Package 'isogeochem' reference manual

Title:	Tools for Stable Isotope Geochemistry
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.
Authors:	David Bajnai [aut, cre] , Julian Tödter [ctb]
Maintainer:	David Bajnai <[email protected]>
License:	GPL (>= 3)
Version:	1.1.1
Built:	2025-02-15 03:24:20 UTC
Source:	https://github.com/davidbajnai/isogeochem

Isotope fractionation factor between A and B

Description

a_A_B() calculates the isotope fractionation factor.

Usage

a_A_B(A, B)
a_A_B(A, B)

Arguments

`A`	Isotope delta value of A (‰).
`B`	Isotope delta value of B (‰).

Details

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

Value

Returns the isotope fractionation factor.

Examples

a_A_B(A = 10, B = 12)

a_A_B(A = 10, B = 12)

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)
A_from_a(a, B)

Arguments

`a`	Isotope fractionation factor between A and B.
`B`	Isotope delta value of B (‰).

Value

Returns the isotope delta value of B (‰).

Examples

A_from_a(a = 1.033, B = -10)

A_from_a(a = 1.033, B = -10)

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)
a13_CO2g_CO2aq(temp)

Arguments

temp

Temperature (°C).

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

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)
a18_c_H2O(temp, min, eq)

Arguments

`temp`	Carbonate growth temperature (°C).
`min`	Mineralogy. Options are `"calcite"`, `"aragonite"`, `apatite`, `siderite`, and `"dolomite"`.
`eq`	Equation used for the calculations. See details.

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

Examples

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

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

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)
a18_CO2acid_c(temp, min)

Arguments

`temp`	Acid digestion temperature (°C).
`min`	Mineralogy. Options are `"calcite"`, `"aragonite"`, and `"dolomite"`.

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

Examples

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

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)
a18_CO2aq_H2O(temp)

Arguments

temp

Temperature (°C).

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

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)
a18_CO2g_H2O(temp)

Arguments

temp

Temperature (°C).

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

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)
a18_CO3_H2O(temp)

Arguments

temp

Temperature (°C).

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

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)
a18_H2O_OH(temp, eq)

Arguments

temp

Temperature (°C).

eq

Equation used for the calculations.

Z20-X3LYP: the theoretical X3LYP/6-311+G(d,p) equation of Zeebe (2020).
Z20-MP2: the theoretical MP2/aug-cc-pVDZ equation of Zeebe (2020).

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

Examples

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

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)
a18_HCO3_H2O(temp)

Arguments

temp

Temperature (°C).

Details

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

Value

Returns the 18O/16O fractionation factor.

References

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)
B_from_a(a, A)

Arguments

`a`	Isotope fractionation factor between A and B.
`A`	Isotope delta value of A (‰).

Value

Returns the Isotope delta value of B (‰).

Examples

B_from_a(a = 1.033, A = 10)

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)
D17O(d18O, d17O, lambda = 0.528)

Arguments

`d18O`	Isotope delta value (‰).
`d17O`	Isotope delta value (‰).
`lambda`	Triple oxygen isotope reference slope. Default `0.528`.

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)

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

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

Arguments

`temp`	Calcite growth temperature (°C).
`d18O_H2O_VSMOW`	Water d18O value expressed on the VSMOW scale (‰).
`D17O_H2O`	D17O value of ambient water calculated using a lambda of `0.528`. Default `0`.
`min`	Mineralogy. Options are `"calcite"` (default) and `"aragonite"`.
`eq17`	Equation used to calculate the 17O/16O fractionation factor between carbonate and water. Options are `"Wostbrock20"` (default) and `"GZ19"`.
`eq18`	Equation used to calculate the 18O/16O fractionation factor between carbonate and water. Options are like in `a18_c_H2O()`. Default `"Daeron19"`.
`lambda`	Triple oxygen isotope reference slope. Default `0.528`.

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:

d18O value of the carbonate expressed on the VSMOW scale (‰).
d17O value of the carbonate expressed on the VSMOW scale (‰).
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

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

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

Arguments

`temp`	Quartz growth temperature (°C).
`d18O_H2O_VSMOW`	Water d18O value expressed on the VSMOW scale (‰).
`D17O_H2O`	D17O value of ambient water calculated using a lambda of `0.528`. Default `0`.
`lambda`	Triple oxygen isotope reference slope. Default `0.528`.

