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gen3sis

Repository of the R-packageGen3sis

https://github.com/project-gen3sis/r-package

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 12 DOI reference(s) in README
  • ○
    Academic publication links
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    Committers with academic emails
    16 of 28 committers (57.1%) from academic institutions
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    Scientific vocabulary similarity
    Low similarity (14.8%) to scientific vocabulary

Keywords

biodiversity ecology evolution mechanistic model modeling r r-package simulation
Last synced: 6 months ago · JSON representation

Repository

Repository of the R-packageGen3sis

Basic Info
Statistics
  • Stars: 33
  • Watchers: 5
  • Forks: 8
  • Open Issues: 10
  • Releases: 0
Topics
biodiversity ecology evolution mechanistic model modeling r r-package simulation
Created almost 6 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License

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 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

{r} install.packages("gen3sis")

you can also install the latest development release from GitHub via

{r} 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 ```{r} library("gen3sis")

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

sim <- runsimulation(config = file.path(datapath, "config/configworldcenter.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 {r} plot_summary(sim)

Check installed version

Make sure you have the latest gen3sis version ```{r}

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:

  • Rcpp Dirk Eddelbuettel and James Joseph Balamuta (2018). Extending R with C++: A Brief Introduction to Rcpp. The American Statistician. 72(1). URL https://doi.org/10.1080/00031305.2017.1375990.

  • BH Dirk Eddelbuettel, John W. Emerson and Michael J. Kane (2021). BH: Boost C++ Header Files. R package. https://CRAN.R-project.org/package=BH

  • Matrix Douglas Bates and Martin Maechler (2019). Matrix: Sparse and Dense Matrix Classes and Methods. R package. https://CRAN.R-project.org/package=Matrix

  • raster Robert J. Hijmans (2021). raster: Geographic Data Analysis and Modeling. R package. https://CRAN.R-project.org/package=raster

  • gdistance van Etten, J. (2017). R package gdistance: Distances and routes on geographical grids. Journal of Statistical Software, 76(1), 1–21. https://doi.org/10.18637/jss.v076.i13

  • sp Roger S. Bivand, Edzer Pebesma, Virgilio Gomez-Rubio, 2013. Applied spatial data analysis with R, Second edition. Springer, NY. https://asdar-book.org/

  • stringr Hadley Wickham (2019). stringr: Simple, Consistent Wrappers for Common String Operations. R package. https://CRAN.R-project.org/package=stringr

  • testthat Hadley Wickham (2011). testthat: Get Started with Testing. The R Journal, vol. 3, no. 1, pp. 5--10, https://journal.r-project.org/archive/2011-1/RJournal2011-1Wickham.pdf

  • formatR Yihui Xie (2021). formatR: Format R Code Automatically. R package. https://CRAN.R-project.org/package=formatR

  • scico Crameri, F. (2018). Scientific colour maps. Zenodo. http://doi.org/10.5281/zenodo.1243862 & Crameri, F., G.E. Shephard, and P.J. Heron (2020). The misuse of colour in science communication, Nature Communications, 11, 5444. doi:10.1038/s41467-020-19160-7

Owner

  • Name: GENƎSIS
  • Login: project-gen3sis
  • Kind: organization
  • Email: oskar@hagen.bio

General Engine for Eco-Evolutionary Simulations

GitHub Events

Total
  • Commit comment event: 1
  • Issues event: 3
  • Watch event: 3
  • Issue comment event: 2
  • Push event: 8
  • Pull request event: 7
Last Year
  • Commit comment event: 1
  • Issues event: 3
  • Watch event: 3
  • Issue comment event: 2
  • Push event: 8
  • Pull request event: 7

Committers

Last synced: 6 months ago

All Time
  • Total Commits: 682
  • Total Committers: 28
  • Avg Commits per committer: 24.357
  • Development Distribution Score (DDS): 0.415
Past Year
  • Commits: 13
  • Committers: 2
  • Avg Commits per committer: 6.5
  • Development Distribution Score (DDS): 0.154
Top Committers
Name Email Commits
Oskar Hagen o****n@o****m 399
ohagen o****n@u****h 130
Benjamin Flueck b****k@a****h 36
benj919 9****9 24
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
Benjamin Flück b****j@g****t 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
richelbilderbeek r****l@r****l 2
Yihui Xie x****e@y****e 2
Fabian Fopp F****n@s****h 1
Fabian Fopp F****n@s****h 1
Fabian Fopp F****n@s****h 1
cakloecker 6****r 1
Matthew Andres Moreno m****n@g****m 1
Fabian Fopp F****n@s****h 1
ZHG z****4@g****m 1
cndesantana c****a@g****m 1
Committer Domains (Top 20 + Academic)
staff-net-vpn-dhcp-8091.ethz.ch: 1 staff-net-vpn-dhcp-7653.ethz.ch: 1 staff-net-vpn-dhcp-3488.ethz.ch: 1 staff-net-vpn-dhcp-3184.ethz.ch: 1 yihui.name: 1 richelbilderbeek.nl: 1 staff-net-vpn-dhcp-6027.ethz.ch: 1 staff-net-vpn-dhcp-5718.ethz.ch: 1 staff-net-vpn-dhcp-4511.ethz.ch: 1 staff-net-vpn-dhcp-1415.ethz.ch: 1 gmx.net: 1 staff-net-vpn-dhcp-6166.ethz.ch: 1 uni-wuerzburg.de: 1 staff-net-vpn-dhcp-7771.ethz.ch: 1 staff-net-vpn-dhcp-2778.ethz.ch: 1 staff-net-vpn-dhcp-7161.ethz.ch: 1 staff-net-vpn-dhcp-3263.ethz.ch: 1 alumni.ethz.ch: 1 usys.ethz.ch: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 61
  • Total pull requests: 18
  • Average time to close issues: 3 months
  • Average time to close pull requests: 9 days
  • Total issue authors: 12
  • Total pull request authors: 10
  • Average comments per issue: 2.26
  • Average comments per pull request: 2.5
  • Merged pull requests: 13
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: about 2 hours
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.33
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ohagen (31)
  • benj919 (11)
  • florianhartig (8)
  • hadley (2)
  • mmore500 (2)
  • Bantau (1)
  • cakloecker (1)
  • FFopp (1)
  • wibach (1)
  • julianoscabral (1)
  • dkStevensNZed (1)
  • alexskeels (1)
Pull Request Authors
  • ohagen (6)
  • florianhartig (2)
  • AdmirJr (2)
  • mmore500 (2)
  • ZHG2017 (1)
  • FFopp (1)
  • julianoscabral (1)
  • richelbilderbeek (1)
  • cakloecker (1)
  • yihui (1)
Top Labels
Issue Labels
bug (17) enhancement (12) documentation (3) good first issue (2) help wanted (1) Low priority (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 636 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 7
  • Total maintainers: 1
cran.r-project.org: gen3sis

General Engine for Eco-Evolutionary Simulations

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 636 Last month
Rankings
Forks count: 8.0%
Stargazers count: 11.0%
Downloads: 14.7%
Average: 17.2%
Dependent repos count: 24.3%
Dependent packages count: 27.9%
Maintainers (1)
oskar@hagen.bio
Last synced: 6 months ago

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