Package: isotopylog
About isotopylogisotopylogis a Python package for analyzing “clumped” isotope kinetic data; it is particularly suited for assessing carbonate clumped isotope (i.e., ∆47) bond reordering and closure temperatures, but will be expanded in the future to include clumped isotopes of other isotopologues (e.g., ∆48) molecular species (e.g., sulfate). This package currently performs two basic functions:it fits ∆47reordering data from carbonate heating experiments (inverse model) andit predicts geologic ∆47evolution given any time/temperature sample history (forward model).For both functions, the package can use any of the available clumped isotope kinetic models: (1) the “pseudo-first-order” model (Passey and Henkes, 2012), (2) the “transient defect/equilibrium defect” model (Henkes et al., 2014), (3) the “pair-diffusion” model (Stolper and Eiler, 2015), and (4) the “disordered kinetic” model (Hemingway and Henkes, 2021).This package allows users to quickly and easily assess whether their clumped isotope measurements reflect primary signatures, or if these values have been reset during diagenetic heating. Similarly, it also allows users to easily assess geologic cooling rates using the apparent “closure” or “blocking” temperatures recorded in carbonates that have been diagenetically heated.Package InformationAuthors:Jordon D. Hemingway (jordon.hemingway@erdw.ethz.ch)Version:0.0.8Release:24 May 2023License:GNU GPL v3 (or greater)url:http://github.com/FluvialSeds/isotopyloghttp://pypi.python.org/pypi/isotopylogdoi:How to CiteWhen analyzing data withisotopylogto be used in a peer-reviewed journal, please cite this package as:J.D. Hemingway.isotopylog: open-source tools for clumped isotope kinetic data analysis, 2020-,http://pypi.python.org/pypi/isotopylog[online; accessed 2023-10-10]Additionally, please cite the following peer-reviewed manuscript describing the deveopment of the package and clumped isotope data treatment:J.D. Hemingway and G.A. Henkes (2021) A disordered kinetic model for clumped isotope bond reordering in carbonates.Earth and Planetary Science Letters,566, 116962.If analyzing data with any of the previously published models, please also cite the relevant manuscript(s):For the pseudo-first-order model: B.H. Passey and G.A. Henkes (2012) Carbonate clumped isotope bond reordering and geospeedometry.Earth and Planetary Science Letters,351, 223–236.For the transient defect/equilibrium defect model: G.A. Henkes et al. (2014) Temperature limits for preservation of primary calcite clumped isotope paleotemperatures.Geochimica et Cosmochimica Acta,139, 362–382.For the pair-diffusion model: D.A. Stolper and J.M. Eiler (2015) The kinetics of solid-state isotope exchange reactions for clumped isotopes: A study of inorganic calcites and apatites from natural and experimental samples.American Journal of Science,315, 363–411.DocumentationThe documentation for the latest release—including detailed package references and comprehensive examples detailing various steps of the data analysis process—is available at:http://isotopylog.readthedocs.ioPackage featuresisotopylogcurrently contains the following features relevant for clumped isotope data analysis:Stores, culls, and plots experimental kinetic isotope dataEasily converts between multiple reference frames (e.g., Ghosh, CDES90, I-CDES)Plots forward-modeled predictions using rate parameters (i.e., k values) in order to visually assess goodness of fitEstimates the rate parameters (i.e., k values) of bond reordering kinetics for a given set of experimental results using any of the following models:Pseudo-first-order model (Passey and Henkes, 2012)Transient defect/equilibrium defect model (Henkes et al., 2014)Paired-diffusion model (Stolper and Eiler, 2015)Disordered kinetic model (Hemingway and Henkes, 2021)Calculates best-fit regularized (“smoothed”) rate distributions using Tikhonov RegularizationAutomated or user-defined regularization valueCan include negative solutions (e.g., for fitting aragonite data with transient ∆47increases)Determines best-fit lognormal rate distributionsDetermines activation energy values using an Arrhenius fit to rate parametersGenerates Arrhenius plots (not possible for negative solutions)Allows quick and easy importing of literature dataCalculates and stores model performance metrics and goodness of fit statisticsAbility to update published model kinetics, either by manually entering kinetic results or by fitting new experimental dataPredicts clumped isotope evolution for a given geologic time/temperature history:Allows users to assess if their results reflect primary signatures or diagenetic overprinting.Includes propagated uncertainty estimates for all heating experiment model fits, Arrhenius activation energy fits, and geologic history forward-model predictions.Includes analytical uncertainty weighting factors when calculating heating experiment rate values.Accounts for model parameter covariance using a numerical Jacobian approach.Future AdditionsFuture versions ofisotopylogwill aim to include:Additional models as they become availableKinetics of new isotopologues and non-carbonate molecular species (e.g., sulfate) as they become availableHow to ObtainSource code can be directly downloaded from GitHub:http://github.com/FluvialSeds/isotopylogBinaries can be installed through the Python package index:$ pip install isotopylogLicenseThis product is licensed under the GNU GPL license, version 3 or greater.Bug ReportsThis software is still in active deveopment. Please report any bugs directly to me at:jordon.hemingway@erdw.ethz.ch