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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.
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 within R, do:
install.packages("DAISIE")
Install DAISIE
from this GitHub repository by running:
install.packages("remotes")
remotes::install_github("rsetienne/DAISIE")
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
Remotes:
rsetienne/DAISIE
For feature requests or bug-reports or other matters, please submit an issue.
master
: build should always pass. @rsetienne has control overdevelop
tomaster
merges.develop
: merge of feature branches, merge withmaster
by @rsetienne iff build passes.
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.
-
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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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