Contents related to the Human-Plant Coevolution model implemented in R.
This repository includes the source files for model, exploration and analyses (library/) and documentation of the HPC model (index.Rmd), the sensitive analysis report (all other Rmarkdown files in the root directory), and a user interface for running and visualising simulations (hpcShinyApp/).
The entire repository is the directory of an R Project that runs in RStudio. Download it to consult and use all files locally. It was created and tested with R 3.6.2 and should be mostly compatible with later versions. There are no package dependency for running the model code (library/hpcModel.(...).R files).
To re-run all experiment analyses (both R and Rmd scripts), the following packages and minimum versions must be installed: ggplot2 (3.3.1), scales (1.1.1), reshape2 (1.4.4), ggpubr (0.4.0), randomForest (4.6-14), kableExtra (0.3.4), magick (2.7.2). Specifically to use the magick package for creating the GIF animations (plots/runPlot/(...).gif), it is required to download and install 'Image Magick' (7.1.0): https://imagemagick.org/. To re-compile the html booklet the following packages are also needed: knitr (1.33), bookdown (0.22). The Shiny app was built with shiny (1.6.0).
Alternatively, explore the following online features:
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Explore single simulation runs using the Shiny App hosted in ShinyApps.io: https://andros-spica.shinyapps.io/HPCShinyApp/
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Consult the HTML version of the model description and the sensitivity analysis report: https://andros-spica.github.io/hpcModel
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See our a presentation overviewing the model and its results, hosted in another repository: https://github.com/Andros-Spica/ENE-Angourakis-et-al-2019
Dedicated article:
Angourakis, Andreas, Jonas Alcaina-Mateos, Marco Madella, and Debora Zurro. 2021 (preprint). ‘Human-Plant Coevolution: A Modelling Framework for Theory-Building on the Origins of Agriculture’. bioRxiv. https://doi.org/10.1101/2021.11.19.469342.
Cite this repository as:
Angourakis, Andreas, & Alcaina-Mateos, Jonas. (2022, Jun 27). Andros-Spica/hpcModel: Human-Plant Coevolution model: source files, simulation interface, sensitivity analysis report and documentation (Version v1.3). Zenodo. http://doi.org/10.5281/zenodo.3881916