by Alain Danet, Alex Genin, Vishwesha Guttal, Sonia Kefi, Sabiha Majumder, Sumithra Sankaran, Florian Schneider (Maintainer)
Published: 01 December 2015
github: fdschneider/caspr (issues | package vignette)
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’.
Alain Danet, Alex Genin, Vishwesha Guttal, Sonia Kefi, Sabiha Majumder, Sumithra Sankaran, Florian Schneider (Maintainer)
To use the package, it can be installed directly from GitHub using the
Contribute to the package
Just a couple of guidelines for contributing code to the package:
- 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).
- 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
Importlist in DESCRIPTION and use the structure
package::function()to apply them in the code.
- 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
0.0.1and 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
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.
- Danet, Alain, Florian D. Schneider, Fabien Anthelme, Sonia Kéfi (2020), Indirect facilitation drives species composition and stability in drylands, Theoretical Ecology, doi: 10.1007/s12080-020-00489-0
- Alexandre Génin, Sabiha Majumder, Sumithra Sankaran, Florian D. Schneider, Alain Danet, Miguel Berdugo, Vishwesha Guttal, Sonia Kéfi (2018), Spatially heterogeneous stressors can alter the performance of indicators of regime shifts, Ecological Indicators, 94 :520-533 doi: 10.1016/j.ecolind.2017.10.071 (pdf)
- Alexandre Génin, Sabiha Majumder, Sumithra Sankaran, Alain Danet, Vishwesha Guttal, Florian D. Schneider, Sonia Kéfi (2018), Monitoring ecosystem degradation using spatial data and the R package spatialwarnings, Methods in Ecology and Evolution, 9 :2067-2075 doi: 10.1111/2041-210X.13058 (pdf)
- Schneider, F.D., Kéfi, S. (2015), Spatially heterogeneous pressure raises risk of catastrophic shifts, Theoretical Ecology, 9 2:207-217 doi: 10.1007/s12080-015-0289-1 (pdf)
- van den Elsen, Erik, Lindsay C. Stringer, Cecilia De Ita, Rudi Hessel, Sonia Kéfi, Florian D. Schneide, Susana Bautista, Angeles G. Mayor, Mara Baudena, Max Rietkerk, Alejandro Valdecantos, Victoriano R. Vallejo, Nichola Geeson, C. Jane Brandt, Luuk Fleskens, Lia Hemerik, Panos Panagos, Sandra Valente, Jan J. Keizer, Gudrun Schwilch, Matteo Jucker Riva, Diana Sietz, Michalakis Christoforou, Diofantos G. Hadjimitsis, Christiana Papoutsa, Giovanni Quaranta, Rosanna Salvia, Ioannis K. Tsanis, Ioannis Daliakopoulos, Heleen Claringbould and Peter C. de Ruiter (2020), Advances in Understanding and Managing Catastrophic Ecosystem Shifts in Mediterranean Ecosystems, Frontiers in Ecology and Evolution, doi: 10.3389/fevo.2020.561101 (pdf)