Pandas error patch

Patches two bugs due to pandas display formatting that appeared with Pandas v.2.0

Data import patch

Patched Pandas DataFrame.from_csv deprecated call

Biogeosciences companion code

This release is the version that accompanies Hemingway et al. (2017) "An inverse method to relate organic carbon reactivity to isotope composition from serial oxidation" Biogeosciences.

PyPI release version

This is the version first uploaded to the Python Package Index (PyPI) and is the version used to generate Chapter 3 of JDH's Ph.D. thesis.

First Full Release

Package features

• Stores and plots thermogram data
• Performs first-order DAEM inverse model to estimate activation energy distributions, f(Ea)
  • Regularizes ("smoothes") f(Ea) using Tikhonov Regularization
    • Automated or user-defined regularization value
• Deconvolves f(Ea) distribution into individual components
  • Automated or user-defined component number selection
  • Allows for combination of Gaussian peaks into a single component
• Calculates isotope values for each f(Ea) component
  • Can automatically blank-correct inputted values using any known blank carbon composition
  • Determines component radiocarbon (Fm) values
  • Determines component ¹³C/¹²C ratios
  • Accounts for the kinetic isotope effect (KIE) during heating
    • Allows for unique KIE compensation for each component
• Calculates and stores model performance metrics and goodness of fit
  statistics
• Determines isotope value uncertainty using Monte Carlo resampling
• Allows for forward-modeling of any arbitrary time-temperature history, e.g. to determine the decomposition rates and isotope fractionation during geologic organic carbon matruation

Additional information

Full documentation is available at:

http://rampedpyrox.readthedocs.io

This product is licensed under the GNU GPL license, version 3 or greater.

Pre-release

This is a pre release of the entire model -- from importing raw RPO thermogram data to calculating best-fit isotopes for each deconvolved peak. This release should be stable in Python3 and should be ready for use by the RPO community.

Note

The class naming conventions used in this release are no longer used! Please upgrade to v.0.0.2. for updated class definitions, naming conventions, and class hierarchy structure. This change will allow for much easier incorporation of other forms of kinetic data.

Not included in this release:

• Thorough documentation and examples
• Monte Carlo methods for calculating isotope uncertainties
• Functions to perform entire model run

Plans for next release:

• Better documentation
• Monte Carlo uncertainty
• Better omega 'auto' functionality in rp.EnergyComplex