messinian_biol_impact

Supplementary code for The marine biodiversity impact of the Late Miocene Mediterranean salinity crisis
Project webpage: REMARE project

Authors

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

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

Requirements

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

Reproducing Results

In the RStudio IDE, open the file messinian_biol_impact.Rproj. This opens the RProject of the same name, and installs the renv package (if not already installed). Then, run

renv::restore()

in the console to install all dependencies required for the analysis. Next, run

source("code/download_data.R")

do download the database from Zenodo. Then, run

source("code/analysis.R")

to run the analysis and produce the figures. This will generate all figures in the figs/ folder, and generate the variables sr_change_whole, sr_change_reg, sr_change_time, and eco_ind_median in the workspace. Instructions on how to generate the maps are in the file code/maps.R.

Repository structure

• code : folder for R scripts
  • analysis.R : R script for main analysis
  • download_data.R : script to download raw data from Zenodo
  • helper_functions.R : utility functions for analysis
  • maps.R : code to generate maps
• data : folder for raw data. Initially empty, will be filled with data from Zenodo once download_data.R is run
• figs : folder for figures. Initially empty, will be filled with figures ofter analysis.R and/or maps.R is run
• renv : folder for renv package
• .Rprofile : R session settings
• .gitignore : untracked files
• LICENSE : Apache 2.0 license text
• README.md : README file with instructions for reproducibility
• messinian_biol_impact.Rproj : RProject file
• renv.lock : lock file for renv package

License

Apache 2.0, see LICENSE file for full text.

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).