Is there a reason you can't use the mxCI() function? It computes confidence intervals based on the profile likelihood. That is, it varies the free parameters and monitors the change in likelihood to get the confidence intervals based on changing the likelihood by a certain amount. It handles missing data just fine because it's using FIML, the same as the estimation routine.
I will consider it given that it takes the missing values into account, instead of using the expected covariance matrix for the parametric bootstrapping. Thank you!
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