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:

d18O value of the quartz expressed on the VSMOW scale (‰).
d17O value of the quartz expressed on the VSMOW scale (‰).
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

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

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)
d18O_c(temp, d18O_H2O_VSMOW, min, eq)

Arguments

`temp`	Carbonate growth temperature (°C).
`d18O_H2O_VSMOW`	Water d18O value expressed on the VSMOW scale (‰).
`min`	Mineralogy. Options are as in `a18_c_H2O()`.
`eq`	Equation used for the calculations. Options depend on mineralogy and are listed in `a18_c_H2O()`.

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().

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"))

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"))

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)
d18O_H2O(temp, d18O_c_VSMOW, min, eq)

Arguments

`temp`	Carbonate growth temperature (°C).
`d18O_c_VSMOW`	Carbonate d18O value expressed on the VSMOW scale (‰).
`min`	Mineralogy. Options are `"calcite"`, `"aragonite"`, and `"dolomite"`.
`eq`	Equation used to calculate the equilibrium 18O/16O oxygen isotope fractionation factor between carbonate and water. Options depend on mineralogy and listed in `a18_c_H2O()`.

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().

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")

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 D47 value

Description

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

Usage

D47(temp, eq)
D47(temp, eq)

Arguments

temp

Carbonate growth temperature (°C).

eq

Equation used for the calculation.

"Petersen19": the synthetic-only composite IUPAC-parameter calibration of Petersen et al. (2019).
"Anderson21": the I-CDES90 calibration of Anderson et al. (2021).
"Fiebig21": the CDES90 calibration of Fiebig et al. (2021).

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

Examples

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

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)
D48(temp, eq)

Arguments

temp

Carbonate growth temperature (°C).

eq

Equation used for the calculation.

"Fiebig21": the CDES90 calibration of Fiebig et al. (2021).
"Swart21": the CDES90 "PBLM1" calibration in Swart et al. (2021).

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

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

Examples

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

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

Devils Hole carbonate d18O time series

Description

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

Usage

devilshole
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

Isotope fractionation value

Description

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

Usage

epsilon(alpha)
epsilon(alpha)

Arguments

alpha

Isotope fractionation factor

Details

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

Value

Returns the isotope fractionation value (‰).

Examples

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

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

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
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

A Pliocene-Pleistocene benthic foraminifera d18O stack

Description

A dataset containing the LR04 benthic d18O stack.

Usage

LR04
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

Oxygen isotope values for meteoric waters

Description

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

Usage

meteoric_water
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

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

Arguments

`d18O_A`	d18O value of component A (‰).
`d17O_A`	d17O value of component A (‰).
`D17O_A`	Alternatively, the D17O value of component A (‰).
`d18O_B`	d18O value of component B (‰).
`d17O_B`	d17O value of component B (‰).
`D17O_B`	Alternatively, the D17O value of component B (‰).
`lambda`	Triple oxygen isotope reference slope. Default `0.528`.
`step`	Output resolution, i.e., step size. Default `10`%.

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:

d18O value of the mixture at x% mixing (‰).
D17O value of the mixture at x% mixing (‰).
relative amount of component B in the mixture (%): from 100% A and 0% B to 0% A and 100% B.
d17O value of the mixture at x% mixing (‰).

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])

# 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)
prime(classical)

Arguments

classical

"Classical delta" values to be converted (‰).

Details

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

Value

Returns the "delta prime" value (‰).

Examples

prime(10) # Return 9.950331

prime(10) # Return 9.950331

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)
temp_d18O(d18O_c_VSMOW, d18O_H2O_VSMOW, min, eq)

Arguments

`d18O_c_VSMOW`	Carbonate d18O value expressed on the VSMOW scale (‰).
`d18O_H2O_VSMOW`	Water d18O value expressed on the VSMOW scale (‰).
`min`	Mineralogy. Options are as in `a18_c_H2O()`.
`eq`	Equation used for the calculations. Options depend on mineralogy and listed in `a18_c_H2O()`.

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().

