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 <email@example.com>|
|License||GPL-2 | GPL-3|
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
mkPower: MakePower Old
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