plotcoda: Convergence plot

In BDgraph: Bayesian Structure Learning in Graphical Models using Birth-Death MCMC

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).

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.

Author(s)

Reza Mohammadi [e-mail]

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, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.18637/jss.v089.i03")}

See Also

bdgraph, bdgraph.mpl, traceplot

Examples

## Not run: 
# 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 )  

## End(Not run)

BDgraph documentation built on Sept. 11, 2024, 5:30 p.m.