Cellular Automata for Spatial Pressure in R
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README.md

R-package caspr

The code provided here is running spatial disturbance models in a cellular automata framework. This is part of a collaborative project between the group of Sonia Kéfi (Institut de Sciences d'Evolution, CNRS, IRD, Université Montpellier, France) and Vishwesha Guttal (Center for Ecological Sciences, Indian Institute of Science, Bangalore, India).

The R-package is build around objects of a particular class ca_model (S3 objects in R) that contain all the model specific information, like the original publication, the update functions, and the cell states. These objects can be handled by a function called ca() which runs the cellular automata over time.

Other functions allow the plotting of single snapshots or timeseries, the generation of initial lattices/grids/landscapes, the calculation of spatial and temporal indicators as provided by the package 'spatialwarnings'.

Contributors

Alain Danet, Alex Genin, Vishwesha Guttal, Sonia Kefi, Sabiha Majumder, Sumithra Sankaran, Florian Schneider (Maintainer)

Install package

To use the package, it can be installed directly from GitHub using the devtools package.

install.packages("devtools")
devtools::install_github("fdschneider/caspr")

Details

Further description of the functions of the package, the models provided and the application of spatial indicators can be found in the package vignette (pdf download) and the package manual (pdf).

Contribute to the package

Just a couple of guidelines for contributing code to the package:

  1. The collaborative work on the package is coordinated via the issues. No uninvited pull-requests, please! Before you start developing a feature, please create an issue and assign yourself (if it does not exist yet).
  2. Clone the repository to your computer and work locally. If you add a new function or modify an existing one please include a valid documentation using roxygen2. If you refer to functions of other packages, put them in the Import list in DESCRIPTION and use the structure package::function() to apply them in the code.
  3. Before you push your commits to GitHub, please be sure that everything works fine by testing the new functionality on your local repository. Test functions that rely on your function, too! If your feature works, create a last commit where you increase the version number in DESCRIPTION by 0.0.1 and mention the related issue in your commit message, e.g. git commit -m "transfer code into R-package #1". If you're not listed yet, add your name to the LICENSE and README.md file.

License

The MIT License (MIT)

Copyright (c) 2015 the authors

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.