smacofx-package

smacofx: Flexible multidimensional scaling methods and SMACOF extensions

Flexible multidimensional scaling (MDS) methods centered around the Majorization algorithm. The package contains various functions, wrappers, methods and classes for fitting, plotting and displaying a large number of different flexible MDS models such as Torgerson scaling, ratio, interval and nonmetric MDS with majorization, Sammon mapping with ratio and interval optimal scaling, multiscale MDS with ratio and interval optimal scaling, Alscal (s-stress) MDS with ratio and interval optimal scaling, elastic scaling with ratio and interval optimal scaling, r-stress MDS for ratio, interval and nonmetric scaling, power stress for interval and ratio optimal scaling, restricted power-stress with ratio and interval optimal scaling, approximate power-stress with ratio scaling, curvilinear component analysis with ratio, interval and ordinal optimal scaling, power curvilinear component analysis with ratio, interval and ordinal optimal scaling, Box-Cox MDS and local MDS. Some functions are suitably flexible to allow any other sensible combination of explicit power transformations for weights, distances and input proximities with implicit ratio, interval or ordinal optimal scaling of the input proximities. Most functions use a majorization algorithm. package

Details

The package provides:

Models:

• alscal... ALSCAL (s-stress) MDS with ratio, interval optimal scaling
• elscal.. Elastic scaling MDS with ratio, interval optimal scaling
• multiscale... Multiscale MDSwith ratio, interval optimal scaling
• rstressMin .. R-Stress MDS with ratio, interval, ordinal optimal scaling
• powerStressMin... power stress MDS (POST-MDS) with ratio, interval optimal scaling
• apStressMin... approximate POST-MDS with ratio, interval optimal scaling
• rpowerStressMin... restricted POST-MDS with ratio, interval optimal scaling
• clca ... curvilinear component analysis with ratio optimal scaling
• clda ... curvilinear distance analysis with ratio optimal scaling (ie.e. clca with Isomap distances)
• bcmds ... Box-Cox MDS with ratio optimal scaling
• lmds... Local MDS with ratio optimal scaling
• sammonmap... Sammon mapping with ratio, interval optimal scaling
• smds ... power curvilinear component analysis with ratio, interval, ordinal optimal scaling
• pclca ... power curvilinear component analysis with ratio, interval, ordinal optimal scaling
• smdda ... sparsified multidimensional distance analsysis with ratio interval scaling (this is smds with Isomap distances)
• spmdda ... sparsified power multidimensional distance analsysis with ratio interval scaling (this is spmds with Isomap distances)
• smds ... sparsified multidimensional scaling with ratio interval scaling (inspired by CLCA, so fitted distances larger than tau are weighted with 0)
• spmds ... sparsified multidimensional scaling with ratio interval scaling (inspired by CLCA, so fitted distances larger than tau are weighted with 0)

Classes and Methods: The objects are of classes that extend the S3 classes smacof and smacofB. For the objects returned by the high-level functions S3 methods for standard generics were implemented, including print, coef, residuals, summary, plot, plot3dstatic. Wrappers and convenience functions for the model objects:

• bootmds ... Bootstrapping an MDS model
• biplotmds ... MDS Biplots
• icExploreGen ... Expore initial configurations
• jackmds ... Jackknife for MDS
• multistart ... Multistart function for MDS
• permtest ... Permutation test for MDS

Wrappers:

• cmdscale ... stats::cmdscale but returns an S3 objects to be used with smacof classes
• sammon... MASS::sammon but returns S3 objects to be used with smacof classes

Examples

data(BankingCrisesDistances)

res<-rStressMin(BankingCrisesDistances[,1:69],type="ordinal",r=2)
res

summary(res)
plot(res)
plot(res,"transplot")
plot(res,"Shepard")

msres<- multistart(res)

res2<-msres$best
permtest(res2)

See Also

Useful links:

• https://r-forge.r-project.org/projects/stops/
• Report bugs at https://r-forge.r-project.org/tracker/?atid=5375&group_id=2037&func=browse

Author(s)

Maintainer : Thomas Rusch thomas.rusch@wu.ac.at (ORCID)

Authors:

• Jan de Leeuw
• Lisha Chen
• Patrick Mair mair@fas.harvard.edu (ORCID)