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 |