Code

Published

• Foraminiferal Isotope Reproduciblity Model (FIRM)
  • Foraminifera are the backbone of paleoceanography. Planktic foraminifera are one of the leading tools for reconstructing water column structure. However, there are unconstrained variables when dealing with uncertainty in the reproducibility of oxygen isotope measurements. This study presents the first results from a simple model of foraminiferal calcification (Foraminiferal Isotope Reproducibility Model; FIRM), designed to estimate uncertainty in oxygen isotope measurements. FIRM uses parameters including location, depth habitat, season, number of individuals included in measurement, diagenesis, misidentification, size variation, and vital effects, to produce synthetic isotope data in a manner reflecting natural processes. Reproducibility is then tested using Monte Carlo simulations. Importantly, this is not an attempt to fully model the entire complicated process of foraminiferal calcification; instead we are trying to include only enough parameters to estimate the uncertainty in foraminiferal δ18O records. Two well-constrained real world datasets are simulated successfully, demonstrating the validity of our model. The results from a series of experiments with the model show that reproducibility is largely controlled by the number of individuals in each measurement, but also strongly a function of local oceanography, if the number of individuals is held constant. Parameters like diagenesis or misidentification have an impact on both the precision and the accuracy of the data. FIRM is a tool to estimate isotopic uncertainty values and to explore the impact of myriad factors on the fidelity of paleoceanographic records, particularly for the Holocene. *Link to paper Link to Repository
• Paragloborotalia kugleri precision
  • This code is just for building the age models used in this paper. The actual data, the revision and update of numerous age models around the Oligocene Miocene boundary, can be found on FigShare. In the future I plan to keep material on Github, rather than the variety of services I’ve tried in the past.
• Test Complexity
  • The test complexity repository explains how the Lowery & Fraass 2019 paper came about and has a walkthrough built on a .rmd file.

In Progress

• StratCore
  • This is an unfinished collection of code that has built up over the years. I do plan to eventually get it flexibly written and published as a paper eventually. It’s all devoted to working with scientific ocean drilling data. Functions are not documented, and I make no promises that any of it will work with anybody elses data.
  • There is code to:
    • Splice core material, both individual samples and to splice together a single lithologic log
    • Apply age models (e.g., paleomag)
    • Remove certain lithologies (e.g., volcanics) and then generate a new faux-depthscale
    • Integrates with the ‘astrochron’ package