gen3sis2: General Engine for Eco-Evolutionary Simulations

Contains an engine for spatially-explicit eco-evolutionary mechanistic models with a modular implementation and several support functions. It allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal spaces on biodiversity patterns as a general term.

Details

Gen3sis2 is implemented in a mix of R and C++ code, and wrapped into an R-package. All high-level functions that the user may interact with are written in R, and are documented via the standard R / Roxygen help files for R-packages. Runtime-critical functions are implemented in C++ and coupled to R via the Rcpp framework. Additionally, the package provides several convenience functions to generate input data, configuration files and plots, as well as tutorials in the form of vignettes that illustrate how to declare models and run simulations.

References

O. Hagen, B. Flück, F. Fopp, J.S. Cabral, F. Hartig, M. Pontarp, T.F. Rangel, L. Pellissier. (2021). gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity. PLoS biology

See also

create_input_config create_spaces_raster run_simulation plot_summary

Author

Maintainer: Oskar Hagen oskar@hagen.bio (space Ecology, WSL and ETH Zürich, Switzerland)

Authors:

• Admir C. de O. Junior admircjunior@gmail.com

• Bouwe Reijenga bouwe.reijenga@earth.ox.ac.uk

• Benjamin Flück benjamin.flueck@alumni.ethz.ch (space Ecology, WSL and ETH Zürich, Switzerland)

• Fabian Fopp fabian.fopp@usys.ethz.ch (space Ecology, WSL and ETH Zürich, Switzerland)

• Juliano S. Cabral juliano.sarmento_cabral@uni-wuerzburg.de (Ecosystem Modeling, Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany)

• Florian Hartig florian.hartig@biologie.uni-regensburg.de (Theoretical Ecology, University of Regensburg, Regensburg, Germany)

• Mikael Pontarp mikael.pontarp@biol.lu.se (Department of Biology, Lund University, Lund, Sweden)

• Thiago F. Rangel rangel.tf@gmail.com (Department of Ecology, Universidade Federal de Goiás, Goiás, Brazil)

• Loïc Pellissier loic.pellissier@usys.ethz.ch (space Ecology, WSL and ETH Zürich, Switzerland) [thesis advisor]

Other contributors:

• ETH Zürich [copyright holder]

• Charles Novaes de Santana charles.novaes@usys.ethz.ch (space Ecology, WSL and ETH Zürich, Switzerland) [contributor]

• Theo Gaboriau theo.gaboriau@unil.ch (Depatment of Computational Biology, Lausanne University, Switzerland) [contributor]

Examples

if (FALSE) { # \dontrun{

# 1. Load gen3sis and all necessary input data is set (space and config).

library(gen3sis2)

# get path to example input inside package
path_config <- system.file("extdata/TestConfigs/TestConfig.R", package = "gen3sis2")
path_space <- system.file("extdata/TestSpaces/geodynamic_spaces/raster", package = "gen3sis2")

# 2. Run simulation

sim <- run_simulation(
  config = path_config, 
  space = path_space,
  output_directory = tempdir())

# 3. Visualize the outputs
# plot summary of entire simulation
plot_summary(sim)
# plot richness at a given time-step 
# this only works if species is saved for this time-step
space_t_3 <- readRDS(file.path(tempdir(),"TestConfig","spaces","space_t_3.rds"))
species_t_3 <- readRDS(file.path(tempdir(),"TestConfig","species","species_t_3.rds"))

plot_richness(species_t_3, space_t_3)   
} # }