stops: STructure Optimized Proximity Scaling

Structure optimized proximity scaling (STOPS) refers to a collection of methods that fit nonlinear distance transformations in multidimensional scaling (MDS) and trade-off the fit with structure considerations to find optimal parameters or optimal configurations. This includes the three variants of cluster optimized proximity scaling (COPS). The package contains various functions, wrappers, methods and classes for fitting, plotting and displaying different MDS models in a STOPS framework like Torgerson scaling, SMACOF, Sammon mapping, elastic scaling, symmetric SMACOF, spherical SMACOF, sstress, rstress, powermds, power elastic scaling, power sammon mapping, powerstress, COPS-0, COPS-C and P-COPS. All of these models can also solely be fit as MDS with power transformations. The package further contains functions for optimization (Adaptive LJ and for Bayesian optimization with treed Gaussian process with jump to linear models) and functions for various structuredness indices.

Author
Thomas Rusch [aut, cre], Jan de Leeuw [aut], Patrick Mair [aut], Kurt Hornik [ctb]
Date of publication
2016-11-30 16:32:06
Maintainer
Thomas Rusch <thomas.rusch@wu.ac.at>
License
GPL-2 | GPL-3
Version
0.0-36
URLs

View on R-Forge

Man pages

BankingCrisesDistances
Banking Crises Distances
CAClimateIndicatorsCountyMedian
Climate Change Indicators of Californian Counties
c_association
c-association calculates the c-association based on the...
c_complexity
c-complexity calculates the c-complexity based on the minimum...
c_dependence
c-dependence calculates c-dependence as the distance...
c_faithfulness
c-faithfulness calculates the c-faithfulness based on the...
c_functionality
c-functionality calculates the c-functionality based on the...
c_linearity
c-linearity calculates c-linearity as the maximum multiple...
c_manifoldness
c-manifoldness calculates c-manifoldness as the maximal...
cmdscale
Wrapper to 'cmdscale' for S3 class
c_mine
wrapper for getting the mine coefficients
c_nonmonotonicity
c-nonmonotonicity calculates the c-nonmonotonicity based on...
conf_adjust
conf_adjust: a function to procrustes adjust two matrices
cop_cmdscale
COPS version of strain
cop_elastic
COPS versions of elastic scaling models (via smacofSym)
coploss
Calculates coploss for given MDS object
coplossMin
Fitting a COPS Model (Variant 1).
coplossMinOLD
Fitting a COPS Model. (old version to be discontinued)
cop_powerelastic
COPS version of elastic scaling with powers
cop_powermds
COPS version of powermds
cop_powersammon
COPS version of sammon with powers
cop_powerstress
COPS version of powerstress
cop_rstress
COPS version of rstress
cops
High Level COPS Function
cop_sammon
COPS version of sammon mapping
cop_sammon2
COPS versions of Sammon mapping models (via smacofSym)
cop_smacofSphere
COPS versions of smacofSphere models
cop_smacofSym
COPS versions of smacofSym models
cop_sstress
COPS version of sstress
cordillera
Calculates the Optics Cordillera
cordillera2
Calculates the Optics cordillera
doubleCenter
double centering
enorm
Explicit Norm
e_optics
OPTICS function
knn_dist
calculate k nearest neighbours from a distance matrix
ljoptim
(Adaptive) Version of Luus-Jaakola Optimization
mkBmat
Auxfunction1
mkPower
MakePower Old
mkPower2
MakePower
mkPowerALTERN
MakePower
oldcordilleraplot
Plot method for OPTICS cordilleras. Deprecated.
pcops
Profile COPS Function (aka COPS Variant 2)
pdist
Squared distances
Pendigits500
Pen digits
plot3d.cmdscale
3D plots: plot3d method for class cmdscale
plot3dstatic
plot3dstatic: static 3D plots
plot3dstatic.cmdscale
3D plots: plot3dstatic method for class cmdscale
plot3dstatic.stops
3D plots: plot3dstatic method for class stops
plot3d.stops
3D plots: plot3d method for class stops
plot.cops
S3 plot method for cops objects
plot.cordillera
Plot method for OPTICS cordilleras
plot.opticse
Plot method for OPTICS results
plot.pcops
S3 plot method for cops objects
plot.smacofP
S3 plot method for smacofP objects
plot.stops
S3 plot method for stops objects
powerStressFast
Power stress minimization by NEWUOA
powerStressFastOLD
Power stress minimization by NEWUOA (old version)
powerStressMin
Power Stress SMACOF
powerStressMinOLD
Power Stress SMACOF
print.cordillera
Print method for OPTICs cordilleras
print.opticse
Print method for OPTICS results
print.summary.opticse
Print method for OPTICS summary Displays summaries of the...
procruster
procruster: a procrustes function
sammon
Wrapper to 'sammon' for S3 class
secularEq
Secular Equation
shrinkB
Finding the shrinkage matrix for COPS-0
shrinkCoploss0
Fitting a COPS Model by shrinking residuals to Zero (COPS-0).
sqdist
Squared distances
stop_cmdscale
STOPS version of strain
stop_elastic
STOPS versions of elastic scaling models (via smacofSym)
stop_flexsmacof
STOPS versions of flexsmacof models (models with a parametric...
stoploss
Calculate the weighted multiobjective loss function used in...
stop_powerelastic
STOPS version of elastic scaling with powers
stop_powermds
STOPS version of powermds
stop_powersammon
STOPS version of sammon with powers
stop_powerstress
STOPS version of powerstress
stop_rstress
STOPS version of rstress
stops
stops: structure optimized proximity scaling
stop_sammon
STOPS version of sammon mapping
stop_sammon2
STOPS versions of Sammon mapping models (via smacofSym)
stop_smacofSphere
STOPS versions of smacofSphere models
stop_smacofSym
STOPS version of smacofSym models
stop_sstress
STOPS version of sstress
summary.opticse
Summary method for OPTICs results
tgpoptim
Bayesian Optimization by a (treed) Bayesian Gaussian Process...
torgerson
Torgerson scaling

