Hi Matt - I think you are right, some of the variables I was marking as nominal had a large number of categories.  When I reclassified these variables I could get Amelia to run. My problem now seems to be that the resulting matrices are non-invertible, though I assume that is a problem with my starting dataset rather than anything to do with Amelia (let me know if it might be otherwise).  I ran and pasted the results of your code below, and am using R version 2.10.1 and Amelia 1.2-16. [1] 0 [1] 0 Thanks - Nick On Mon, Apr 26, 2010 at 11:52 AM, Matt Blackwell &lt;blackwel(a)fas.harvard.edu wrote: > Hi Nick, > We need just a bit more information to figure what is going on. Which > version of R and Amelia are you using? > Amelia seems to be having a problem checking to see if your data has > any variables that do not vary. It crashing on this is usually not a > good thing. I would make the following observations. First, Gary is > right that you may have too many variables. Second, it seems that you > are marking a lot of these variables as nominal. Note that this add a > dummy variable for each category of the nominal variable. Thus, if you > had 10 variables, all with 4 categories, that would put an additional > 20 covariates into the imputation model. With the number of nominal > variables you have, that could get problematic. > It might also be helpful if you could post the output to the following R > code: > This will give us a sense for what the invariance of the data looks like. > Cheers, > matt. > On Sun, Apr 25, 2010 at 9:31 AM, Nick Menzies &lt;nmenzies(a)fas.harvard.edu> wrote: > > Hi Matt, I am having trouble implementing Amelia in a dataset of 50,000 > > observations and ~200 variables. > > After running the code: > > a.out1 <- amelia(dataHIV, m = 5, noms = c("v000", "v001", "v003", > > "v004", > > "v006", > >   "v014", "v016", "v101", "v102", "v116", "v113", "v119", "v120", > >   "v121", "v122", "v123", "v124", "v125", "v127", "v128", "v129", > > "religion", "currentmaritalshort", "morethanoneunion", "region", > > "cluster", "v103", "ethny", "radioteleall", "transportall", "country"), > > ords = c("v013", "v106", "v105"), idvars = c("caseid", "idnumber", > > "hivid", > > "hcaseid", "acaseid")) > > I get the output: > > Error in if (sum(non.vary == 0)) { : > >   argument is not interpretable as logical > > In addition: Warning message: > > In FUN(X[[4L]], ...) : NAs introduced by coercion > > I implemented the suggestion made in post below -- I have downloaded and > > am > > using the most recent Amelia II version -- but am still unable to run > > the > > program, even when I trim the dataset down to a small number of > > variables, > > and delete out invariant variables. I also get warnings that some > > nominal > > variables have many categories, but assume this is unrelated > > > http://lists.gking.harvard.edu/lists/amelia_at_lists_gking_harvard_edu/2010… > > Do you have any suggestions? > > Thanks for your help - Nick > > -- > > > Nick Menzies > > nick.menzies(a)gmail.com > > 404 217 1076 > > > > > -- > > > Nick Menzies > > nick.menzies(a)gmail.com > > 404 217 1076 > -- Nick Menzies nick.menzies(a)gmail.com 404 217 1076