, 369-388. doi:10.1016/j.gca.2020.07.045

Guo, W., and Zhou, C. (2019). Triple oxygen isotope fractionation in the DIC-H2O-CO2 system: A numerical framework and its implications. Geochimica et Cosmochimica Acta, 246, 541-564. doi:10.1016/j.gca.2018.11.018

See Also

Other equilibrium_carbonate: D47(), D48(), d18O_c()

Examples

d17O_c(temp = 10, d18O_H2O_VSMOW = -1) # Returns the data frame (length = 3)
prime(d17O_c(temp = 10, d18O_H2O_VSMOW = -1)[, 2]) # Returns the d'17O value
d17O_c(temp = 10, d18O_H2O_VSMOW = -1)[, 3] # Returns the D17O value

Triple oxygen isotope values of quartz

Description

d17O_qz() calculates the equilibrium d18O, d17O, and D17O values of quartz grown at a given temperature.

Usage

d17O_qz(temp, d18O_H2O_VSMOW, D17O_H2O = 0, lambda = 0.528)

Arguments

Details

\theta_{A/B} = \frac{\alpha^{17}_{A/B}}{\alpha^{18}_{A/B}}

\delta'^{17}O_{H2O,VSMOW} = \beta \times \delta'^{18}O_{H2O,VSMOW} + \gamma \textrm{ , where } \beta=0.528 \textrm{ and } \gamma = 0

\Delta^{17}O_{SiO2,VSMOW} = \delta'^{17}O_{SiO2,VSMOW} - \lambda \times \delta'^{18}O_{SiO2,VSMOW}

NOTE:

\theta_{quartz/water} = -\frac{1.85}{T} + 0.5305

\alpha^{18}_{quartz/water} = e^{(\frac{4280}{T^{2}} - \frac{3.5}{T})}

Value

Returns a data frame:

1. d18O value of the quartz expressed on the VSMOW scale (‰).

2. d17O value of the quartz expressed on the VSMOW scale (‰).

3. D17O value of the quartz expressed on the VSMOW scale (‰).

References

Sharp, Z.D., Gibbons, J.A., Maltsev, O., Atudorei, V., Pack, A., Sengupta, S., Shock, E.L. and Knauth, L.P. (2016). A calibration of the triple oxygen isotope fractionation in the SiO2-H2O system and applications to natural samples. Geochimica et Cosmochimica Acta, 186, 105-119. doi:10.1016/j.gca.2016.04.047

Examples

d17O_qz(temp = 10, d18O_H2O_VSMOW = 0) # Returns the data frame (length = 3)
d17O_qz(temp = 10, d18O_H2O_VSMOW = 0)[, 3] # Returns the D17O value

Water d18O value

Description

d18O_H2O() calculates the d18O value of the ambient water from the d18O value of a carbonate and its growth temperature.

Usage

d18O_H2O(temp, d18O_c_VSMOW, min, eq)

Arguments

Value

Returns the water d18O value expressed on the VSMOW scale (‰).

Note

Use to_VSMOW() and to_VPDB() to convert between the VSMOW and VPDB scales.

References

References are listed in the description of a18_c_H2O().

See Also

d18O_c() calculates the equilibrium d18O value of a carbonate grown at a given temperature. temp_d18O() calculates growth temperatures from oxygen isotope data.

Examples

d18O_H2O(temp = 33.7, d18O_c_VSMOW = 14.58,
         min = "calcite", eq = "Coplen07")
d18O_H2O(temp = 25, d18O_c_VSMOW = to_VSMOW(-7.47),
         min = "aragonite", eq = "GK86")

Equilibrium carbonate d18O value

Description

d18O_c() calculates the equilibrium d18O value of a carbonate grown at a given temperature.

Usage

d18O_c(temp, d18O_H2O_VSMOW, min, eq)

Arguments

Value

Returns the equilibrium carbonate d18O value expressed on the VSMOW scale (‰).

Note

Use to_VSMOW() and to_VPDB() to convert between the VSMOW and VPDB scales.

References

References are listed in the description of a18_c_H2O().

