Covariance matrices for `hyperSpec`

objects

```
# S4 method for hyperSpec,missing
cov(
x,
y = NULL,
use = "everything",
method = c("pearson", "kendall", "spearman")
)
cov_pooled(x, groups, ..., regularize = NULL)
```

## Arguments

- x
`hyperSpec`

object.

- y
Not supported.

- use, method
handed to `stats::cov()`

- groups
Factor indicating the groups.

- ...
Ignored.

- regularize
(numeric):
Regularization of the covariance matrix.
Set `0`

to switch off.
Default is `1e-5 * max(abs(cov_p))`

, where `cov_p`

is a pooled
covariance matrix before regularization.

`cov_pooled()`

calculates pooled covariance like, e.g., in LDA.

## Value

Covariance `matrix`

of size `nwl(x)`

x `nwl(x)`

.

## Examples

```
image(cov(faux_cell))
pcov <- cov_pooled(faux_cell, faux_cell$region)
plot(pcov$means)
image(pcov$COV)
```