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 lisa Carlesso posted on Sunday, October 25, 2015 - 10:46 am
Hello

I am about to start an LPA analysis and have a categorical distal outcome that I would like to relate the classes to as well as other covariates that I would like use to predict class membership. I have read the article from 2014 on auxiliary variables in 3 step approaches, but it is not clear to me if it is possible to do this all together, particularly including the other covariates as predictors of class membership. Can you please clarify?

thank you
 Linda K. Muthen posted on Monday, October 26, 2015 - 9:22 am
You would need to use manual 3-step for this. See Web Note 21, Section 3.2.
 lisa Carlesso posted on Tuesday, October 27, 2015 - 7:18 am
Thank you. I am familiar with BCH and had planned on using it, however I was confused by table 6 of webnote 21 that recommends BCH for continuous and DCAT for categorical. Are you suggesting that I try BCH even though my distal outcome is categorical?
 Linda K. Muthen posted on Tuesday, October 27, 2015 - 9:50 am
I would use the recommendations in Web Note 21.
 lisa Carlesso posted on Thursday, January 21, 2016 - 12:15 pm
Hello again,

I have run the LPA (with 3 classes) as mentioned above to a categorical distal outcome and in the output for one of the classes I am getting an OR of 1 with a 95 % CI of (1.0, 1.0). The other 2 classes are fine. Do you know why this may be the case?

thank you
 Bengt O. Muthen posted on Thursday, January 21, 2016 - 4:14 pm
See the FAQ onour website:

Odds ratio interpretation for categorical distal outcomes using DCAT
 lisa Carlesso posted on Thursday, January 21, 2016 - 5:24 pm
Thank you that was very helpful. In this particular case, my last class is the one whose OR I am most interested in. Is there a way to change the order of how the classes fall out? I have read about using DEFINE but I am not sure if that could work.
 Bengt O. Muthen posted on Friday, January 22, 2016 - 4:27 pm
You use starting values to change classes around. Request SVALUES in the output from your original run and use them in a second run where you switch them for the classes so you get the last class you want.
 lisa Car posted on Thursday, November 17, 2016 - 10:45 am
Seeing as the recommended model for binary outcomes cannot accommodate covariates, I am wondering what your opinion is on using logistic regression after the fact as an option to explore them?
 Bengt O. Muthen posted on Thursday, November 17, 2016 - 1:45 pm
You can use the manual 3-step approach described in our papers.
 lisa Car posted on Friday, November 18, 2016 - 10:19 am
Hi again,

I have tried using the manual 3-step as suggested and when I get to the final step I cannot get the model to converge. My model has 3 classes, a number of covariates and 2 binary distal outcomes. The following error message appears.
THE ESTIMATED COVARIANCE MATRIX FOR THE Y VARIABLES IN CLASS 1 COULD NOT BE INVERTED. PROBLEM INVOLVING VARIABLE INCIDCFK. COMPUTATION COULD NOT BE COMPLETED IN ITERATION 3. CHANGE YOUR MODEL AND/OR STARTING VALUES. THIS MAY BE DUE TO A ZERO ESTIMATED VARIANCE, THAT IS, NO WITHIN-CLASS VARIATION FOR THE VARIABLE.

I have tried increasing STARTS up to 800 100 with no avail.

thank you
 Bengt O. Muthen posted on Friday, November 18, 2016 - 2:18 pm
Send output to Support along with your license number.
 lisa Car posted on Monday, November 21, 2016 - 1:37 pm
So the model works with a continuous distal outcome but not a categorical one however I am getting class shifting. Does something special need to be done for a categorical distal outcome in the manual 3 sep approach?
 Bengt O. Muthen posted on Monday, November 21, 2016 - 4:51 pm
No.
 DavidBoyda posted on Monday, April 16, 2018 - 9:41 pm
Dear support,

If I have categorical variables, and temporal order is not an issue, can i use DCAT instead of r3step to predict class membership instead of using it for distals? (e.g N > dummy coded age categories)
 Bengt O. Muthen posted on Tuesday, April 17, 2018 - 4:29 pm
I don't see how that would work.
 Katharine Buek posted on Monday, November 26, 2018 - 8:18 am
I have a 10-class LCA model with two binary distal outcomes. I'm using the Auxiliary with DCAT, but getting the following error message:

