R: Calculate distances between object vectors in a SOM

object.distances {kohonen} | R Documentation

## Calculate distances between object vectors in a SOM

### Description

This function calculates the distance between objects using the distance functions, weights and other attributes of a trained SOM. This function is used in the calculation of the U matrix in function `plot.kohonen` using the `type = "dist.neighbours" argument.`

### Usage

    object.distances(kohobj, type = c("data", "codes"), whatmap)

### Arguments

`kohobj` | An object of class `kohonen`.
`type` | Whether to calculate distances between the data objects, or the codebook vectors.
`whatmap` | What data layers to use. If unspecified the data layers defined in the kohonen object are used.

### Value

An object of class `dist`, which can be directly fed into (e.g.) a hierarchical clustering.

### Author(s)

Ron Wehrens

### References

R. Wehrens and J. Kruisselbrink, submitted, 2017.

### See Also

`unit.distances`, `supersom`

### Examples

    data(wines)
    set.seed(7)
    sommap <- supersom(list(measurements = scale(wines),
                            vintages = vintages),
                       grid = somgrid(6, 4, "hexagonal"))
    obj.dists <- object.distances(sommap, type = "data")
    code.dists <- object.distances(sommap, type = "codes")

[Package kohonen version 3.0.4 Index]