See Also

d18O_H2O() calculates the d18O value of the ambient water from the d18O value of a carbonate and its growth temperature.

Other equilibrium_carbonate: D47(), D48(), d17O_c()

Examples

d18O_c(33.7, -13.54, min = "calcite", eq = "Coplen07")
to_VPDB(d18O_c(temp = 12, d18O_H2O_VSMOW = -6.94,
               min = "aragonite", eq = "GK86"))

Devils Hole carbonate d18O time series

Description

A dataset containing the d18O values of the "original" Devils Hole cores.

Usage

devilshole

Format

A data frame with 442 rows and 4 variables:

age

Interpolated uranium-series age of the sample expressed as thousands of years before present (ka).

d18O_VSMOW

Carbonate d18O value expressed on the VSMOW scale (‰).

d18O_error

Standard deviation on the d18O value.

core

Name of the core (DHC2-8, DHC2-3, DH-11).

Source

doi:10.3133/ofr20111082

References

Winograd, I. J., Landwehr, J. M., Coplen, T. B., Sharp, W. D., Riggs, A. C., Ludwig, K. R., & Kolesar, P. T. (2006). Devils Hole, Nevada, d18O record extended to the mid-Holocene. Quaternary Research, 66(2), 202-212. doi:10.1016/j.yqres.2006.06.003

See Also

Other "datasets": GTS2020, LR04, meteoric_water

Isotope fractionation value

Description

epsilon() converts isotope fractionation factors to isotope fractionation values.

Usage

epsilon(alpha)

Arguments

Details

\epsilon^{i}E_{A/B} = \alpha^{i}E_{A/B} - 1

Value

Returns the isotope fractionation value (‰).

See Also

a_A_B() calculates the isotope fractionation factor between A and B.

Examples

epsilon(a18_H2O_OH(25, "Z20-X3LYP"))

Oxygen isotope values for meteoric waters

Description

A dataset containing a compilation of d17O and d17O values of various meteoric waters.

Usage

meteoric_water

Format

A data frame with 156 rows and 4 variables:

Sample

Sample ID as in the original publication.

d17O

Water d17O value expressed on the VSMOW scale (‰).

d18O

Water d18O value expressed on the VSMOW scale (‰).

Reference

Abbreviated reference for the data point.

References

Luz, B., & Barkan, E. (2010). Variations of 17O/16O and 18O/16O in meteoric waters. Geochimica et Cosmochimica Acta, 74(22), 6276–6286. doi:10.1016/j.gca.2010.08.016

Aron, P. G., Levin, N. E., Beverly, E. J., Huth, T. E., Passey, B. H., Pelletier, E. M., Poulsen, C. J., Winkelstern, I. Z., & Yarian, D. A. (2021). Triple oxygen isotopes in the water cycle. Chemical Geology, 565, 116770. doi:10.1016/j.chemgeo.2020.120026

See Also

Other "datasets": GTS2020, LR04, devilshole

Mixing curves in triple oxygen isotope space

Description

mix_d17O() produces mixing curves between two endmembers (A and B) in triple oxygen isotope space (d18O vs. D17O).

Usage

mix_d17O(
  d18O_A,
  d17O_A,
  D17O_A,
  d18O_B,
  d17O_B,
  D17O_B,
  lambda = 0.528,
  step = 10
)

Arguments

Details

If both d17O and D17O values are specified for a component, the function uses the d17O values for the calculations.

Value

Returns a data frame:

1. d18O value of the mixture at x% mixing (‰).

2. D17O value of the mixture at x% mixing (‰).

3. relative amount of component B in the mixture (%): from 100% A and 0% B to 0% A and 100% B.

4. d17O value of the mixture at x% mixing (‰).

See Also

d17O_c() calculates equilibrium calcite d18O, d17O, and D17O values for a given temperature.

Examples

# The two functions below yield the same output.
mix_d17O(d18O_A = d17O_c(10, -1)[1], d17O_A = d17O_c(10, -1)[2],
         d18O_B = d17O_c(100,0)[1], d17O_B = d17O_c(100, 0)[2])
mix_d17O(d18O_A = d17O_c(10, -1)[1], D17O_A = d17O_c(10, -1)[3],
         d18O_B = d17O_c(100,0)[1], D17O_B = d17O_c(100, 0)[3])

Converting delta to delta prime

Description

prime() converts "classical delta" values to "delta prime" values.

