Ridge Estimation of Precision Matrices from High-Dimensional Data

Proper L2-penalized ML estimators for the precision matrix as well as supporting functions to employ these estimators in a graphical modeling setting.


The R-package rags2ridges performs L2-penalized estimation of precison (and covariance) matrices. The package contains proper L2-penalized ML estimators for the precision matrix as well as supporting functions to employ these estimators in a (integrative or meta-analytic) graphical modeling setting. The package has a modular setup and features fast and efficient algorithms. The released and tested version of rags2ridges is available at CRAN (Comprehensive R Archive Network). It can be easily be installed from within R by running

install.packages("rags2ridges")

If you wish to install the latest version of rags2ridges directly from the master branch here at GitHub, run

#install.packages("devtools")  # Uncomment if devtools is not installed
devtools::install_github("CFWP/rags2ridges")

Note, that this version is in development and is different from the version at CRAN. As such, it may be unstable. Be sure that you have the package development prerequisites if you wish to install the package from the source.

When installed, run news(package = "rags2ridges") to view the latest notable changes to rags2ridges.

For previous versions of rags2ridges, visit the archive at CRAN.

Relevant publications to rags2ridges include (ordered according to year):

  1. Peeters, C.F.W., Bilgrau, A.E., & van Wieringen, W.N. (2016). "rags2ridges: Ridge Estimation of Precision Matrices from High-Dimensional Data". R package, version 2.1.1
  2. Peeters, C.F.W., van de Wiel, M.A., & van Wieringen, W.N. (2016) "The Spectral Condition Number Plot for Regularization Parameter Determination". Available as arXiv:1608.04123v1 [stat.CO].
  3. van Wieringen, W.N. & Peeters, C.F.W. (2016). "Ridge Estimation of Inverse Covariance Matrices from High-Dimensional Data", Computational Statistics & Data Analysis, vol. 103: 284-303 (doi:10.1016/j.csda.2016.05.012). Also available as arXiv:1403.0904v3 [stat.ME].
  4. Bilgrau*, A.E., Peeters*, C.F.W., Eriksen, P.S., Boegsted, M., & van Wieringen, W.N. (2015). "Targeted Fused Ridge Estimation of Inverse Covariance Matrices from Multiple High-Dimensional Data Classes". Available as arXiv:1509.07982v1 [stat.ME].
  5. van Wieringen, W.N. & Peeters, C.F.W. (2015). "Application of a New Ridge Estimator of the Inverse Covariance Matrix to the Reconstruction of Gene-Gene Interaction Networks". In: di Serio, C., Lio, P., Nonis, A., and Tagliaferri, R. (Eds.) `Computational Intelligence Methods for Bioinformatics and Biostatistics'. Lecture Notes in Computer Science, vol. 8623. Springer, pp. 170-179 (doi:10.1007/978-3-319-24462-4_15).

Please cite the relevant publications if you use rags2ridges.

News

Reference manual

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install.packages("rags2ridges")

2.2 by Carel F.W. Peeters, 7 months ago


http://www.bigstatistics.nl/carel-fw-peeters


Browse source code at https://github.com/cran/rags2ridges


Authors: Carel F.W. Peeters [cre, aut], Anders Ellern Bilgrau [aut], Wessel N. van Wieringen [aut]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports igraph, stats, methods, expm, reshape, ggplot2, Hmisc, fdrtool, snowfall, sfsmisc, utils, grDevices, graphics, gRbase, RBGL, graph

Suggests KEGGgraph, testthat

Linking to Rcpp, RcppArmadillo


Depended on by ragt2ridges.


See at CRAN