sem package and AMOS

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/

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
AMOS.

I hope this helps,
 John

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/

--------------------------------
John Fox, Professor
Department of Sociology
McMaster University
Hamilton, Ontario, Canada
http://socserv.mcmaster.ca/jfox/