# mdpeer: Graph-Constrained Regression with Enhanced Regularization Parameters Selection

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

## Man pages

- 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...

## Files in this package

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 |