R code mcmcplots function

Question

Is there a way to make the R mcmcplot() function not open a browser when it's called? I need to run my R code on a cluster and if mcmcplot() tries to open a browser, it will puke.

Can the output be dumped to a file maybe?

Answer 1

That function writes everything to a file and also opens it in a browser. If you dont want to open the browser I would recommend editing the function to pass whether or not you want to open in a browser as an argument. You can retreive the function by just typing its name without any parenthesis.

mcmcplot

then copy that output to a editor and at the beginning change the name of the function and add teh argument:

mcmcplotnew=function (mcmcout, parms = NULL, regex = NULL, random = NULL, 
    leaf.marker = "[\\[_]", dir = tempdir(), filename = "MCMCoutput", 
    extension = "html", title = NULL, heading = title, col = NULL, 
    lty = 1, xlim = NULL, ylim = NULL, style = c("gray", "plain"), 
    greek = FALSE,ShouldIPlotinbrowser=T)   #new argument here

then there are much more parts of the function

then at the end there is

    cat("\r", rep(" ", getOption("width")), "\r", sep = "")
    cat("\n</div>\n</div>\n", file = htmlfile, append = TRUE)
    .html.end(htmlfile)
    full.name.path <- paste("file://", htmlfile, sep = "")
    browseURL(full.name.path)
    invisible(full.name.path)
}

Where you have the browsURL line, make it something like:

if(ShouldIPlotinbrowser) { browseURL(full.name.path) }

Then initialize that function before you run it with:

mcmcplotnew(whatever, usual, arguments,then,ShouldIPlotinbrowser=F)

Answer 2

Looking at the source, it seems not. There is an unconditional call to browseURL() there. Maybe by making a dummy version of that function which does nothing in your global namespace, it's effect can be avoided.

browseURL <- identity

This may break other browser activity as well, so after the mcmcplot calls, you may want to

rm(browseURL)

Alternatively, copy all the code from mcmcplot except for the browseURL line and use that function instead.