OpenMx Help
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).
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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.
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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')
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.
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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
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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)
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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_
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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)
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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?
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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.
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