mgmfit:

Description

Estimation of Mixed Graphical Models using L1-constrained neighborhood regression.

Usage

mgmfit(data, type, lev, lambda.sel = "EBIC", folds = 10, 
       gam = .25, d=2, rule.reg = "AND", pbar = TRUE, 
       method = "glm", missings = 'error', weights = NA, 
       ret.warn = TRUE, binary.sign = FALSE)

Arguments

data

n x p data matrix

type

p-vector containing the types of variable ("g" Gaussian, "p" Poisson, "c" Categorical)

lev

p-vector containing the number of levels for each variable p (lev=1 for all continuous variables)

lambda.sel

Procedure to select the lambda-parameter for L1-penalized regressions. The two options are cross validation "CV" and "EBIC" (default). While cross-validation (CV) is used in the paper (see below), the Extended Bayesian Information Criterion (EBIC, see Barber et al., 2015) is a useful alternative in cases where the CV requirement that all categories are present in each fold is not met or in cases where CV is computationally unfeasible.

folds

The number of folds to be used for cross-validation in case lambda.sel="CV". Defaults to folds=10.

gam

Gamma hyperparameter when lambda.sel="EBIC". Defaults to gam=.25 (Barber et al., 2015).

Degrees of augmented interactions. The degree of augmented interactions reflects our belief about the maximal degree in the true graph. (see Loh & Wainwright, 2013)

rule.reg

Rule for combining the two parameters obtained for each edge due to the neighborhood-regression approach. The "OR"-rule determines conditional dependence if at least one of the two parameters is non-zero, the "AND"-rule determines conditional dependence if both parameters are non-zero.

pbar

Shows a progress-bar if TRUE.

method

For each neighborhood regression, method = "glm" uses the appropriate link function for each variable type. method = "linear" uses linear regression for each variable, no matter of which type it is (for categorical variables, this method predicts each indicator variable using linear regression).

missings

Handling of missing values. The default missings = 'error' returns an error message in case there are missing data. missings = 'casewise.zw' sets the weight of missing cases to zero. For stationary graphs, this is the equivalent to casewise deletion. In time varying graphs, this avoids corruption of the time scale, which would be the consequence of casewise deletion. For details, please see Haslbeck and Waldorp (2015).

weights

Weights for observations. Defaults to 1 for each observation.

ret.warn

If FALSE warnings are surpressed.

binary.sign

The default in mgm is to assign no sign to interactions involving categorical variables. This is because for the case where the number of categories m > 2, every interaction has to involve > 1 parameter and hence no sign of the interaction can be defined. However, for the case = 2 we have one parameter describing the interaction between the binary variable at hand and any other binary or continuous variable. If binary.sign = TRUE and if the binary variable is in (0,1) then the sign of this interaction will be recovered and returned in the sign matrix (see below).

Value

Returns a list containing:

call

A list with all function inputs except the data

adj

Adjacency matrix

wadj

Weighted adjacency matrix; Please note that we collapsed the interaction parameters involving categorical variables into one value by taking the mean of the absolute values; for the actual interaction parameters inspect wpar.matrix

mpar.matrix

This matrix includes all estimated parameters in one matrix. If there are only continuous variables in the dataset this matrix has the same dimensions as wadj. If there are categorical variables in the dataset, the matrix has the dimensions of the overcomplete representations. NA values indicate parameters that are not estimated (because they are redundant). For details see Friedman, Hastie and Tibshirani (2010).

signs

A p x p matrix that gives the sign of the edge parameters, if defined. The sign is defined for edges between two continuous variables, where the edge weight is equal to the single parameter. It is not defined for interactions involving categorical variables, where dependency depends on more than one parameter. In case a sign is defined it is indicated as -1 or 1, if a sign is undefined there is a 0 entry. If an edge is absent, there is NA entry.

edgecolor

A p x p matrix that is equivalent to the signs matrix, however, contains color names. This is useful for plotting the graphical model (for instance with the qgraph package) and indicating the sign (negative = red, positive = green, undefined = grey) for each edge in the graph.

node.models

A list that includes for each node: a list of estimated parameters, the selected regularization parameter, the threshold parameter and the EBIC of the model (if applicable).

par.labels

A vector matching with the dimensions of mpar.matrix indicating which parameter belongs to the interaction between which variables.

warnings

A list of all warnings produced during execution. Useful to have when warnings are surpressed in console output (ret.warn = TRUE).

References

Barber, R. F., & Drton, M. (2015). High-dimensional Ising model selection with Bayesian information criteria. Electronic Journal of Statistics, 9, 567-607.

Friedman, J., Hastie, T., & Tibshirani, R. (2010). Regularization paths for generalized linear models via coordinate descent. Journal of statistical software, 33(1), 1. Chicago.

Haslbeck, J., & Waldorp, L. J. (2015). Structure estimation for mixed graphical models in high-dimensional data. arXiv preprint arXiv:1510.05677.

Loh, P. L., & Wainwright, M. J. (2013). Structure estimation for discrete graphical models: Generalized covariance matrices and their inverses. The Annals of Statistics, 41(6), 3022-3049.

Yang, E., Baker, Y., Ravikumar, P., Allen, G., & Liu, Z. (2014). Mixed graphical models via exponential families. In Proceedings of the Seventeenth International Conference on Artificial Intelligence and Statistics (pp. 1042-1050).

Examples

Run this code


## Not run: ------------------------------------
# 
# # Autism example dataset
# dim(autism_data$data)
# 
# # Fit mixed graphical model
# fitobj <- mgmfit(data = autism_data$data, 
#                  type = autism_data$type, 
#                  lev = autism_data$lev, 
#                  lambda.sel = 'EBIC') 
# 
# round(fitobj$wadj,2) # Weighted adjacency matrix
# 
# # Visualize the adjacency matrix using the qgraph package
# library(qgraph)
# colnames(fitobj$wadj) <- autism_data$colnames
# qgraph(fitobj$wadj, 
#        legend=TRUE, 
#        nodeNames=autism_data$colnames, 
#        layout='spring', 
#        edge.color=fitobj$edgecolor)
## ---------------------------------------------