Computes the variation matrix (Aitchison 1986, definition 4.4).
variation(x, ...)# S4 method for CompositionMatrix
variation(x)
A matrix
.
A CompositionMatrix
object.
Currently not used.
N. Frerebeau
Aitchison, J. (1986). The Statistical Analysis of Compositional Data. London: Chapman and Hall, p. 64-91.
Greenacre, M. J. (2019). Compositional Data Analysis in Practice. Boca Raton: CRC Press.
## Data from Aitchison 1986
data("hongite")
## Coerce to compositional data
coda <- as_composition(hongite)
## Variation matrix
## (Aitchison 1986, definition 4.4)
(varia <- variation(coda))
## Cluster dendrogram
d <- as.dist(varia)
h <- hclust(d, method = "ward.D2")
plot(h)
## Heatmap
stats::heatmap(
varia,
distfun = stats::as.dist,
hclustfun = function(x) stats::hclust(x, method = "ward.D2"),
symm = TRUE,
scale = "none"
)
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