nexus (version 0.3.0)

variation: Variation Matrix

Description

Computes the variation matrix (Aitchison 1986, definition 4.4).

Usage

variation(x, ...)
# S4 method for CompositionMatrix
variation(x)

Value

A matrix.

Arguments

x

A CompositionMatrix object.

...

Currently not used.

Author

N. Frerebeau

References

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.

See Also

Other statistics: aggregate(), condense(), covariance(), dist, mahalanobis(), margin(), mean(), pip(), quantile(), scale(), variance(), variance_total()

Examples

## 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"
)