fuzzySim 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 one or more species simultaneously.
It can then calculate e.g. fuzzy change and fuzzy similarity among (fuzzy) species distributions and/or among (fuzzy) regional species compositions, avoiding the use of thresholds and instead using fuzzy logic versions of known similarity indices.
Package fuzzySim can be installed from CRAN, where it is updated relatively often:
install.packages("fuzzySim")
The development version may include more recent enhancements and small bug fixes. fuzzySim was created long before I knew GitHub, and it's still normally maintained on its original platform, R-Forge. So, you can normally install the latest version from there:
install.packages("fuzzySim", repos="http://R-Forge.R-project.org")
Sadly, R-Forge servers are sometimes offline, so I try to also keep an updated version of the development version here on GitHub:
remotes::install_github("AMBarbosa/fuzzySim")
Find out more about the package, along with usage manuals and literature examples, at https://fuzzysim.r-forge.r-project.org/