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isogeochem: Tools for Stable Isotope Geochemistry

website·Indexed 30 days ago

https://davidbajnai.github.io/isogeochem/index.html

An R package providing tools for stable isotope geochemistry, including functions for calculating isotope fractionation factors, oxygen isotope thermometry, dual clumped isotope thermometry, and conversions between VPDB and VSMOW scales. It includes utilities for error-considering linear regression (york_fit) and access to isotope stratigraphy data such as the Geologic Time Scale 2020.

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What's inside isogeochem

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  6. Example usage of york_fit

    This example demonstrates how to perform a York regression with specific x/y values and their corresponding errors.
    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)
)

# Expected output includes:
# $slope: 1.061775
# $slope_se: 0.1599487
# $intercept: -0.05293936
# $intercept_se: 0.3416549
# $w: 0.3412216 0.3175568 0.3412216
# $sigma: 0.1167873
# $R2: 0.9822171
# $pval: 0.09518642

  8. Recalculate calcite δ18O values using updated IUPAC Acid Fractionation Factors

    The original Kim and O'Neil (1997) equation used an 18O/16O acid fractionation factor (AFF) of 1.01050 at 25 °C. To update these values to the current IUPAC recommendation (1.010254), you must first convert the calcite δ18O to the δ18O of CO2 produced from acid digestion using the old AFF, and then convert back to calcite δ18O using the new AFF.
    # Convert d18O_calcite to d18O_CO2acid using the "old" AFF (1.01050)
d18O_CO2acid = A_from_a(a = 1.01050, B = d18O_calcite)

# Get the current IUPAC recommended AFF for calcite at 25°C
AFF_new = a18_CO2acid_c(25, "calcite")

# Convert d18O_CO2acid to d18O_calcite using the "new" AFF
d18O_calcite_newAFF = B_from_a(a = AFF_new, d18O_CO2acid)

  9. Example usage of d17O_c() for carbonate isotope analysis

    This example demonstrates how to calculate triple oxygen isotope values for a carbonate grown at 10°C in water with a d18O of -1‰, and how to extract specific values from the resulting data frame.
    # Calculate d18O, d17O, and D17O values
results <- d17O_c(temp = 10, d18O_H2O_VSMOW = -1)
print(results)
# Output: d18O_c: 32.43637, d17O_c: 16.91669, D17O_c: -0.07931083

# Extract the D17O value specifically
d17o_val <- results[, 3]
print(d17o_val)
# Output: -0.07931083

# Calculate the d'17O value using the prime() function on the d17O column
prime(results[, 2])
# Output: 16.7752

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