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.

AuthorThomas Rusch [aut, cre], Jan de Leeuw [aut], Patrick Mair [aut], Kurt Hornik [ctb]
Date of publication2016-11-30 16:32:06
MaintainerThomas Rusch <>
LicenseGPL-2 | GPL-3

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/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/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

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