canneddist: Canned Dissimilarities with their Vernacular Names

In jarioksa/natto: An Extreme 'vegan' Package of Experimental Code

Canned Dissimilarities with their Vernacular Names

Description

Function is a storehouse for dissimilarity indices that can be called by their vernacular names. The function is based on designdist (vegan package).

Usage

canneddist(x, method, help = FALSE)

Arguments

x	Input data.
method	Vernacular name for a dissimilarity index.
help	List available indices and their definitions instead of calculating dissimilarities.

Details

Function wraps popular dissimilarity indices for designdist allowing these to be called by their popular names. It can have synonymous names for one dissimilarity index. Use argument help=TRUE to see the current selection of indices and their definitions.

The function uses the main notation of designdist where terms are based on sums and paired minima or sum of squares and crossproducts of pairs of sampling units. For vectors x and y the "quadratic" terms are J = sum(x*y), A = sum(x^2), B = sum(y^2), and "minimum" terms are J = sum(pmin(x,y)), A = sum(x) and B = sum(y), and "binary" terms are either of these after transforming data into binary form (number of shared species J, and number of species for each row, A, B.). Number of columns (species) is notated as P, and the number of sampling units is N.

There is a huge number of indices, and the current selection is far from comprehensive (but it can easily expanded). See References for sources. Many sources use different notation, but they were changed to the notation described above. For instance, in popular (but strange) 2x2 contingency table notation for binary data a = J, b = A-J, c = B-J, d = P-A-B+J. Some of formulae may be surprising, but they are mathematically equivalent to traditional ones. I challenge you to inspect Euclidean distance, and once you see how it is derived, try Chord distance.

Value

Function returns a dist object of dissimilarities.

Author(s)

Jari Oksanen

References

Clarke, K.R., Somerfield, P.J. & Chapman, M.G. (2006). On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray-Curtis coefficient for denuded assemblages. J. Exp. Marine Biol. & Ecol. 330, 55-80. (bray0).

Hubálek, Z. (1982). Coefficients of association and similarity, based on binary (presence-absence) data: an evaluation. Biological Review 57, 669–689.

Legendre, P. & Legendre, L. (2012). Numerical Ecology. 3rd English Ed., Elsevier.

Yue, J.C. & Clayton, M.K. (2005). A similarity measure based on species proportions. Communications in Statistics Theory and Methods 34, 2123–2131. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1080/STA-200066418")}.

See Also

Function is a wrapper to designdist. vegan function betadiver is a similar collection of canned indices for beta diversity, and many of these are well-known dissimilarity indices.

Examples

data(spurn)
## Ochiai dissimilarity
canneddist(spurn, "ochiai")

jarioksa/natto documentation built on Feb. 20, 2025, 3:29 p.m.