OpenMx Developer Forums

We talked about this at the beginning of the summer, but it was never followed up on, so now, instead of always going to the about piebald page when the logo is clicked as Michael had it, that behavior only happens on the front page. Otherwise it takes you home, as users generally expect.

Here are the minutes from our first meeting after the OpenMx 1.0 release. We made a list of objectives for the short term. These tasks involve code cleanup and rewriting some components of the library.

Objectives:

• rewrite mxEval. Handle definition variables.
• correctly transform cbind(), rbind(), and t() into matrix objects behind the scenes
• error handling in the backend
• pass algebra dependency graph to the backend
• mxRowObjective - complete NA reduction algebra

In OpenMx 1.0, it will be possible to use square brackets inside MxMatrix labels only when the row and column arguments of the square brackets are numeric literal values. Specifically, if you wish to use a definition variable in either the row or column argument, then you must place that reference in an algebra and then reference the algebra from the MxMatrix label.

As we get close to the release of OpenMx 1.0, it is time to begin compiling a list of the new features we would like to see in the post-1.0 development cycle. I'll start the discussion with two features that have been on my mind.

Rewrite of mxEval

I'm trying to spec out a least-squares based optimizer using the mxAlgebraObjective, but I've been unable to include data in an algebra. Is that possible/feasible, or do I need to move to mxRObjective?

Hi,

I have been learning how to structure the analyses and scripts for examining twin data and I am having some trouble with 'adding a covariate'. When I run the following code.(which I didn't write)...............

mxModel("Sibs",
mxMatrix( type="Lower", nrow=ntv, ncol=ntv, free=TRUE, values=1, name="Chol" ),
mxAlgebra( expression=Chol %*% t(Chol), name="expCov" ),

#regressing out covariate
mxMatrix( type="Full", nrow=1, ncol=ntv, free=TRUE, values=0, labels="intercept", name="grandMean" ),

folks,
short and sweet: how can OpenMx access user-written functions and functions from other packages? e.g., i would like to access alpha and sumx in the following code:

alpha <- .3
sumx <- function (x) {
sum(x)
}
x <- c(1, 2, 3)
testModel <- mxModel("testModel", mxAlgebra(expression="alpha * sumx(x)", name="test"))
mxRun(testModel)

Example:

Running modelThreshReparam3
Error: The expected covariance matrix associated with the FIML objective in model 'modelThreshReparam3' is not of the same length as the dimnames provided by the objective function.

This should read:

Running modelThreshReparam3
Error: The expected covariance matrix associated with the FIML objective in model 'modelThreshReparam3' is not of the same length as the dimnames provided by the objective function.
The expected covariance matrix is of dimension 4x4, but the length of the dimnames in the objective function is 3

Hi

I tried running a model with vs. without a feedback loop. There is some penalty if there's feedback in the model, but not as much as I would have expected. This is in a system with 48 latent+observed variables, so I would have thought that inverting 2 48x48 matrices every iteration would have slowed things down a lot more. But perhaps the inversion routine is pretty smart about cases like this. Script attached.

> system.time(twinACEFit <- mxRun(twinACEModel))
Running twinACE
user system elapsed
239.818 0.429 240.693
> #summary(twinACEFit)
>

Is there a function to output an mxModel to a file? I was running a simulation, and rather than extracting a few specific elements, I wanted to save the results from each model fit to a file. I tried dput(). While a file was written, I can not retrieve it using dget(). My ideal would be to be able to save the entirety of mxModel for future reference. Ideas?