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Dear MplusTeam, is it possible to specify a random variance in threelevel models? (random Level 2 variance) Mplus starts, but doesn't open an Output. if I manually open the Output  it is truncated after the Input commands. regards christoph 


We don't have that yet for 3level  there should have been a stoppage. 


thanks, I also tried to model the variance using model constraints. But specific constaints are also not allowed with type threelevel. Do you have any other suggestions for the following problem. I have threelevel data (student, class, school). I want to regress L2variance on L3variables. The outcome is a continuous SESmeasure. Thus, the L2variance is a measure of within school (between class) segregation. Between school differences in the L2variance should capture school differences in within school segregation, which in turn should be explained by school level variables. My next idea was to use a twostep approach. First, estimate a null model for ses and save the factor scores. then I will use the factor scores b2_ses and b3_ses to calculate the between class/within school variance for each school. Finally, I would use standard regression at school level. Is this a reasonable approach, or are there any other (better) possibilities? and a final question. Do I get it right, that the factor scores in the output (SES, b2_ses, b3_ses) refer to decomposision xijn = xwijn (SES) + xb2jn (b2_ses) + xb3n (b3_ses)? Thanks 


The two step approach sounds reasonable. I would recommend instead of running a three level model to run a twolevel model with random variance (drop the top level). Get plausible values for the random variance. You can than run the second step using type=imputation and regress these plausible values on predictors. See the plausible value note if you are not familiar with this process. http://statmodel.com/download/Plausible.pdf Add the top level to the second step, so your second step model will be run either as type=complex or type=twolevel with the ML estimator. The answer to the last question is yes. 


Thanks, I'm not sure if I get this right. The random variance in the 2levelmodel will capture the variance differences between classes (L2). In the next step I would drop L1, and regress the L2PVs on L3 predictors. Thus, I will explain why some classes (L2units) are more SEShomogenous than others. But this way, I can't differentiate whehter SEShomogeneity is due to schoolSEShomogeneity or due to within school segregation (i.e heterogenous school, but homogenous classes). Isn't it? I want to explain, why in some schools the (latent) class means deviate more from the (latent) school mean, than in others schools? 


Just to back up: Is my Interpretation of the random variance (in the 2level case) correct? And are PVs generally "better" than ML or IRT factor scores? Thanks Christoph 


Maybe you have to estimate the latent class means in the first step and then use these PV in the second step  where you would have to run a twolevel model with school specific variance. PV are better than single estimate such as factor scores. You can also just use sample statistics at least for exploratory purposes, such as sample variance within classroom. 


Thanks a lot, that helps! One final question: The outcome has several missing values (25%). Thus, I would have used multilevel MI to deal with the missing data. But after MI I need bayes estimation (to estimate PV), which is not suited for multiple data sets. So what would you recommend for this problem? Is it possible to use auxiliary variables as missing correlates in the PV estimation step? 


There are two ways to proceed I think. 1. Avoid the MI. Instead just use the specification for missing data variable: missing=all(999); (that way the imputation is internal) Alternatively 2. In principle you can proceed in the second step with "manual MI". You would run each imputed data set separately and then combine the results manually using the standard imputation formulas. 


The first Approach seems quite comfortable. If I use an intercept only model for the PV estimation, cases with missing values would be excluded, isn't it? Thus, latent means are based on "listwise" data and might be biased? Or should I use groupmean centered covariates? This should also lead to "unweigthed" class means, isn't it? Christoph 


Yes ... I would not recommend using the intercept only univariate model given the missing data. The variables that could be related should be included (the way you would include these in the imputation model). So a model like that %within% Y1Y10 with Y1Y10 %between% Y1Y10 with Y1Y10 is better to use even if you just want the PV for Y1_between. I do not see advantages in using groupmean centering, as compared to the above suggestion. Groupmean centering could be detrimental, see http://www.statmodel.com/bmuthen/articles/Article_127.pdf 


Now I get it, thanks a lot! 


Dear MplusTeam, a further question emerged. How many PVs would you suggest would be neccesary for the latent class means. best Christoph 


The more you do the better but I would do 10. Make sure these don't come from consecutive iterations. If you are using data imputation use thin=100 in the data imputation command (that is the default actually so you don't need to do anything). If you are using the factor scores, that 100 is not there for you by default  so add thin=100 to the analysis command (or save 1000 factor scores and take draws that are 100 apart). 


I'd like to back up if I get the PV applications right (referring to example 11.7). SAVEDATA: FILE = ex11.7plaus.dat; SAVE = FSCORES (20); 1.) If I use Savedata and Fscores descriptives of the PVs (means, median, ...) are saved in ex11.7plaus.dat for each case. 2.) If I want to save each of the 20 PVs per case in 20 files, I have to use DATA IMPUTATION: NDATASETS = 20; SAVE = ex11.7imp*.dat; 3.) When I use the data imputation command, Mplus automatically uses a thinning interval of 100, 4.) ... which does also affect the PV Distribution in ex11.7plaus.dat??? 5.) Single PVs can only be saved by using "data imputation". 6.) If I use PVs in a twolevel model for a catogorical (binary) variable X, the PV X_B is the threshold on a probit scale? (If this is correct, what might be the reason when the threshold from the imputation model and the mean threshold based on the PVs differ?) Thanks Christoph 


14. Yes 5. No. See page 838 in the user's guide. You can save the plausible values in one file with the FACTORS command, also you can control the thinking there as well SAVE = FSCORES(20 100) will give you the thinning of 100. 6. No. The cluster specific threshold is "threshold parameter  X_B" X_B is the cluster specific deviation from the average threshold parameter which is the nonrandom threshold parameter 


Thanks! regarding 5: thus, if I only use savedata and factors, the pvs will be saved in one file, whereas data imputation will save the pvs in multiple files? regarding 6: if X is continous X_B is the cluster specific mean? 


Yes on both 

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