bootstrap likelihood ratio test (BLRT) for GMM with definition variables

Posted on Fri, 04/13/2018 - 14:42

Veronica_echo Joined: 02/23/2018

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Hi everyone,

I would like to conduct BLRT test for 2 nested GMM model with definition variables. I referred to a previous post
https://openmx.ssri.psu.edu/node/4329 and it worked well on my computer. However, when I run the comparison of my model, it reported errors. I attached a screenshot of LRT without and with bootstrap in the attachment. And here is the information of my OpenMx Version:

> mxVersion()
OpenMx version: 2.9.6 [GIT v2.9.6]
R version: R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0
MacOS: 10.13.4
Default optimiser: CSOLNP
NPSOL-enabled?: Yes
OpenMP-enabled?: Yes

Thanks in advance!

Replied on Fri, 04/13/2018 - 16:25

AdminRobK Joined: 01/24/2014

Script?

You should post your current script.

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Replied on Sat, 04/14/2018 - 09:08

Veronica_echo Joined: 02/23/2018

Thanks for kind and prompt

Thanks for kind and prompt reply. I've attached dataset and codes I am using. Thanks in advance!

File attachments

LGC1.dat

BLRT_error.R

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Replied on Sun, 04/15/2018 - 13:43

AdminRobK Joined: 01/24/2014

I reproduce the error you

I reproduce the error you report. I think this is a bug. A model using an MxExpectationMixture will run if the mixture components contain definition variables but the data are in the container model, and not the mixture-component. But, mxGenerateData() raises an error if it sees definition variables inside an MxModel object that doesn't contain an MxData object.

The bug-fix will seemingly require modifying the behavior of mxGenerateData() when used with models that have MxExpectationMixture.

As a workaround, try putting the MxData object inside the mixture components class1, class2, and class3, and see it that makes a difference. Alternately, you could try defining sloLoads differently, so that its labels are paste0("GMM2Class.data.T", 1:10) when used with the two-component model, and paste0("GMM3Class.data.T", 1:10) when used with the three-component model.

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Replied on Tue, 04/17/2018 - 11:02

Veronica_echo Joined: 02/23/2018

Thanks for advice

Thanks for your kind advice. I've tried to put the raw data in each class. However, every time I tried run it, R studio would be terminated since "R encountered a fatal error" and I don't know why. Also, relabeling the definition variables did not work either. I've included the updated version with data in the attachment. Thank you.

File attachments

BLRT_relabel.R

BLRT_add data in class.R

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Replied on Tue, 04/17/2018 - 11:51

Veronica_echo Joined: 02/23/2018

Another error

BTW, it seems that the function mxBootstrap() does not work well if I put mxData outside the class1, class2 and class3. But it works if I put the data in each class. Thanks.

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Replied on Tue, 04/17/2018 - 12:07

jpritikin Joined: 05/23/2012

mxBootstrap

Yes, these are symptoms of the same problem with mxGenerateData.

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Replied on Tue, 05/01/2018 - 14:17

AdminRobK Joined: 01/24/2014

Wait, I don't think that's

Wait, I don't think that's the case. mxBootstrap() is for nonparametric bootstrapping, so its behavior doesn't depend upon mxGenerateData().

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Replied on Tue, 05/01/2018 - 15:04

jpritikin Joined: 05/23/2012

Rob is correct

What exactly is going wrong with mxBootstrap?

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Replied on Mon, 04/16/2018 - 14:51

jpritikin Joined: 05/23/2012

investigating

Something is going wrong with data generation.

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Replied on Mon, 04/16/2018 - 15:37

jpritikin Joined: 05/23/2012

a bunch of stuff related to inherited MxData was broken

Yeah, you can probably get your stuff to work with the current version of OpenMx by copying the data into the class components. Anyway, fixed in v2.9.6-48-g17adc932f

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Replied on Tue, 04/17/2018 - 11:06

Veronica_echo Joined: 02/23/2018

Thank you

Tried it, but R studio would be terminated every time. And glad to know it will be fixed. May I know when v2.9.6-48-g17adc932f will be available (approximated date is good enough)? Thank you very much!

