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.

git branching workflow

• master: build should always pass. @rsetienne has control over develop to master merges.
• develop: merge of topic 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. (2021). The robustness of a simple dynamic model of island biodiversity to geological and eustatic change. bioRxiv. https://doi.org/10.1101/2021.07.26.453064

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. (2022). A simple island biodiversity model is robust to trait dependence in diversification and colonization rates. biRrxiv. https://doi.org/10.1101/2022.01.01.474685