THE ESTIMATED COVARIANCE MATRIX FOR THE Y VARIABLES IN CLASS 1 COULD NOT
BE INVERTED. PROBLEM INVOLVING VARIABLE NICU. COMPUTATION COULD
NOT BE COMPLETED IN ITERATION 12. CHANGE YOUR MODEL AND/OR STARTING
VALUES. THIS MAY BE DUE TO A ZERO ESTIMATED VARIANCE, THAT IS, NO WITHIN-CLASS
VARIATION FOR THE VARIABLE.
THE MODEL ESTIMATION DID NOT TERMINATE NORMALLY. ESTIMATES CANNOT
BE TRUSTED.


What does this mean? There are certainly several class indicator variables for which there is only a single value in a given latent class. Is this causing my problem and what can i do about it?
 Bengt O. Muthen posted on Monday, November 26, 2018 - 12:02 pm
Please send your Step 1 LPA that shows this message - data and output - to Support along with your license number.
 Katharine Buek posted on Friday, November 30, 2018 - 9:47 am
I see your note above regarding start values:

"You use starting values to change classes around. Request SVALUES in the output from your original run and use them in a second run where you switch them for the classes so you get the last class you want."

Where can I find example code to show me how to do this?

Thanks
 Bengt O. Muthen posted on Friday, November 30, 2018 - 4:48 pm
It's a very simple idea. Say that you have 1 continuous LPA indicator and 2 classes. Say that your estimates in the first run come out as

%c#1%
[y*1];
%c#2%
[y*-1];

Then you change that to

%c#1%
[y*-1];
%c#2%
[y*1];

For the rest, see the SVALUES option in the UG.
 Katharine Buek posted on Monday, December 03, 2018 - 7:25 am
Ok, so I think I see what you are saying. I have the starting values for all the variables in each class. I just specify these in the input re-ordering the classes the way I want them? i.e. Class 8 starting values become class 1 starting values, for instance?
 Katharine Buek posted on Monday, December 03, 2018 - 8:05 am
Also, hopefully a quick question. With the DCAT output, I'd like to get the OR or RR comparing each class to every other (pairwise comparisons), rather than just the chi-squares. Is there a way to do this?
 Katharine Buek posted on Monday, December 03, 2018 - 8:40 am
Oh, and to clarify my most recent question, I am referring to ORs/RRs for the distal outcome... not the indicator items used in the LCA, which come up as part of the LCA output by default.
 Bengt O. Muthen posted on Tuesday, December 04, 2018 - 2:52 pm
Q1: Right.

Q2 - Q3: See the FAQ on our website:

Odds ratio confidence interval from logOR estimate and SE
 Katharine Buek posted on Tuesday, December 04, 2018 - 4:22 pm
As far as I can tell, the DCAT output does not give log ORs for comparing each class (pairwise). It just gives chi square tests. I was wondering if it was possible to get these somehow.
 Tihomir Asparouhov posted on Tuesday, December 04, 2018 - 4:35 pm
If you are using the DCAT option the output should look like this

Prob S.E. Odds Ratio S.E. 2.5% C.I. 97.5% C.I.

Class 1
Category 1 0.487 0.045 1.000 0.000 1.000 1.000
Category 2 0.513 0.045 3.933 0.793 2.379 5.486
Class 2
Category 1 0.254 0.032 1.000 0.000 1.000 1.000
Category 2 0.746 0.032 10.947 2.361 6.318 15.575
Class 3
Category 1 0.504 0.034 1.000 0.000 1.000 1.000
Category 2 0.496 0.034 3.672 0.925 1.860 5.485

Chi-Square P-Value Degrees of Freedom

Overall test 228.783 0.000 2
Class 1 vs. 2 19.018 0.000 1
Class 1 vs. 3 0.079 0.778 1
Class 2 vs. 3 26.816 0.000 1


