is.nested

<p>A matrix indicating the relation between samples (first column) and parent groups.</p>

hierarchy

<p>Multi-level diversity partitioning requires the groups at different hierarchical levels to be nested. i.e. two samples that belong to a common parent group cannot have different grandparent groups. The best example of nested hierarchy is taxonomy: e.g. two species that belong to the same genus cannot belong to different families. This function checks whether the groups specified in a hierarchy table have a nested structure.</p>

partitioning

levels

nestedness

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>.

is.nested: Check if hierachy is nested

Description

Usage

Arguments

Value

Details

Examples