Package Reference Documentation

The following classes and methods form the isotopylog package:

isotopylog classes

isotopylog.EDistribution(kds, **kwargs) Class for inputting, storing, and visualizing clumped isotope activation energies.
isotopylog.HeatingExperiment(dex, T, tex, …) Class for inputting, storing, and visualizing clumped isotope heating experiment data.
isotopylog.kDistribution(params, model, T, …) Class for inputting, storing, and visualizing clumped isotope rate data.

isotopylog methods

isotopylog.calc_L_curve(he[, ax, kink, …]) Function to choose the “best” omega value for regularization following the Tikhonov Regularization method.
isotopylog.derivatize(num, denom) Method for derivatizing numerator, num, with respect to denominator, denom.
isotopylog.fit_Arrhenius(T, lnk[, lnk_std, …]) Determines the activation energy by fitting an Arrhenius plot.
isotopylog.fit_Hea14(he[, logy, p0]) Fits D evolution data using the transient defect/equilibrium model of Henkes et al.
isotopylog.fit_HH21(he[, nu_max, nu_min, …]) Fits D evolution data using the distributed activation energy model of Hemingway and Henkes (2021).
isotopylog.fit_HH21inv(he[, nu_max, nu_min, …]) Fits D evolution data using the distributed activation energy model of Hemingway and Henkes (2021).
isotopylog.fit_PH12(he[, logy, p0, thresh]) Fits D evolution data using the first-order model approximation of Passey and Henkes (2012).
isotopylog.fit_SE15(he[, p0, mp, z]) Fits D evolution data using the paired diffusion model of Stolper and Eiler (2015).
isotopylog.geologic_history(t, T, ed, d0[, …]) Predicts the D47 evolution when a given ipl.EDistribution model is subjected to any arbitrary time-temperature history.

References

The following references were used during creation of the core isotopylog pacakge or provide information regarding the choice of user-inputted parameters.

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  • Hansen (1994) Numerical Algorithms, 6, 1-35.
  • Gonfiantini (1995) IAEA Technical Report, 825.
  • Assonov and Brenninkmeijer (2003) Rapid Comm. Mass Spec., 17, 1017–1029.
  • Barkan and Luz (2005) Rapid Comm. Mass Spec., 19, 3737–3742.
  • Ghosh et al. (2006) Geochim. Cosmochim. Ac., 70, 1439–1456.
  • Brand (2010) Pure Appl. Chem., 82, 1719–1733.
  • Dennis et al. (2011) Geochim. Cosmochim. Ac., 75, 7117–7131.
  • Forney and Rothman (2012) J. Royal Soc. Inter., 9, 2255–2267.
  • Passey and Henkes (2012) Earth Planet. Sci. Lett., 351, 223–236.
  • Passey et al. (2014) Geochim. Cosmochim. Ac., 141, 1–25.
  • Henkes et al. (2014) Geochim. Cosmochim. Ac., 139, 362–382.
  • Stolper and Eiler (2015) Am. J. Sci., 315, 363–411.
  • Daëron et al. (2016) Chem. Geol., 442, 83–96.
  • Bonifacie et al. (2017) Geochim. Cosmochim. Ac., 200, 255–279.
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  • Chen et al. (2019) Geochim. Cosmochim. Ac., 258, 156–173.
  • Anderson et al. (2021) Geophys. Res. Lett., 48, e2020GL092069.
  • Bernasconi et al. (2021) Geochem., Geophys., Geosys., 22, e2020GC009588.
  • Hemingway and Henkes (2021) Earth Planet. Sci. Lett., 566, 116962.
  • Looser et al. (2023) Geochim. Cosmochim. Ac., 350, 1–15.