messinian_db

Supplementary code for "A revised marine fossil record of the Mediterranean before and after the Messinian Salinity Crisis" (Agiadi et al 2024, DOI: 10.5194/essd-2024-75). Generates summary statistics, figures, and maps.

Project webpage: REMARE project

Authors

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

Daniel García-Castellanos (contributor)
Geociencias Barcelona
email: danielgc [at] geo3bcn.csic.es
Web page: digital.csic.es/cris/rp/rp07103
ORCID: 0000-0001-8454-8572

Konstantina Agiadi (principal investigator, contributor)
University of Vienna
email: konstantina.agiadi [at] univie.ac.at
Web page: sites.google.com/view/kagiadi
ORCID: 0000-0001-8073-559X

License

Apache 2.0, see LICENSE file for full text.

Requirements

Base R (version >= 4.0) and the RStudio IDE.

Reproduction

In the RStudio IDE, open the file messinian_db.Rproj. This opens the RProject of the same name, and should automatically install the renv package (if not already installed). First, run

renv::restore()

to install all required packages and their dependencies. Then run

source("code/download_data.R")

to download the latest version of the database from Zenodo. Then, run

source("code/make_table_and_plots.R")

in the console to produce the summary statistics of the database (stored in the variable table). You can view the values by running

table

in the console, and inspect the figures in figs/. Details on producing the map are given in the file code/make_maps.R.

Repository structure

• code : folder with R code
  • make_table_and_plots.R : script to generate table 1 and figures
  • make_maps.R : script to generate the maps
  • download_data.R : script to download data from Zenodo
• data : folder for raw data. Initially empty, will be filled with downloaded data after the script in code/download_data.R is run.
• figs : folder for figures. Initially empty
• renv : folder used by the renv package
• .gitignore : untracked files
• .Rprofile : session info
• messinian_db.Rproj : RProject file
• README : README file
• renv.lock : lock file for renv package

References

This repository downloads and uses data from

• Agiadi, K., Hohmann, N., Gliozzi, E., Thivaiou, D., Francesca, B., Taviani, M., Bianucci, G., Collareta, A., Londeix, L., Faranda, C., Bulian, F., Koskeridou, E., Lozar, F., Mancini, A. M., Dominici, S., Moissette, P., Bajo Campos, I., Borghi, E., Iliopoulos, G., … Garcia-Castellanos, D. (2024). Revised marine fossil record of the Mediterranean before and after the Messinian Salinity Crisis [Data set]. Zenodo. https://doi.org/10.5281/zenodo.13358435

Funding

This work was supported by the Austrian Science Fund (FWF) project “Late Miocene Mediterranean Marine Ecosystem Crisis” (2022–2026), Project no. V 986, DOI 10.55776/V986 (PI: K.Agiadi).