bootmds.pcops: MDS Bootstrap for pcops objects

In cops: Cluster Optimized Proximity Scaling

MDS Bootstrap for pcops objects

Description

Performs a bootstrap on an MDS solution. It works for derived dissimilarities only, i.e. generated by the call dist(data). The original data matrix needs to be provided, as well as the type of dissimilarity measure used to compute the input dissimilarities.

Usage

## S3 method for class 'pcops'
bootmds(
  object,
  data,
  method.dat = "pearson",
  nrep = 100,
  alpha = 0.05,
  verbose = FALSE,
  ...
)

Arguments

object	Object of class smacofP if used as method or another object inheriting from smacofB (needs to be called directly as bootmds.smacofP then).
data	Initial data (before dissimilarity computation).
method.dat	Dissimilarity computation used as MDS input. This must be one of "pearson", "spearman", "kendall", "euclidean", "maximum", "manhattan", "canberra", "binary".
nrep	Number of bootstrap replications.
alpha	Alpha level for condfidence ellipsoids.
verbose	If 'TRUE', bootstrap index is printed out.
...	Additional arguments needed for dissimilarity computation as specified in sim2diss.

Details

In order to examine the stability solution of an MDS, a bootstrap on the raw data can be performed. This results in confidence ellipses in the configuration plot. The ellipses are returned as list which allows users to produce (and further customize) the plot by hand. See bootmds for more.

Value

An object of class 'smacofboot', see bootmds. With values

• cov: Covariances for ellipse computation

• bootconf: Configurations bootstrap samples

• stressvec: Bootstrap stress values

• bootci: Stress bootstrap percentile confidence interval

• spp: Stress per point (based on stress.en)

• stab: Stability coefficient

Examples

dats <- na.omit(PVQ40[,1:5])
diss <- dist(t(dats))   ## Euclidean distances 
fit <- pcops(diss,loss="rstress",itmaxi=50) #this is just for illustration: increase itmaxi    
set.seed(123)
resboot <- bootmds(fit, dats, method.dat = "euclidean", nrep = 2)

cops documentation built on Sept. 30, 2024, 9:22 a.m.