R: Structure Optimized Proximity Scaling

# Structure Optimized Proximity Scaling

## Documentation for package ‘stops’ version 1.9-1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

BankingCrisesDistances | Banking Crises Distances
biplotmds.stops | S3 method for stops objects
bootmds.stops | MDS Bootstrap for stops objects
coef.stops | S3 coef method for stops objects
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_shepardness | c-shepardness calculates the c-shepardness as the correlation between a loess smoother of the transformed distances and the transformed dissimilarities
c_skinniness | c-skinniness
c_sparsity | c-sparsity
c_striatedness | c-striatedness
c_stringiness | c-stringiness
jackmds.stops | MDS Jackknife for stops objects
knn_dist | calculate k nearest neighbours from a distance matrix
ljoptim | (Adaptive) Version of Luus-Jaakola Optimization
match_partial_ignorecase_nopunct | function for lookup that partially matched and ignores cases and punctuation
Pendigits500 | Pen digits
plot.stops | S3 plot method for stops objects
print.stops | S3 print method for stops objects
print.summary.stops | S3 print method for summary.stops
residuals.stops | S3 residuals method for stops
stoploss | Calculate the weighted multiobjective loss function used in STOPS
stops | High Level STOPS Function
stop_apstress | STOPS version of approximated power stress models.
stop_bcmds | STOPS version of Box Cox Stress
stop_clca | STOPS version of CLCA.
stop_cldae | STOPS version of CLDA with free epsilon.
stop_cldak | STOPS version of CLDA with free k.
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_smddae | STOPS version of sparsified multidimensional distance analysis for fixed eps and tau
stop_smddak | STOPS version of sparsified multidimensional distance analysis for fixed k and tau
stop_smds | STOPS version of sparsified MDS.
stop_spmddae | STOPS version of sparsified post multidimensional distance analysis for fixed tau and epsilon.
stop_spmddak | STOPS version of sparsified post multidimensional distance analysis for fixed tau and k.
stop_spmds | STOPS version of sparsified POST-MDS for fixed tau
stop_sstress | STOPS version of sstress
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.