Intro

Supplementary data and code for "Nonparametric estimation of age-depth models from sedimentological and stratigraphic information" (Hohmann et al. 2024, DOI: 10.5194/egusphere-2024-2857.

Authors

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

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

Requirements

Base R (version >= 4) and the RStudio IDE.

Usage

Open the file nonparam_est_adm_supp.Rproj in RStudio. This will set all paths correctly, and install the renv package if necessary. The run

renv::restore()

to install all dependencies required for the analyses.

To reproduce the results, run

source("code/analyses.R")

in the RStudio console. This will run both analyses (site 1266 and Steinbruch Schmidt), generate all figues and save them in the figs/ folder, and save the data under data/res/site690_data.Rdata and data/res/sbs_data.Rdata.

Repository structure

• code : folder for code
  • analysis_steinbruch_schmidt.R : code for Steinbruch Schmidt example
  • analysis_site1266.R : code for the PETM example
  • plot_steinbruch_schmidt.R : generate plots and statistics for sbs example
  • plots_site_1266.R : generate plots and statistics for sbs example
  • analyses.R : runs all examples
  • Helper functions: condensation_plot.R sed_rate_plot.R median_sedrate_l.R petm_recovery_stats.R
• data : folder for data
  • res : folder for results
    • sbs_data.RData : estimated age-depth models for steinbruch schmidt
    • site1266_data.RData : estimated age-depth models for site 1266
  • raw : folder for raw data, read only!
    • SbS_XRF_forfactor3.csv : data for Steinbruch Schmidt example, from da Silva (2020, 2024)
    • murphy_et_al_2010_1-s2.0-S0016703710003108-mmc3.txt : raw data from ODP site 1266, from Murphy et al. (2010)
    • murphy_et_al_2010_1-s2.0-S0016703710003108-mmc3.csv : tabular data from ODP site 1266, from Murphy et al. (2010)
• figs : folder for figures. Initially empty, filled after code/analyses.R or the plotting scripts (code/plot*.R) are run
• renv : folder for renv package
• .gitignore : untracked files
• .Rprofile : R session settings
• LICENSE : Apache 2.0 license text
• nonparam_est_adm_supp.Rproj : R project file
• README : Readme file
• renv.lock : lock file of the renv package

References

Data in data/raw/SbS_XRF_forfactor3.csv and parts of the code in code/analysis_steinbruch_schmidt.R are from

• da Silva, A.-C. (2024). Anchoring the Late Devonian mass extinction in absolute time by integrating climatic controls and radio-isotopic dating: Supplementary code (v1.0.0). Zenodo. DOI: 10.5281/zenodo.12516430, In supplement to Da Silva, AC., Sinnesael, M., Claeys, P. et al. Anchoring the Late Devonian mass extinction in absolute time by integrating climatic controls and radio-isotopic dating. Sci Rep 10, 12940 (2020). DOI: 10.1038/s41598-020-69097-6

The materials are protected by copyright and shared under the CC BY 4.0 license.

Data in data/raw/murphy_et_al_2010_1-s2.0-S0016703710003108-mmc3.csv is from

• Murphy, B. H., Farley, K. A., & Zachos, J. C. (2010). An extraterrestrial 3He-based timescale for the Paleocene--Eocene thermal maximum (PETM) from Walvis Ridge, IODP Site 1266. Geochimica et Cosmochimica Acta, 74(17), 5098--5108. https://doi.org/10.1016/j.gca.2010.03.039

The dataset is protected by copyright and shared under the CC BY 3.0 license

Citation

Please cite this code as

• Hohmann, N., & Jarochowska, E. (2025). Supplementary data and code for "Nonparametric estimation of age-depth models from sedimentological and stratigraphic data" (v1.1.0). Zenodo. https://doi.org/10.5281/zenodo.15489276

Copyright

Copyright 2023-2025 Utrecht University.

License

Apache 2.0 License, see LICENSE file for full license text.

Funding information

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.