prabclus (version 2.3-4)

stressvals: 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)

Value

A list with components

MDSstress

vector of stress values.

mdsout

list of full outputs of isoMDS.

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?).

Author

Christian Hennig https://www.unibo.it/sitoweb/christian.hennig/en

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.

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