What is coenocliner?

coenocliner is an R package to simulate species abundance (count) data along environmental gradients.

One of the key ways quantitative ecologists attempt to understand the properties and behaviour of the methods they use or dream up is through the use of simulated data.

Rather than have to reinvent the wheel each time I wanted to simulate some new data for a paper or to work on a new approach, I decided to start my own R package to contain a range of simulators encapsulating different response models, numbers of gradients, etc.

Features

At the moment, coenocliner is limited in what it can do practically.

The main response model is the Gaussian response, which is a symmetric model of the parameters; the optimum, tolerance and height of the response curve. Count data can be generated from this model from either a Poisson or negative binomial distribution, using the parameterised Gaussian response as the expectation or mean of the distribution.

Additional response models include:

  • The generalised beta response function.

A further feature of coenocliner that I hope to develop is to include simulation wrapper functions that replicate the simulation methods used in research papers. A working example is simJamil, which produces simlations from a Gaussian logit response following the scheme described in Jamil and Ter Braak (2013).

Development

I would like to see coenocliner be as inclusive as possible; if you have code to simulate ecological species or community data that is just sitting around, consider adding it to coenocliner. In the meantime, I’m happy just having something tangible for my own use without having to remember the expressions for some of the response models.

Currently coenocliner is licensed under the GPL v2, but I’m happy to reconsider this if you want to contribute code under a more permissive licence.

Installation

No binary packages are currently available for coenocliner. If you have the correct development tools you can compile the package yourself after downloading the source code from github. Once I work out how to link git with svn I’ll start a project on R-forge which will host binary packages of coenocliner.

If you use Hadley Wickham’s devtools package then you can install coenocliner directly from github using functions that devtools provides. To do this, install devtools from CRAN via

install.packages("devtools")

then run

require("devtools")
install_github("coenocliner", "gavinsimpson")

Bugs, feature requests

Bug reports and feature requests should be filed as issues on github.

Licence

coenocliner is released under the GNU General Public Licence Version 2.

References

Jamil, Tahira, and Cajo J F Ter Braak. 2013. “Generalized Linear Mixed Models Can Detect Unimodal Species-Environment Relationships.” PeerJ 1 (9~jul): e95.