iNEXT.3D: Interpolation and Extrapolation for Three Dimensions of Biodiversity

Biodiversity is a multifaceted concept covering different levels of organization from genes to ecosystems. 'iNEXT.3D' extends 'iNEXT' to include three dimensions (3D) of biodiversity, i.e., taxonomic diversity (TD), phylogenetic diversity (PD) and functional diversity (FD). This package provides functions to compute standardized 3D diversity estimates with a common sample size or sample coverage. A unified framework based on Hill numbers and their generalizations (Hill-Chao numbers) are used to quantify 3D. All 3D estimates are in the same units of species/lineage equivalents and can be meaningfully compared. The package features size- and coverage-based rarefaction and extrapolation sampling curves to facilitate rigorous comparison of 3D diversity across individual assemblages. Asymptotic 3D diversity estimates are also provided. See Chao et al. (2021) <doi:10.1111/2041-210X.13682> for more details.

Version: 1.0.4
Depends: R (≥ 4.0)
Imports: stats, tibble, ggplot2, reshape2, tidytree, phyclust, dplyr, ape, Rcpp
LinkingTo: Rcpp
Suggests: testthat, knitr, rmarkdown, gridExtra, ggthemes
Published: 2024-03-28
Author: Anne Chao [aut, cre], KaiHsiang Hu [ctb]
Maintainer: Anne Chao <chao at stat.nthu.edu.tw>
BugReports: https://github.com/AnneChao/iNEXT.3D/issues
License: GPL (≥ 3)
URL: https://sites.google.com/view/chao-lab-website/software/inext-3d
NeedsCompilation: yes
Citation: iNEXT.3D citation info
Materials: NEWS
CRAN checks: iNEXT.3D results

Documentation:

Reference manual: iNEXT.3D.pdf
Vignettes: iNEXT.3D Vignette (Feb. 2024)

Downloads:

Package source: iNEXT.3D_1.0.4.tar.gz
Windows binaries: r-devel: iNEXT.3D_1.0.4.zip, r-release: iNEXT.3D_1.0.4.zip, r-oldrel: iNEXT.3D_1.0.4.zip
macOS binaries: r-release (arm64): iNEXT.3D_1.0.4.tgz, r-oldrel (arm64): iNEXT.3D_1.0.4.tgz, r-release (x86_64): iNEXT.3D_1.0.4.tgz
Old sources: iNEXT.3D archive

Reverse dependencies:

Reverse imports: iNEXT.4steps, iNEXT.beta3D

Linking:

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