pair_dis: Pairwise dissimilarity

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

View source: R/pair_dis.R

Description

Computation of pairwise dissimilarities based on Hill numbers diversity partitioning

Usage

1
pair_dis(countable, qvalue, tree, hierarchy, 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.

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, anttonalberdi@gmail.com

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

1
2
3
4
5
6

anttonalberdi/hilldiv documentation built on Feb. 14, 2021, 5:08 p.m.