generalized_unifrac: Generalized UniFrac

In ecodive: Parallel and Memory-Efficient Ecological Diversity Metrics

Generalized UniFrac

Description

Generalized UniFrac beta diversity metric.

Usage

generalized_unifrac(
  counts,
  tree = NULL,
  alpha = 0.5,
  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').
alpha	How much weight to give to relative abundances; a value between 0 and 1, inclusive. Setting alpha=1 is equivalent to weighted_normalized_unifrac().
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, a pair of samples' abundances (A and B) on each of those branches, and abundance weighting 0 \le \alpha \le 1:

D = \displaystyle \frac{\sum_{i = 1}^{n} L_i(\frac{A_i}{A_T} + \frac{B_i}{B_T})^{\alpha}|\displaystyle \frac{\frac{A_i}{A_T} - \frac{B_i}{B_T}}{\frac{A_i}{A_T} + \frac{B_i}{B_T}} |}{\sum_{i = 1}^{n} L_i(\frac{A_i}{A_T} + \frac{B_i}{B_T})^{\alpha}}

See vignette('unifrac') for details and a worked example.

References

Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, Collman RG, Bushman FD, Li H 2012. Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics, 28(16). \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/bts342")}

See Also

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

Examples

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

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