iNEXT.3D-package {iNEXT.3D}

Interpolation and Extrapolation for three dimensions of biodiversity

Description

iNEXT.3D (iNterpolation and EXTrapolation for three dimensions of biodiversity) is a sequel to iNEXT (Hsieh et al., 2016). Here the three dimensions (3D) of diversity refer to taxonomic diversity (TD), phylogenetic diversity (PD) and functional diversity (FD). An online version "iNEXT.3D Online" (https://chao.shinyapps.io/iNEXT_3D/) is also available for users without an R background.

A unified framework based on Hill numbers (for TD) and their generalizations (Hill-Chao numbers, for PD and FD) is adopted to quantify 3D. In this framework, TD quantifies the effective number of species, PD quantifies the effective total branch length, mean-PD (PD divided by tree depth) quantifies the effective number of lineages, and FD quantifies the effective number of virtual functional groups (or functional "species"). Thus, TD, mean-PD, and FD are all in the same units of species/lineage equivalents and can be meaningfully compared; see Chao et al. (2014) for the basic standardization theory for TD, and Chao et al. (2021) for a review of the unified theory for 3D.

For each of the three dimensions of biodiversity, iNEXT.3D features two statistical analyses (non-asymptotic and asymptotic):

(1) A non-asymptotic approach based on interpolation and extrapolation for 3D diversity (i.e., Hill-Chao numbers)

iNEXT.3D computes the estimated 3D diversity for standardized samples with a common sample size or sample completeness. This approach aims to compare diversity estimates for equally-large (with a common sample size) or equally-complete (with a common sample coverage) samples; it is based on the seamless rarefaction and extrapolation (R/E) sampling curves of Hill-Chao numbers for q = 0, 1 and 2. For each dimension of biodiversity, iNEXT.3D offers three types of R/E sampling curves:

* Sample-size-based (or size-based) R/E sampling curves: This type of sampling curve plots the diversity estimates with respect to sample size.

* Coverage-based R/E sampling curves: This type of sampling curve plots the diversity estimates with respect to sample coverage.

* Sample completeness curve: This curve depicts how sample coverage varies with sample size. The sample completeness curve provides a bridge between the size- and coverage-based R/E sampling curves.

(2) An asymptotic approach to infer asymptotic 3D diversity (i.e., Hill-Chao numbers)

iNEXT.3D computes the estimated asymptotic 3D diversity and also plots 3D diversity profiles (q-profiles) for q between 0 and 2, in comparison with the observed diversity. Typically, the asymptotic estimates for q \geq 1 are reliable, but for q < 1 (especially for q = 0, species richness), the asymptotic estimates represent only lower bounds. iNEXT.3D also features a time-profile (which depicts the observed and asymptotic estimate of PD or mean PD with respect to reference times), and a tau-profile (which depicts the observed and asymptotic estimate of FD with respect to threshold level tau).

There are six main functions in this package:

1. iNEXT3D computes standardized 3D diversity of order q = 0, 1 and 2 for rarefied and extrapolated samples at specified sample coverage values and sample sizes.

2. ggiNEXT3D visualizes the output from the function iNEXT3D.

3. ObsAsy3D computes observed and asymptotic diversity of order q between 0 and 2 (in increments of 0.2) for 3D diversity; it also computes observed and asymptotic PD for specified reference times, and observed and asymptotic FD for specified threshold levels.

4. ggObsAsy3D visualizes the output from the function ObsAsy3D.

5. estimate3D computes 3D diversity of order q = 0, 1 and 2 with a particular set of user-specified level of sample sizes or sample coverage values.

6. DataInfo3D provides basic data information based on the observed data.

Author(s)

Anne Chao, Kai-Hsiang Hu

Maintainer: Anne Chao <[e-mail]>

References

Chao, A., Henderson, P. A., Chiu, C.-H., Moyes, F., Hu, K.-H., Dornelas, M. and Magurran, A. E. (2021). Measuring temporal change in alpha diversity: a framework integrating taxonomic, phylogenetic and functional diversity and the iNEXT.3D standardization. Methods in Ecology and Evolution, 12, 1926-1940.

Hsieh, T. C., Ma, K. H. and Chao, A. (2016). iNEXT: An R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods in Ecology and Evolution, 7, 1451-1456.