[R] polycor package

[yrosseel]

> 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.