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DAISIE

DAISIE

https://github.com/rsetienne/daisie

Science Score: 59.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 33 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    7 of 19 committers (36.8%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.5%) to scientific vocabulary

Keywords from Contributors

phylogenetics
Last synced: 6 months ago · JSON representation

Repository

DAISIE

Basic Info
  • Host: GitHub
  • Owner: rsetienne
  • License: gpl-3.0
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 43.7 MB
Statistics
  • Stars: 9
  • Watchers: 5
  • Forks: 11
  • Open Issues: 21
  • Releases: 23
Created over 7 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing License

README.md

DAISIE: Dynamic Assembly of Island biota through Speciation, Immigration and Extinction

CRAN_Status_Badge GitHub R package version DOI

Branch|GHA logo|Codecov logo ---|---|--- master|R build status|codecov.io develop|R build status|codecov.io

DAISIE is an R package that simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction.

The model can be fitted to both empirical dated phylogenies and simulated data.

  • For an overview of the simulation functionality see here.
  • Details and an overview of the maximum likelihood inference capabilities to estimate parameters see here.
  • For details on comparing between two diversity dependence models see here.

The DAISIE package has a stable version on CRAN and a development version on GitHub.

DAISIE is now part of an ecosystem of packages! Check out DAISIEprep to help preparing your phylogenetic data for DAISIE.

From CRAN

From within R, do:

r install.packages("DAISIE")

From GitHub

Install DAISIE from this GitHub repository by running:

r install.packages("remotes") remotes::install_github("rsetienne/DAISIE")

Using DAISIE as a package dependency

From CRAN

To your DESCRIPTION file, add DAISIE as any normal package.

If your package directly uses DAISIE:

Imports: DAISIE

If your package uses DAISIE in its peripherals (e.g. vignettes and tests):

Suggests: DAISIE

From GitHub

Remotes: rsetienne/DAISIE

Support/Questions

For feature requests or bug-reports or other matters, please submit an issue.

Feature branches

  • master: build should always pass. @rsetienne has control over develop to master merges.
  • develop: merge of feature branches, merge with master by @rsetienne iff build passes.

Contributors

DAISIE was originally developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore and Bart Haegeman. It is continuously maintained by members of the @tece-lab, at the University of Groningen.

References

  • Etienne R. S., Valente, L., Phillimore, A. B., Haegeman, B., Lambert, J. W., Neves, P., Xie, S., Bilderbeek, R. J. C., & Hildenbrandt, H. (2021). DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction. R package version 4.0.2. https://cran.r-project.org/package=DAISIE. https://doi.org/10.5281/zenodo.4054058

  • Valente, L., Etienne, R.S., & Phillimore, A.B. (2014). The effects of island ontogeny on species diversity and phylogeny. Proceedings of the Royal Society B: Biological Sciences, 281(1784), 20133227–20133227. http://doi.org/10.1098/rspb.2013.3227

  • Valente, L., Phillimore, A.B., & Etienne, R.S. (2015). Equilibrium and non-equilibrium dynamics simultaneously operate in the Galápagos islands. Ecology Letters, 18(8), 844–852. http://doi.org/10.1111/ele.12461

  • Valente, L., Etienne, R.S., & Dávalos, L.M. (2017). Recent extinctions disturb path to equilibrium diversity in Caribbean bats. Nature Ecology & Evolution, 1(2), 0026. http://doi.org/10.1038/s41559-016-0026

  • Valente, L., Illera, J.C., Havenstein, K., Pallien, T., Etienne, R.S., & Tiedemann, R. (2017). Equilibrium Bird Species Diversity in Atlantic Islands. Current Biology, 27(11), 1660-1666. https://doi.org/10.1016/j.cub.2017.04.053

  • Valente, L., Phillimore, A.B., & Etienne, R.S. (2018). Using molecular phylogenies in island biogeography: It’s about time. Ecography, 1–3. http://doi.org/10.1111/ecog.03503

  • Valente, L., Etienne, R.S., & Garcia-R., J.C. (2019). Deep Macroevolutionary Impact of Humans on New Zealand’s Unique Avifauna. Current Biology 29 (15): 2563-2569.e4. https://doi.org/10.1016/j.cub.2019.06.058

  • Valente, L., Phillimore, A.B., Melo, M., Warren, B.H., Clegg, S.M., Havenstein, K., Tiedemann, R., Illera, J.C., Thebaud, C., Aschenbach, T. & Etienne, R.S. (2020). A Simple Dynamic Model Explains the Diversity of Island Birds Worldwide. Nature 579 (7797): 92–96. https://doi.org/10.1038/s41586-020-2022-5

  • Hauffe, T., Delicado, D., Etienne, R.S., & Valente, L. (2020). Lake expansion elevates equilibrium diversity via increasing colonization. Journal of Biogeography 47: 1849–1860. https://doi.org/10.1111/jbi.13914

  • Valente, L., Kristensen, N., Phillimore, A. B., & Etienne, R. S. (2021). Report of programming bugs in the DAISIE R package: consequences and correction. https://doi.org/10.32942/osf.io/w5ntf

  • Santos Neves, P.*, Lambert, J. W.*, Valente, L., & Etienne, R. S. (2022). The robustness of a simple dynamic model of island biodiversity to geological and sea-level change. Journal of Biogeography 49: 2091-2104. https://doi.org/10.1111/jbi.14519

  • Lambert, J. W., Santos Neves, P., Bilderbeek, R. L. C., Valente, L., Etienne, R. S. (2022). The effect of mainland dynamics on data and parameter estimates in island biogeography. bioRxiv. https://doi.org/10.1101/2022.01.13.476210

