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The Shellbed Condensator

DOI fair-software.eu

Shiny app to visualize the effects of changing sedimentation rates on formation of fossil accumulations.

Authors

Niklas Hohmann (Maintainer) Utrecht University
email: n.h.hohmann [at] uu.nl
Web page: 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

R (version >= 3.0.2), RStudio IDE.

Online Usage

The app can be used online at stratigraphicpaleobiology.shinyapps.io/shellbed_condensator. Online usage does not require an installation of R.

Offline Usage

Open the file ShellbedCondensator.Rproj in the RStudio IDE. This will open the RProject, and install the renv package (if not already installed). Then run

renv::restore()

in the console to install all dependencies required for the app. To run the app, use

shiny::runApp()

Repository structure

  • LICENSE.md : Apache 2.0 license text
  • README.md : Readme file
  • CITATION.cff : Citation info
  • app.R : R code to start app. Contains app architecture
  • renv.lock : lockfile for renv package
  • zenodo.json : Zenodo metadata
  • renv : folder for renv package
  • src : Folder for code
    • condensator.R : Generates model outputs from user input
    • condensator_plot.R : Generates plots from model outputs
  • www : Folder with pictures used in the app
    • people : Folder with pictures of authors
    • logos : Folder with logos
    • geology : Folder with pictures of shell accumulations and stratigraphic columns
  • .github : GitHub actions

License

Apache 2.0, see LICENSE file for details

Citation

To cite the app, please use

References

The model underlying the app is described in

  • Hohmann, N.: Incorporating Information on Varying Sedimentation Rates in Paleontological Analyses. PALAIOS, 2021. doi: 10.2110/palo.2020.038

The app uses the shiny package:

  • Chang W, Cheng J, Allaire J, Sievert C, Schloerke B, Xie Y, Allen J, McPherson J, Dipert A, Borges B (2022). shiny: Web Application Framework for R. R package version 1.7.3, https://CRAN.R-project.org/package=shiny.

Funding information

Online access to the App is made possible by the IDUB programme of the University of Warsaw (Grant BOB-IDUB-622-18/2022).
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. European Union and European Research Council logos