The pairwise comparison and the OR are given in that output, i.e., the OR comparison for Class 1 and Class 2 has a p-value of 0.000, although the P-value is coming from the test of Prob in class 1 - Prob in class 2 = 0 rather than odds ratio.
 Katharine Buek posted on Thursday, December 06, 2018 - 7:32 am
Thank you, the chi squares are not particularly useful to me, but are you suggesting that I can create confidence intervals for each of the ORs in the upper part of the output, and compare them to each other that way? i.e., if the OR for class 2 is not inside the CI for the class 1 OR, then they are significantly different?
 Tihomir Asparouhov posted on Thursday, December 06, 2018 - 10:01 am
In my example above the T-statistics for class 1 v.s. class 2 is sqrt(19.018)=4.361.

The point estimate for the log odds ratio is
log(0.487/0.513)-log(0.254/0.746)=1.025

From here you can get an estimate for its SE
1.025/4.361=0.235 and a confidence interval for the log odds ratio as
[1.025-1.96*0.235, 1.025+1.96*0.235]=[0.565,1.486]

The problem of this approach is that the T-statistic is coming from a different scale for the same test - so it is up to you if you want to use it but this is what is available at this time.

The T-statistic is for the test P11-P12=0, while what you are using it for is
log(P11/(1-P11)) - log(P12/(1-P12))=0.

Even though the two tests are equivalent and asymptotically they will yield the same conclusion because of the different parameterization scale they are expected to have slightly different T-statistics. If you decide to use the above approach to construct CI for the log odds ratio you have to treat them as an approximation.

I don't agree that the chi-squares are not useful. They do the same thing that the log OR confidence intervals do - they are simply in a different parameterization scale, but there is no evidence that one test is superior than the other.
 Tihomir Asparouhov posted on Thursday, December 06, 2018 - 10:14 am
Actually I just realized that you can indeed obtain the exact SE and confidence interval. It is a bit more complicated however.It goes like this
Var(P11-P12)=((0.487-0.254)/4.361)^2=0.003049
Since Var(P11)=0.045^2 and Var(P12)=0.032^2 you get Cov(P11,P12)=-0.000097. You can then apply the delta method for
log(P11/(1-P11)) - log(P12/(1-P12)) to obtain the exact value.
 Sam Crawley posted on Thursday, December 06, 2018 - 5:46 pm
Hi,

I have a binary distal outcome for a latent class analysis, and two binary IVs. I want to estimate the relationship between the IVs and the outcome variable for each latent class.

Web note 21 suggests that DCAT should be used for a categorical outcome. However, as far as I know, this can't be used when there are other covariates in the model.

Is this correct? Should I use BCH (as per Web note 21) in this case?

Thanks.
 Bengt O. Muthen posted on Friday, December 07, 2018 - 3:54 pm
Use the "manual" approach in Section 3 of Web Note 15 declaring the distal as categorical.
 Kierra Sattler posted on Friday, February 08, 2019 - 1:38 pm
Hello,

For the manual approach, how do I estimate a categorical outcome across the classes? When I try to run the below model I get an error about parameterization, but this cannot be used with mixture.

Classes = c(2);
nominal = N;
categorical = anycps3t;

Analysis:
Type = mixture;

Model:

%OVERALL%

anycps3t;

%C#1%
[N#1@4.114;
[N#2@-4.940];
[N#3@-9.685];

anycps3t;

%C#2%
[N#1@6.082];
[N#2@13.808];
[N#3@8.833];

anycps3t;



*** WARNING in MODEL command
All variables are uncorrelated with all other variables within class.
Check that this is what is intended.
*** ERROR in MODEL command
Variances for categorical outcomes can only be specified using
PARAMETERIZATION=THETA with estimators WLS, WLSM, or WLSMV.
Variance given for: ANYCPS3T
 Bengt O. Muthen posted on Saturday, February 09, 2019 - 11:06 am
Change from anycps3t to [anycps37$1]. This is the threshold for a binary variable. With an ordinal variable you can have ..$2, ...$3 etc.
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