DAISIE

Branch	Travis	Codecov
master
develop
richel_mainland_extinction
pedro_ontogeny
sebastian_archipelago
shu_traits
josh_nonoceanic
luis

Dynamic Assembly of Island biota through Speciation, Immigration and Extinction in R

This is a development version before the official release on CRAN.

Installing DAISIE

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

Because the DAISIE package is located in the folder DAISIE, do:

devtools::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

git branching model

• 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.
• pedro_ontogeny: @Neves-P's topic branch adding island ontongeny functionality for simulation and parameter estimation.
• richel_mainland_extinction: @richelbilderbeek's topic branch adding dynamic mainland processes.
• shu_traits: @xieshu95's topic branch adding lineage trait functionality
• sebastian_archipelago: @sebmader topic branch adding archipelago dynamics to DAISIE in C++

@Neves-P's is responsible for day-to-day merging and repository maintenance. For questions open an issue or contact @Neves-P's.

Contributors

DAISIE was originally developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore and Bart Haegeman.

Additional members working on expanding DAISIE at the TECE lab, University of Groningen are: Joshua Lambert, Pedro S. Neves, Richel J. C. Bilderbeek, Sebastian Mader, Shu Xie

References

Etienne, R. S., Valente, L. M., Phillimore, A. B., & Haegeman, B., (2018). DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction. R package version 1.6.0.

Valente, L. M., 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. M., 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. M., 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., 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