similarity: Similarity

In tabula: Analysis and Visualization of Archaeological Count Data

Similarity

Description

Similarity

Usage

similarity(object, ...)

## S4 method for signature 'matrix'
similarity(
  object,
  method = c("brainerd", "bray", "jaccard", "morisita", "sorenson")
)

## S4 method for signature 'data.frame'
similarity(
  object,
  method = c("brainerd", "bray", "jaccard", "morisita", "sorenson")
)

Arguments

object	A m \times p numeric matrix or data.frame of count data (absolute frequencies giving the number of individuals for each category, i.e. a contingency table). A data.frame will be coerced to a numeric matrix via data.matrix().
...	Currently not used.
method	A character string specifying the method to be used (see details). Any unambiguous substring can be given.

Details

\beta-diversity can be measured by addressing similarity between pairs of samples/cases.

bray, jaccard, morisita and sorenson indices provide a scale of similarity from 0-1 where 1 is perfect similarity and 0 is no similarity. brainerd is scaled between 0 and 200.

brainerd

Brainerd-Robinson quantitative index.

bray

Bray-Curtis similarity (Sorenson quantitative index).

jaccard

Jaccard qualitative index.

morisita

Morisita-Horn quantitative index.

sorenson

Dice-Sorenson index (Sorenson qualitative index).

For jaccard and sorenson, data are standardized on a presence/absence scale (0/1) beforehand.

Value

A stats::dist object.

Author(s)

N. Frerebeau

References

Magurran, A. E. (1988). Ecological Diversity and its Measurement. Princeton, NJ: Princeton University Press. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/978-94-015-7358-0")}.

See Also

index_binomial(), index_brainerd(), index_bray(), index_jaccard(), index_morisita(), index_sorenson()

Other diversity measures: heterogeneity(), occurrence(), plot_diversity, plot_rarefaction, profiles(), rarefaction(), richness(), she(), simulate(), turnover()

Examples

## Data from Huntley 2004, 2008
data("pueblo")

## Brainerd-Robinson measure
(C <- similarity(pueblo, "brainerd"))
plot_spot(C)

## Data from Magurran 1988, p. 166
data("aves")

## Jaccard measure (presence/absence data)
similarity(aves, "jaccard") # 0.46

# Bray and Curtis modified version of the Sorenson index (count data)
(sim <- similarity(aves, "bray")) # 0.44

# Bray and Curtis dissimilarity
1 - sim

tabula documentation built on April 4, 2025, 5:09 a.m.