[R] sem package and AMOS

John Fox jfox at mcmaster.ca
Mon Feb 2 23:45:46 CET 2009

Dear Anthony,

sem() does FIML estimation, not 2SLS, and so it's hard to understand
why you're getting "nearly identical" parameter estimates but very
different coefficient standard errors and model chi-squares. In fact,
unless the problem is very ill-conditioned, the parameter estimates
should be the same within rounding error, as should the model
chi-square. There is some room for small differences in the standard
errors -- sem() uses a numerical Hessian and I'm not sure what AMOS
does -- but large differences are indicative of some problem. 

I suspect that you're not fitting quite the same model in sem() and

I hope this helps,

On Mon, 02 Feb 2009 14:50:26 -0600
 Anthony Dick <adick at uchicago.edu> wrote:
> Hello-
> I am using R to build my initial models, but need to use AMOS to
> compare the models of two groups (adults vs. kids). The problem is I
> am getting different results with R and AMOS for the initial models
> of the separate groups (and the R results make more sense).
> The parameter estimates (path coefficients and variances) from both
> programs are nearly identical, but the model chi-squares (and
> significance estimates of the parameter estimates) are different. I
> am using Maximum Likelihood in AMOS. R I think defaults to
> two-stage-least squares estimate, and AMOS 16 does not implement
> 2SLS.
> I am using fMRI data, so the error variances are likely correlated,
> and the data non-normal to varying degrees. Is 2SLS the better way to
> go for these kinds of data?
> Is there a way to change the default method for R sem? I couldn't
> find this in the ?help. I note I have run some of the AMOS examples
> in R and have gotten identical results across platforms, so I believe
> the problem is not in specifying things incorrectly across platforms.
> Also, the dfs are identical for both analyses. I must use AMOS to do
> model comparison (and thus maximum likelihood), but would like to
> achieve similar results across platforms for the basic models before
> I proceed, and would like to track down the reason for the
> difference.
> Thanks,
> Anthony
> -- 
> Anthony Steven Dick, Ph.D.
> Post-Doctoral Fellow
> Human Neuroscience Laboratory
> Department of Neurology
> The University of Chicago
> 5841 S. Maryland Ave. MC-2030
> Chicago, IL 60637
> Phone: (773)-834-7770
> Email: adick at uchicago.edu
> Web: http://home.uchicago.edu/~adick/
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John Fox, Professor
Department of Sociology
McMaster University
Hamilton, Ontario, Canada

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