OpenMx Help

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Picture of user. neale Joined: 07/31/2009

Improving OS X OpenMx Performance with Default libRblas

We have found that the default blas (basic linear algebra system) libraries supplied with R for MAC OS X have poor performance. Specifically, the following three commands, executed as root in a Terminal.app window reduces OpenMx execution time by 75% in some cases (ymmv).

cd /Library/Frameworks/R.framework/Libraries
sudo rm libRblas.dylib
sudo ln -s libRblas.0.dylib libRblas.dylib

Note that these commands simply reconfigure the link, they don't actually delete any libraries. To *undo* these commands one could do the following:

cd /Library/Frameworks/R.framework/Libraries

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Picture of user. Mike Cheung Joined: 10/08/2009

Installing OpenMx in Fedora distribution

I have observed this for a while in two 32-bit and one 64-bit computers with Fedora 13.

When I installed OpenMx inside R with a root account by source('http://openmx.psyc.virginia.edu/getOpenMx.R'), I got the following errors:

** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/usr/lib/R/library/OpenMx/libs/OpenMx.so':
/usr/lib/R/library/OpenMx/libs/OpenMx.so: cannot restore segment prot after reloc: Permission denied
ERROR: loading failed
* removing ‘/usr/lib/R/library/OpenMx’

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Picture of user. Mike Cheung Joined: 10/08/2009

Versions 0.9.0 vs. 0.5.2

Hello all,

I am fitting some variance known models (akin to meta-analysis). To handle models with possible covariates, I use a RAM model. The results based on 0.5.2 are comparable to those based on other statistical packages. After upgraded to 0.9.0, the results look odd.

The followings are an example. The -2LL of the 0.5.2 and 0.9.0 versions are 27.79916 and 29.02565, respectively. Any suggestions are highly appreciated. Thanks.

Regards,
Mike

yi <- c(-0.264,-0.230,0.166,0.173,0.225,0.291,0.309,0.435,0.476,0.617,0.651,0.718,0.740,0.745,0.758,0.922,0.938,0.962,1.522,1.844)

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No user picture. Simo Joined: 07/25/2010

OpenMx script - error message

Hi there,

I am new to OpenMx and trying to fit a factor model. The main part of the script used is shown below:

> manifests <-names(hetcor_T)
> latents <-c("F1","F2","F3","F4")
> twofactorModel<-mxModel(name = "Four Factor Model Path Specification",type="RAM",manifestVars = manifests, latentVars = manifests,
+ mxData(observed=cov(hetcor_T),type="cov",numObs=709),
+ # residual variances
+ mxPath(from= manifests, arrows=2), # latent variances and covariance
+ mxPath(from= latents, arrows=2), # factor loadings for business performance measure variables
+ mxPath(
+ from=c("F1"),

Posted on
No user picture. joespher Joined: 07/28/2010

what's the estimator in OpenMx?

Dear all:
I'm a new learner of OpenMX and R , I want to use it to do simple SEM analysis, but I can't find the estimator information in OpenMxUserGuide. please tell me how can I find and how can I understand the estimator in OpenMx .

Posted on
Picture of user. mspiegel Joined: 07/31/2009

parameters of 1 factor factor examples

I'm posting a link to a comment from one of the news updates, because those comments appear without a listing in the "Recent Threads" panel on the right-hand side of the page.

http://openmx.psyc.virginia.edu/2010/08/openmx-050

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No user picture. newsomjr Joined: 10/13/2009

Error: The expected covariance matrix associated with the FIML objective in model 'MZ' is not of the same length as the dimnames

I received this error when trying to run a latent growth curve model:

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

I used the traceback() function to try to determine the error and received the following output:

9: stop(msg, call. = FALSE)
8: updateObjectiveDimnames(.Object, job, model@name, "FIML")
7: genericObjModelConvert(flatObjective, job, model, namespace,
flatJob)
6: genericObjModelConvert(flatObjective, job, model, namespace,
flatJob)

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No user picture. rlucas Joined: 11/17/2009

Should version 0.5 be slower on some models?

I have been running some models that decompose multi-wave data into a stable trait component, an autoregressive trait component, and a state component. I have eight waves, with three indicators at each wave, 600 observations, and I'm using raw data (and there are missing data). With the data I have, these models (and some variants) can take a little while to run. But I've noticed that they actually run considerably slower with version .5.0 than with .3.0 (I hadn't upgraded until .5.0 came out).

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Picture of user. Mike Cheung Joined: 10/08/2009

Jacobian matrix

Hi,

I am trying to implement the Satorra-Bentler robust standard error. It requires the Jacobian matrix in the calculations. Apparently, the Jacobian matrix is called "cJac" in npsolWrap.c. I would like to see whether it is possible to access "cJac" in OpenMx. Thanks in advance.

Regards,
Mike

Posted on
Picture of user. smedland Joined: 08/04/2009

Code mistake or Bug?

Hi
I am teaching tomorrow and I have a werid glich in my code that I can't resolve
I am modeling the correlations between 3 variables in a very straight forward script. I then want to drop one of the correlations. the difference in fits between the full model and the reduced model is huge and the correlation is not being set to zero
Where have I gone wrong - I can't spot it typo(?)
thanks
Sarah

data(twinData)
selVars <- c('wt1','ht1','bmi1')
nv <- 3
factorData <- subset(twinData, zyg<=5, selVars)

SatModel <- mxModel("saturated",
mxModel("Cor",