Structure Optimized Proximity Scaling

Documentation for package ‘stops’ version 1.0-1

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apStressMin	Approximate Power Stress SMACOF
BankingCrisesDistances	Banking Crises Distances
bcStressMin	An MDS version for minimizing BoxCox Stress (Chen & Buja 2013)
cmds	normalization function Classical Scaling
cmdscale	Wrapper to 'cmdscale' for S3 class
coef.stops	S3 coef method for stops objects
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 columns in confs
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 columns in confs 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 of each pair if nonidentical columns
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 columns of confs
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 fitted distance matrix. This can help with avoiding degenerate solutions. 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 correlation of all columns of the configuration.
c_manifoldness	c-manifoldness calculates c-manifoldness as the aggregated maximal correlation coefficient (i.e., Pearson correlation of the ACE transformed variables) 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 columns in confs 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 function for local MDS (Chen & Buja 2006)
mkBmat	MkBmat function (internal)
mkPower	MakePower Old
mkPower2	MakePower
Pendigits500	Pen digits
plot.cmdscaleE	S3 plot method for cmdscaleE
plot.smacofP	S3 plot method for smacofP objects
plot.stops	S3 plot method for stops objects
plot3d.cmdscaleE	S3 plot3d method for class cmdscaleE
plot3d.stops	S3 plot3d method for class stops
plot3dstatic	plot3dstatic: static 3D plots
plot3dstatic.cmdscaleE	3D plots: plot3dstatic method for class cmdscaleE
plot3dstatic.stops	S3 plot3dstatic method for class stops
powerStressMin	Power Stress SMACOF
print.cmdscale	S3 print method for cmdscale
print.sammon	S3 print method for sammon objects
print.stops	S3 print method for stops objects
print.summary.smacofP	S3 print method for summary.smacofP
print.summary.stops	S3 print method for summary.stops
procruster	procruster: a procrustes function
residuals.stops	S3 residuals method for stops
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_apstress	STOPS version of approximated power stress models.
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_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 for proximities and distances
stop_powermds	STOPS version of powermds
stop_powersammon	STOPS version of sammon with powers
stop_powerstress	STOPS version of powerstress
stop_rpowerstress	STOPS version of restricted powerstress
stop_rstress	STOPS version of rstress
stop_sammon	STOPS version of Sammon mapping
stop_sammon2	Another STOPS version 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.cmdscale	S3 summary method for cmdscale
summary.sammon	S3 summary method for sammon
summary.smacofP	S3 summary method for smacofP
summary.stops	S3 summary method for stops
Swissroll	Swiss roll
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