Thu, 09/03/2009 - 12:44

running a tri-bivariate ACE model, and the results can be all over the show (with no convergence warnings), depending on the start values: for instance C wandering from .998 to .054 for one variable.

Any thoughts?

Here are the results, and script fragment

Results starting at a, c, and e at .6

A1 A2 A3 C1 C2 C3 E1 E2 E3 var1 0.284 NA NA 0.282 NA NA 0.434 NA NA var2 -0.292 0.027 NA 0.998 0.434 NA 0.294 0.539 NA var3 0.224 -0.028 0.206 0.366 0.458 0.196 0.411 0.570 0.598 [1] 7550.711

Now, starting at a=.6, c=.3, e=.4

A1 A2 A3 C1 C2 C3 E1 E2 E3 var1 0.560 NA NA 0.006 NA NA 0.434 NA NA var2 0.652 0.343 NA 0.054 0.118 NA 0.294 0.539 NA var3 0.636 0.477 0.277 -0.047 -0.047 0.124 0.411 0.570 0.598 [1] 7550.711

relevant fragment

share = mxModel("share", mxMatrix("Lower", nrow=nVar, ncol=nVar, free=TRUE, values=.6, name="a", byrow=TRUE), # Additive genetic path coefficient mxMatrix("Lower", nrow=nVar, ncol=nVar, free=TRUE, values=.6, name="c", byrow=TRUE), # Common environmental path coefficient mxMatrix("Lower", nrow=nVar, ncol=nVar, free=TRUE, values=.6, name="e", byrow=TRUE), # Unique environmental path coefficient # Multiply by each path coefficient by its inverse to get variance component mxAlgebra(a %*% t(a), name="A"), # additive genetic variance mxAlgebra(c %*% t(c), name="C"), # common environmental variance mxAlgebra(e %*% t(e), name="E") # unique environmental variance ) mzModel = mxModel(share, name="MZ", expMZMeans, # MZ ACE algebra mxAlgebra(rbind (cbind(A+C+E , A+C), cbind(A+C , A+C+E)), dimnames = list(selVars, selVars), name="expCov"), mxData(mzData, type="raw"), mxFIMLObjective("expCov", "expMean") ) dzModel = mxModel(share, name="DZ", expDZMeans, mxAlgebra(rbind (cbind(A+C+E , .5%x%A+C), cbind(.5%x%A+C, A+C+E) ), dimnames = list(selVars, selVars), name="expCov"), mxData(dzData, type="raw"), mxFIMLObjective("expCov", "expMean") ) #Build and Run ACE model twinACEModel = mxModel("twinACE",mzModel, dzModel, mxAlgebra(MZ.objective + DZ.objective, name="twin"), mxAlgebraObjective("twin") ) twinACEFit = mxRun(twinACEModel)

Interestingly, rewriting the script so that it uses three-models so that the MZ and DZ sub-models both do their algebra off a single set of ace and ACE matrices and algebras contained in the third shared model eliminates this instability, with the same solution reliably emerging from diverse starts.

The output fragment you provide indicates strongly that the model is not identified. Different parameter estimates emerge, but the -2lnL is the same. I expect that somehow the information from one group is not being used in the model-fitting.

my error was to assume that there was a global space of matrix names across the supermodel and all contained groups so matrix names acted like labels equating all matrices with the same name to be the same.

The fix here was to use the name of the mz group in the algebra of the dz group, linking the two algebras to the same underlying matrices.

It will important to clearly explain the scope of labels and names to users, and that information from different groups has to be imported by using the object's full name, including the originating group.

Easy enough once you know :-)

Hmmm.... That is interesting. We're trying to do the consolidation of the algebra in a smart way. It must be eliminating either some multiplication or a place where your first model had two parameters plus a constraint. I'd need to work through the model step by step and see where the two sets of convariance algebra differ.