unweighted_unifrac: Unweighted UniFrac

In ecodive: Parallel and Memory-Efficient Ecological Diversity Metrics

Unweighted UniFrac

Description

Unweighted UniFrac beta diversity metric.

Usage

unweighted_unifrac(counts, tree = NULL, pairs = NULL, cpus = n_cpus())

Arguments

counts	An OTU abundance matrix where each column is a sample, and each row is an OTU. Any object coercible with as.matrix() can be given here, as well as phyloseq, rbiom, SummarizedExperiment, and TreeSummarizedExperiment objects.
tree	A phylo-class object representing the phylogenetic tree for the OTUs in counts. The OTU identifiers given by colnames(counts) must be present in tree. Can be omitted if a tree is embedded with the counts object or as attr(counts, 'tree').
pairs	Which combinations of samples should distances be calculated for? The default value (NULL) calculates all-vs-all. Provide a numeric or logical vector specifying positions in the distance matrix to calculate. See examples.
cpus	How many parallel processing threads should be used. The default, n_cpus(), will use all logical CPU cores.

Value

A dist object.

Calculation

Given n branches with lengths L and a pair of samples' abundances (A and B) on each of those branches:

D = \displaystyle \frac{\sum_{i = 1}^{n} L_i(|A_i - B_i|)}{\sum_{i = 1}^{n} L_i(max(A_i,B_i))}

Abundances in A and B are coded as 1 or 0 to indicate their presence or absence, respectively, on each branch.

See https://cmmr.github.io/ecodive/articles/unifrac.html for details and a worked example.

References

Lozupone C, Knight R 2005. UniFrac: A new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology, 71(12). \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1128/AEM.71.12.8228-8235.2005")}

See Also

Other beta_diversity: bray_curtis(), canberra(), euclidean(), generalized_unifrac(), gower(), jaccard(), kulczynski(), manhattan(), variance_adjusted_unifrac(), weighted_normalized_unifrac(), weighted_unifrac()

Examples

    # Example counts matrix
    ex_counts
    
    # Unweighted UniFrac distance matrix
    unweighted_unifrac(ex_counts, tree = ex_tree)
    
    # Only calculate distances for A vs all.
    unweighted_unifrac(ex_counts, tree = ex_tree, pairs = 1:3)
    

ecodive documentation built on Aug. 23, 2025, 1:13 a.m.