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ecolottery - Backward- and forward-in-time simulation of ecological communities

License: GPL v3 CRAN_Status_Badge Build Status AppVeyor Build Status

The package allows quick and efficient simulation of community composition under diverse combinations of environmental filtering and neutral birth-death dynamics. The package offers a coalescent-based, backward-in-time algorithm, named coalesc. The package also includes a forward-in-time simulation algorithm, named forward, to investigate a broader set of niche-based dynamics, albeit at the expense of greater resources and computation time.

coalesc_abc is another core function of the package, to perform Approximate Bayesian Computation (ABC) and infer parameters of the processes from observed community composition. This function relies on the coalesc function for intensive simulation of biodiversity parrtterns in ABC analyses.

Installing the package

The version 1.0.0 is available on CRAN, https://cran.r-project.org/web/packages/ecolottery/index.html

install.packages("ecolottery")

The development version on Github can be installed using the devtools package:

devtools::install_github("frmunoz/ecolottery/pkg", build_vignettes = TRUE)

How to use the package

The two main functions of the package are coalesc() and forward(). You can learn more on how to use them by looking at the introduction vignette.

If you want to see how coalesc_abc() allows estimating parameters of community assembly with the ABC approach, have a look at the Barro Colorado vignette.