Computes the variation matrix (Aitchison 1986, definition 4.4).
Arguments
- x
A
CompositionMatrix
object.- ...
Currently not used.
Value
A matrix
.
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))
#> A B C D E
#> A 0.00000000 0.2592742 1.5328586 0.08281464 0.1385604
#> B 0.25927416 0.0000000 3.0006804 0.54727146 0.6490135
#> C 1.53285862 3.0006804 0.0000000 1.11145146 0.9476375
#> D 0.08281464 0.5472715 1.1114515 0.00000000 0.1870579
#> E 0.13856035 0.6490135 0.9476375 0.18705791 0.0000000
## 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"
)