Dear Leonore, On Wed, Apr 10, 2013 at 5:51 PM, Leonore Wigger <leonore.wig...@unil.ch> wrote: > Question: I have specified a blacklist. I would have expected this to > completely disallow the arcs on the blacklist. But the result shows that > some of the blacklisted arcs have a strength > 0 (rows 7,8,10,11). It > seems that only the arc that was blacklisted in both directions was > actually banned (x1-x2, in rows 9 and 12). What is the reason for this? > Is there a way to completely disallow all blacklisted arcs, such that > their strength is 0.0? Or is there a compelling reason why that should > not be done?
Because by default boot.strength() runs with "cpdag = TRUE". This means that reversible arcs can have positive strength in both directions. You should set "cpdag = FALSE" to get the result you are expecting. In that case the probabilities of the arc directions should be taken with a grain of salt, as they can be influenced by many things (optimized = TRUE/FALSE, order of the variables in the data set) unless you are doing causal modelling. > This code makes 50 different networks from the same data, then uses them > as input for custom.strength. The networks are constructed using the > algorithm "hc". A different network is produced every time "hc" is > invoked because a random starting network is supplied to the parameter > "start". I would like to do the same thing, but use "mmhc" instead of > "hc". However, in my hands, the networks that are constructed by "mmhc" > are all identical, and I am not sure how to introduce a random element > into the construction. Question: Which parameters do I need to give to > "mmhc" in order to obtain a different network every time it is run on > the same data set? This is not surprising, because mmhc() does not have a "start" argument, so it's starting from the same network over and over. There is no way to provide a random seed to mmhc(), so the only way to perturb it is through bootstrap. Marco -- Marco Scutari, Ph.D. Research Associate, Genetics Institute (UGI) University College London (UCL), United Kingdom ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
