DarwinCAT

Description

A web application to experiment and visualize how evolution is distorted by the geological record, focusing on carbonate platforms.

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

Peter Burgess
University of Liverpool
Email: pmb42 [at] liverpool.ac.uk
Web page: liverpool.ac.uk/environmental-sciences/staff/peter-burgess

License

Apache 2.0 License, see LICENSE file for license text.

Online Usage

The app is available online at stratigraphicpaleobiology.shinyapps.io/DarwinCAT
Online access works with a web browser and does not require any coding skills or installations.

Offline Usage

Running the app offline requires R version 3.3 or later, RStudio, and the R packages "renv", "shiny" and "png".

Open the R project: Go to File -> Open Project, then navigate to the DarwinCAT folder and open the DarwinCAT Rproject file (file ending .Rproj). This will bootstrap the renv package.
Run
```
renv::restore()
```
This will install all packages dependencies required to run the app.
Now you can start the app by running the command
```
shiny::runApp()
```

Further Work

Next steps in development of the App are (in no specific order):

Branch off ProxyCAT, an app that focuses on preservation of proxy records
Publish lesson plans for different skill/knowledge levels

Repository structure

LICENSE.md : Apache 2.0 license text
README.md : Readme file
app.R : Main app
renv.lock : lock file from R package renv
CITATION.cff : Citation format file
.zenodo.json : Metadata for zenodo
DarwinCAT.Rproj : Rproject file
.Rprofile : Rprofile file generated by renv
.gitignore : Untracked files
data : Folder for data
- age_depth_models_for_shiny_app.Rdata : R workspace containing the age depth models generated by CarboCAT in Matlab
renv : Folder used by the R package renv
src : Folder for functions called by the app
- getAgeDepthModel.R : returns age depth models based on user input
- getEvolutionarySimulations.R : makes evolutionary simulation based on user inputs
- global_variables.R : loads data & global variables into workspace
- makeBasinTransectPlot.R : plot basin transect generated by CarboCAT
- makeWheelerDiagram.R : plot Wheeler diagram generated by CarboCAT
- makeTimeDomainPlot.R : plot trait simulations in time
- makeAgeDepthModelPlot.R : plots age depth models
- makeStratDomainPlot.R : plot evolutionary simulations in stratigraphic domain
- transform_ts.R : transfroms time series from time to depth domain
- prepare_download_trait_evo.R : prepares download of trait evol. data
- prepare_download_strat_pal.R : prepares download of strat pal data
- prepare_download_upload_data.R : prepares download in upload data tab
- process_upload_data.R : preprocesses data uploaded by users
www : Folder with pictures used in the app

Citation

To cite the app, please use

Hohmann, Niklas, Jarochowska, Emilia, & Burgess, Peter. (2023). DarwinCAT (1.2.0). Zenodo. DOI: 10.5281/zenodo.7851988

The app uses datasets generated by CarboCAT, a forward model of carbonate sedimentation developed by Peter Burgess. If you use or cite the app, please cite CarboCAT:

Burgess, P.M., 2013, CarboCAT: A cellular automata model of heterogeneous carbonate strata: Computers & Geosciences, v. 53, p. 129–140, doi: 10.1016/j.cageo.2011.08.026.

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.

MindTheGap-ERC / DarwinCAT