OpenMx General Help
http://openmx.ssri.psu.edu/taxonomy/term/7/0
enStaying informed with OpenMx
http://openmx.ssri.psu.edu/thread/470
<div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>The easiest way to keep up with the latest changes to the OpenMx software is to subscribe to receive email notification of any news updates. Assuming that you are logged in, click on the "My account" link on the left-hand panel of your screen. Next click on "Subscriptions" and then "Content types". Enable the checkbox for "News" and click on "Save". Once you have followed these steps, you will start receiving an email whenever something is posted under the "Recent News" section of the website (the top left panel, underneath the Guinea Pig). If you are concerned about inbox cluttering, it's ok you can expect a fairly low frequency of announcements.</p>
</div></div></div><div class="field field-name-taxonomy-forums field-type-taxonomy-term-reference field-label-above"><div class="field-label">Forums: </div><div class="field-items"><div class="field-item even"><a href="/forums/openmx-help/openmx-general-help">OpenMx General Help</a></div></div></div>Tue, 30 Mar 2010 14:24:47 +0000mspiegel470 at http://openmx.ssri.psu.eduWelcome to the OpenMx General Help Forum
http://openmx.ssri.psu.edu/thread/17-welcome-openmx-general-help-forum
<div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>This forum is designed for general questions about how to use OpenMx. If you can't find another place where your question fits, then this is the place to be!</p>
</div></div></div><div class="field field-name-taxonomy-forums field-type-taxonomy-term-reference field-label-above"><div class="field-label">Forums: </div><div class="field-items"><div class="field-item even"><a href="/forums/openmx-help/openmx-general-help">OpenMx General Help</a></div></div></div>Fri, 31 Jul 2009 18:51:09 +0000Steve17 at http://openmx.ssri.psu.eduPower estimation for the detection of rG and rE
http://openmx.ssri.psu.edu/thread/4195
<div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>How can one estimate the power for the detection of significant rG and rE in multivariate Cholesky models?</p>
<p>Specifically, the analysis employed a trivariate Cholesky (AE providing the best fit, with all significant rGs, and one significant rE). The CIs have been calculated for all estimates. The sample is on the small side: 200 same-sex pairs (half MZ, half DZ) and may have been underpowered for the other smaller rEs but I’m not sure what size effect I had enough power to detect. </p>
<p>I can estimate power for variance components in univariate decomposition models but cannot find anything specific to multivariate models or correlations. Any advice or script to get a power estimate specific to correlations would be super helpful!</p>
<p>Thanks in advance,<br />
M</p>
</div></div></div><div class="field field-name-taxonomy-forums field-type-taxonomy-term-reference field-label-above"><div class="field-label">Forums: </div><div class="field-items"><div class="field-item even"><a href="/forums/openmx-help/openmx-general-help">OpenMx General Help</a></div></div></div>Thu, 20 Oct 2016 23:41:48 +0000Marianna4195 at http://openmx.ssri.psu.eduHow to set the value of a computed parameter to that computed value?
