variation {nexus} | R Documentation |
Variation Matrix
Description
Computes the variation matrix (Aitchison 1986, definition 4.4).
Usage
variation(x, ...)
## S4 method for signature 'CompositionMatrix'
variation(x)
Arguments
x |
A |
... |
Currently not used. |
Value
A matrix
.
Author(s)
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"
)
[Package nexus version 0.6.0 Index]