dist function

Distance Matrix Computation (including Aitchison distance)

This function overwrites dist function to contain Aitchison distance between compositions.

dist(x, method = "euclidean", ...)

Arguments

• x: compositions method
• method: the distance measure to be used. This must be one of "aitchison", "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". Any unambiguous substring can be given.
• ...: arguments passed to dist function

Returns

dist returns an object of class "dist".

Examples

X = exp(matrix(rnorm(10*50), ncol=50, nrow=10))

(d <- dist(X, method = 'aitchison'))
plot(hclust(d))

# In contrast to Euclidean distance
dist(rbind(c(1,1,1), c(100, 100, 100)), method = 'euc') # method = 'euclidean'
# using Aitchison distance, only relative information is of importance
dist(rbind(c(1,1,1), c(100, 100, 100)), method = 'ait') # method = 'aitchison'

See Also

See functions dist.