STructure Optimized Proximity Scaling


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Documentation for package ‘stops’ version 0.0-34

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stops-package stops: structure optimized proximity scaling
BankingCrisesDistances Banking Crises Distances
CAClimateIndicatorsCountyMedian Climate Change Indicators of Californian Counties
cmdscale Wrapper to 'cmdscale' for S3 class
conf_adjust conf_adjust: a function to procrustes adjust two matrices
coploss Calculates coploss for given MDS object
coplossMin Fitting a COPS Model (Variant 1).
cops High Level COPS Function
cop_cmdscale COPS version of strain
cop_elastic COPS versions of elastic scaling models (via smacofSym)
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
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
c_association c-association calculates the c-association based on the maximal information coefficient We define c-association as the maximum association between any two dimensions - or use the determinant of the MINE matrix - TBD
c_complexity c-complexity calculates the c-complexity based on the minimum cell number We define c-complexity as the maximum minimum cell number between any two dimensions - or use the determinant of the MINE matrix? - TBD
c_dependence c-dependence calculates c-dependence as the distance correlation
c_faithfulness c-faithfulness calculates the c-faithfulness based on the index by Chen and Buja 2013 (M_adj) with equal input neigbourhoods
c_functionality c-functionality calculates the c-functionality based on the maximum edge value We define c-functionality as the mean functionality between any two dimensions - or use the determinant of the MINE matrix? - TBD
c_linearity c-linearity calculates c-linearity as the maximum multiple correlation
c_manifoldness c-manifoldness calculates c-manifoldness as the maximal correlation coefficient
c_mine wrapper for getting the mine coefficients
c_nonmonotonicity c-nonmonotonicity calculates the c-nonmonotonicity based on the maximum asymmetric score We define c-nonmonotonicity as the maximum nonmonotonicity between any two dimensions - or use the determinant of the MINE matrix? - TBD
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
oldcordilleraplot Plot method for OPTICS cordilleras. Deprecated.
pcops Profile COPS Function (aka COPS Variant 2)
pdist Squared distances
Pendigits500 Pen digits
plot.cops S3 plot method for cops objects
plot.cordillera Plot method for OPTICS cordilleras
plot.opticse Plot method for OPTICS results
plot.smacofP S3 plot method for smacofP objects
plot.stops S3 plot method for stops objects
plot3d.cmdscale 3D plots: plot3d method for class cmdscale
plot3d.stops 3D plots: plot3d method for class stops
plot3dstatic plot3dstatic: static 3D plots
plot3dstatic.cmdscale 3D plots: plot3dstatic method for class cmdscale
plot3dstatic.stops 3D plots: plot3dstatic method for class stops
powerStressFast Power stress minimization by NEWUOA
powerStressMin 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 reachability plot. Currently its the five points summary of the reachabilities and a stem and leaf display. The latter should not be confused with the reachability plot. If you need the latter, use plot()
procruster procruster: a procrustes function
sammon Wrapper to 'sammon' for S3 class
secularEq Secular Equation
shrinkB Finding the shrinkage matrix for COPS-0
shrinkCoploss Fitting a COPS Model by shrinking residuals to Zero (COPS-0).
sqdist Squared distances
stoploss Calculate the weighted multiobjective loss function used in STOPS
stops stops: structure optimized proximity scaling
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 f() transformation to be determined)
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
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 Prior (with jumps to linear models) surrogate model Essentially a wrapper for the functionality in tgp that has the same slots as optim with defaults for STOPS models.
torgerson Torgerson scaling