http://openmx.ssri.psu.edu/thread/4181
<div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>Is there a function to put the computed value of all parameters determined by a bracket address (e.g. var[1,1] ) into the appropriate values cell(s) in the model?</p>
<p>Background and use-case: OpenMx allows us to use labels to set the value of a parameter (matrix cell). Here's a RAM model where I insert the value of covXY into the row 2, column1 of the symmetric path (S) matrix: </p>
<p><div class="geshifilter"><pre class="rsplus geshifilter-rsplus" style="font-family:monospace;">m1$S
$labels
x y
x <span style="color: #ff0000;">"x_with_x"</span> <span style="color: #ff0000;">"covXY[1,1]"</span>
y <span style="color: #ff0000;">"covXY[1,1]"</span> <span style="color: #ff0000;">"y_with_y"</span> </pre></div></p>
<p><div class="geshifilter"><pre class="rsplus geshifilter-rsplus" style="font-family:monospace;">$values
x y
x <span style="color: #ff0000;">1.198632</span> <span style="color: #ff0000;">0.000000</span>
y <span style="color: #ff0000;">0.000000</span> <span style="color: #ff0000;">2.018483</span></pre></div></p>
<p>For summary and plot (in umx) the x-y covariance path is MIA. That zero should in fact be .97, as we can verify with <span class="geshifilter"><code class="rsplus geshifilter-rsplus">mxEval<span style="color: #080;">(</span>covXY<span style="color: #080;">[</span><span style="color: #ff0000;">1</span>,<span style="color: #ff0000;">1</span><span style="color: #080;">]</span>, m1<span style="color: #080;">)</span></code></span>.</p>
<p>Now, I can mxEval the relevant parameters, and get the right answer, and even manually push this to the correct place. But is there an "update computed cells" function to do all this automatically?</p>
</div></div></div><div class="field field-name-taxonomy-forums field-type-taxonomy-term-reference field-label-above"><div class="field-label">Forums: </div><div class="field-items"><div class="field-item even"><a href="/forums/openmx-help/openmx-general-help">OpenMx General Help</a></div></div></div>Sat, 03 Sep 2016 16:59:23 +0000tbates4181 at http://openmx.ssri.psu.eduRmpi
http://openmx.ssri.psu.edu/thread/4130
<div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>I am trying to parallelize OpenMx on a computing cluster at my university. I'm using Rmpi, and I keep getting the same error: </p>
<p>Error in { : task 18 failed - "job.num is at least 2."<br />
Calls: %dopar% -> <anonymous><br />
Execution halted<br />
--------------------------------------------------------------------------<br />
mpirun has exited due to process rank 0 with PID 1077 on<br />
node compute-0-11.local exiting improperly. There are two reasons this could occur:</anonymous></p>
<p>1. this process did not call "init" before exiting, but others in<br />
the job did. This can cause a job to hang indefinitely while it waits<br />
for all processes to call "init". By rule, if one process calls "init",<br />
then ALL processes must call "init" prior to termination.</p>
<p>2. this process called "init", but exited without calling "finalize".<br />
By rule, all processes that call "init" MUST call "finalize" prior to<br />
exiting or it will be considered an "abnormal termination"</p>
<p>This may have caused other processes in the application to be<br />
terminated by signals sent by mpirun (as reported here).<br />
--------------------------------------------------------------------------</p>
<p>Googling led me to this website: https://github.com/snoweye/Rmpi_PROF/blob/master/R/Rparutilities.R. Evidently "job.num is at least 2" is given when mpi.comm.size(comm) - 1
</p><p>Does anyone know why this is happening? I've tried getting OpenMx to not parallelize on its own and I've tried using OpenMx to do the parallelization as opposed to another package, and neither works. What am I doing wrong?</p>
</div></div></div><div class="field field-name-taxonomy-forums field-type-taxonomy-term-reference field-label-above"><div class="field-label">Forums: </div><div class="field-items"><div class="field-item even"><a href="/forums/openmx-help/openmx-general-help">OpenMx General Help</a></div></div></div>Tue, 19 Apr 2016 00:36:43 +0000jonno3124130 at http://openmx.ssri.psu.eduStandard Errors versus Confidence Intervals
http://openmx.ssri.psu.edu/thread/4129
<div class="field field-name-upload field-type-file field-label-hidden"><div class="field-items"><div class="field-item even"><table class="sticky-enabled">
<thead><tr><th>Attachment</th><th>Size</th> </tr></thead>
<tbody>
<tr class="odd"><td><span class="file"><img class="file-icon" alt="Binary Data" title="application/octet-stream" src="/modules/file/icons/application-octet-stream.png" /> <a href="http://openmx.ssri.psu.edu/sites/default/files/example_0.R" type="application/octet-stream; length=2587" title="example.R">example.R</a></span></td><td>2.53 KB</td> </tr>
