Missing Data Modeling  
Mplus Discussion >
Mplus has several options for the estimation of models with missing data. Mplus provides maximum likelihood (ML) estimation under MCAR (missing completely at random) and MAR (missing at random; Little & Rubin, 2002) for continuous, censored, binary, ordered categorical (ordinal), unordered categorical (nominal), counts, or combinations of these variable types. MAR means that missingness can be a function of observed covariates and observed outcomes. For censored and categorical outcomes using the weighted least squares estimators, missingness is allowed to be a function of the observed covariates but not the observed outcomes. Non-ignorable missing data modeling is possible using maximum likelihood where categorical outcomes represent indicators of missingness and where missingness may be influenced by continuous and categorical latent variables (Muthén et al., 2003).

Multiple data sets generated using multiple imputation (Schafer, 1997) can be analyzed using a special feature of Mplus. Parameter estimates are averaged over the set of analyses, and standard errors are computed using the average of the standard errors over the set of analyses and the between analysis parameter estimate variation.

In all models, missingness is not allowed for the observed covariates because they are not part of the model. The outcomes are modeled conditional on the covariates and the covariates have no distributional assumption. Covariate missingness can be modeled if the covariates are explicitly brought into the model and given a distributional assumption. With missing data, the standard errors for the parameter estimates are computed using the observed rather than the expected information matrix (Kenward & Molenberghs, 1998). Bootstrap standard errors and confidence intervals are also available with missing data.
Thread (Start New Thread) Last Post Last Poster Posts
Missing data4-10-17  7:06 pmBengt O. Muthen667
Fit indexes11-14-16  7:48 amBengt O. Muthen39
Data with structural missingness6-21-11  10:26 amLinda K. Muthen11
Missing by design9-12-16  5:13 amSimon L Chrétien110
Interpreting 'estimated sample statistics'10-01-14  5:56 pmBengt O. Muthen11
Sample statistics in latent growth modeling with missing data9-30-02  2:36 pmLinda K. Muthen2
Significance of correlations in LGM modeling with missing data11-22-16  6:10 amLinda K. Muthen18
Significance of correlations in LGM modeling with missing data10-03-02  4:25 pmAnonymous1
Missing data in binary outcomes8-05-16  2:19 pmLinda K. Muthen24
Robust standard errors and missing data9-04-09  12:30 pmBengt O. Muthen4
Degrees of freedom for missing data models4-02-03  2:27 pmAnonymous5
Specifying a Saturated Model10-03-03  5:20 pmLinda K. Muthen2
Standardized coefficients in latent growth modeling with missing data2-06-04  7:38 amLinda K. Muthen2
Multiple imputation3-06-17  6:07 pmBengt O. Muthen559
Dummy interpretation12-21-13  2:53 amhassan zeb1
Test for MCAR10-20-14  9:48 amLinda K. Muthen17
Missing data modeling5-18-15  2:40 pmBengt O. Muthen41
Missing at Random and Not7-21-08  2:47 pmLinda K. Muthen13
Monte Carlo simulations with missing data10-09-15  8:52 amBengt O. Muthen28
Missing in EFA/CFA2-16-14  11:17 amLinda K. Muthen36
Missing Data, Complex Samples, and Categorical Data11-12-16  5:13 amslck.dgn@hotmail.com29
Sample size10-22-16  8:37 amBengt O. Muthen9
Two part growth model4-13-16  12:51 pmBengt O. Muthen12
Multiple Group MIMIC model with censored data and MI9-25-08  10:22 amLinda K. Muthen4
Growth model with missing time points5-27-15  10:10 amLinda K. Muthen6
Ordered Polytomous data5-08-05  6:44 amLinda K. Muthen12
Chi-square diff test with weights and missing data11-20-06  5:02 pmLinda K. Muthen5
Comparison of two models2-05-09  1:15 pmBengt O. Muthen7
MODEL INDIRECT not available with multiple imputation8-15-16  3:50 pmBengt O. Muthen31
MISSING ARE command 6-23-05  3:52 amLinda K. Muthen2
Missing data by design8-12-05  9:26 amLMuthen2
What does the H1 option do? Why are intercepts included?8-17-05  2:20 pmLinda K. Muthen2
Reconciling Sample Size Counts9-01-05  2:19 pmLinda K. Muthen2
Factor scores9-18-05  3:10 pmLinda K. Muthen2
WLSMV missing data3-30-17  9:23 amBengt O. Muthen49