Usage

prime(classical)

Arguments

Details

\delta'^{17}O = 1000 \times \ln(\frac{\delta^{17}O}{1000}+1)

Value

Returns the "delta prime" value (‰).

See Also

unprime() converts "delta prime" values to "classical delta" values.

Examples

prime(10) # Return 9.950331

Clumped isotope thermometry

Description

temp_D47() calculates carbonate growth temperature from D47 value.

Usage

temp_D47(D47_CDES90, D47_error, eq)

Arguments

Details

The D47 vs temperature equations are listed at D47().

Value

Returns the carbonate growth temperature (°C). If D47_error is specified temp_D47() returns a data frame.

References

References are listed at D47().

See Also

D47() calculates the equilibrium carbonate D47 value.

Other thermometry: temp_D48(), temp_d18O()

Examples

temp_D47(D47_CDES90 = 0.577, eq = "Petersen19")

Dual clumped isotope thermometry

Description

temp_D48() calculates carbonate growth temperature from D47 and D48 values.

Usage

temp_D48(
  D47_CDES90,
  D48_CDES90,
  D47_error,
  D48_error,
  ks,
  add = FALSE,
  col = "black",
  pch = 19
)

Arguments

Details

The function calculates a D47 value as an intersect of two curves: the equilibrium D47 vs D48 curve from Fiebig et al. (2021) and the kinetic slope. The resulting D47 value is then converted to temperature using the temp_D47() function and the equilibrium D47_CDES90 vs temperature equation of Fiebig et al. (2021).

Value

Returns the carbonate growth temperature (°C). If both D47_error and D48_error are specified temp_D48() returns a data frame.

Contributors

The source code of this function contains elements from the reconPlots package, available at https://github.com/andrewheiss/reconPlots

References

References are listed at D48() and D47().

See Also

D47() calculates the equilibrium carbonate D47 value. D48() calculates the equilibrium carbonate D48 value.

Other thermometry: temp_D47(), temp_d18O()

Examples

temp_D48(0.617, 0.139, ks = -0.6)
temp_D48(0.546, 0.277, ks = -1)

Oxygen isotope thermometry

Description

temp_d18O() calculates carbonate growth temperature from oxygen isotope data.

Usage

temp_d18O(d18O_c_VSMOW, d18O_H2O_VSMOW, min, eq)

Arguments

Value

Returns the carbonate growth temperature (°C).

Note

Use to_VSMOW() and to_VPDB() to convert between the VSMOW and VPDB scales.

References

References are listed in the description of a18_c_H2O().

See Also

d18O_c() calculates the equilibrium d18O value of a carbonate grown at a given temperature.

d18O_H2O() calculates the d18O value of the ambient water from the d18O value of a carbonate and its growth temperature.

Other thermometry: temp_D47(), temp_D48()

Examples

temp_d18O(d18O_c_VSMOW = 14.58, d18O_H2O_VSMOW = -13.54,
          min = "calcite", eq = "Coplen07")

Converting isotope delta from VSMOW to VPDB

Description

to_VPDB() convert d18O value expressed on the VSMOW scale to the VPDB scale.

Usage

to_VPDB(d18O_VSMOW, eq = "IUPAC")

Arguments

Details

The IUPAC recommended equation to convert between the scales is:

\delta^{18}O_{VPDB} = 0.97001 \times \delta^{18}O_{VSMOW} - 29.99

Value

Returns the d18O value expressed on the VPDB scale (‰).

References

References are listed at to_VSMOW().

See Also

to_VSMOW() converts d18O values expressed on the VPDB scale to the VSMOW scale.

Examples

to_VPDB(0)
to_VPDB(0, eq = "Coplen83")

Converting isotope delta from VPDB to VSMOW

Description

to_VSMOW() converts d18O value expressed on the VPDB scale to the VSMOW scale.

