BGGM - Bayesian Gaussian Graphical Models

Fit Bayesian Gaussian graphical models. The methods are separated into two Bayesian approaches for inference: hypothesis testing and estimation. There are extensions for confirmatory hypothesis testing, comparing Gaussian graphical models, and node wise predictability. These methods were recently introduced in the Gaussian graphical model literature, including Williams (2019) <doi:10.31234/osf.io/x8dpr>, Williams and Mulder (2019) <doi:10.31234/osf.io/ypxd8>, Williams, Rast, Pericchi, and Mulder (2019) <doi:10.31234/osf.io/yt386>.

Last updated 23 days ago

bayes-factorsbayesian-hypothesis-testinggaussian-graphical-models

9.61 score 54 stars 1 packages 103 scripts 783 downloads

GGMncv - Gaussian Graphical Models with Nonconvex Regularization

Estimate Gaussian graphical models with nonconvex penalties <doi:10.31234/osf.io/ad57p>, including the atan Wang and Zhu (2016) <doi:10.1155/2016/6495417>, seamless L0 Dicker, Huang, and Lin (2013) <doi:10.5705/ss.2011.074>, exponential Wang, Fan, and Zhu <doi:10.1007/s10463-016-0588-3>, smooth integration of counting and absolute deviation Lv and Fan (2009) <doi:10.1214/09-AOS683>, logarithm Mazumder, Friedman, and Hastie (2011) <doi:10.1198/jasa.2011.tm09738>, Lq, smoothly clipped absolute deviation Fan and Li (2001) <doi:10.1198/016214501753382273>, and minimax concave penalty Zhang (2010) <doi:10.1214/09-AOS729>. There are also extensions for computing variable inclusion probabilities, multiple regression coefficients, and statistical inference <doi:10.1214/15-EJS1031>.

Last updated 3 years ago

6.10 score 4 stars 2 packages 21 scripts 322 downloads

vICC - Varying Intraclass Correlation Coefficients

Compute group-specific intraclass correlation coefficients, Bayesian testing of homogenous within-group variance, and spike-and-slab model selection to determine which groups share a common within-group variance in a one-way random effects model <10.31234/osf.io/hpq7w>.

Last updated 4 years ago

3.54 score 7 stars 3 scripts 150 downloads

GGMnonreg - Non-Regularized Gaussian Graphical Models

Estimate non-regularized Gaussian graphical models, Ising models, and mixed graphical models. The current methods consist of multiple regression, a non-parametric bootstrap <doi:10.1080/00273171.2019.1575716>, and Fisher z transformed partial correlations <doi:10.1111/bmsp.12173>. Parameter uncertainty, predictability, and network replicability <doi:10.31234/osf.io/fb4sa> are also implemented.

Last updated 3 years ago

3.48 score 6 stars 4 scripts 695 downloads

IRCcheck - Irrepresentable Condition Check

Check the irrepresentable condition (IRC) in both L1-regularized regression <doi:10.1109/TIT.2006.883611> and Gaussian graphical models. The IRC requires that the important and unimportant variables are not correlated, at least not all that much, and it is necessary for consistent model selection. Exploring the IRC as a function of the number of variables, assumed sparsity, and effect size can provide valuable insights into the model selection properties of L1-regularization.

Last updated 4 years ago

3.00 score 2 stars 1 scripts 130 downloads