Performs graph-constrained regularization in which regularization parameters are selected with the use of a known fact of equivalence between penalized regression and Linear Mixed Model solutions. Provides implementation of three different regression methods where graph-constraints among coefficients are accounted for. 'crPEER' (Partially Empirical Eigenvectors for Regression with Constant Ridge, Constant Ridge PEER) method utilizes additional Ridge term to handle the non-invertibility of a graph Laplacian matrix. 'vrPEER' (Variable Reduction PEER) method performs variable-reduction procedure to handle the non-invertibility of a graph Laplacian matrix. Finally, 'RidgePEER' method employs a penalty term being a linear combination of graph-originated and Ridge-originated penalty terms, whose two regularization parameters are ML estimators from corresponding Linear Mixed Model solution. Notably, in 'RidgePEER' method a graph-originated penalty term allows imposing similarity between coefficients based on graph information given whereas additional Ridge-originated penalty term facilitates parameters estimation: it reduces computational issues arising from singularity in a graph-originated penalty matrix and yields plausible results in situations when graph information is not informative or when it is unclear whether connectivities represented by a graph reflect similarities among corresponding coefficients.

Author | Marta Karas [aut, cre], Damian Brzyski [ctb], Jaroslaw Harezlak [ctb] |

Date of publication | 2016-11-25 19:48:06 |

Maintainer | Marta Karas <marta.karass@gmail.com> |

License | GPL-2 |

Version | 0.1.0 |

**Adj2Lap:** Compute a graph Laplacian matrix from a graph Adjacency...

**crPEER:** Graph-constrained regression with additional Ridge term to...

**dist2sim:** Transform Distance matrix to Similarity matrix

**L2L.normalized:** Compute normalized version of a graph Laplcian matrix

**mdpeer:** mdpeer: Performs graph-constrained regression with enhanced...

**RidgePEER:** Graph-constrained estimation with enhanced regulariazation...

**RidgePEER.cv:** Graph-constrained estimation with regulariazation parameter...

**vizu.mat:** Visualize matrix data in a form of a heatmap

**vrPEER:** Graph-constrained regression with variable-reduction...

mdpeer

mdpeer/inst

mdpeer/inst/doc

mdpeer/inst/doc/Introduction_and_usage_examples.R

mdpeer/inst/doc/Introduction_and_usage_examples.html

mdpeer/inst/doc/Introduction_and_usage_examples.Rmd

mdpeer/NAMESPACE

mdpeer/R

mdpeer/R/RidgePEER.R
mdpeer/R/L2Lnormalized.R
mdpeer/R/vizumat.R
mdpeer/R/mdpeer.R
mdpeer/R/GraceTest_C.R
mdpeer/R/dist2sim.R
mdpeer/R/RidgePEER_cv.R
mdpeer/R/A2L.R
mdpeer/R/vrPEER.R
mdpeer/R/crPEER.R
mdpeer/vignettes

mdpeer/vignettes/Introduction_and_usage_examples.Rmd

mdpeer/README.md

mdpeer/MD5

mdpeer/build

mdpeer/build/vignette.rds

mdpeer/DESCRIPTION

mdpeer/man

mdpeer/man/dist2sim.Rd
mdpeer/man/mdpeer.Rd
mdpeer/man/vizu.mat.Rd
mdpeer/man/RidgePEER.cv.Rd
mdpeer/man/RidgePEER.Rd
mdpeer/man/crPEER.Rd
mdpeer/man/L2L.normalized.Rd
mdpeer/man/vrPEER.Rd
mdpeer/man/Adj2Lap.Rd
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