
I think the brms package (https://github.com/paulbuerkner/brms) or the blavaan package (http://ecmerkle.github.io/blavaan/) have support for SEM. I've never done it myself, so I unfortunately can't give you any direction for that in particular. However, I have used stan in multilevel metaanalysis regression (combining multiple CRISPRa experiments to find determinants of CRISPRa activity, see https://github.com/timydaley/CRISPRasgRNAdeterminants/blob/master/metaAnalysis/NeuronAndSelfRenewalMetaMixtureRegression.Rmd) and had some success.

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I think the brms package (https://github.com/paulbuerkner/brms) or the blavaan package (http://ecmerkle.github.io/blavaan/) have support for SEM. I've never done it myself, so I unfortunately can't give you any direction for that in particular. However, I have used stan in multilevel metaanalysis regression (combining multiple CRISPRa experiments to find determinants of CRISPRa activity, see https://github.com/timydaley/CRISPRasgRNAdeterminants/blob/master/metaAnalysis/NeuronAndSelfRenewalMetaMixtureRegression.Rmd) and had some success.