<tr class="even"><td><span class="file"><img class="file-icon" alt="Binary Data" title="application/octet-stream" src="/modules/file/icons/application-octet-stream.png" /> <a href="http://openmx.ssri.psu.edu/sites/default/files/fake.data_.R" type="application/octet-stream; length=8143" title="fake.data_.R">fake.data_.R</a></span></td><td>7.95 KB</td> </tr>
</tbody>
</table>
</div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>When I run this code (a threshold model for ordinal data), the standard errors are incredibly large but the confidence intervals are relatively narrow. Are any of the results trustworthy? I've tried simplifying the thresholds (using labeling to reduce the number of parameters) but it doesn't help. I'm not sure why this data is so hard to model.</p>
<p>If I treat the ordinal data as if it were quantitative, I have no trouble fitting a common factor model.</p>
<p>I've also noticed that when I used mxGenerateData, the resulting data is noticeably different from the original. The original ordinal data goes from 0 to 9. mxGenerateData changes this to 1 to 10 - which I could live with, but the percentage of 1s is MUCH larger than the percentage of 0s for each of the seven ordinal variables.</p>
</div></div></div><div class="field field-name-taxonomy-forums field-type-taxonomy-term-reference field-label-above"><div class="field-label">Forums: </div><div class="field-items"><div class="field-item even"><a href="/forums/openmx-help/openmx-general-help">OpenMx General Help</a></div></div></div>Mon, 18 Apr 2016 02:11:12 +0000rabil4129 at http://openmx.ssri.psu.eduHow to use "mxFitFunctionAlgebra" instead of "mxAlgebraObjective"
http://openmx.ssri.psu.edu/thread/4113
<div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>This code used to work using "mxAlgebraObjective", but now says I have to use "mxFitFunctionAlgebra" instead of "mxAlgebraObjective".</p>
<p>###############<br />
models_1_v4
Model_1_t1_v4,<br />
Model_1_t2_v4,<br />
mxAlgebra(<br />
Model_1_t1_v4.objective+<br />
Model_1_t2_v4.objective,<br />
name="multi"),</p>
<p># mxAlgebraObjective("multi"),</p>
<p> mxFitFunctionAlgebra(algebra = "multi")<br />
)</p>
<p>m1_fit_v4
##################</p>
<p>I tried changing ".objective" to ".fitfunction" but this did not work either. What am I doing wrong?</p>
</div></div></div><div class="field field-name-taxonomy-forums field-type-taxonomy-term-reference field-label-above"><div class="field-label">Forums: </div><div class="field-items"><div class="field-item even"><a href="/forums/openmx-help/openmx-general-help">OpenMx General Help</a></div></div></div>Thu, 10 Mar 2016 16:22:21 +0000rabil4113 at http://openmx.ssri.psu.eduOutput from mxFactorScores - Order of rows?
http://openmx.ssri.psu.edu/thread/4109
<div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>In the help file for mxFactorScores, it says:</p>
<p>The rows are in the order of the _sorted_ data.</p>
<p>I'm not sure what this means. The data I have is in order by date and it's clear that the estimated factor scores for "ML" are no longer in the same order. There are two correlated factors each with 2 indicators (and nothing else). How can I get the factor scores into the same order as the rest of the data?</p>
<p>BTW, I'm using OpenMx 2.3.1 under R 3.2.2 (Ubuntu 15.04). mxFactorScores does not work with the RAM model so I converted it to LISREL in order to get the factor scores. (I had this problem before but I don't remember if it was ever resolved.)</p>
</div></div></div><div class="field field-name-taxonomy-forums field-type-taxonomy-term-reference field-label-above"><div class="field-label">Forums: </div><div class="field-items"><div class="field-item even"><a href="/forums/openmx-help/openmx-general-help">OpenMx General Help</a></div></div></div>Mon, 07 Mar 2016 18:27:43 +0000rabil4109 at http://openmx.ssri.psu.eduHandling Exogenous Latent Variables in OpenMx
http://openmx.ssri.psu.edu/thread/4099
<div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>Suppose you have two exogenous latent variable. (There will be directed paths from them to a response variable.) Is the covariance between the two exogenous latent variables part of the model? That is, do I have to include a path specification for the covariance or otherwise the covariance will be constrained to zero? I understand that the covariances among exogenous manifest variables are not part of the model.</p>
</div></div></div><div class="field field-name-taxonomy-forums field-type-taxonomy-term-reference field-label-above"><div class="field-label">Forums: </div><div class="field-items"><div class="field-item even"><a href="/forums/openmx-help/openmx-general-help">OpenMx General Help</a></div></div></div>Tue, 16 Feb 2016 14:54:59 +0000rabil4099 at http://openmx.ssri.psu.eduHow can you tell if OpenMx is using multiple cores?
