Similarity between rangemaps can allow the detection of associations among species distributions, with important applications in macroecology, biogeography and conservation planning. Commonly used similarity indices use counts of species occurrences and co-occurrences in discrete localities, regions or grid cells. However, gridding rangemaps distorts species’ distribution limits, generally overestimating their overlap and sometimes overriding important geographical barriers (Barbosa & Estrada, in press). This tutorial shows how to calculate similarity between ungridded rangemaps with R. First, download, install and open R, which is freely available at CRAN.

Functions to calculate the areas of pairwise intersection and union between rangemaps and to assess rangemap similarity are implemented in R package fuzzySim (Barbosa, 2015). The first of these functions needs some other packages to work. You can paste the following code in the R console (and then press enter) to install all of these packages if they’re not already there:

for (pkg in c("fuzzySim", "tools", "PBSmapping", "maptools", "sp")) {
if (pkg == "fuzzySim")  rp <- "http://R-Forge.R-project.org"
else  rp <- "http://cran.rstudio.com"
if (!requireNamespace(pkg, quietly = TRUE)) install.packages(pkg, repos = rp)
}

Now you’ll need some shapefile rangemaps to compare. You can use my sample rangemap set for experimenting. Download it to your R working directory – find out which it is by typing getwd() – and unzip it. You should now have some shapefiles in a folder called “imagine_rangemaps” in your R working directory. The following code will get you a matrix containing the areas of pair-wise intersection (in the lower triangle) and union (in the upper triangle) of the shapefiles in this folder (the diagonal contains the area of each individual rangemap):

require(fuzzySim)
my_rangemaps <- list.files(path = "imagine_rangemaps", pattern = ".shp", full.names = TRUE)
my_rangemaps
rangemap_matrix <- pairwiseRangemaps(my_rangemaps, projection = 3035, Ncpu = 1, nchunks = 1, filename = "rangemap_matrix.csv")
rangemap_matrix

This calculation can be very intensive and slow if you have many and/or large rangemaps, due to the time needed for spatial operations between maps. If your computer has more than one core that you can use, you can increase Ncpu (e.g., replace Ncpu = 1 with Ncpu = 3 in the command above; you can find out the number of cores in your machine by typing parallel::detectCores()) to get parallel computing. If there are many rangemaps, you should also set nchunks = "decreasing" for the matrix to be calculated in parts and the memory cleaned between one part and the next.

Once you have your rangemap_matrix, you can use it to calculate pairwise similarity between the rangemaps, using a variety of indices. Jaccard is the one used by default:

rangemap_jac <- rangemapSim(rangemap_matrix)
rangemap_jac

Check out the help files of these functions (help(pairwiseRangemaps); help(rangemapSim)) for additional options and information. And that’s it! You can e-mail me with any suggestions or concerns, but first remember to check for updates to the package or this tutorial at http://fuzzysim.r-forge.r-project.org. This tutorial was built with RStudio + rmarkdown + knitr. Thanks!

References

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)

Barbosa A.M. & Estrada A. (in press) Calcular corotipos sin dividir el territorio en OGUs: una adaptacion de los indices de similitud para su utilizacion directa sobre areas de distribucion. In: Areas de distribucion: entre puentes y barreras. Universidad de Granada, Spain.