Published on *OpenMx* (http://openmx.psyc.virginia.edu)

By *Dorothy Bishop*

Created *03/24/2010 - 12:47*

Wed, 03/24/2010 - 12:47 — Dorothy Bishop [1]

This is an elementary nonurgent question but an answer would help me understand OpenMx better.

In trying to teach myself a bit more I have been playing around with a couple of multivariate ACE twin scripts. There's one by Hermine Maes that I downloaded from:

http://www.vipbg.vcu.edu/~vipbg/OpenMx/MultivariateTwin_MatrixRaw.R [2]

and another I think by Steve Boker that is in the slides from

http://www.vipbg.vcu.edu/~vipbg/OpenMx/OpenMxSession8.pdf [3]

They differ in how they specify covariance matrices for the saturated model:

The Maes script gives:

mxMatrix( type="Lower", nrow=ntv, ncol=ntv, free=TRUE, values=pathstartvalue, name="CholMZ" ),

mxAlgebra( expression=CholMZ %*% t(CholMZ), name="ExpCovMZ" ),

mxAlgebra( expression=diag2vec(ExpCovMZ), name="ExpVarMZ"),

The Boker script gives:

mxMatrix( "Diag", ntv, ntv, free=T, values=meanestvalue, lbound=.001, name="EVmzf" ),

mxMatrix( "Stand", ntv, ntv, free=T, values=.5, lb=-.99, ub=.99, name="ERmzf" ),

mxAlgebra( expression= EVmzf %*% ERmzf %*% EVmzf, name="ECmzf" ),

I assume they are mathematically equivalent, with the Boker script estimating the correlation matrix (ERmzf) with the Stand matrix.

My problem is that when I try to run the Boker script, I get:

Error: The job for model 'multi' exited abnormally with the error message: Expected covariance matrix is not positive definite

I understand what the error message is saying – I'm just wondering why you'd want to estimate the covariance matrix this way, if it can give a 'not positive definite' result?

Or maybe this was an example to demonstrate the perils of not using a regular Cholesky decomposition ?

It's possible that the dataset I'm using is not the one it was written for.

**Links:**

[1] http://openmx.psyc.virginia.edu/users/dorothy-bishop

[2] http://www.vipbg.vcu.edu/~vipbg/OpenMx/MultivariateTwin_MatrixRaw.R

[3] http://www.vipbg.vcu.edu/~vipbg/OpenMx/OpenMxSession8.pdf

[4] http://openmx.psyc.virginia.edu/thread/465

[5] http://openmx.psyc.virginia.edu/thread/450

[6] http://openmx.psyc.virginia.edu/forums/openmx-help/openmx-general-help