Zou, Yi;
Peng, Zhao;
Wu, Naicheng;
Lai, Jiangshan;
Peres-Neto, Pedro R;
Axmacher, Jan;
(2024)
An R package using rarefaction metrics to estimate α- and β-diversity for incomplete samples.
Diversity and Distributions
, 31
(1)
, Article e13954. 10.1111/ddi.13954.
Preview |
Text
Axmacher_Diversity and Distributions - 2025 - Zou - rarestR An R Package Using Rarefaction Metrics to Estimate ‐ and ‐Diversity.pdf Download (869kB) | Preview |
Abstract
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.
| Type: | Article |
|---|---|
| Title: | An R package using rarefaction metrics to estimate α- and β-diversity for incomplete samples |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1111/ddi.13954 |
| Publisher version: | https://onlinelibrary.wiley.com/journal/14724642 |
| Language: | English |
| Additional information: | This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2025 The Author(s). Diversity and Distributions published by John Wiley & Sons Ltd. |
| Keywords: | alpha-diversity | beta-diversity | dissimilarity | expected species | sample size | species composition | species richness |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL SLASH UCL > Provost and Vice Provost Offices > UCL SLASH > Faculty of S&HS UCL > Provost and Vice Provost Offices > UCL SLASH > Faculty of S&HS > Dept of Geography |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10200499 |
Archive Staff Only
 |
View Item |
