This repository contains the data, code, and manuscript editing history for
Trayler, R. B., Meyers, S. R., Sageman, B. B., Schmitz, M. D., (in prep) Bayesian Integration of Astrochronology and Radioisotope Geochronology.
The code, installation instructions, and user guide for the {astroBayes} R package can be found at github.com/robintrayler/astroBayes.
The breakdown of the files and R scripts in this repository is below. If you would like to reproduce the tests in the manuscript run the scripts in the ./R/ directory in the order listed below. Note that the results directory is empty in this repository as it is too large to archive on GitHub.
These scripts are designed to be run in parallel on a fairly powerful desktop computer or cluster. Otherwise, they will take several days or weeks to complete and will generate approximately 1 terabyte of results files. It is not recommended to run them on a personal laptop.
├── data
└── BCL # data for Bridge Creek Limestone case study
└── cyclostratigraphic_record.csv # greyscale data
└── meyers_radioisotopic_dates.csv # dates from Meyers et al. (2012)
└── updated_radioisotopic_dates.csv # updated dates for BCL
└── layer_boundaries.csv # layer boundary positions for modeling
└── target_frequency.csv # target frequencies for modeling
└── CIP2 # CIP2 testing data
└── cyclostrat_data.csv # synthetic cyclostratigraphic data
└── layer_boundaries.csv # layer boundary positions for modeling
└── radioisotopic_dates.csv # dates used for stability modeling
└── true_age.csv # true age model
└── target_frequency.csv # target frequencies for modeling
└── TD1 # TD1 testing data
└── cyclostrat_data.csv # synthetic cyclostratigraphic data
└── layer_boundaries.csv # layer boundary positions for modeling
└── radioisotopic_dates.csv # dates used for stability modeling
└── true_age.csv # true age model
└── target_frequency.csv # target frequencies for modeling
├── R # R scripts to to reproduce figures and calculations
└── CIP2_stability.R # runs 1,000 CIP2 models with the same inputs
└── CIP2_validation.R # runs 4,000 CIP2 models with randomly placed dates
└── CIP2_outlier_analysis.R # runs 1,000 CIP2 with randomly placed outliers
└── TD1_stability.R # runs 1,000 TD1 models with the same inputs
└── TD1_validation.R # runs 4,000 TD1 models with randomly placed dates
└── TD1_outlier_analysis.R # runs 1,000 TD1 with randomly placed outliers
└── CIP2_hiatus_sensitvity # tests sensitivity of hiatus duration to date position
└── BCL_case_study.R # Bridge Creek Limestone case study
└── model_reproducibility.R # calculates the reproducibility of the 95% CI
└── proportion_constrained.R # calculates proportion of true age model within 95% CI
└── outlier_proportion_contained.R # calculates proportion of true age model within 95% CI for models with outliers
└── figure_2.R # generates figure 2
└── figure_3.R # generates figure 3
└── figure_8.R # generates figure 8
├── figures # output directory for pdf figures
└── final figures # cleaned up figures for publication
├── results # contains the model results for stability and validation models
└── stability_validation # contains the outputs of CIP2_stability.R and TD1_stability.R
└── random_age_validation # contains the outputs of CIP2_validation.R and TD1_validation.R
├── manuscript.md # pandoc markdown formatted manuscript
This manuscript is written in Pandoc flavored markdown. Follow the instructions here to install Pandoc. The manuscript also relies on the pandoc-crossref filter to handle figure, table, and section numbering.
The manuscript file, manuscript.md can be compiled into a nicely formatted PDF by running the following pandoc command.
pandoc -s -f markdown+mark -o manuscript.pdf --pdf-engine=xelatex --filter pandoc-crossref --citeproc --number-sections manuscript.md