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Replied on Tue, 04/17/2018 - 12:05

jpritikin Joined: 05/23/2012

os/x builds

You could try the builds [here](https://vipbg.vcu.edu/vipbg/OpenMx2/software/bin/macosx/travis/)

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Replied on Fri, 04/20/2018 - 11:50

AdminRobK Joined: 01/24/2014

Specifically, you could try

Specifically, you could try downloading this MacOS package binary and installing it.

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Replied on Sat, 04/21/2018 - 12:16

Veronica_echo Joined: 02/23/2018

Requirement for R version

Thanks for your kind reply. I tried, however, it seems not available for R version 3.4.4. I am wondering if it has specific requirement for r version. Thank you very much!

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Replied on Fri, 04/27/2018 - 14:05

AdminRobK Joined: 01/24/2014

R version

I am wondering if it has specific requirement for r version.

Not that I know of. But, I'm not involved in building OpenMx for MacOS. Are you downloading the file and installing the package from that local file?

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Replied on Sun, 04/29/2018 - 19:33

Veronica_echo Joined: 02/23/2018

Yep, and here is the

Yep, and here is the screenshot

File attachments

Screen Shot 2018-04-29 at 7.31.46 PM.png

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Replied on Mon, 04/30/2018 - 10:30

AdminRobK Joined: 01/24/2014

You might need to

You might need to additionally pass argument repos=NULL to install.packages() to install a local file.

You use RStudio, right? It's also possible to install a local file with RStudio's package-installation interface.

Also, the extension of a MacOS package binary should be .tgz, not .tar.

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Replied on Mon, 04/30/2018 - 21:32

Veronica_echo Joined: 02/23/2018

Yes, it works now. Thank you

Yes, it works now. Thank you very much!

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Replied on Tue, 05/01/2018 - 11:35

Veronica_echo Joined: 02/23/2018

One more question

I run mxCompare(model1, model2, boot=TRUE) on my computer using 4 cores overnight, but it did not work... I mean I did not get any result until now... Should it take longer? If so, I may want to run it on cluster. May I know how to upgrade the package on cluster? Thank you very much!

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Replied on Tue, 05/01/2018 - 12:25

jpritikin Joined: 05/23/2012

cluster

Who manages your cluster? You'll probably want to talk to that person for guidance.

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Replied on Tue, 05/01/2018 - 12:42

Veronica_echo Joined: 02/23/2018

Thanks for your kind advice!

Thanks for your kind advice! I firstly may want to check if the BLRT for definition variables is available for linux system. If so, which version should be used? Thank you very much!

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Replied on Tue, 05/01/2018 - 13:04

jpritikin Joined: 05/23/2012

def vars

What's implemented is data generation assuming that def vars are fixed. If that's what you want then it should work. You can test whether data generation works the way you expect with mxGenerateData

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Replied on Tue, 05/01/2018 - 13:06

AdminRobK Joined: 01/24/2014

I agree with Joshua

I agree with Joshua: the best person to ask is your cluster's sysadmin. If I had to guess, I would recommend following the instructions under "Unix installation" here, except with an additional shell command:



git clone git@github.com:OpenMx/OpenMx.git

cd OpenMx/

git checkout stable

make install

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Replied on Sun, 04/29/2018 - 17:40

News

Recent Posts

bootstrap likelihood ratio test (BLRT) for GMM with definition variables

Script?

Thanks for kind and prompt

I reproduce the error you

Thanks for advice

Another error

mxBootstrap

Wait, I don't think that's

Rob is correct

investigating

a bunch of stuff related to inherited MxData was broken

Thank you

os/x builds

Specifically, you could try

Requirement for R version

R version

Yep, and here is the

You might need to

Yes, it works now. Thank you

One more question

cluster

Thanks for your kind advice!

def vars

I agree with Joshua

Yes, I think so

News

Recent Posts