polycor package
The reason I was working with a correlation matrix is because I wanted to calculate polychoric correlations first before submitting it to the actual sem command. I was unsure whether R would use polychoric correlations when indicating which of the variables are ordered. A final question on the sample.cov=hetcor command. Does this not assume it is a sample variance-covariance rather than a correlation matrix (as calculated using the polycor package)?
Yes. Sample.cov should always be a covariance matrix, not a correlation matrix. It is pretty useless for categorical data.
I also tried using the command (thanks for the tip!)
sem.cdu= sem(cdu, data=germany2009, ordered=c("cdupid", "MERKELLIKE",
"CDULIKE", "MERKELPROX", "CDUPROX"))
but I always get the error result:
semcdu=sem(cdu, data=germany2009, ordered=c("cdupid", "MERKELLIKE",
"CDULIKE", "MERKELPROX", "CDUPROX"), fixed.x=F)
Error in tmp[cbind(REP$row[idx], REP$col[idx])] <- partable$free[idx] :
NAs are not allowed in subscripted assignments
It looks like you have some issues with your model specification. Could you remove all '~~' statements and try again? If the problem remains, please send me your R script, and a snippet of the data (just enough to replicate the error). Yves.