R: Stress values for different dimensions of Kruskal's MDS

stressvals {prabclus} | R Documentation

## Stress values for different dimensions of Kruskal's MDS

### Description

Computes Kruskal's nonmetric multidimensional scaling `isoMDS` on `alleleobject` or `prab`-objects for different output dimensions in order to compare stress values.

### Usage

      stressvals(x,mdsdim=1:12,trace=FALSE)

### Arguments

`x` | object of class `alleleobject` or `link{prab}`. generated by `alleleinit` or `prabinit`.
`mdsdim` | integer vector of MDS numbers of dimensions to be tried.
`trace` | logical. `trace`-argument for `isoMDS` (should trace information be printed during execution?).

### Details

Note that zero distances between non-identical objects are replaced by the smallest nonzero distance divided by 10 to prevent `isoMDS` from producing an error.

### Value

A list with components

`MDSstress` | vector of stress values.
`mdsout` | list of full outputs of `isoMDS`.

### Author(s)

Christian Hennig chrish@stats.ucl.ac.uk http://www.homepages.ucl.ac.uk/~ucakche

### Examples

      options(digits=4)
      data(tetragonula)
      set.seed(112233)
      taiselect <- sample(236,40)
    # Use data subset to make execution faster.
      tnb <-
      coord2dist(coordmatrix=tetragonula.coord[taiselect,],
        cut=50,file.format="decimal2",neighbors=TRUE)
      ta <- alleleconvert(strmatrix=tetragonula[taiselect,])
      tai <- alleleinit(allelematrix=ta,neighborhood=tnb$nblist)
      stressvals(tai,mdsdim=1:3)$MDSstress

[Package prabclus version 2.2-6 Index]