index_div {hilldiv}

Diversity index computation

Description

Computes common diversity indices related to Hill numbers. If the input is a vector, the function computes the indices of a single sample, while if the input is a matrix (OTU table), the function computes individual diversity indices for each sample (column). An ultrametic OTU tree is required for computing phylogenetic diversity indices (Faith's PD, Allen's H and Rao's Q). If the relative abundances of each sample (vector or each column of the matrix) do not sum to 1, TSS normalisation is applied.

Usage

index_div(abund, tree, index)

Arguments

abund

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.

tree

An ultrametic tree of class 'phylo'. The tip labels must match the names of the vector values (if one sample) or matrix rows (if multiple samples). Use the function match_data() if the OTU names do not match.

index

Diversity index to be computed ("richness", "shannon", "simpson", "faith", "allen", "rao"). Default without tree argument: index="richness". Default with tree argument: index="faith".

Details

Diversity index computation

Author(s)

Antton Alberdi, [e-mail]

References

Alberdi, A., Gilbert, M.T.P. (2019). A guide to the application of Hill numbers to DNA-based diversity analyses. Molecular Ecology Resources, 19, 804-817.

Jost, L. (2006). Entropy and diversity. Oikos, 113, 363-375.

Rao, C. R. (1982). Diversity and dissimilarity coefficients: A unified approach. Theoretical Population Biology, 21, 24-43.

Shannon, C. E. (1948). A mathematical theory of communication. The Bell System Technical Journal, 27, 379-423.

See Also

hill_div, div_part

Examples

data(bat.diet.otutable)
data(bat.diet.tree)
data(bat.diet.hierarchy)
#One sample
bat.diet.sample <- bat.diet.otutable[,1]
index_div(bat.diet.sample)
index_div(bat.diet.sample,index="shannon")
#Multiple samples
index_div(bat.diet.otutable)
index_div(bat.diet.otutable,tree=bat.diet.tree,index="faith")
#Incidence-based
bat.diet.otutable.incidence <- to.incidence(bat.diet.otutable,bat.diet.hierarchy)
index_div(bat.diet.otutable.incidence)
index_div(bat.diet.otutable.incidence,index="simpson")
index_div(to.incidence(bat.diet.otutable,bat.diet.hierarchy),tree=bat.diet.tree)