Dear Prof. Gelman: Thanks for providing such a simple, replicable example. I got the same results you describe under Windows XP Pro with: > sessionInfo() R version 2.2.1, 2005-12-20, i386-pc-mingw32
attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: lme4 lattice Matrix "0.995-1" "0.12-11" "0.995-1" Unfortunately, I'm missing something in my attempts to move beyond this. First, I tried "traceback()", which gave me a standard cryptogram, which I couldn't decypher. Then I typed "mcmcsamp" and learned that it consists solely of a call to 'standardGeneric("mcmcsamp")'. The help file for 'standardGeneric' sent me to "?GenericFunctions", which sent me further to "showMethods", which produced the following: showMethods("mcmcsamp") Function "mcmcsamp": object = "mer" object = "lmer" (inherited from object = "mer") Then I confirmed that the object "M1" created by the "lmer" call indeed had class "lmer". From there, I tried several things without success. The help("GenericFunctions") file mentioned 'dumpMethod' and 'dumpMethods'. > dumpMethods("mcmcsamp") # produced nothing I could find. > dumpMethods("mcmcsamp", file="mcmcsamp.R") # produced a file named "mcmcsamp.R" of official length 0 KB # containing nothing, as far as I could tell. > dumpMethods("mcmcsamp", file="mcmcsamp.R", signature="lmer") # also generated an empty file. > dumpMethod("mcmcsamp", "lmer") [1] "mcmcsamp.lmer.R" # Produced a file 'mcmcsamp.lmer.R' in the working directory, #which contained only the following: setMethod("mcmcsamp", "lmer", NULL ) I also tried 'trace(mcmcsamp)' and 'trace("mcmcsamp", browser, exit = browser)' before running the function giving the error message. Nothing I saw from that seemed useful. I'd be much obliged to anyone who could help understand how I could diagnose this issue. Best Wishes, Spencer Graves Andrew Gelman wrote: > I am working with lmer() in the latest release of Matrix, doing various > things including writing a function called mcsamp() that acts as a > wrapper for mcmcsamp() and automatically runs multiple chains, diagnoses > convergence, and stores the result as a bugs object so it can be > plotted. I recognize that at this point, mcmcsamp() is somewhat of a > placeholder (since it doesn't work on a lot of models) but I'm sure it > will continue to be improved so I'd like to be able to work with it, as > a starting point if necessary. > > Anyway, I couldn't get mcmcsamp() to work with the saveb=TRUE option. > Here's a simple example: > > y <- 1:10 > group <- rep (c(1,2), c(5,5)) > M1 <- lmer (y ~ 1 + (1 | group)) # works fine > mcmcsamp (M1) # works fine > mcmcsamp (M1, saveb=TRUE) > > This last gives an error message: > > Error in "colnames<-"(`*tmp*`, value = c("(Intercept)", "log(sigma^2)", : > length of 'dimnames' [2] not equal to array extent > > Thanks for your help. > Andrew > ______________________________________________ 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