README.md

In rsetienne/DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

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

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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 depedence models see here.

Installing DAISIE

N.B.: MacOS users may experience issues when installing DAISIE, especially when on MacOS Big Sur. If that is you case, please see here for detailed installation instructions.

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

From CRAN

From within R, do:

install.packages("DAISIE")

From GitHub

Install DAISIE from this GitHub repository by running:

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

rsetienne/DAISIE documentation built on Oct. 25, 2023, 4:32 a.m.