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Cheddar: analysis and visualisation of ecological communities in R
Article first published online: 23 NOV 2012
© 2012 The Authors. Methods in Ecology and Evolution © 2012 British Ecological Society
Methods in Ecology and Evolution
Volume 4, Issue 1, pages 99–104, January 2013
How to Cite
Hudson, L. N., Emerson, R., Jenkins, G. B., Layer, K., Ledger, M. E., Pichler, D. E., Thompson, M. S. A., O'Gorman, E. J., Woodward, G., Reuman, D. C. (2013), Cheddar: analysis and visualisation of ecological communities in R. Methods in Ecology and Evolution, 4: 99–104. doi: 10.1111/2041-210X.12005
- Issue published online: 24 JAN 2013
- Article first published online: 23 NOV 2012
- Manuscript Accepted: 4 OCT 2012
- Manuscript Received: 18 JUL 2012
- body mass;
- ecological network;
- food chain;
- food web;
- trophic height;
- trophic level
- There has been a lack of software available to ecologists for the management, visualisation and analysis of ecological community and food web data. Researchers have been forced to implement their own data formats and software, often from scratch, resulting in duplicated effort and bespoke solutions that are difficult to apply to future analyses and comparative studies.
- We introduce Cheddar – an R package that provides standard, transparent implementations of a wide range of food web and community-level analyses and plots, focussing on ecological network data that are augmented with estimates of body mass and/or numerical abundance.
- The package allows analysis of individual communities, as well as collections of communities, allowing examination of changes in structure through time, across environmental gradients, or due to experimental manipulations. Several commonly analysed food web data sets are included and used in worked examples.
- This is the first time these important features have been combined in a single package that helps improve research efficiency and serves as a unified framework for future development.