Installation | What hilldiv3 does | The data | Alpha diversity (within a sample) | Which taxa carry the Hill power sum? | Partitioning and dissimilarity | Where to next | References
Package: hilldiv3 3.1.0.9000
Antton Alberdi
hilldiv3: Integral Analysis of Diversity Based on Hill Numbers
Measures and compares the diversity of biological communities (e.g. tables of operational taxonomic units (OTUs), amplicon sequence variants (ASVs) or metagenome-assembled genomes (MAGs)) based on Hill numbers, in a unified framework for neutral, phylogenetic and functional diversity measurement, diversity partitioning, (dis)similarity measurement, diversity profiles, evenness, redundancy and attribution of Hill power-sum weight and beta dissimilarity to taxa and sets. The statistical framework encompasses richness, Shannon and Simpson diversity, Faith's phylogenetic diversity (PD), Rao's quadratic entropy and Sorensen- and UniFrac-type dissimilarities, all grounded in a single Hill-number framework. Methods are described in Jost (2007) <doi:10.1890/06-1736.1>, Chao et al. (2010) <doi:10.1098/rstb.2010.0272>, Chiu et al. (2014) <doi:10.1890/12-0960.1> and reviewed in Alberdi & Gilbert (2019) <doi:10.1111/1755-0998.13014>. Optional import adapters interoperate with the Bioconductor packages 'phyloseq', 'SummarizedExperiment' and 'TreeSummarizedExperiment', which are available from <https://bioconductor.org>.
Authors:
hilldiv3_3.1.0.9000.tar.gz
hilldiv3_3.1.0.9000.zip(r-4.7-any)hilldiv3_3.1.0.9000.zip(r-4.6-any)hilldiv3_3.1.0.9000.zip(r-4.5-any)
hilldiv3_3.1.0.9000.tgz(r-4.6-any)hilldiv3_3.1.0.9000.tgz(r-4.5-any)
hilldiv3_3.1.0.9000.tar.gz(r-4.7-any)hilldiv3_3.1.0.9000.tar.gz(r-4.6-any)
hilldiv3_3.1.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hilldiv3/json (API)
| # Install 'hilldiv3' in R: |
| install.packages('hilldiv3', repos = c('https://alberdilab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/alberdilab/hilldiv3/issues
Pkgdown/docs site:https://alberdilab.github.io
Datasets:
- gut_counts - Simulated gut microbiome MAG count table
- gut_traits - Functional traits for the simulated gut MAGs
- gut_tree - Phylogeny for the simulated gut MAGs
Last updated from:263360c04c. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 159 | ||
| source / vignettes | OK | 181 | ||
| linux-release | OK | 158 | ||
| macos-release | OK | 120 | ||
| macos-oldrel | OK | 116 | ||
| windows-devel | OK | 120 | ||
| windows-release | OK | 128 | ||
| windows-oldrel | OK | 116 | ||
| wasm-release | OK | 107 |
Exports:hillcontribhilldisshilldivhillevenhillpairhillparthillprofhillredhillsharehillsimmatch_datatraits2disttss
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Simulated gut microbiome MAG count table | gut_counts |
| Functional traits for the simulated gut MAGs | gut_traits |
| Phylogeny for the simulated gut MAGs | gut_tree |
| Attribute Hill dissimilarity to taxa or sets | hillcontrib |
| Hill numbers-based dissimilarity | hilldiss |
| Hill numbers computation | hilldiv |
| Hill-number evenness | hilleven |
| Pairwise Hill numbers-based dissimilarity | hillpair |
| Hill numbers diversity partitioning | hillpart |
| Diversity profile across a range of orders | hillprof |
| Hill numbers redundancy | hillred |
| Allocate Hill power-sum weight to taxa or sets | hillshare |
| Hill numbers-based similarity | hillsim |
| Match and align a count table to a tree or distance matrix | match_data |
| Plot a diversity profile | plot.hill_profile |
| Plot a redundancy fit | plot.hill_redundancy |
| Convert a trait table into a distance matrix | traits2dist |
| Total Sum Scaling normalisation | tss |