CRAN/E | hilldiv

hilldiv

Integral Analysis of Diversity Based on Hill Numbers

Installation

About

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.

Citation hilldiv citation info
github.com/anttonalberdi/hilldiv
Bug report File report

Key Metrics

Version 1.5.1
R ≥ 3.1.0
Published 2019-10-01 1640 days ago
Needs compilation? no
License GPL-3
CRAN checks hilldiv results

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Maintainer

Maintainer

Antton Alberdi

antton.alberdi@bio.ku.dk

Authors

Antton Alberdi

aut / cre

Material

Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Depends

R ≥ 3.1.0

Imports

stats
ggplot2
scales
ggpubr
RColorBrewer
data.table
ape
vegan
geiger
qgraph
FSA