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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: | 1.0.6 |
| Depends: | R (≥ 4.0) |
| Imports: | stats, tibble, ggplot2, reshape2, tidytree, phyclust, dplyr, ape, Rcpp |
| LinkingTo: | Rcpp |
| Suggests: | testthat, knitr, rmarkdown, gridExtra, ggthemes |
| Published: | 2024-08-22 |
| DOI: | 10.32614/CRAN.package.iNEXT.3D |
| 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 |
| Reference manual: | iNEXT.3D.pdf |
| Vignettes: |
iNEXT.3D Vignette (Feb. 2024) (source) |
| Package source: | iNEXT.3D_1.0.6.tar.gz |
| Windows binaries: | r-devel: iNEXT.3D_1.0.6.zip, r-release: iNEXT.3D_1.0.6.zip, r-oldrel: iNEXT.3D_1.0.6.zip |
| macOS binaries: | r-release (arm64): iNEXT.3D_1.0.6.tgz, r-oldrel (arm64): iNEXT.3D_1.0.6.tgz, r-release (x86_64): iNEXT.3D_1.0.6.tgz, r-oldrel (x86_64): iNEXT.3D_1.0.6.tgz |
| Old sources: | iNEXT.3D archive |
| Reverse imports: | iNEXT.4steps, iNEXT.beta3D |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.