STructure Optimized Proximity Scaling


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Documentation for package ‘stops’ version 0.0-44

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stops-package stops: structure optimized proximity scaling
BankingCrisesDistances Banking Crises Distances
bcStressMin An MDS version for minimizing BoxCox Stress (Chen & Buja 2013)
CAClimateIndicatorsCountyMedian Climate Change Indicators of Californian Counties
cmds normalization function Classical Scaling
cmdscale Wrapper to 'cmdscale' for S3 class
conf_adjust conf_adjust: a function to procrustes adjust two matrices
c_association c-association calculates the c-association based on the maximal information coefficient We define c-association as the aggregated association between any two dimensions
c_clumpiness c-clumpiness
c_clusteredness c-clusteredness calculates c-clusteredness as the OPTICS cordillera. The higher the more clustered.
c_complexity c-complexity Calculates the c-complexity based on the minimum cell number We define c-complexity as the aggregated minimum cell number between any two dimensions This is one of few c-structuredness indices not between 0 and 1, but can be between 0 and (theoretically) infinity
c_convexity c-convexity
c_dependence c-dependence calculates c-dependence as the aggregated 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 aggregated functionality between any two dimensions
c_hierarchy c-hierarchy captures how well a partition/ultrametric (obtained by hclust) explains the configuration distances. Uses variance explained for euclidean distances and deviance explained for everything else.
c_inequality c-inequality calculates c-inequality (as in an economic measure of inequality) as Pearsons coefficient of variation of the distance matrix this is one of few c-structuredness indices not between 0 and 1, but 0 and infinity
c_linearity c-linearity calculates c-linearity as the aggregated multiple correlations
c_manifoldness c-manifoldness calculates c-manifoldness as the aggregated maximal correlation coefficient (i.e., Pearson correlation of the ACE transformedvariables) of all pairwise combinations of two different columns in confs. If there is an NA (happens usually when the optimal transformation of any variable is a constant and therefore the covariance is 0 but also one of the sds in the denominator), it gets skipped.
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 aggregated nonmonotonicity between any two dimensions this is one of few c-structuredness indices not between 0 and 1
c_outlying c-outlying
c_regularity c-regularity calculates c-regularity as 1 - OPTICS cordillera for k=2. The higher the more regular.
c_skinniness c-skinniness
c_sparsity c-sparsity
c_striatedness c-striatedness
c_stringiness c-stringiness
doubleCenter double centering
enorm Explicit Norm
knn_dist calculate k nearest neighbours from a distance matrix
ljoptim (Adaptive) Version of Luus-Jaakola Optimization
lmds An MDS version for local MDS (Chen & Buja 2006)
mkBmat Auxfunction1
mkPower MakePower Old
mkPower2 MakePower
pdist Squared distances
Pendigits500 Pen digits
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
powerStressMin Power Stress SMACOF
procruster procruster: a procrustes function
sammon Wrapper to 'sammon' for S3 class
secularEq Secular Equation
sqdist Squared distances
stoploss Calculate the weighted multiobjective loss function used in STOPS
stops stops: structure optimized proximity scaling
stop_bcstress STOPS version of Box Cox Stress
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_isomap1 STOPS version of isomap to optimize over integer k.
stop_isomap2 STOPS version of isomap over real epsilon.
stop_lmds STOPS version of lMDS
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
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