fitCovGraph and fitConGraph from the ggm package are used in computing these networks (Marchetti, Drton and Sadeghi, 2014).findGraph(S, n, type = "cor", gamma = 0.5, method = c('stepup','stepdown','brute'),
reverseSteps = TRUE, startSig = TRUE)cor_auto will be used."cor" for estimating a correlation network or "pcor" for estimating a partial correlation network"brute" for brute force search (testing all possible models), "stepup" for stepwise up model search and "stepdown" for stepwise down model search.method is "stepup" or "stepdown", should the stepping be reversed if a minimum is found? For example, if in stepwise up search a best model is found, should the search be continued by looking at if differTRUE the initial model in if method is "stepup" or "stepdown" is the model in which all edges that are insignificant using Holm adjustment are deleted. Otherwise, "stepup" will EBICglasso should be preferred in larger datasets.Giovanni M. Marchetti, Mathias Drton and Kayvan Sadeghi (2014). ggm: A package for Graphical Markov Models. R package version 2.0. http://CRAN.R-project.org/package=ggm