diff --git a/README.md b/README.md index b636ff7..16e26fb 100644 --- a/README.md +++ b/README.md @@ -27,26 +27,22 @@ Web page: [liverpool.ac.uk/environmental-sciences/staff/peter-burgess](https://w Apache 2.0 License, see LICENSE file for license text. -## Requirements - -R version 3.0.2 or later -R packages "renv", "shiny" and "png" - -## Resources - -The app uses datasets generated by [CarboCAT](https://github.com/csdms-contrib/carbocat), a forward model of carbonate sedimentation developed by [Peter Burgess](https://www.liverpool.ac.uk/environmental-sciences/staff/peter-burgess/). If you use or cite the app, please cite CarboCAT: +## Online Usage -- 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](https://www.sciencedirect.com/science/article/pii/S0098300411002949). +The app is available online at [stratigraphicpaleobiology.shinyapps.io/DarwinCAT](https://stratigraphicpaleobiology.shinyapps.io/DarwinCAT/) +Online access works with a web browser and does not require any coding skills or installations. ## Offline Usage -1. Install the _renv_ package by running the following code in R: +Running the app offline requires R version 3.0.2 or later, RStudio, and the R packages "renv", "shiny" and "png" + +1. Install the _renv_ package by running the following code in RStudio: ``` R if (!require("renv", quietly = TRUE)) install.packages("renv") ``` -2. Open the R project: In RStudio, go to _File -> Open Project_, then navigate to the DarwinCAT folder and open the DarwinCAT Rproject file (file ending _.Rproj_) +2. Open the R project: Go to _File -> Open Project_, then navigate to the DarwinCAT folder and open the DarwinCAT Rproject file (file ending _.Rproj_) 3. Run ``` R @@ -60,37 +56,49 @@ The app uses datasets generated by [CarboCAT](https://github.com/csdms-contrib/c shiny::runApp() ``` -## Online Usage - -The app is available on [stratigraphicpaleobiology.shinyapps.io/DarwinCAT](https://stratigraphicpaleobiology.shinyapps.io/DarwinCAT/) - -## Citation - -To cite the app, please use +## Further Work -Hohmann, Niklas, Jarochowska, Emilia, & Burgess, Peter. (2023). DarwinCAT (1.0.0). Zenodo. [DOI: 10.5281/zenodo.7851989](https://doi.org/10.5281/zenodo.7851989) +Next steps in development of the App are (in no specific order): +1. Add option to download data (time series & stratigraphic time series) +2. Add option to upload user time series +3. Branch off _ProxyCAT_, an app that focuses on preservation of proxy records +4. 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 - - _getAgeDepthModel.R_ : returns age depth models based on user input - - _getEvolutionarySimulations.R_ : makes evolutionary simulation based on user inputs - _makeAgeDepthModelPlot.R_ : plots age depth models - _makeStratDomainPlot.R_ : plot evolutionary simulations in stratigraphic domain -- _www_ : Folder with pictures used in the app - - _people_ : Folder with pictures of authors - - _logos_ : Folder with logos - - _geology_ : Folder with basin transect and wheeler diagram produced by CarboCAT -- _app.R_ : Main app +- _www_ : Folder with pictures used in the app + +## Citation + +To cite the app, please use + +- Hohmann, Niklas, Jarochowska, Emilia, & Burgess, Peter. (2023). DarwinCAT (1.0.0). Zenodo. [DOI: 10.5281/zenodo.7851989](https://doi.org/10.5281/zenodo.7851989) + +The app uses datasets generated by [CarboCAT](https://github.com/csdms-contrib/carbocat), a forward model of carbonate sedimentation developed by [Peter Burgess](https://www.liverpool.ac.uk/environmental-sciences/staff/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](https://www.sciencedirect.com/science/article/pii/S0098300411002949). ## Funding