  • Xie, S., Valente, L., Etienne, R. S. (2023). Can we ignore trait-dependent colonization and diversification in island biogeography? Evolution. https://doi.org/10.1093/evolut/qpad006

  • Michielsen, N. M., Goodman, S. M., Soarimalala, V., van der Geer, A. A. E., Dávalos, L. M., Saville, G. I., Upham, N., Valente, L. (2023). The macroevolutionary impact of recent and imminent mammal extinctions on Madagascar. Nature Communications 14 (14). https://doi.org/10.1038/s41467-022-35215-3

  • Lambert, J.W., Roeble, L., Pannetier T., Etienne, S. R., Valente, L. (2025). Using phylogenetic data for island biogeography analyses: The DAISIEprep package. 206 (108324) https://doi.org/10.1016/j.ympev.2025.108324

Owner

  • Name: Rampal S. Etienne
  • Login: rsetienne
  • Kind: user
  • Location: Groningen, The Netherlands
  • Company: University of Groningen

GitHub Events

Total
  • Release event: 1
  • Delete event: 1
  • Issue comment event: 1
  • Member event: 1
  • Push event: 172
  • Pull request review comment event: 4
  • Pull request review event: 7
  • Pull request event: 25
  • Create event: 8
Last Year
  • Release event: 1
  • Delete event: 1
  • Issue comment event: 1
  • Member event: 1
  • Push event: 172
  • Pull request review comment event: 4
  • Pull request review event: 7
  • Pull request event: 25
  • Create event: 8

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 2,442
  • Total Committers: 19
  • Avg Commits per committer: 128.526
  • Development Distribution Score (DDS): 0.536
Past Year
  • Commits: 201
  • Committers: 7
  • Avg Commits per committer: 28.714
  • Development Distribution Score (DDS): 0.284
Top Committers
Name Email Commits
Neves-P p****s@r****l 1,133
joshwlambert j****t@r****l 402
rsetienne r****e@g****m 345
rsetienne r****e@g****m 180
xieshu95 x****5@g****m 122
richelbilderbeek r****l@r****l 122
luislvalente l****e@g****m 34
Hanno Hildenbrandt h****t@r****l 33
O. Dehayem Nanwou o****u@r****l 26
= = 22
Ornela Dehayem Nanwou o****m@g****m 7
P.M. Santos neves P****7@W****L 6
rscherrer r****r@e****u 3
hanno h****o@D****4 2
P.M. Santos neves P****7@w****l 1
Luis Valente l****e@c****l 1
Luis Valente l****s@L****l 1
Luis Valente l****e@n****l 1
Yangshen0325 8****5 1
Committer Domains (Top 20 + Academic)
rug.nl: 4 workspace.rug.nl: 2 naturalis.nl: 1 client-145-120-39-6.surfnet.eduroam.rug.nl: 1 evobio.eu: 1 richelbilderbeek.nl: 1 gmail.om: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 57
  • Total pull requests: 77
  • Average time to close issues: 3 months
  • Average time to close pull requests: 7 days
  • Total issue authors: 5
  • Total pull request authors: 9
  • Average comments per issue: 1.3
  • Average comments per pull request: 0.77
  • Merged pull requests: 63
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 27
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 day
  • Issue authors: 0
  • Pull request authors: 4
  • Average comments per issue: 0
  • Average comments per pull request: 0.11
  • Merged pull requests: 20
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Neves-P (45)
  • richelbilderbeek (6)
  • joshwlambert (3)
  • Yangshen0325 (2)
  • romainfrancois (1)
Pull Request Authors
  • Neves-P (37)
  • rsetienne (26)
  • luislvalente (5)
  • HHildenbrandt (3)
  • xieshu95 (3)
  • joshwlambert (2)
  • Yangshen0325 (1)
  • O-Dehayem (1)
  • rscherrer (1)
Top Labels
Issue Labels
refactor (19) bug (5) High priority (5) Low Priority (2) depends (1) enhancement (1) suggestion (1) Medium Priority (1)
Pull Request Labels
bug (3) High priority (3) enhancement (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 308 last-month
  • Total docker downloads: 20,392
  • Total dependent packages: 3
  • Total dependent repositories: 12
  • Total versions: 13
  • Total maintainers: 1
cran.r-project.org: DAISIE

Dynamical Assembly of Islands by Speciation, Immigration and Extinction

  • Versions: 13
  • Dependent Packages: 3
  • Dependent Repositories: 12
  • Downloads: 308 Last month
  • Docker Downloads: 20,392
Rankings
Forks count: 5.8%
Dependent repos count: 8.4%
Dependent packages count: 11.0%
Docker downloads count: 12.8%
Average: 15.6%
Stargazers count: 17.5%
Downloads: 38.2%
Maintainers (1)
r.s.etienne@rug.nl
Last synced: 7 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
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.github/workflows/test-coverage.yaml actions
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  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 4.1.0 depends
  • doMC * enhances
  • DDD >= 5.0 imports
  • Matrix * imports
  • Rcpp >= 1.0.10 imports
  • deSolve * imports
  • doParallel * imports
  • foreach * imports
  • graphics * imports
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  • stats * imports
  • subplex * imports
  • tensor * imports
  • testit * imports
  • utils * imports
  • ape * suggests
  • covr * suggests
  • dplyr * suggests
  • ggplot2 * suggests
  • ggtree >= 3.0.0 suggests
  • gridExtra * suggests
  • knitr * suggests
  • phytools * suggests
  • purrr * suggests
  • rmarkdown * suggests
  • testthat >= 2.1.0 suggests
  • tibble * suggests
  • tidyr * suggests
  • tidytree * suggests
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite