Rarefaction Curves with the Rarefy Package

Rarefy is a new R package that offers a suite of new functions useful to perform rarefaction analysis based on any diversity metric. It can calculate the expected values of a given taxonomic, functional, or phylogenetic index for a reduced sampling size while considering a spatially constrained and distance-based ordering of the sampling units. Rarefy and the functions within this package offer an advanced solution for ecologists seeking to “rarefy” any diversity metric while taking into account the contributions of a distance-based ordination of sampling units. This approach provides more ecologically meaningful and unbiased estimates of expected diversities. In this chapter, we will explore the concept of rarefaction, its evolution to incorporate spatial autocorrelation, and its application with different types of metrics while examining the functions available in Rarefy.