http://openmx.ssri.psu.edu/thread/4092
<div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>I'm running OpenMx on 4 different computers running Ubuntu 15.04 and the latest version of OpenMx and current versions of R. On one, when look at the output for htop, it seems clear that all 4 cores are being used by OpenMx. Yet on two of the others, htop seems to indicate that not all 4 cores are being used simultaneously and the same model takes 2 to 3 times longer to run. I've tried using the suggestion to tell OpenMx to use more threads - but this seems to have no effect and I never had to do this on the computer that seems to be using all 4 cores and runs the model much more quickly. I don't think its processing power is greater than the other computers. When I used to install OpenMx, it seemed that it asked you if you wanted parallel processing enabled. But lately it no longer asks.</p>
</div></div></div><div class="field field-name-taxonomy-forums field-type-taxonomy-term-reference field-label-above"><div class="field-label">Forums: </div><div class="field-items"><div class="field-item even"><a href="/forums/openmx-help/openmx-general-help">OpenMx General Help</a></div></div></div>Wed, 20 Jan 2016 23:44:36 +0000rabil4092 at http://openmx.ssri.psu.eduaccess model estimated parameters (EP) without calling summary?
http://openmx.ssri.psu.edu/thread/4083
<div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>Hi OpenMxers,<br />
I want to determine automatically which order to put models into mxCompare so that the model with more degrees of freedom comes first.</p>
<p>Both models have been run, and I can access a models number of estimated parameters from summary(model).</p>
<p>summary() however, can be costly in terms of execution time: Is there a way to access the EP (or df) property from the model directly without calling summary?</p>
<p>Besten Wünsche,<br />
tim</p>
<p>FYI, the situation I am trying to automate is avoiding this:</p>
<pre>
|Model | EP|Delta-2LL |Delta df|p | AIC|Compare with Model |
|:------------|--:|:----------|:------|:--|--------:|:------------------|
|fix_C_2_zero | 25| | | | 2227.444| |
|Final | 27|1.29e-05 |-2 | | 2231.444|fix_C_2_zero |
Warning message:
In pchisq(otherSummary$Minus2LogLikelihood - refSummary$Minus2LogLikelihood, :
NaNs produced
</pre></div></div></div><div class="field field-name-taxonomy-forums field-type-taxonomy-term-reference field-label-above"><div class="field-label">Forums: </div><div class="field-items"><div class="field-item even"><a href="/forums/openmx-help/openmx-general-help">OpenMx General Help</a></div></div></div>Thu, 26 Nov 2015 18:46:00 +0000tbates4083 at http://openmx.ssri.psu.edumxTryHard status codes
http://openmx.ssri.psu.edu/thread/4045
<div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>Dear all, </p>
<p>I have been running a model within a loop over several variables, which does not converge well for all variables. Therefore, I applied mxTryHard. There are two things I noticed: </p>
<p>1) for models that run well without calling mxTryHard the best fit does not seem to change using mxTryHard, but the status code changes from 0 to -1</p>
<p>> fit1
> fit1$output$Minus2LogLikelihood<br />
[1] 4595.342<br />
> fit1$output$status<br />
$code<br />
[1] 0<br />
$status<br />
[1] 0</p>
<p>fit2
> fit2$output$Minus2LogLikelihood<br />
[1] 4595.342<br />
fit2$output$status<br />
$code<br />
[1] -1</p>
<p>$status<br />
[1] 0</p>
<p>2) even when I set "intervals=F" (like in the example above) the mxTryHard option computes intervals. </p>
