BDgraph (version 2.74)

plotcoda: Convergence plot

Description

Visualizes the cumulative occupancy fractions of all possible links in the graph. It can be used for monitoring the convergence of the sampling algorithms, BDMCMC and RJMCMC.

Usage

plotcoda(bdgraph.obj, thin = NULL, control = TRUE, main = NULL, 
                  verbose = TRUE, ...)

Arguments

bdgraph.obj

object of S3 class "bdgraph", from function bdgraph. It also can be an object of S3 class "ssgraph", from the function ssgraph::ssgraph() of R package ssgraph::ssgraph().

thin

option for getting fast result for a cumulative plot according to part of the iteration.

control

logical: if TRUE (default) and the number of nodes is greater than 15, then 100 links randomly is selected for visualization.

main

graphical parameter (see plot).

verbose

logical: if TRUE (default), report/print the calculation progress.

...

system reserved (no specific usage).

Author

Reza Mohammadi

Details

Note that a spending time for this function depends on the number of nodes. For fast result, you can choose bigger value for the 'thin' option.

References

Mohammadi, R. and Wit, E. C. (2019). BDgraph: An R Package for Bayesian Structure Learning in Graphical Models, Journal of Statistical Software, 89(3):1-30, tools:::Rd_expr_doi("10.18637/jss.v089.i03")

See Also

bdgraph, bdgraph.mpl, traceplot

Examples

if (FALSE) {
# Generating multivariate normal data from a 'circle' graph
data.sim <- bdgraph.sim(n = 50, p = 6, graph = "circle", vis = TRUE)
  
bdgraph.obj <- bdgraph(data = data.sim, iter = 10000, burnin = 0 , save = TRUE)
   
plotcoda(bdgraph.obj)  
}