Package: sharp 1.4.6

sharp: Stability-enHanced Approaches using Resampling Procedures

In stability selection (N Meinshausen, P Bühlmann (2010) <doi:10.1111/j.1467-9868.2010.00740.x>) and consensus clustering (S Monti et al (2003) <doi:10.1023/A:1023949509487>), resampling techniques are used to enhance the reliability of the results. In this package, hyper-parameters are calibrated by maximising model stability, which is measured under the null hypothesis that all selection (or co-membership) probabilities are identical (B Bodinier et al (2023a) <doi:10.1093/jrsssc/qlad058> and B Bodinier et al (2023b) <doi:10.1093/bioinformatics/btad635>). Functions are readily implemented for the use of LASSO regression, sparse PCA, sparse (group) PLS or graphical LASSO in stability selection, and hierarchical clustering, partitioning around medoids, K means or Gaussian mixture models in consensus clustering.

Authors:Barbara Bodinier [aut, cre]

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Bug tracker:https://github.com/barbarabodinier/sharp/issues

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66 exports 13 stars 2.11 score 38 dependencies 103 scripts 313 downloads

Last updated 8 months agofrom:d2cc3d9bc6. Checks:OK: 5 NOTE: 2. Indexed: yes.

Exports:AdjacencyAggregatedEffectsArgmaxArgmaxIdBiSelectionBlockLambdaGridCalibrationPlotCARTClusteringClusteringAlgoClusteringPerformanceClustersCombineCoMembershipConsensusMatrixConsensusScoreDBSCANClusteringEnsembleEnsemblePredictionsExplanatoryPerformanceFDPFoldsGMMClusteringGraphGraphComparisonGraphicalAlgoGraphicalModelGroupPLSHierarchicalClusteringIncrementalIncrementalPlotKMeansClusteringLambdaGridGraphicalLambdaGridRegressionLambdaSequenceLinearSystemMatrixOpenMxMatrixOpenMxModelPAMClusteringPenalisedGraphicalPenalisedLinearSystemPenalisedOpenMxPenalisedRegressionPFERPlotIncrementalPLSPredictPLSRecalibrateRefitResampleSelectedVariablesSelectionAlgoSelectionPerformanceSelectionPerformanceGraphSelectionProportionsSparseGroupPLSSparsePCASparsePLSSplitSquareStabilityMetricsStabilityScoreStableStructuralModelVariableSelectionWeightBoxplot

Dependencies:abindaudiobeeprclicodetoolscpp11digestfakeforeachfuturefuture.applyglassoFastglmnetglobalsgluehugeigraphiteratorslatticelifecyclelistenvmagrittrMASSMatrixmclustnloptrparallellypkgconfigplotrixrbibutilsRcppRcppEigenRdpackrlangshapesurvivalvctrswithr