FUZZY SIMILARITY IN SPECIES DISTRIBUTIONS
fuzzySim is an R package that builds on some functions preliminarily published in the modTools blog (such as spCodes, splist2presabs, binarySimilarity and simMatrix). It implements fuzzy versions of the latter two functions to account for fuzziness / uncertainty / vagueness when comparing species presence-absence patterns or regional species compositions and when calculating beta diversity. It also includes functions to generate fuzzy occurrence data, namely through trend surface analysis, inverse distance interpolation, or generalized linear modelling of binary occurrence (including the favourability function); and to make fuzzy comparison of model predictions, including niche model overlap, fuzzy intersection / union, fuzzy range change, etc.
fuzzySim is publicly available on CRAN, but is more frequently updated on R-Forge. A simple step-by-step tutorial on installation and usage is available as well. If you use/cite fuzzySim functions, or find articles that do, please let me know so I can keep track of them and help justify the work dedicated to developing the package!
A more graphical and directly mappable version of fuzzySim for QGIS is also in preparation – you can download the current (experimental!) functions from here, place them in your “.qgis2/processing/rscripts” folder (search for it in your computer; you may need to toggle “show hidden files” to see it) and give them a try. You need to have installed QGIS > 2.0, R with the fuzzySim package, and tell QGIS (under Processing – Options and configuration – Providers) where your R instalation is. Feedback welcome!
If you use a fuzzySim function, please remember to cite:
Barbosa A.M. (2015) fuzzySim: applying fuzzy logic to binary similarity indices in ecology. Methods in Ecology and Evolution, 6: 853-858 (DOI: 10.1111/2041-210X.12372)