StratPal_paleoverse_materials

Materials and examples for the Paleoverse lecture "Building modeling pipelines for stratigraphic paleobiology in R" (Oct 31st 2024)

Author

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

Usage

Open the StratPal_paleoverse_materials.Rproj file in the RStudio IDE. This will automatically set all paths correctly, and install the renv package (if not already installed).

Then, run

renv::restore()

to install all required packages in their correct version. The examples were created in R v4.4.1, but will also run in R versions >= 4.2.

After installing all packages, open the file examples/examples.R to examine the code and interact with it.

Other resources

Other resources mentioned during the lecture are:

• Publication on the effect of incompleteness on the recognition of the mode of evolution: Hohmann, N., Koelewijn, J.R., Burgess, P., Jarochowsk, E. Identification of the mode of evolution in incomplete carbonate successions. BMC Ecol Evo 24, 113 (2024). DOI: 10.1186/s12862-024-02287-2
• Interactive web application to explore stratigraphic paleobiology:
  • Browser version: DarwinCAT
  • Github: github.com/MindTheGap-ERC/DarwinCAT
• Open educational resources (OERs) for a workshop on modeling stratigraphic paleobiology in R: Hohmann, N., Liu, X., & Jarochowska, E. (2024). Materials for workshop on building modeling pipelines in stratigraphic paleobiology (v1.0.0). Zenodo. DOI: 10.5281/zenodo.13769443
• Rudimentary shiny app showing transformation of phylogenetic trees using age-depth models : github.com/MindTheGap-ERC/phylo_stratpal
• Package webpages:
  • StratPal: mindthegap-erc.github.io/admtools/
  • admtools: mindthegap-erc.github.io/StratPal/
• Project webpage: mindthegap-erc.github.io/

Citation

To cite this work, please use

• Hohmann, N. (2024). Materials and examples for the Paleoverse lecture "Building modeling pipelines for stratigraphic paleobiology in R" (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.14001502

Copyright

Copyright 2023-2024 Netherlands eScience Center and Utrecht University

License

Apache 2.0 License, see LICENSE file for license text.

Repository structure

• examples:
  • examples.R : coding examples shown during the interactive coding part of the lecture
• renv: folder for renv package
• .gitignore: untracked files
• .Rprofile: R session settings
• LICENSE: Apache 2.0 license text
• README.md: Readme file
• renv.lock: lock file for renv package
• StratPal_paleoverse_materials.Rproj : R project file

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.