documentation/pair_dis.md

In anttonalberdi/hilldiv: Integral Analysis of Diversity Based on Hill Numbers

pair_dis()

Last update: hilldiv 1.4.2

Computation of pairwise dissimilarities among samples or groups is a common practice in ecology. The function pair_dis() enables generation of pairwise dissimilarity matrices from count tables, making use of functions div_part() and beta_dis(). It is possible to generate pairwise beta diversity values as well as the four (dis)similarity metrics incorporated in hilldiv, i.e. UqN, VqN, SqN and VqN. The function enables generating pairwise distance matrices between samples or any parent group as specified in the hierarchy table.

Arguments

| Arguments | Description | | ------------- | ------------- | | countable | A count table (matrix/data.frame) indicating the absolute or relative OTU/ASV abundances of multiple samples. Columns must refer to samples and rows to OTUs/ASVs. | | qvalue | A positive number, usually between 0 and 5, but most commonly 0, 1 or 2. It can be an integer or contain decimals. | | 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 parent group(s). | | level | Hierarchical level at which to compute the pairwise dissimilarities. Only meaningful if a hierarchy table is provided. | | metric | A vector containing any combination of "C", "U", "V" or "S". If not provided, all metrics will be computed. |

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")

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