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.

Version: | 0.1.0 |

Depends: | R (≥ 3.3.1) |

Imports: | MASS, glmgraph, magic, reshape2, ggplot2, scalreg, glmnet, nlme, nloptr |

Suggests: | knitr, rmarkdown |

Published: | 2016-11-25 |

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

Maintainer: | Marta Karas <marta.karass at gmail.com> |

License: | GPL-2 |

NeedsCompilation: | no |

Materials: | README |

CRAN checks: | mdpeer results |

Reference manual: | mdpeer.pdf |

Vignettes: |
Introduction and usage examples |

Package source: | mdpeer_0.1.0.tar.gz |

Windows binaries: | r-devel: mdpeer_0.1.0.zip, r-release: mdpeer_0.1.0.zip, r-oldrel: mdpeer_0.1.0.zip |

OS X El Capitan binaries: | r-release: mdpeer_0.1.0.tgz |

OS X Mavericks binaries: | r-oldrel: mdpeer_0.1.0.tgz |

Please use the canonical form
`https://CRAN.R-project.org/package=mdpeer`
to link to this page.