Examples

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

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

Clumped isotope thermometry

Description

temp_D47() calculates carbonate growth temperature from D47 value.

Usage

temp_D47(D47_CDES90, D47_error, eq)
temp_D47(D47_CDES90, D47_error, eq)

Arguments

`D47_CDES90`	Carbonate D47 values expressed on the CDES90 scale (‰).
`D47_error`	Error on the D47 value. Optional.
`eq`	Equation used for the calculation. Options are as in `D47()`.

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().

Examples

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

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

Arguments

`D47_CDES90`	Carbonate D47 values expressed on the CDES90 scale (‰).
`D48_CDES90`	Carbonate D48 values expressed on the CDES90 scale (‰).
`D47_error`	Error on the D47 value. Optional.
`D48_error`	Error on the D48 value. Optional.
`ks`	Kinetic slope. Has to be negative!
`add`	Add graphics to an already existing plot? Default: `FALSE`.
`col`	Graphical parameter. Optional.
`pch`	Graphical parameter. Optional.

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().

Examples

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

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

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")
to_VPDB(d18O_VSMOW, eq = "IUPAC")

Arguments

d18O_VSMOW

d18O values expressed on the VSMOW scale (‰).

eq

Equation used for the conversion.

"IUPAC" (default): the IUPAC recommended equation listed in Brand et al. (2014) and Kim et al. (2015).
"Coplen83": the equation listed in Coplen et al. (1983) and the Hoefs book.

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().

Examples

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

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")
to_VSMOW(d18O_VPDB, eq = "IUPAC")

Arguments

d18O_VPDB

d18O values expressed on the VPDB scale (‰).

eq

Equation used for the conversion.

"IUPAC" (default): the IUPAC recommended equation listed in Brand et al. (2014) and Kim et al. (2015).
"Coplen83": the equation listed in Coplen et al. (1983) and the Hoefs book.

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

Examples

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

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)
unprime(prime)

Arguments

prime

"Delta prime" values to be converted (‰).

Details

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

Value

Returns the "classical delta" value (‰).

Examples

unprime(9.950331) # Return 10

unprime(9.950331) # Return 10

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)
X_absorption(temp, pH, S)

Arguments

`temp`	The temperature of the solution (°C).
`pH`	The pH of the solution.
`S`	The salinity of the solution (g/kg or ‰).

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)

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

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)
X_DIC(temp, pH, S)

Arguments

`temp`	The temperature of the solution (°C).
`pH`	The pH of the solution.
`S`	The salinity of the solution (g/kg or ‰).

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)

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

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

Arguments

`x`	vector of x values.
`y`	vector of y values. Has to be same the length as x.
`x_err`	Error on the x values. Has to be same the length as x.
`y_err`	Error on the y values. Has to be same the length as x.
`r`	Correlation coefficient of x_err and y_err at each data point. Default: `0` (independent errors). Has to be same the length as x. Optional.

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))

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

Arguments

`x`	x values of the data points.
`slope`	regression slope.
`slope_se`	Standard error of the slope.
`intercept`	regression intercept.
`intercept_se`	Standard error of the intercept.
`cl`	Confidence level. Default: `0.95`.
`weights`	Weights of the data points. If given, mean & SD of x are computed with the weights. Has to be same the length as x. Optional.
`add`	Add graphics to an already existing plot? Default: `FALSE`.
`col`	Graphical parameter. Optional.

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

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)

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

Package 'isogeochem'

Help Index

Isotope fractionation factor between A and B

Description

Usage

Arguments

Details

Value

See Also

Examples

Isotope delta from fractionation factor

Description

Usage

Arguments

Value

See Also

Examples

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

Description

Usage

Arguments

Details

Value

References

See Also

18O/16O fractionation factor between carbonate and water

Description

Usage

Arguments

Details

Value

References

See Also

Examples

18O/16O acid fractionation factor

Description

Usage

Arguments

Details

Value

References

See Also

Examples

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

Description

Usage

Arguments

Details

Value

References

See Also

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

Description

Usage

Arguments

Details

Value

References

See Also

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

Description

Usage

Arguments

Details

Value

References

See Also

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

Description

Usage

Arguments

Value

References

See Also

Examples

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

Description

Usage

Arguments

Details