kdisteuclid: a way to obtain Euclidean distance matrices

In ade4: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

Description

a way to obtain Euclidean distance matrices

Usage

kdisteuclid(obj, method = c("lingoes", "cailliez", "quasi"))

Arguments

obj	an object of class kdist
method	a method to convert a distance matrix in a Euclidean one

Value

returns an object of class kdist with all distances Euclidean.

Note

according to the program DistPCoa of P. Legendre and M.J. Anderson
http://www.fas.umontreal.ca/BIOL/Casgrain/en/labo/distpcoa.html

Author(s)

Daniel Chessel
Stéphane Dray [e-mail]

References

Gower, J.C. and Legendre, P. (1986) Metric and Euclidean properties of dissimilarity coefficients. Journal of Classification, 3, 5–48.

Cailliez, F. (1983) The analytical solution of the additive constant problem. Psychometrika, 48, 305–310.

Lingoes, J.C. (1971) Somme boundary conditions for a monotone analysis of symmetric matrices. Psychometrika, 36, 195–203.

Legendre, P. and Anderson, M.J. (1999) Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments. Ecological Monographs, 69, 1–24.

Legendre, P., and L. Legendre. (1998) Numerical ecology, 2nd English edition edition. Elsevier Science BV, Amsterdam.

Examples

w <- c(0.8, 0.8, 0.377350269, 0.8, 0.377350269, 0.377350269) # see ref.
w <- kdist(w)
w1 <- c(kdisteuclid(kdist(w), "lingoes"), kdisteuclid(kdist(w), "cailliez"), 
  kdisteuclid(kdist(w), "quasi"))
print(w, print = TRUE)
print(w1, print = TRUE)

data(eurodist)
par(mfrow = c(1, 3))
eu1 <- kdist(eurodist) # an object of class 'dist'
plot(data.frame(unclass(c(eu1, kdisteuclid(eu1, "quasi")))), asp = 1)
title(main = "Quasi")
abline(0,1)
plot(data.frame(unclass(c(eu1, kdisteuclid(eu1, "lingoes")))), asp = 1)
title(main = "Lingoes")
abline(0,1)
plot(data.frame(unclass(c(eu1, kdisteuclid(eu1, "cailliez")))), asp = 1)
title(main = "Cailliez")
abline(0,1)

ade4 documentation built on May 2, 2019, 5:50 p.m.