Reproducible Research Platform Study 1 Player Bundle

RRP Study 1 Reproducible Research Platform (RRP) project including the RStudio IDE for reproducing the study "The archaeology, chronology and stratigraphy of Madjedbebe (Malakunanja II): A site in northern Australia with early occupation". Overview This RRP project repository demonstrates how published data with R-Studio and R Markdown on RRP can be reproduced (data taken from [1]). Original scripts could in principle be run directly from the git repository as provided by the authors (run_original_version_to_reproduce_study_results.Rmd). However, we demonstrate how such data stored in a research data management system (RDMS) and minor modifications to the scripts can generate the original figures and results (run_rrp_version_to_reproduce_study_results.Rmd). The report and figures are stored in the results folder of RRP. This special folder can be used to register relevant outputs to the RDMS and demonstrates the round trip to make important results FAIR. The main outcome of this example is: Usage of RStudio and R Markdwon for analysis and report generation reproducing a published study. Features Integration with RRP and openBIS ELN-LIMS: Mounts data from the RDMS openBIS in RRP for direct use in RStudio. RStudio: Keeping user habits allowing to work with a familiar IDE. Installation Prerequisites Local Docker installation. Steps Download and extract the .zip file Run the play script for your operating system Linux / macOS: play Windows: play.bat or play.ps1 Usage Workflow Overview Re-run analysis: In the Launcher RStudio can be opened in a new tab and the file run_original_version_to_reproduce_study_results.Rmd or run_rrp_version_to_reproduce_study_results.Rmd be opened. Results generation: Using Run all or Knit (in RStudio) the whole study report can be compiled and results will be saved under results among other outputs such as figures. Directory Structure ├── .binder/ # Environment specifications, R version, packages etc. ├── .rrp/ # Specification of openBIS server and required data from RDMS openBIS ELN-LIMS (e.g. data) ├── src/ # Original study package adopted for RRP ├── 1989-excavation-report-Madjedbebe # Original study data repository ├── LICENSE # License ├── README.md # This file ├── run_original_version_to_reproduce_study_results.Rmd # Reproduces published story directly from git repository └── run_rrp_version_to_reproduce_study_results.Rmd # Reproduces published story with data registered in our RDMS allowing for potential extension. Contributing We welcome contributions to improve this repository! Please follow these steps: Fork the repository. Create a new branch for your feature or bug fix. Submit a pull request with a clear description of your changes. Authors and acknowledgment Andreas P. Cuny, ETH Zurich initial implementation We acknowledge Ben Marwick, [e-mail], author of the original study repository License This project is licensed under the Apache 2.0 License. See LICENSE file for details. The data in 1989-excavation-report-Madjedbebe is CC0-licenced and the code MIT-licensed, copyright 2015 Ben Marwick. Copyright © 2020-2025 ETH Zurich, Andreas P. Cuny, D-BSSE, CSB Group References Clarkson, C., Mike Smith, Ben Marwick, Richard Fullagar, Lynley A. Wallis, Patrick Faulkner, Tiina Manne, Elspeth Hayes, Richard G. Roberts, Zenobia Jacobs, Xavier Carah, Kelsey M. Lowe, Jacqueline Matthews, S. Anna Florin 2015 The archaeology, chronology and stratigraphy of Madjedbebe (Malakunanja II): A site in northern Australia with early occupation. Journal of Human Evolution Volume 83, June 2015, Pages 46–64 http://dx.doi.org/10.1016/j.jhevol.2015.03.014