stops: STructure Optimized Proximity Scaling
Version 0.0-36

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.

Browse man pages Browse package API and functions Browse package files

AuthorThomas Rusch [aut, cre], Jan de Leeuw [aut], Patrick Mair [aut], Kurt Hornik [ctb]
Date of publication2016-11-30 16:32:06
MaintainerThomas Rusch <thomas.rusch@wu.ac.at>
LicenseGPL-2 | GPL-3
Version0.0-36
URL http://r-forge.r-project.org/projects/stops/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("stops", repos="http://R-Forge.R-project.org")

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

Functions

BankingCrisesDistances Man page
CAClimateIndicatorsCountyMedian Man page
Pendigits500 Man page
c_association Man page Source code
c_complexity Man page Source code
c_dependence Man page Source code
c_faithfulness Man page Source code
c_functionality Man page Source code
c_linearity Man page Source code
c_manifoldness Man page Source code
c_mine Man page Source code
c_nonmonotonicity Man page Source code
cmdscale Man page Source code
coef.cops Source code
coef.stops Source code
conf_adjust Man page Source code
cop_cmdscale Man page Source code
cop_elastic Man page Source code
cop_powerelastic Man page Source code
cop_powermds Man page Source code
cop_powersammon Man page Source code
cop_powerstress Man page Source code
cop_rstress Man page Source code
cop_sammon Man page Source code
cop_sammon2 Man page Source code
cop_smacofSphere Man page Source code
cop_smacofSym Man page Source code
cop_sstress Man page Source code
coploss Man page Source code
coplossMin Man page Source code
coplossMinOLD Man page Source code
cops Man page Source code
cordillera Man page Source code
cordillera2 Man page Source code
doubleCenter Man page Source code
e_optics Man page Source code
enorm Man page Source code
knn_dist Man page Source code
ljoptim Man page Source code
mkBmat Man page Source code
mkPower Man page Source code
mkPower2 Man page Source code
mkPowerALTERN Man page Source code
oldcordilleraplot Man page Source code
pcops Man page Source code
pdist Man page Source code
plot.cmdscale Source code
plot.cops Man page Source code
plot.cordillera Man page Source code
plot.opticse Man page Source code
plot.pcops Man page Source code
plot.smacofP Man page Source code
plot.stops Man page Source code
plot3d.cmdscale Man page Source code
plot3d.stops Man page Source code
plot3dstatic Man page Source code
plot3dstatic.cmdscale Man page Source code
plot3dstatic.stops Man page Source code
powerStressFast Man page Source code
powerStressFastOLD Man page Source code
powerStressMin Man page Source code
powerStressMinOLD Man page Source code
print.cmdscale Source code
print.cops Source code
print.cordillera Man page Source code
print.opticse Man page Source code
print.pcops Source code
print.sammon Source code
print.stops Source code
print.summary.cordillera Source code
print.summary.opticse Man page Source code
print.summary.smacofP Source code
print.summary.stops Source code
procruster Man page Source code
residuals.stops Source code
sammon Man page Source code
secularEq Man page Source code
shrinkB Man page Source code
shrinkCoploss0 Man page Source code
sqdist Man page Source code
stop_cmdscale Man page Source code
stop_elastic Man page Source code
stop_flexsmacof Man page Source code
stop_powerelastic Man page Source code
stop_powermds Man page Source code
stop_powersammon Man page Source code
stop_powerstress Man page Source code
stop_rstress Man page Source code
stop_sammon Man page Source code
stop_sammon2 Man page Source code
stop_smacofSphere Man page Source code
stop_smacofSym Man page Source code
stop_sstress Man page Source code
stoploss Man page Source code
stops Man page Source code
stops-package Man page
summary.cmdscale Source code
summary.cordillera Source code
summary.opticse Man page Source code
summary.sammon Source code
summary.smacofP Source code
summary.stops Source code
tgpoptim Man page Source code
torgerson Man page Source code

