Dynamic Assembly Model of Colonization, Local Extinction and Speciation

Simulates and computes (maximum) likelihood of a dynamical model of community assembly that takes into account phylogenetic history.

DAMOCLES

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Dynamic Assembly Model of Colonization, Local Extinction and Speciation in R.

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

Installing DAMOCLES

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

From CRAN

From within R, do:

install.packages("DAMOCLES")

From GitHub

Install DAMOCLES from this GitHub repository by running:

install.packages("remotes")
remotes::install_github("rsetienne/DAMOCLES")

Using DAMOCLES as a package dependency

From CRAN

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

If your package directly uses DAMOCLES:

Imports:
  DAMOCLES

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

Suggests:
  DAMOCLES

From GitHub

Remotes:
  rsetienne/DAMOCLES

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.

Contributors

DAMOCLES was originally developed by Rampal S. Etienne and Alex Pigot

Additionally there are others working on expanding DAMOCLES at the TECE lab, University of Groningen.

References

Pigot, A. L., & Etienne, R. S. (2015). A new dynamic null model for phylogenetic community structure. Ecology Letters, 18(2), 153-163. https://doi.org/10.1111/ele.12395