Package: iNEXT.3D 1.0.6
Anne Chao
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.
Authors:
iNEXT.3D_1.0.6.tar.gz
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iNEXT.3D.pdf |iNEXT.3D.html✨
iNEXT.3D/json (API)
NEWS
# Install 'iNEXT.3D' in R: |
install.packages('iNEXT.3D', repos = c('https://annechao.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/annechao/inext.3d/issues
- Brazil_rainforest_abun_data - Abundance data
- Brazil_rainforest_distance_matrix - Species pairwise distance matrix for species in the dataset 'Brazil_rainforest_abun_data'
- Brazil_rainforest_phylo_tree - Phylogenetic tree for 'Brazil_rainforest_abun_data'
- Fish_distance_matrix - Species pairwise distance matrix for species in the dataset 'Fish_incidence_data'
- Fish_incidence_data - Incidence data
- Fish_phylo_tree - Phylogenetic tree for 'Fish_incidence_data'
Last updated 2 months agofrom:e9866d52a5. Checks:OK: 1 WARNING: 8. Indexed: yes.
Target | Result | Date |
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Doc / Vignettes | OK | Sep 02 2024 |
R-4.5-win-x86_64 | WARNING | Sep 02 2024 |
R-4.5-linux-x86_64 | WARNING | Sep 02 2024 |
R-4.4-win-x86_64 | WARNING | Sep 02 2024 |
R-4.4-mac-x86_64 | WARNING | Sep 02 2024 |
R-4.4-mac-aarch64 | WARNING | Sep 02 2024 |
R-4.3-win-x86_64 | WARNING | Sep 02 2024 |
R-4.3-mac-x86_64 | WARNING | Sep 02 2024 |
R-4.3-mac-aarch64 | WARNING | Sep 02 2024 |
Exports:DataInfo3Destimate3DggiNEXT3DggObsAsy3DiNEXT3DObsAsy3D
Dependencies:apeclicolorspacecpp11digestdplyrfansifarverfsgenericsggplot2gluegtableisobandlabelinglatticelazyevallifecyclemagrittrMASSMatrixmgcvmunsellnlmephyclustpillarpkgconfigplyrpurrrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbletidyrtidyselecttidytreeutf8vctrsviridisLitewithryulab.utils