Files

.Rinstignore
DESCRIPTION
NAMESPACE
NEWS
R
R/BankingCrisesDistances-data.R
R/CAClimateIndicatorsCountyMedian-data.R
R/Pendigits500-data.R
R/cops.R
R/cordillera.R
R/extras.R
R/optics.R
R/optimizations.R
R/powerstress.R
R/stops-package.R
R/stops.R
R/structurednessindices.R
build
build/vignette.rds
data
data/BankingCrisesDistances.rda
data/CAClimateIndicatorsCountyMedian.rda
data/Pendigits500.rda
inst
inst/CITATION
inst/doc
inst/doc/stops.html
inst/doc/stops.html.asis
man
man/BankingCrisesDistances.Rd
man/CAClimateIndicatorsCountyMedian.Rd
man/Pendigits500.Rd
man/c_association.Rd
man/c_complexity.Rd
man/c_dependence.Rd
man/c_faithfulness.Rd
man/c_functionality.Rd
man/c_linearity.Rd
man/c_manifoldness.Rd
man/c_mine.Rd
man/c_nonmonotonicity.Rd
man/cmdscale.Rd
man/conf_adjust.Rd
man/cop_cmdscale.Rd
man/cop_elastic.Rd
man/cop_powerelastic.Rd
man/cop_powermds.Rd
man/cop_powersammon.Rd
man/cop_powerstress.Rd
man/cop_rstress.Rd
man/cop_sammon.Rd
man/cop_sammon2.Rd
man/cop_smacofSphere.Rd
man/cop_smacofSym.Rd
man/cop_sstress.Rd
man/coploss.Rd
man/coplossMin.Rd
man/coplossMinOLD.Rd
man/cops.Rd
man/cordillera.Rd
man/cordillera2.Rd
man/doubleCenter.Rd
man/e_optics.Rd
man/enorm.Rd
man/knn_dist.Rd
man/ljoptim.Rd
man/mkBmat.Rd
man/mkPower.Rd
man/mkPower2.Rd
man/mkPowerALTERN.Rd
man/oldcordilleraplot.Rd
man/pcops.Rd
man/pdist.Rd
man/plot.cops.Rd
man/plot.cordillera.Rd
man/plot.opticse.Rd
man/plot.pcops.Rd
man/plot.smacofP.Rd
man/plot.stops.Rd
man/plot3d.cmdscale.Rd
man/plot3d.stops.Rd
man/plot3dstatic.Rd
man/plot3dstatic.cmdscale.Rd
man/plot3dstatic.stops.Rd
man/powerStressFast.Rd
man/powerStressFastOLD.Rd
man/powerStressMin.Rd
man/powerStressMinOLD.Rd
man/print.cordillera.Rd
man/print.opticse.Rd
man/print.summary.opticse.Rd
man/procruster.Rd
man/sammon.Rd
man/secularEq.Rd
man/shrinkB.Rd
man/shrinkCoploss0.Rd
man/sqdist.Rd
man/stop_cmdscale.Rd
man/stop_elastic.Rd
man/stop_flexsmacof.Rd
man/stop_powerelastic.Rd
man/stop_powermds.Rd
man/stop_powersammon.Rd
man/stop_powerstress.Rd
man/stop_rstress.Rd
man/stop_sammon.Rd
man/stop_sammon2.Rd
man/stop_smacofSphere.Rd
man/stop_smacofSym.Rd
man/stop_sstress.Rd
man/stoploss.Rd
man/stops.Rd
man/summary.opticse.Rd
man/tgpoptim.Rd
man/torgerson.Rd
tests
tests/testthat
tests/testthat/test-cmdscalesammon.R
tests/testthat/test-cops.R
tests/testthat/test-cordillera.R
tests/testthat/test-optics.R
tests/testthat/test-optimization.R
tests/testthat/test-powerstress.R
tests/testthat/test-stops.R
tests/testthat/testthat.R
vignettes
vignettes/stops.Rmd
vignettes/stops.html.asis
stops documentation built on May 21, 2017, 3:49 a.m.