On 8/21/07, Horace Tso <[EMAIL PROTECTED]> wrote: > Deepayan, you're right. Now I realize anyone could write a densityplot > function to apply on a different class of objects. I guess I should write to > the author of lme4 which from what I could see does not describe a > densityplot. By the way, it is used in Baayen, Davidson, and Bates (2006).
You're right. It's my bad for not documenting that the coda package is required for plots of the results of mcmcsamp. I was trying to piggy-back on the work that the authors of the coda package had done on diagnostics, etc. It was actually Deepayan and I who added the lattice-based plots to the coda package for exactly this purpose (did you remember that, Deepayan?). In some ways it might be better to remove the dependence on coda and write the classes and methods in the lme4 package. That way I can use S4 classes and irritate all those people who rail against S4 classes and methods (and you know who you are). > >>> "Deepayan Sarkar" <[EMAIL PROTECTED]> 8/21/2007 11:17:39 AM >>> > On 8/21/07, Horace Tso <[EMAIL PROTECTED]> wrote: > > Hi folks, > > > > This is really minor but to someone not familiar with the various tentacles > > of the lmer package it could be really annoying. I was trying to plot the > > posterior density of the fixed effect parameters of a lmer model, > > > > > hr.mcmc = mcmcsamp(hr.lmer, n=50000) > > > densityplot(hr.mcmc, plot.points=F) > > > > There is this error, > > > > "Error in densityplot(hr.mcmc, plot.points = F) : > > no applicable method for "densityplot" " > > > > It kind of smells like something I've come across before. So I checked the > > mcmcsamp help page, and alas, the example suggests that the package coda is > > needed. > > > > >From the help page of densityplot alone, there is no way one could figure > > >out this dependency. It says, together with histogram, it is part of > > >lattice. > > > > Could the function author *please* make clarification in future editions of > > lattice. > > There is nothing to clarify. densityplot() is a generic function, and > it is not possible for the author of the generic function to > anticipate and document all possible methods, especially those in > other packages. I would say that since you are using mcmcsamp(), it's > perfectly reasonable to expect you to look at its help page to figure > out what you can do with the results. > > What gave you the idea that densityplot would work on the result of > mcmcsamp in the first place? > > -Deepayan > > ______________________________________________ > R-help@stat.math.ethz.ch 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. > > ______________________________________________ > R-help@stat.math.ethz.ch 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. > ______________________________________________ R-help@stat.math.ethz.ch 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.