<p>Can you help?<br />
Thanks in advance</p>
</div></div></div><div class="field field-name-taxonomy-forums field-type-taxonomy-term-reference field-label-above"><div class="field-label">Forums: </div><div class="field-items"><div class="field-item even"><a href="/forums/openmx-help/openmx-general-help">OpenMx General Help</a></div></div></div>Tue, 15 Sep 2015 20:55:35 +0000Rachel4045 at http://openmx.ssri.psu.eduCan't move paths
http://openmx.ssri.psu.edu/thread/4042
<div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>Hi, I'm using Onyx, which I think is based on OpenMx, for a confirmatory factor analysis.</p>
<p>I'm using a Macbook Air, and I can't work out how to modify the path arrows so they look neat. Can anyone help?</p>
<p>There is nothing in the documentation. The models in the examples all look nice, whereas everytime I add a path or covariance path, the program sticks them in anywhere and I can't move the end-points around to different parts of the observed or latent variable.</p>
<p>Please help!</p>
<p>Jay.</p>
</div></div></div><div class="field field-name-taxonomy-forums field-type-taxonomy-term-reference field-label-above"><div class="field-label">Forums: </div><div class="field-items"><div class="field-item even"><a href="/forums/openmx-help/openmx-general-help">OpenMx General Help</a></div></div></div>Mon, 14 Sep 2015 04:10:31 +0000Anonymous4042 at http://openmx.ssri.psu.eduModifying an Existing Model
http://openmx.ssri.psu.edu/thread/4036
<div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>I created a model (using a function) saved as "x". I would like to change a label in the A matrix. Here are the labels for the A matrix:</p>
<p>> x$matrices$A$labels<br />
v_1 v_2 v_3 mu<br />
v_1 NA NA NA "b_1"<br />
v_2 NA NA NA "b_2"<br />
v_3 NA NA NA "b_3"<br />
mu NA NA NA NA </p>
<p>I would like to change "b_3" to "b_2":</p>
<p>> x$matrices$A$labels[3,4]
Error: Right-hand side of assignment operator has illegal value FullMatrix, SymmMatrix, FullMatrix, and FullMatrix</p>
<p>Why does this not work?</p>
</div></div></div><div class="field field-name-taxonomy-forums field-type-taxonomy-term-reference field-label-above"><div class="field-label">Forums: </div><div class="field-items"><div class="field-item even"><a href="/forums/openmx-help/openmx-general-help">OpenMx General Help</a></div></div></div>Tue, 01 Sep 2015 17:59:10 +0000rabil4036 at http://openmx.ssri.psu.eduConstraining mxAlgebra across submodels
http://openmx.ssri.psu.edu/thread/4012
<div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even"><p>Hi,</p>
<p>This is actually quite a quick question and the title says most of it already.<br />
Anyway, is there anyway to constrain mxAlgebra objects across multiple submodels?</p>
<p>I would like to constrain estimated heritability of two separate twin models to be the same while allowing each submodel to have separate parameter estimations. </p>
<p>Unfortunately I was unable to find a way to do so. I have tried mxConstraint(modelA.algebra1==modelA.algebra2) but that seemed not to work.</p>
<p>I would be thankful for any reply! </p>
</div></div></div><div class="field field-name-taxonomy-forums field-type-taxonomy-term-reference field-label-above"><div class="field-label">Forums: </div><div class="field-items"><div class="field-item even"><a href="/forums/openmx-help/openmx-general-help">OpenMx General Help</a></div></div></div>Fri, 26 Jun 2015 07:52:28 +0000WuandMu4012 at http://openmx.ssri.psu.edu