Data

Tools

Indexes

Applications

Experiments

Open Sustainable Technology

gen3sis

A spatially-explicit eco-evolutionary mechanistic model with a modular implementation that allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal landscapes.
https://github.com/project-Gen3sis/R-package

Category: Biosphere
Sub Category: Ecological and Environmental Modeling

Keywords

biodiversity ecology evolution mechanistic model modeling r r-package simulation

Keywords from Contributors

open-science

Last synced: about 18 hours ago
JSON representation

Repository metadata

Repository of the R-packageGen3sis

README.md

gen3sis

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 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

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

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 CI R-CMD-check tests

DEVELOPMENT R-CMD-check

MASTER R-CMD-check

How to use

Run one 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

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("gen3sis version:", packageVersion("gen3sis"))

How to contribute

In short, the main branches of the gen3sis repo are:

  • master – reflects the current CRAN release. 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.

Great that you are contributing! For guidelines on contributing to this project, please refer to the CONTRIBUTING.md file on github.

Credits

We thank the developers of the following methods and dependencies:

Citation (https://github.com/project-gen3sis/R-package/blob/master/)

citEntry(
  entry = "Article",
  author = {Oskar Hagen and Benjamin Flueck and Fabian Fopp and Juliano S. Cabral and Florian Hartig and Mikael Pontarp and Thiago F. Rangel and Loïc Pellissier},
  title = "gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity",
  doi = "10.1371/journal.pbio.3001340",
  year = 2021,
  month = "July",
  publisher = "PLoS",
  volume = 19,
  number = 7,
  pages = 31,
  journal = "PLoS Biology",
  
  textVersion = paste("Hagen O, Flueck B, Fopp F, Cabral JS, Hartig F, Pontarp M, Rangel TF, Pellissier L. (2021) gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity. PLoS Biology, 19(7), 1-31, https://doi.org/10.1371/journal.pbio.3001340"))

Owner metadata

GitHub Events

Total
Last Year

Committers metadata

Last synced: 1 day ago

Total Commits: 682
Total Committers: 26
Avg Commits per committer: 26.231
Development Distribution Score (DDS): 0.224

Commits in past year: 13
Committers in past year: 2
Avg Commits per committer in past year: 6.5
Development Distribution Score (DDS) in past year: 0.154

Name Email Commits
Oskar Hagen o****n@o****m 529
Benjamin Flueck b****k@a****h 36
benj919 9****9 26
Fabian Fopp F****n@F****l 16
florianhartig f****g 13
loic-pellissier 6****r 11
Fabian Fopp F****n@s****h 7
Fabian Fopp F****n@s****h 7
Fabian Fopp F****n@s****h 5
Fabian Fopp F****n@s****h 5
Juliano Sarmento Cabral j****l@u****e 4
Fabian Fopp F****n@s****h 3
Yihui Xie x****e@y****e 2
richelbilderbeek r****l@r****l 2
Fabian Fopp F****n@s****h 2
Fabian Fopp F****n@s****h 2
Fabian Fopp F****n@s****h 2
Fabian Fopp F****n@s****h 2
Fabian Fopp F****n@s****h 1
Fabian Fopp F****n@s****h 1
Fabian Fopp F****n@s****h 1
Fabian Fopp F****n@s****h 1
Matthew Andres Moreno m****n@g****m 1
ZHG z****4@g****m 1
cakloecker 6****r 1
cndesantana c****a@g****m 1

Committer domains:

Issue and Pull Request metadata

Last synced: 19 days ago

Total issues: 60
Total pull requests: 19
Average time to close issues: 3 months
Average time to close pull requests: 9 days
Total issue authors: 11
Total pull request authors: 10
Average comments per issue: 2.3
Average comments per pull request: 2.37
Merged pull request: 13
Bot issues: 0
Bot pull requests: 0

Past year issues: 2
Past year pull requests: 7
Past year average time to close issues: N/A
Past year average time to close pull requests: about 1 hour
Past year issue authors: 1
Past year pull request authors: 2
Past year average comments per issue: 0.0
Past year average comments per pull request: 0.29
Past year merged pull request: 3
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/project-Gen3sis/R-package

Top Issue Authors

  • ohagen (31)
  • benj919 (11)
  • florianhartig (8)
  • hadley (2)
  • mmore500 (2)
  • Bantau (1)
  • cakloecker (1)
  • FFopp (1)
  • wibach (1)
  • julianoscabral (1)
  • alexskeels (1)

Top Pull Request Authors

  • ohagen (7)
  • florianhartig (2)
  • mmore500 (2)
  • AdmirJr (2)
  • FFopp (1)
  • richelbilderbeek (1)
  • cakloecker (1)
  • yihui (1)
  • ZHG2017 (1)
  • julianoscabral (1)

Top Issue Labels

  • bug (17)
  • enhancement (12)
  • documentation (3)
  • good first issue (2)
  • help wanted (1)
  • Low priority (1)

Top Pull Request Labels

Package metadata

cran.r-project.org: gen3sis

General Engine for Eco-Evolutionary Simulations

  • Homepage: https://github.com/project-Gen3sis/R-package
  • Documentation: http://cran.r-project.org/web/packages/gen3sis/gen3sis.pdf
  • Licenses: GPL-3
  • Latest release: 1.6.0 (published 4 months ago)
  • Last Synced: 2025-12-23T13:32:17.311Z (2 days ago)
  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 643 Last month
  • Rankings:
    • Forks count: 7.999%
    • Stargazers count: 11.02%
    • Downloads: 14.675%
    • Average: 17.169%
    • Dependent repos count: 24.3%
    • Dependent packages count: 27.852%
  • Maintainers (1)

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • Matrix * imports
  • Rcpp >= 0.12.16 imports
  • gdistance * imports
  • grDevices * imports
  • methods * imports
  • raster * imports
  • sp * imports
  • stringr * imports
  • tools * imports
  • utils * imports
  • formatR * suggests
  • knitr * suggests
  • markdown * suggests
  • rmarkdown * suggests
  • testthat >= 2.1.0 suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite

Score: 13.55598825130635