An R package using rarefaction metrics to estimate α- and β-diversity for incomplete samples

Aim: Species abundance data is commonly used to study biodiversity patterns. In this context, comparing α- and β-diversity across incomplete samples can lead to biases. Therefore, it is essential to employ methods that enable standardised and accurate comparisons of α- and β-diversity across varying sample sizes. In addition, biodiversity studies also often require robust estimates of the total number of species within a community and the number of species shared by two communities. Innovation: Rarefaction methods are commonly used to calculate α-diversity for standardised sample sizes, and they can also serve as the basis for calculating β-diversity. In this application note, we present rarestR, a new R package designed for calculating abundance-based α- and β-diversity measures for inconsistent samples using rarefaction-based metrics. The package also includes parametric extrapolation techniques to estimate the total expected number of species within a community, as well as the total number of species shared between two communities. Additionally, rarestR provides visualisation tools for curve-fitting associated with these estimators. Main Conclusions: Overall, the rarestR package is a valuable tool for comparing α- and β-diversity values among incomplete samples, such as those involving highly mobile or species-rich taxa. In addition, our species estimators offer a complementary approach to non-parametric methods, including the Chao series of estimators.