Usage

to_VSMOW(d18O_VPDB, eq = "IUPAC")

Arguments

Details

The IUPAC recommended equation to convert between the scales is:

\delta^{18}O_{VSMOW} = 1.03092 \times \delta^{18}O_{VPDB} + 30.92

Value

Returns the d18O value expressed on the VSMOW scale (‰).

References

Coplen, T. B., Kendall, C., & Hopple, J. (1983). Comparison of stable isotope reference samples. Nature, 302, 236-238. doi:10.1038/302236a0

Brand, W. A., Coplen, T. B., Vogl, J., Rosner, M., & Prohaska, T. (2014). Assessment of international reference materials for isotope-ratio analysis (IUPAC Technical Report). Pure and Applied Chemistry, 86(3), 425-467. doi:10.1515/pac-2013-1023

Kim, S.-T., Coplen, T. B., & Horita, J. (2015). Normalization of stable isotope data for carbonate minerals: Implementation of IUPAC guidelines. Geochimica et Cosmochimica Acta, 158, 276-289. doi:10.1016/j.gca.2015.02.011

See Also

to_VPDB() converts d18O values expressed on the VSMOW scale to the VPDB scale.

Examples

to_VSMOW(0)
to_VSMOW(0, eq = "Coplen83")

Converting delta prime to delta

Description

unprime() converts "delta prime" values to "classical delta" values.

Usage

unprime(prime)

Arguments

Details

\delta^{17}O = 1000 \times e^{(\frac{\delta'^{17}O}{1000}+1)}

Value

Returns the "classical delta" value (‰).

See Also

prime() converts "classical delta" values to "delta prime" values.

Examples

unprime(9.950331) # Return 10

Error-considering linear regression

Description

york_fit() calculates the regression parameters of an error-considering linear regression.

Usage

york_fit(x, y, x_err, y_err, r = 0)

Arguments

Details

Regression fitting method according to York et al. (2004). The algorithm is described in the appendix of Wacker et al. (2014).

Value

A list with regression parameters:

• slope and its standard error

• intercept and its standard error

• weights of the points (normalized to 1)

• residual standard error (sigma)

• R2

• p-value (two-tailed t-test).

Contributors

Julian Tödter

References

York, D., Evensen, N. M., López Martínez, M., & De Basabe Delgado, J. (2004). Unified equations for the slope, intercept, and standard errors of the best straight line. American Journal of Physics, 72(3), 367-375. doi:10.1119/1.1632486

Wacker, U., Fiebig, J., Tödter, J., Schöne, B. R., Bahr, A., Friedrich, O., et al. (2014). Empirical calibration of the clumped isotope paleothermometer using calcites of various origins. Geochimica et Cosmochimica Acta, 141, 127-144. doi:10.1016/j.gca.2014.06.004

Examples

york_fit(
  x = c(1, 2, 3),
  y = c(1.1, 1.9, 3.2),
  x_err = c(0.1, 0.2, 0.1),
  y_err = c(0.2, 0.1, 0.2))

Regression confidence intervals

Description

york_plot() calculates and optionally plots the confidence intervals of an (error-considering) linear regression.

Usage

york_plot(
  x,
  slope,
  slope_se,
  intercept,
  intercept_se,
  cl = 0.95,
  weights = -1,
  add = FALSE,
  col = "black"
)

Arguments

Details

The algorithm is described in the appendix of Wacker et al. (2014).

Value

A list with regression parameters:

• slope and its standard error

• intercept and its standard error

• weights of the points (normalized to 1)

• residual standard error (sigma)

• R2

• p-value (two-tailed t-test).

Contributors

Julian Tödter

References

Wacker, U., Fiebig, J., Tödter, J., Schöne, B. R., Bahr, A., Friedrich, O., et al. (2014). Empirical calibration of the clumped isotope paleothermometer using calcites of various origins. Geochimica et Cosmochimica Acta, 141, 127-144. doi:10.1016/j.gca.2014.06.004

Examples

york_plot(
  x = c(1, 2, 3),
  slope = 1.06,
  slope_se = 1.60,
  intercept = -0.05,
  intercept_se = 0.34,
  cl = 0.98)