similarity-method: Similarity

Description Usage Arguments Details Value Author(s) References See Also Examples

Description

Similarity

Usage

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similarity(object, ...)

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

## S4 method for signature 'IncidenceMatrix'
similarity(object, method = c("jaccard", "sorenson"), ...)

Arguments

object

A m x p matrix of count data.

...

Further arguments to be passed to internal methods.

method

A character string specifying the method to be used (see details). Any unambiguous substring can be given.

Details

β-diversity can be measured by addressing similarity between pairs of samples/cases (Brainerd-Robinson, Jaccard, Morisita-Horn and Sorenson indices). Similarity between pairs of taxa/types can be measured by assessing the degree of co-occurrence (binomial co-occurrence).

Jaccard, Morisita-Horn and Sorenson indices provide a scale of similarity from 0-1 where 1 is perfect similarity and 0 is no similarity. The Brainerd-Robinson index is scaled between 0 and 200. The Binomial co-occurrence assessment approximates a Z-score.

binomial

Binomial co-occurrence assessment. This assesses the degree of co-occurrence between taxa/types within a dataset. The strongest associations are shown by large positive numbers, the strongest segregations by large negative numbers.

brainerd

Brainerd-Robinson quantitative index. This is a city-block metric of similarity between pairs of samples/cases.

bray

Sorenson quantitative index (Bray and Curtis modified version of the Sorenson index).

jaccard

Jaccard qualitative index.

morisita

Morisita-Horn quantitative index.

sorenson

Sorenson qualitative index.

Value

similarity() returns a stats::dist object.

Author(s)

N. Frerebeau

References

Brainerd, G. W. (1951). The Place of Chronological Ordering in Archaeological Analysis. American Antiquity, 16(04), 301-313. doi: 10.2307/276979.

Bray, J. R. & Curtis, J. T. (1957). An Ordination of the Upland Forest Communities of Southern Wisconsin. Ecological Monographs, 27(4), 325-349. doi: 10.2307/1942268.

Kintigh, K. (2006). Ceramic Dating and Type Associations. In J. Hantman and R. Most (eds.), Managing Archaeological Data: Essays in Honor of Sylvia W. Gaines. Anthropological Research Paper, 57. Tempe, AZ: Arizona State University, p. 17-26.

Magurran, A. E. (1988). Ecological Diversity and its Measurement. Princeton, NJ: Princeton University Press. doi: 10.1007/978-94-015-7358-0.

Robinson, W. S. (1951). A Method for Chronologically Ordering Archaeological Deposits. American Antiquity, 16(04), 293-301. doi: 10.2307/276978.

See Also

Other diversity: heterogeneity-index, richness-index, turnover-index

Examples

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## Data from Huntley 2008
ceramics <- CountMatrix(
  data = c(16, 9, 3, 0, 1,
           13, 3, 2, 0, 0,
           9, 5, 2, 5, 0,
           14, 12, 3, 0, 0,
           0, 26, 4, 0, 0,
           1, 26, 4, 0, 0,
           0, 11, 3, 13, 0,
           0, 0, 17, 0, 16,
           0, 0, 18, 0, 14),
  nrow = 9, byrow = TRUE
)
rownames(ceramics) <- c("Atsinna", "Cienega", "Mirabal", "PdMuertos",
                        "Hesh", "LowPesc", "BoxS", "Ojo Bon", "S170")
colnames(ceramics) <- c("DLH-1", "DLH-2a", "DLH-2b", "DLH-2c", "DLH-4")

## Brainerd-Robinson measure (count data)
C <- similarity(ceramics, "brainerd")
plot_spot(C)

## Data from Magurran 1988, p. 166
data("birds", package = "folio")

## Plot spot diagram
birds <- as_count(birds)

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

## Sorenson measure (presence/absence data)
similarity(birds, "sorenson") # 0.63

# Jaccard measure (Bray's formula ; count data)
similarity(birds, "bray") # 0.44

# Morisita-Horn measure (count data)
similarity(birds, "morisita") # 0.81

tabula documentation built on May 25, 2021, 5:11 p.m.