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General Engine for Eco-Evolutionary Simulations

This is the repository for the R-package of the gen3sis engine project-gen3sis git.

gen3sis is a spatially-explicit eco-evolutionary mechanistic model with a modular implementation. It allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal spaces.

gen3sis is licensed under a GPLv3 License deriving from ETHZ 2020 <doi.org/10.5905/ethz-1007-251> and has package authorship according to: http://epub.wu.ac.at/3269/1/Report114.pdf

How to cite

  • O Hagen, B Flueck, F Fopp, JS Cabral, F Hartig, M Pontarp, TF Rangel, L Pellissier (2021) gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity. PLOS Biology. doi:10.1371/journal.pbio.3001340

How to install

you can install the latest development release from GitHub via

devtools::install_github(repo = "ohagen/gen3sis_rf", dependencies = TRUE, build_vignettes = TRUE)

Below the status of the automatic CI R-CMD-check tests for the main branches:

  • DEVELOPMENT R-CMD-check

  • MASTER R-CMD-check

How to use

Run one simulation

Load and run a simulation with the desired config and spaces. Example data is provided with the package.

library("gen3sis2")

datapath <- system.file(file.path("extdata", "WorldCenter"), package = "gen3sis")

sim <- run_simulation(config = file.path(datapath, "config/config_worldcenter.R"),
               space = file.path(datapath, "space"),
               output_directory = tempdir(),
               verbose=0)

A summary statistics is stored at ‘sim’ more data can be save using the observer function

Visualize a simulation

Plot the summary statistics of a simulation

plot_summary(sim)

Check installed version

Make sure you have the latest gen3sis version

#print package version
paste("gen3sis2 version:", packageVersion("gen3sis2"))

How to contribute

Great that you are considering contributing! We welcome contributions from the community, whether they are bug fixes, new features, documentation improvements, or anything else that can help improve the package. Feel free to also reach out over e-mail to discuss ideas. For guidelines on contributing to this project, please refer to the CONTRIBUTING.md file. In short, the main branches of this repo are:

  • master – reflects the current CRAN release (if at all). Only hotfixes or release-ready changes are merged here, typically just before CRAN submission.
  • development – serves as the main working branch. All new features, improvements, and fixes should be merged here from separate feature or bugfix branches.

Credits

We thank the developers of the following methods and dependencies: