pair_dis {hilldiv}

Pairwise dissimilarity

Description

Computation of pairwise dissimilarities based on Hill numbers diversity partitioning

Usage

pair_dis(countable, qvalue, tree, hierarchy, level, metric)

Arguments

countable

A matrix indicating the relative abundances of multiple samples. Columns should be samples and rows OTUs.

qvalue

A positive integer or decimal number (>=0), usually between 0 and 3.

tree

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.

hierarchy

A matrix indicating the relation between samples (first column) and groups.

level

If '1' dissimilarities are computed across samples, while if '2' dissimilarities are computed across groups, as specified by the hierarchy table. level=1.

metric

A vector containing any combination of "C", "U", "V" or "S". If not provided, all metrics will be computed. metric="U", metric=c("U","S").

Details

Pairwise dissimilarity

Value

A list of matrices containing pairwise beta diversities and dissimilarity metrics.

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.

Chao, A., Chiu, C.H., & Hsieh, T. C. (2012). Proposing a resolution to debates on diversity partitioning. Ecology, 93, 2037-2051.

Jost, L. (2007). Partitioning diversity into independent alpha and beta components. Ecology, 88, 2427-2439.

See Also

hill_div, div_part, beta_dis

Examples

data(bat.diet.otutable)
data(bat.diet.tree)
data(bat.diet.hierarchy)
pair_dis(bat.diet.otutable,qvalue=1)

pair_dis(bat.diet.otutable,qvalue=1,tree=bat.diet.tree,metric="V")

pair_dis(bat.diet.otutable,qvalue=0,hierarchy=bat.diet.hierarchy,level="2")