The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
Tools for analysing, comparing, visualising and partitioning diversity based on Hill numbers. 'hilldiv' is an R package that provides a set of functions to assist analysis of diversity for diet reconstruction, microbial community profiling or more general ecosystem characterisation analyses based on Hill numbers, using OTU/ASV tables and associated phylogenetic trees as inputs. The package includes functions for (phylo)diversity measurement, (phylo)diversity profile plotting, (phylo)diversity comparison between samples and groups, (phylo)diversity partitioning and (dis)similarity measurement. All of these grounded in abundance-based and incidence-based Hill numbers. The statistical framework developed around Hill numbers encompasses many of the most broadly employed diversity (e.g. richness, Shannon index, Simpson index), phylogenetic diversity (e.g. Faith's PD, Allen's H, Rao's quadratic entropy) and dissimilarity (e.g. Sorensen index, Unifrac distances) metrics. This enables the most common analyses of diversity to be performed while grounded in a single statistical framework. The methods are described in Jost et al. (2007) <doi:10.1890/06-1736.1>, Chao et al. (2010) <doi:10.1098/rstb.2010.0272> and Chiu et al. (2014) <doi:10.1890/12-0960.1>; and reviewed in the framework of molecularly characterised biological systems in Alberdi & Gilbert (2019) <doi:10.1111/1755-0998.13014>.
| Version: | 1.5.1 |
| Depends: | R (≥ 3.1.0) |
| Imports: | stats, ggplot2, scales, ggpubr, RColorBrewer, data.table, ape, vegan, geiger, qgraph, FSA |
| Published: | 2019-10-01 |
| DOI: | 10.32614/CRAN.package.hilldiv |
| Author: | Antton Alberdi [aut, cre] |
| Maintainer: | Antton Alberdi <antton.alberdi at bio.ku.dk> |
| BugReports: | https://github.com/anttonalberdi/hilldiv/issues |
| License: | GPL-3 |
| URL: | https://github.com/anttonalberdi/hilldiv |
| NeedsCompilation: | no |
| Citation: | hilldiv citation info |
| CRAN checks: | hilldiv results |
| Reference manual: | hilldiv.pdf |
| Package source: | hilldiv_1.5.1.tar.gz |
| Windows binaries: | r-devel: hilldiv_1.5.1.zip, r-release: hilldiv_1.5.1.zip, r-oldrel: hilldiv_1.5.1.zip |
| macOS binaries: | r-release (arm64): hilldiv_1.5.1.tgz, r-oldrel (arm64): hilldiv_1.5.1.tgz, r-release (x86_64): hilldiv_1.5.1.tgz, r-oldrel (x86_64): hilldiv_1.5.1.tgz |
Please use the canonical form https://CRAN.R-project.org/package=hilldiv to link to this page.
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.