Package - pnovack-gottshall/ecospace

ecospace: R Package for Simulating Community Assembly and Ecological Diversification Using Ecospace Frameworks

ecospace is an R package that implements stochastic simulations of community assembly (ecological diversification) using customizable ecospace frameworks (functional trait spaces). Simulations model the 'neutral', 'redundancy', 'partitioning', and 'expansion' models of Bush and Novack-Gottshall (2012) and Novack-Gottshall (2016a, b). The package provides a wrapper to calculate common ecological disparity and functional ecology statistical dynamics as a function of species richness. Functions are written so they will work in a parallel-computing environment.

The package also contains a sample data set, functional traits for Late Ordovician (Type Cincinnatian) fossil species from the Kope and Waynesville formations.

The most recent public release of the code is on CRAN at:

http://cran.r-project.org/web/packages/ecospace

You can install the most recent public release version in R using:

install.packages("ecospace")

The latest pre-release version can be found at GitHub:

https://github.com/pnovack-gottshall/ecospace

Or downloaded directly in R using:

library(devtools)
devtools::install_github("pnovack-gottshall/ecospace")
library(ecospace)

References

Novack-Gottshall, P.M. 2016a. General models of ecological diversification. I. Conceptual synthesis. Paleobiology 42: 185-208.

Novack-Gottshall, P.M. 2016b. General models of ecological diversification. II. Simulations and empirical applications. Paleobiology 42: 209-239.

Bush, A. and P.M. Novack-Gottshall. 2012. Modelling the ecological-functional diversification of marine Metazoa on geological time scales. Biology Letters 8: 151-155.

Reprints are available at https://www.researchgate.net/profile/Philip_Novack-Gottshall/contributions.

The most recent commit is currently: Travis-CI Build Status (Travis CI)

This package is authored by Phil Novack-Gottshall (mailto:pnovack-gottshall@ben.edu) and offered under CC0.

The current total number of downloads of the ecospace package from the RStudio CRAN mirror is: Number of Downloads

Github

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Releases

v1.2.1 - Nov 5, 2017

  1. Addition of 'increm' argument to calc_metrics() for those wishing to only calculate statistics on the entire sample (instead of incrementally). (Thanks to Craig McClain, Felipe Opazo, Stewart Edie, and Katie Collins for the recommendation.)
  2. Improved descriptions of statistics in calc_metrics help file.

v1.1.1 - Jan 8, 2017

ecospace v. 1.1.1 (2017-01-06)

  • Slightly faster calculation of H, life habit richness
  • Minor fixes: typos in documentation and updated references

v1.0.0 - Nov 2, 2015

R Package for Simulating Community Assembly and Ecological Diversification Using Ecospace Frameworks

ecospace is an R package that implements stochastic simulations of community assembly (ecological diversification) using customizable ecospace frameworks (functional trait spaces). Simulations model the 'neutral', 'redundancy', 'partitioning", and "expansion" models of Bush and Novack-Gottshall (2012) as implemented in Novack-gottshall (In pressA,B). The package provides a wrapper to calculate common ecological disparity and functional diversity statistical dynamics as a function of species richness. Functions are written so they will work in a parallel-computing environment.

The package also contains a sample data set, functional traits for Late Ordovician (Type Cincinnatian) fossil species from the Kope and Waynesville formations.

References

Bush, A. and P.M. Novack-Gottshall. 2012. Modelling the ecological-functional diversification of marine Metazoa on geological time scales. Biology Letters 8: 151-155.

Contact Phil Novack-Gottshall (pnovack-gottshall@ben.edu) for a pre-print of the following articles in review, which provide more information on the package and its utility.

Novack-Gottshall, P.M. In review at Paleobiology (submitted Oct. 5, 2015). General models of ecological diversification. I. Conceptual synthesis.

Novack-Gottshall, P.M. In review at Paleobiology (submitted Oct. 5, 2015). General models of ecological diversification. II. Simulations and empirical applications.

Further information

Further information is available at https://cran.r-project.org/web/packages/ecospace/

Development versions will be posted to https://github.com/pnovack-gottshall/ecospace

This code is authored by Phil Novack-Gottshall and offered under CC0.