EBICglasso: Compute Gaussian graphical model using graphical lasso based...

In qgraph: Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation

Compute Gaussian graphical model using graphical lasso based on extended BIC criterium.

Description

This function uses the glasso package (Friedman, Hastie and Tibshirani, 2011) to compute a sparse gaussian graphical model with the graphical lasso (Friedman, Hastie and Tibshirani, 2008). The tuning parameter is chosen using the Extended Bayesian Information criterium (EBIC).

Usage

EBICglasso(S, n, gamma = 0.5, penalize.diagonal = FALSE, nlambda = 100, 
            lambda.min.ratio = 0.01, returnAllResults = FALSE, checkPD = TRUE, 
            penalizeMatrix, countDiagonal = FALSE, refit = FALSE, threshold = FALSE,
            verbose = TRUE, ...)

Arguments

S	A covariance or correlation matrix
n	Sample size used in computing S
gamma	EBIC tuning parameter. 0.5 is generally a good choice. Setting to zero will cause regular BIC to be used.
penalize.diagonal	Should the diagonal be penalized?
nlambda	Number of lambda values to test.
lambda.min.ratio	Ratio of lowest lambda value compared to maximal lambda
returnAllResults	If TRUE this function does not return a network but the results of the entire glasso path.
checkPD	If TRUE, the function will check if S is positive definite and return an error if not. It is not advised to use a non-positive definite matrix as input as (a) that can not be a covariance matrix and (b) glasso can hang if the input is not positive definite.
penalizeMatrix	Optional logical matrix to indicate which elements are penalized
countDiagonal	Should diagonal be counted in EBIC computation? Defaults to FALSE. Set to TRUE to mimic qgraph < 1.3 behavior (not recommended!).
refit	Logical, should the optimal graph be refitted without LASSO regularization? Defaults to FALSE.
threshold	Logical, should elements of the precision matrix that are below (log(p*(p-1)/2)) / sqrt(n) be removed (both before EBIC computation and in final model)? Set to TRUE to ensure high specificity.
verbose	Logical, should progress output be printed to the console?
...	Arguments sent to glasso

Details

The glasso is run for 100 values of the tuning parameter logarithmically spaced between the maximal value of the tuning parameter at which all edges are zero, lamba_max, and lambda_max/100. For each of these graphs the EBIC is computed and the graph with the best EBIC is selected. The partial correlation matrix is computed using wi2net and returned. When threshold = TRUE, elements of the inverse variance-covariance matrix are first thresholded using the theoretical bound (Jankova and van de Geer, 2018).

Value

A partial correlation matrix

Author(s)

Sacha Epskamp <[e-mail]>

References

Friedman, J., Hastie, T., & Tibshirani, R. (2008). Sparse inverse covariance estimation with the graphical lasso. Biostatistics, 9(3), 432-441. Chicago

Jerome Friedman, Trevor Hastie and Rob Tibshirani (2011). glasso: Graphical lasso-estimation of Gaussian graphical models. R package version 1.7. http://CRAN.R-project.org/package=glasso

Foygel, R., & Drton, M. (2010, November). Extended Bayesian Information Criteria for Gaussian Graphical Models. In NIPS (pp. 604-612). Chicago

Revelle, W. (2014) psych: Procedures for Personality and Psychological Research, Northwestern University, Evanston, Illinois, USA, http://CRAN.R-project.org/package=psych Version = 1.4.4.

Bates, D., and Maechler, M. (2014). Matrix: Sparse and Dense Matrix Classes and Methods. R package version 1.1-3. http://CRAN.R-project.org/package=Matrix

Jankova, J., and van de Geer, S. (2018) Inference for high-dimensional graphical models. In: Handbook of graphical models (editors: Drton, M., Maathuis, M., Lauritzen, S., and Wainwright, M.). CRC Press: Boca Raton, Florida, USA.

Examples

## Not run: 
### Using bfi dataset from psych ###
library("psych")
data(bfi)

# Compute correlations:
CorMat <- cor_auto(bfi[,1:25])

# Compute graph with tuning = 0 (BIC):
BICgraph <- EBICglasso(CorMat, nrow(bfi), 0, threshold = TRUE)

# Compute graph with tuning = 0.5 (EBIC)
EBICgraph <- EBICglasso(CorMat, nrow(bfi), 0.5, threshold = TRUE)

# Plot both:
layout(t(1:2))
BICgraph <- qgraph(BICgraph, layout = "spring", title = "BIC", details = TRUE)
EBICgraph <- qgraph(EBICgraph, layout = "spring", title = "EBIC")

# Compare centrality and clustering:
layout(1)
centralityPlot(list(BIC = BICgraph, EBIC = EBICgraph))
clusteringPlot(list(BIC = BICgraph, EBIC = EBICgraph))

## End(Not run)

qgraph documentation built on Nov. 3, 2023, 5:07 p.m.