x |
There are 2 options: (1) x is an n by d data matrix (2) a d by d sample covariance matrix. The program automatically identifies the input matrix by checking the symmetry. (n is the sample size and d is the dimension).
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lambda |
A sequence of decreasing positive numbers to control the regularization when method = "mb", "glasso" or "tiger", or the thresholding in method = "ct". Typical usage is to leave the input lambda = NULL and have the program compute its own lambda sequence based on nlambda and lambda.min.ratio. Users can also specify a sequence to override this. When method = "mb", "glasso" or "tiger", use with care - it is better to supply a decreasing sequence values than a single (small) value.
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nlambda |
The number of regularization/thresholding parameters. The default value is 30 for method = "ct" and 10 for method = "mb", "glasso" or "tiger".
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lambda.min.ratio |
If method = "mb", "glasso" or "tiger", it is the smallest value for lambda, as a fraction of the upperbound (MAX) of the regularization/thresholding parameter which makes all estimates equal to 0. The program can automatically generate lambda as a sequence of length = nlambda starting from MAX to lambda.min.ratio*MAX in log scale. If method = "ct", it is the largest sparsity level for estimated graphs. The program can automatically generate lambda as a sequence of length = nlambda, which makes the sparsity level of the graph path increases from 0 to lambda.min.ratio evenly.The default value is 0.1 when method = "mb", "glasso" or "tiger", and 0.05 method = "ct".
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sym |
Symmetrize the output graphs. If sym = "and", the edge between node i and node j is selected ONLY when both node i and node j are selected as neighbors for each other. If sym = "or", the edge is selected when either node i or node j is selected as the neighbor for each other. The default value is "or". ONLY applicable when method = "mb" or "tiger".
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verbose |
If verbose = FALSE, tracing information printing is disabled. The default value is TRUE.
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