canberra: Canberra

In ecodive: Parallel and Memory-Efficient Ecological Diversity Metrics

Canberra

Description

Canberra beta diversity metric.

Usage

canberra(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.

OTUs must be removed if they are absent from both samples.

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

  x <- c(4, 0, 3, 0, 6)[-4]
  y <- c(0, 8, 0, 0, 5)[-4]
  sum(abs(x-y) / (x+y)) / length(x)  
  #>  0.7727273

References

Lance GN and Williams WT 1967. A general theory of classificatory sorting strategies II. Clustering systems. The computer journal, 10(3). \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/comjnl/10.3.271")}

See Also

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

Examples

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

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