pair_dis: Pairwise dissimilarity
In hilldiv: Integral Analysis of Diversity Based on Hill Numbers

Description Usage Arguments Details Value Author(s) References See Also Examples

Computation of pairwise dissimilarities based on Hill numbers diversity partitioning

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

`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").

Pairwise dissimilarity

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

Antton Alberdi, anttonalberdi@gmail.com

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.

hill_div, div_part, beta_dis

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")