richelbilderbeek/r-package

Repository of the R-packageGen3sis

General Engine for Eco-Evolutionary Simulations

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

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 landscapes.

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

The main methods are described here:

• O Hagen, B Flueck, F Fopp, JS Cabral, F Hartig, M Pontarp, TF Rangel, L Pellissier (2021) gen3sis: the general engine for eco-evolutionary simulations on the origins of biodiversity. bioRxiv. doi:10.1101/2021.03.24.436109

How to install gen3sis

gen3sis is avabaile on CRAN. You can install the latest CRAN release via

install.packages("gen3sis")

you can also install the latest development release from GitHub via

devtools::install_github(repo = "project-gen3sis/R-package/", 
  dependencies = TRUE, build_vignettes = TRUE)

Below the status of the automatic Travis CI tests on the master branch

How to run one simple simulation

Load and run a simulation with the desired config and landscapes. Exemple data is provided with the package

library("gen3sis")

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

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

A summary statistics is stored at 'sim' more data can be save using the oberver function

How to visualize a simulation

Plot the summary statistics of a simulation

plot_summary(sim)

Check package version

Make sure you have the latest gen3sis version

#print package version
paste("gen3sis version:", packageVersion("gen3sis"))