kulczynski: Kulczynski

In ecodive: Parallel and Memory-Efficient Ecological Diversity Metrics

Kulczynski

Description

Kulczynski beta diversity metric.

Usage

kulczynski(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.

t = \displaystyle \sum_{i = 1}^{n} min(x_i,y_i)

D = \displaystyle 1 - 0.5(\frac{t}{\sum_{i = 1}^{n} x_i} + \frac{t}{\sum_{i = 1}^{n} y_i})

  x <- c(4, 0, 3, 2, 6)
  y <- c(0, 8, 0, 0, 5)
  t <- sum(pmin(x,y))
  1 - (t/sum(x) + t/sum(y)) / 2  
  #>  0.6410256

References

Kulcynski S 1927. Die Pflanzenassoziationen der Pieninen. Bulletin International de l'Académie Polonaise des Sciences et des Lettres, Classe des Sciences Mathématiques et Naturelles, Série B: Sciences Naturelles.

See Also

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

Examples

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

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