Repository for "Identification of the mode of evolution in incomplete carbonate successions".

Niklas Hohmann Utrecht University
email: n.hohmann [at] uu.nl
Web page: uu.nl/staff/NHohmann
Orcid: 0000-0003-1559-1838

Jan Roel Koelewijn
Utrecht University
Orcid: 0000-0002-4668-3797

Emilia Jarochowska
Utrecht University
email: e.b.jarochowska [at] uu.nl
Web page: uu.nl/staff/EBJarochowska
Orcid: 0000-0001-8937-9405

Apache 2.0, see LICENSE file for full license text

Base R and Rstudio.
Packages paleoTS, renv, DAIME, ggplot2 and their dependencies.

Open the Rproject file "stratigraphy_paper.Rproj" in Rstudio. This will bootstrap the renv package if it is not installed yet. Next, run

renv::restore()

This will install all required packages and their dependencies needed in the project.

• README.md : Readme file
• LICENSE : Apache 2.0 license text
• .gitignore : Files not tracked by git
• Stratigraphy_paper.Rproj : Rstudio project file
• renv : Folder generated by renv package
• data : Folder for data
  • matlab_outputs : Folder with raw data generated by CarboCATLite in Matlab
    • scenarioA_matlab_outputs.mat : raw data of scenario A
    • scenarioB_matlab_outputs.mat : raw data of scenario B
    • scenarioA_and_B_matlab_to_R.mat : function to extract ADMs from CarboCATLite outputs
    • get_adm_from_carbocat_outputs.m : ADMs from CarboCATLite for import in R
  • R_outputs : Folder with data generated by R
    • ageDepthModelsScenariosAandB.Rdata : ADMs from scenario A and B
    • results_modes_of_evolution.Rdata
• code : Folder with main code
  • analysis_tests_and_simulations.R
  • simulate_and_test_modes_of_evolution.R
  • import_adm_to_R.R
  • multiplot.R
  • process_adm_from_matlab.R : Import ADMs from Matlab into R
• figs : Folder with figures
• tables : Folder with tables

This document describes how to the used in the publication INSERT TITLE HERE

REPEATABILITY OF DATA GENERATION Below is a description of the pipeline uses to generate the data used in the publication. Note that all data generated by the following steps, including test results, are already provided. The aim of the following description is reproducability

1. Run basin simulations: Go into the folder scenarioX (where X=A or B), open the file“carboCATGUI.m” in Matlab and run it. In the window that appears, first click “initialize”. Once the window shows the initial platform parameters, click “run CA model”. The run itself can take a while. Once it is done, a file “scenarioXMatlabOutputs.mat” will appear in the folder. It contains all model outputs.
2. Extract age-depth models from model outputs: Copy the files “scenarioXMatlabOutputs.mat” into the main folder. Open the file “extractADMFromCarboCAT.m” in Matlab and run it. It extracts age-depth models from the model outputs, and stores them in a file named “scenariosAandBMatlabToR.mat”.
3. Import age-depth models into R: Open the file “importADMToR.R” in R, and run it. It will import the age-depth models into R and save them as a workspace named “scenariosAandB.Rdata”. This workspace contains all age-depth models used.
4. Test modes of evolution Open the file "testModesOfEvolution.R" in R and run it. It will test how well the different modes of evolution are recognized in the different scenarios, and save the results as a workspace named "resultsTestModesOfEvo.Rdata".

Co-funded by the European Union (ERC, MindTheGap, StG project no 101041077). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them.