match_data: Match and align a count table to a tree or distance matrix

In hilldiv3: Integral Analysis of Diversity Based on Hill Numbers

Match and align a count table to a tree or distance matrix

Description

Subsets and reorders a count table so that its taxa match those of a phylogenetic tree or a functional distance matrix, dropping taxa absent from the reference. This realises the match_data() helper that hilldiv2's documentation referred to but never provided.

Usage

match_data(data, tree = NULL, dist = NULL)

Arguments

data	A count matrix/data.frame (taxa x samples) with row names.
tree	A phylo tree (optional).
dist	A distance matrix (optional).

Value

The count matrix restricted to and ordered by the shared taxa.

Examples

counts <- matrix(1:6, nrow = 3,
                 dimnames = list(c("t1", "t2", "t3"), c("s1", "s2")))
tree <- ape::read.tree(text = "((t1:1,t2:1):1,t4:2);")
match_data(counts, tree = tree)

hilldiv3 documentation built on Oct. 6, 2026, 5:06 p.m.