Nothing
summary.graphicalVAR <- function(object,...) print(object,...)
# Print method
print.graphicalVAR <- function(x, ...){
name <- deparse(substitute(x))[[1]]
if (nchar(name) > 10) name <- "object"
cat("=== graphicalVAR results ===")
cat("\nNumber of nodes:",nrow(x[['kappa']]),
"\nNumber of tuning parameters tested:",nrow(x[['path']]),
"\nEBIC hyperparameter:",x[['gamma']],
"\nOptimal EBIC:",x[['EBIC']],
"\n\nNumber of non-zero Partial Contemporaneous Correlations (PCC):",sum(x[['PCC']][upper.tri(x[['PCC']],diag=FALSE)]!=0) ,
"\nPCC Sparsity:",mean(x[['PCC']][upper.tri(x[['PCC']],diag=FALSE)]==0) ,
"\nNumber of PCC tuning parameters tested:",length(unique(x$path$kappa)),
paste0("\nPCC network stored in ",name,"$PCC"),
"\n\nNumber of non-zero Partial Directed Correlations (PDC):",sum(x[['PDC']][upper.tri(x[['PDC']],diag=FALSE)]!=0) ,
"\nPDC Sparsity:",mean(x[['PDC']][upper.tri(x[['PDC']],diag=FALSE)]==0) ,
"\nNumber of PDC tuning parameters tested:",length(unique(x$path$beta)),
paste0("\nPDC network stored in ",name,"$PDC"),
paste0("\n\nUse plot(",name,") to plot the estimated networks.")
)
}
# Plot method
plot.graphicalVAR <- plot.gVARmodel <- function(x, include = c("PCC","PDC"), repulsion = 1, horizontal = TRUE, titles = TRUE, sameLayout = TRUE, unweightedLayout = FALSE,...){
qtitle <- function (x)
{
text(par("usr")[1] + (par("usr")[2] - par("usr")[1])/40,
par("usr")[4] - (par("usr")[4] - par("usr")[3])/40, x,
adj = c(0, 1))
}
if (length(include)>1){
if (horizontal){
layout(t(seq_along(include)))
} else {
layout(seq_along(include))
}
}
# Choose directed or undirected:
if (unweightedLayout){
wPCC <- 1*(x$PCC!=0)
wPDC <- 1*(x$PDC!=0)
} else {
wPCC <- x$PCC
wPDC <- x$PDC
}
if (sameLayout & all(c("PCC","PDC") %in% include)){
Layout <- qgraph::averageLayout(as.matrix(wPCC), as.matrix(wPDC), repulsion=repulsion)
}
Res <- list()
for (i in seq_along(include)){
if ("PCC" == include[i]){
if (sameLayout & all(c("PCC","PDC") %in% include)){
Res[[i]] <- qgraph::qgraph(x$PCC, layout = Layout, ..., repulsion=repulsion)
} else {
L <- qgraph::qgraph(wPCC,DoNotPlot=TRUE,...,repulsion=repulsion)$layout
Res[[i]] <- qgraph::qgraph(x$PCC, layout = L,..., repulsion=repulsion)
}
if (titles){
qtitle("Partial Contemporaneous Correlations")
}
}
if ("PDC" == include[i]){
if (sameLayout & all(c("PCC","PDC") %in% include)){
Res[[i]] <- qgraph::qgraph(x$PDC, layout = Layout, ..., repulsion=repulsion, directed=TRUE)
} else {
L <- qgraph::qgraph(wPDC,DoNotPlot=TRUE,...,repulsion=repulsion, directed=TRUE)$layout
Res[[i]] <- qgraph::qgraph(x$PDC,layout=L, ..., repulsion=repulsion, directed=TRUE)
}
if (titles){
qtitle("Partial Directed Correlations")
}
}
}
invisible(Res)
}
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