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Welcome to fuzzySim project!

fuzzySim is an R package for calculating fuzzy similarity in species occurrence patterns.

It includes functions for data preparation, such as converting species lists (long format) to presence-absence tables (wide format), obtaining unique abbreviations of species names, or transposing (parts of) complex data frames; and sample data sets for providing practical examples.

It can convert binary presence-absence to fuzzy occurrence data, using e.g. trend surface analysis, inverse distance interpolation or prevalence-independent environmental favourability modelling, for multiple species simultaneously.

It then calculates fuzzy similarity among (fuzzy) species distributions and/or among (fuzzy) regional species compositions. Currently available similarity indices are Jaccard, Sørensen, Simpson, and Baroni-Urbani & Buser.

Some of the fuzzySim functions are also being implemented within a graphical-interface extension for the QGIS Processing Toolbox - you can download their current versions 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!


Install and load

To install fuzzySim directly from R-Forge, paste the following command in the R console (when connected to the internet):

install.packages("fuzzySim", repos="http://R-Forge.R-project.org")

This should work if you have the latest version of R; otherwise, it may either fail (producing a message like "package 'fuzzySim' is not available for your R version") or install an older version of fuzzySim. To check the version that you have actually installed, type citation(package="fuzzySim"). To install the latest version of the package, you can either upgrade R or download the compressed fuzzySim package source files to your disk (.zip or .tar.gz available here or here) and then install the package from there, e.g. with R menu "Packages - Install packages from local zip files" (Windows), or "Packages & Data - Package installer, Packages repository - Local source package" (Mac), or "Tools - Install packages - Install from: Package Archive File" (RStudio).

You only need to install (each version of) the package once, but then every time you re-open R you need to load it by typing:

library(fuzzySim)

You can then check out the package help files and try some of the provided examples:

help("fuzzySim")

References

If you use fuzzySim in publications, please cite the following paper:

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)

To see how to cite the package itself, load it in R and type citation(package="fuzzySim").


Find out more

There's an illustrated beginners tutorial of fuzzySim (updated 22 Jul 2015), and a reference manual based on the package help files.

Here's a poster made to present fuzzySim at Rencontres R 2014.

There's also a beginners tutorial on species distribution modelling with fuzzySim (updated 29 Oct 2015), and a course manual on model building with fuzzySim and model evaluation with modEvA (in Spanish).

Recently, I've added a tutorial on rangemap comparison (updated 12 Feb 2016).

Go here for further info on the package and its origins.

The R-Forge project summary page you can find here.