Files in this package

stops/.Rinstignore
stops/DESCRIPTION
stops/NAMESPACE
stops/NEWS
stops/R
stops/R/BankingCrisesDistances-data.R
stops/R/CAClimateIndicatorsCountyMedian-data.R
stops/R/Pendigits500-data.R
stops/R/cops.R
stops/R/cordillera.R
stops/R/extras.R
stops/R/optics.R
stops/R/optimizations.R
stops/R/powerstress.R
stops/R/stops-package.R
stops/R/stops.R
stops/R/structurednessindices.R
stops/build
stops/build/vignette.rds
stops/data
stops/data/BankingCrisesDistances.rda
stops/data/CAClimateIndicatorsCountyMedian.rda
stops/data/Pendigits500.rda
stops/inst
stops/inst/CITATION
stops/inst/doc
stops/inst/doc/stops.html
stops/inst/doc/stops.html.asis
stops/man
stops/man/BankingCrisesDistances.Rd
stops/man/CAClimateIndicatorsCountyMedian.Rd
stops/man/Pendigits500.Rd
stops/man/c_association.Rd
stops/man/c_complexity.Rd
stops/man/c_dependence.Rd
stops/man/c_faithfulness.Rd
stops/man/c_functionality.Rd
stops/man/c_linearity.Rd
stops/man/c_manifoldness.Rd
stops/man/c_mine.Rd
stops/man/c_nonmonotonicity.Rd
stops/man/cmdscale.Rd
stops/man/conf_adjust.Rd
stops/man/cop_cmdscale.Rd
stops/man/cop_elastic.Rd
stops/man/cop_powerelastic.Rd
stops/man/cop_powermds.Rd
stops/man/cop_powersammon.Rd
stops/man/cop_powerstress.Rd
stops/man/cop_rstress.Rd
stops/man/cop_sammon.Rd
stops/man/cop_sammon2.Rd
stops/man/cop_smacofSphere.Rd
stops/man/cop_smacofSym.Rd
stops/man/cop_sstress.Rd
stops/man/coploss.Rd
stops/man/coplossMin.Rd
stops/man/coplossMinOLD.Rd
stops/man/cops.Rd
stops/man/cordillera.Rd
stops/man/cordillera2.Rd
stops/man/doubleCenter.Rd
stops/man/e_optics.Rd
stops/man/enorm.Rd
stops/man/knn_dist.Rd
stops/man/ljoptim.Rd
stops/man/mkBmat.Rd
stops/man/mkPower.Rd
stops/man/mkPower2.Rd
stops/man/mkPowerALTERN.Rd
stops/man/oldcordilleraplot.Rd
stops/man/pcops.Rd
stops/man/pdist.Rd
stops/man/plot.cops.Rd
stops/man/plot.cordillera.Rd
stops/man/plot.opticse.Rd
stops/man/plot.pcops.Rd
stops/man/plot.smacofP.Rd
stops/man/plot.stops.Rd
stops/man/plot3d.cmdscale.Rd
stops/man/plot3d.stops.Rd
stops/man/plot3dstatic.Rd
stops/man/plot3dstatic.cmdscale.Rd
stops/man/plot3dstatic.stops.Rd
stops/man/powerStressFast.Rd
stops/man/powerStressFastOLD.Rd
stops/man/powerStressMin.Rd
stops/man/powerStressMinOLD.Rd
stops/man/print.cordillera.Rd
stops/man/print.opticse.Rd
stops/man/print.summary.opticse.Rd
stops/man/procruster.Rd
stops/man/sammon.Rd
stops/man/secularEq.Rd
stops/man/shrinkB.Rd
stops/man/shrinkCoploss0.Rd
stops/man/sqdist.Rd
stops/man/stop_cmdscale.Rd
stops/man/stop_elastic.Rd
stops/man/stop_flexsmacof.Rd
stops/man/stop_powerelastic.Rd
stops/man/stop_powermds.Rd
stops/man/stop_powersammon.Rd
stops/man/stop_powerstress.Rd
stops/man/stop_rstress.Rd
stops/man/stop_sammon.Rd
stops/man/stop_sammon2.Rd
stops/man/stop_smacofSphere.Rd
stops/man/stop_smacofSym.Rd
stops/man/stop_sstress.Rd
stops/man/stoploss.Rd
stops/man/stops.Rd
stops/man/summary.opticse.Rd
stops/man/tgpoptim.Rd
stops/man/torgerson.Rd
stops/tests
stops/tests/testthat
stops/tests/testthat/test-cmdscalesammon.R
stops/tests/testthat/test-cops.R
stops/tests/testthat/test-cordillera.R
stops/tests/testthat/test-optics.R
stops/tests/testthat/test-optimization.R
stops/tests/testthat/test-powerstress.R
stops/tests/testthat/test-stops.R
stops/tests/testthat/testthat.R
stops/vignettes
stops/vignettes/stops.Rmd
stops/vignettes/stops.html.asis