OpenMx Help

Posted on
No user picture. jkarch Joined: 03/15/2011

Recommended stable OpenMx Version

I am a bit confused what the latest stable OpenMx Version is. The last news announcement is for 2.0.1, the install script installs 2.2.4 on my linux supercomputer and fails to install 2.2.2 on my mac laptop (see http://openmx.psyc.virginia.edu/thread/3997).

Posted on
Picture of user. carey Joined: 10/19/2009

Funky confidence intervals

Are the default confidences intervals for mxCI 95% or 90%? Or is there something funky in the documentation of mxCI? My understanding of a 95% confidence interval is that it is equivalent to a two-tailed test with alpha = .05. That is, it delimits the 2.5% most extreme values at the low end and the 2.5% most extreme values at the high end, leaving the 95% most likely values between the confidence intervals.

Posted on
No user picture. jkarch Joined: 03/15/2011

OpenMx 2.0.1 installation fails for R 3.2.0 on OS X

If I do

source('http://openmx.psyc.virginia.edu/getOpenMx.R')

the result is

You are now installing OpenMx 2.0.
OpenMx 2.0 has a number of exciting new features, described in more detail at
http://openmx.psyc.virginia.edu/2014/10/openmx-version-20-officially-released
and in the OpenMx User's Guide.
Most OpenMx-1.4 scripts will work under OpenMx 2.0, but users who wish to download and install the previous stable version can run
source('http://openmx.psyc.virginia.edu/getOpenMx1.R')

Posted on
No user picture. bhuibregtse Joined: 03/06/2014

NA values hit for thresholds

I am using a modified script for a bivariate twin analysis with two dichotomous variables.

I am stuck with the error message: "Error: In model 'Sat' I was expecting 1 thresholds in column 'nssi1' of matrix/algebra 'DZf.expThresDZf' but I hit NA values after only 0 thresholds. You need to increase the number of thresholds for 'nssi1' and give them values other than NA"

Another user had a similar issue- see previous discussion: (http://openmx.psyc.virginia.edu/thread/2953). However, I do not believe my problem has to do with the mxFactor command, factors in general, or NAs in my data.

Posted on
Picture of user. carey Joined: 10/19/2009

mxFitFunctionAlgebra question

Attached are two outputs, one from OpenMx 2.0.1.4157 using OS X on a Mac and the other from OpenMx 2.2.2 on Red Hat Linux. In both situations the models converge when I use mxExpectationNormal and mxFitFunctionML. But when I manually set the fit function to -log(likelihood) using mxFitFunctionAlgebra, mxRun crashes in both operating systems (albeit with different errors).
Am perplexed.
Greg

Posted on
Picture of user. carey Joined: 10/19/2009

mxExpectationGREML error

Why does this give an error when the code is taken directly from the documentation to mxExpectationGREML?

> require(OpenMx)
> mxVersion()
OpenMx version: 2.0.1.4157
R version: R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin10.8.0
Default optimiser: NPSOL
> # the following are the first three commands from the Examples from
> # the documentation to mxExpectationGREML
> dat <- cbind(rnorm(100),rep(1,100))
> colnames(dat) <- c("y","x")
>
> ge <- mxExpectationGREML(V="V",yvars="y",Xvars=list("X"),addOnes=FALSE)

Posted on
No user picture. Anbupalam Joined: 09/01/2012

Installation under Linux

I get the following error message when I tried to install OpenMx through R 3.1.1 or R 3.2.0

OpenMx/libs/OpenMx.so: undefined symbol: npoptn_

Posted on
No user picture. CM Joined: 05/12/2015

speed issue with mxRun

Dear All,

I am writing on behalf of a user of our local cluster.

The OpenMX install is fairly recent (just with source('http://openmx.psyc.virginia.edu/getOpenMx.R' in R). The script in question is rather long and starts with loading OpenMX:

require(OpenMx)

and subsequently snowfall:

library(snowfall)
sfInit(parallel = T, cpus = 64)
sfLibrary(OpenMx)

Posted on
No user picture. jacobucc Joined: 05/27/2014

Specifying Unique mxFitFunction

Hi,
I am new to 2.0 and am playing around with specifying a non-standard fit function, and have hit some road bumps in trying to start with specifying the ML fit through mxFitFunctionAlgebra. Attached is the reproducible script. Error message is:

Error: The job for model 'One Factor' exited abnormally with the error message: MxComputeGradientDescent: fitfunction One Factor.fitfunction is not finite ()

If mxFitFunctionAlgebra() is used, does it have to include a gradient specification?

Posted on
No user picture. Lux Whitehaven Joined: 02/02/2015

Restricted Model Cholesky; how to drop/fix parameters?

Hello everyone,

I'm a graduate student currently learning OpenMX, and I am unfortunately still a novice at OpenMX and genetic modeling in general. I've so far successfully run multivariate Cholesky analyses with OpenMX in R studio, and gotten interpretable data.

However, I am now trying to drop parameters on my current Cholesky model, to get a "best fit" reduced model for my data. I am having trouble understanding how I might do this; I understand it would involve fixing certain parameters at zero, but given my code, I am completely at a loss as to how I might go about this.