OpenMx Help
CharlesD
Joined: 04/30/2013
Returned matrices (expCov, expMean, A,S, etc) only reflect last row of data
Hi folks. I mentioned this to Joshua who asked me to post it here for further input. While wondering about some strange output in one of my functions the other day I discovered that the matrices output by openmx only reflect the last calculated row of data. I believe this only becomes evident when definition variables are used, such that the A S or M matrices (when using RAM format, though I don't believe it's limited to this case) depend on the definition variable.
cvanhulle
Joined: 05/07/2010
syntax problem with saturated model
Hi, I modified a twin model so that I could look at the saturated model. The twin model runs fine, but I get the following error with the saturated model
Error in mxModel("SAT", mxMatrix(type = "Full", nrow = ntv, ncol = ntv, :
argument is missing, with no default
For some reason R stops reading after ncol=ntv. The rest of the syntax is below:
mxMatrix( type="Full", nrow=ntv, ncol=ntv, free=TRUE, values=.6, label=c("dz11","dz21","dz22"), name="MZL" ),
- Read more about syntax problem with saturated model
- 5 comments
- Log in or register to post comments
jkarch
Joined: 03/15/2011
Obtain number of Objective function evaluations
Hi,
I am interested in obtaining both the number of major iterations and the overall number of objective function evaluations (how many times is the log likelihood and its gradient computed).
I found model@output$iterations and model@output$evaluations. model@output$iterations is the number of major iterations. model@output$evaluations contains a vector with two integer entries. Does somebody know what the entries are?
saralonn
Joined: 12/11/2012
Fail to install OpenMx on Ubuntu
I am trying to install OpenMx under R 3.0.2 on Linux (Ubuntu) but without success and get the following error message, could you please help me understand what is the problem?
Have tried to run it both as root and as an ordinary user. With the same results during the build process.
The config.log file from the configure build script is attached.
Below you find the output from when I try to download, build and install OpenMx and if I run the configure script manually ( ./configure) the build process will result in the same error.
sysadmin@cpf-calc1:/var/run$ sudo -i R
- Read more about Fail to install OpenMx on Ubuntu
- 2 comments
- Log in or register to post comments
rpmb
Joined: 05/18/2014
R 3.1.0 (OS X Mavericks) Install
Followed the installation procedures for OS X Mavericks R 3.1.0 (re: downloaded R-3.1.0-snowleopard.pkg), but got this error when trying to load the package:
> source('http://openmx.psyc.virginia.edu/getOpenMx.R')
trying URL 'http://openmx.psyc.virginia.edu/sequential/bin/macosx/contrib/3.1/OpenMx_1.4-3059.tgz'
Content type 'application/x-gzip' length 3952270 bytes (3.8 Mb)
opened URL
==================================================
downloaded 3.8 Mb
The downloaded binary packages are in
- Read more about R 3.1.0 (OS X Mavericks) Install
- 2 comments
- Log in or register to post comments
CarolKan
Joined: 04/17/2014
mxFactor command
Dear all
I am trying to run a saturated model but there is something wrong in the way I have have ordered the variables, as I received this error message:
# Error: In model 'Sat' column 'dm1' is not an ordered factor. Use mxFactor() on this column.
So, I did the following after the reshape command:
TwDEP_DM <- reshape(DEP_DM, idvar = c("PAIRID", "ZYG"), timevar = "TVAB", direction = "wide")
colnames(TwDEP_DM) <- c('PAIRID', 'ZYG', 'dm1', 'dep1', 'age1','dm2', 'dep2', 'age2')
TwDEP_DM$dm1 <- mxFactor(TwDEP_DM$dm1, levels=c(0:2), ordered = TRUE)
- Read more about mxFactor command
- 5 comments
- Log in or register to post comments
CarolKan
Joined: 04/17/2014
Q
Q
- Read more about Q
- 6 comments
- Log in or register to post comments
CarolKan
Joined: 04/17/2014
OpenMX installation on R version 3.1.0 Mac
Dear all
I am a new user to OpenMX and cannot download it onto the new version of R (see error message below) and I do not know how to download the older version of R (ie. 3.0) onto my Mac.
Any help will be much appreciated,
Carol
> source('http://openmx.psyc.virginia.edu/getOpenMx.R')
Warning: unable to access index for repository http://openmx.psyc.virginia.edu/sequential/bin/macosx/contrib/3.1
package ‘OpenMx’ is available as a source package but not as a binary
- Read more about OpenMX installation on R version 3.1.0 Mac
- 6 comments
- Log in or register to post comments
brandmaier
Joined: 02/04/2010
Standardized estimates under equality constraints
I was wondering how OpenMx treats standardized estimates under equality constraints.
I ran a linear latent growth curve model in OpenMx and constrained all residual variances to be equal. Not surprisingly, they all get to be the same unstandardized estimate. However, OpenMx reports only a single standardized estimate for the residual, which happens to be the one associated with the first observation. Even if the unstandardized estimates are constrained to be equal, the unstandardized ones need not be and in reality seldom are the same.
[code]
brandmaier
Joined: 02/04/2010
Sticky issue: Problems with tar
When installing OpenMx on OSX 10.9.2, I ran into the following error:
"tar: Option --delete is not supported"
Particularly, this error happens after successful compilation when the npsol-related files are deleted from the resulting gzip file. On my machine, tar does in fact not support the "--delete" option. For Mac users, MacPorts provides gnutar, which does the job. However, with the default path of MacPorts, one needs to explicitly create another symlink:
sudo ln -s /opt/local/bin/gnutar /usr/bin/gnutar
and change line 268 in the Makefile to:
- Read more about Sticky issue: Problems with tar
- 1 comment
- Log in or register to post comments