bray_curtis: Bray-Curtis

In ecodive: Parallel and Memory-Efficient Ecological Diversity Metrics

Bray-Curtis

Description

Bray-Curtis beta diversity metric.

Usage

bray_curtis(counts, weighted = TRUE, 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.
weighted	If TRUE, the algorithm takes relative abundances into account. If FALSE, only presence/absence is considered.
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

In the formulas below, x and y are two columns (samples) from counts. n is the number of rows (OTUs) in counts.

D = \displaystyle \frac{\sum_{i = 1}^{n} |x_i - y_i|}{\sum_{i = 1}^{n} (x_i + y_i)}

  x <- c(4, 0, 3, 2, 6)
  y <- c(0, 8, 0, 0, 5)
  sum(abs(x-y)) / sum(x+y)  
  #>  0.6428571

References

Sorenson T 1948. A method of establishing groups of equal amplitude in plant sociology based on similarity of species content. Kongelige Danske Videnskabernes Selskab, 5.

Bray JR and Curtis JT 1957. An ordination of the upland forest communities of southern Wisconsin. Ecological Monographs, 27(4). \Sexpr[results=rd]{tools:::Rd_expr_doi("10.2307/1942268")}

See Also

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

Examples

    # Example counts matrix
    ex_counts
    
    # Bray-Curtis weighted distance matrix
    bray_curtis(ex_counts)
    
    # Bray-Curtis unweighted distance matrix
    bray_curtis(ex_counts, weighted = FALSE)
    
    # Only calculate distances for A vs all.
    bray_curtis(ex_counts, pairs = 1:3)
    

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