tree_depth

A phylogenetic tree of class 'phylo'. The tip labels must match the row names in the OTU table. Use the function match_data() if the OTU names do not match.

tree

A vector or a matrix/data.frame indicating the relative abundances of one or multiple samples, respectively. If a matrix/data.frame is provided, columns must refer to samples and rows to OTUs.

abund

Computes phylogenetic tree depth based from a phylogenetic tree and a vector of (relative) abundances.

phylogeny

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>.

tree_depth: Tree depth

Description

Usage

Arguments

Value

Details

See Also

Examples