Does Mplus impute missing data/ role of EM?11-19-12  12:06 pmLinda K. Muthen25
Implications of type = missing3-17-15  8:00 amBengt O. Muthen11
Dont want deletion in logistic regression12-08-15  9:47 amLinda K. Muthen33
Robust standard errors under MAR3-24-06  6:07 amLinda K. Muthen6
Wrong mean estimates with FIML?5-31-15  3:12 pmLinda K. Muthen23
Side effects of including missing data8-21-06  3:58 pmBengt O. Muthen12
Missing occasions in growth model 6-27-06  10:40 pmShige Song9
LCA and Multiple Imputed Datasets9-24-15  5:22 pmLinda K. Muthen29
Missing with WLSMV3-06-13  9:53 amLinda K. Muthen10
MAR or Not MAR?2-26-12  10:42 amBengt O. Muthen6
DIFFTEST with type=missing10-25-06  7:46 amLinda K. Muthen5
Using TYPE=Imputation1-31-07  8:34 amBengt O. Muthen2
FIML and power analysis2-24-07  4:24 pmBengt O. Muthen2
Missing values, MI, and growth mixture model4-22-17  5:33 pmBengt O. Muthen21
Missing on Y variables only2-02-16  5:53 pmBengt O. Muthen9
Maximum number of missing data patterns?12-13-16  6:29 pmBengt O. Muthen4
FQL Estimation6-04-07  10:47 amLinda K. Muthen2
Multiple mediation, FIML, and bootstrap1-09-15  2:43 pmLinda K. Muthen14
Missing DV in a latent curve model6-28-07  9:51 amLinda K. Muthen4
Reliability test7-17-07  6:20 pmBengt O. Muthen2
FIML vs MI2-27-15  8:58 pmNara Jang40
Nonignorable Missing Data11-17-16  2:56 pmBengt O. Muthen27
Joint-Modeling Survival and Repeated Measure 1-12-12  9:46 amLinda K. Muthen9
MI Datasets Generated Outside of Mplus4-20-15  6:23 amLinda K. Muthen12
Setting a minimum standard for missing data11-24-07  9:23 amLinda K. Muthen2
SQM and Missing Values12-19-07  9:04 amLinda K. Muthen2
Imputation and memory limits11-28-11  1:37 amKristine Khachatryan5
Residual degrees of freedom with Missing Data3-22-08  9:41 amLinda K. Muthen2
FIML not allowed with censored Y?4-04-08  6:27 pmLinda K. Muthen2
Pairwise deletion and number of valid case4-14-16  11:49 amLinda K. Muthen11
Auxilary Vars. to make data MAR4-21-08  8:00 amLinda K. Muthen2
Multi-level CFa with missing data6-14-08  4:00 pmBengt O. Muthen2
Missing Data Estimators8-01-08  9:50 amLinda K. Muthen2
Auxiliary function of missing data12-12-16  4:31 pmBengt O. Muthen35
Missing on x-variable - solution?9-11-15  12:42 pmLyndsay Boggess33
Missing Weight Variable in Complex Survey Data3-28-14  11:21 amLinda K. Muthen12
MI and successful computations9-14-08  10:08 amLinda K. Muthen7
Estimated means with MI and LGCM 11-21-08  7:58 amLinda K. Muthen2
Sample size1-29-09  6:00 amLinda K. Muthen2
Missing data in groups and zero variance11-26-15  6:37 pmLinda K. Muthen14
Missing data in analysis with count outcomes3-17-10  2:54 pmLinda K. Muthen8
Correlations and covariances8-12-15  7:30 pmBengt O. Muthen4
Errors for replication8-08-12  5:58 pmLinda K. Muthen7
Missing on x-variables 10-12-16  4:05 pmBengt O. Muthen53
Auxiliary command and Graham's models10-25-10  6:04 pmLinda K. Muthen9
Multiple Imputation - asymptotic covariance matrix7-29-09  4:46 pmLinda K. Muthen2
Multiple Imputation Syntax2-07-13  9:55 amLinda K. Muthen7
Missing data, nonzero residuals, zero chi-sq9-02-09  1:56 pmBengt O. Muthen3
Missingness fully dependent on grouping variable10-02-09  8:56 amLinda K. Muthen4
Mplus crash with imputated datasets10-12-09  2:47 pmWouter Steenbeek0
The PATTERN option10-23-09  1:37 pmLinda K. Muthen5
Number of observation4-11-14  6:12 amBengt O. Muthen18
Fit with missing data5-11-10  9:42 amLinda K. Muthen12
Non-ignorable missing data in longitudinal studies5-13-16  2:12 pmBengt O. Muthen16
Probabilistic latent semantic analysis3-29-10  2:44 pmLinda K. Muthen2
Multivariate normality7-16-10  3:24 pmTom Fisseha7
Multiple Imputation in Mplus 69-08-16  1:28 pmBengt O. Muthen17
Missing data in categorical outcomes (MAR)6-16-10  8:16 amLinda K. Muthen2
Threshold for multilevel simulation9-12-10  12:58 pmBengt O. Muthen14
Imputation and Latent Class Analysis2-16-17  9:09 amJon Heron9
Individual and aggregated results for imputation7-21-10  10:12 amLinda K. Muthen2
Plausible value12-09-15  1:39 pmLisa M. Yarnell45
Multiple imputation with complex survey data8-13-10  9:47 amLinda K. Muthen2
Missing data options for version 62-03-11  2:50 pmLinda K. Muthen6
Out of range values6-07-13  9:18 amJenny L. 5
Class label switching and global maximum?5-31-14  2:02 pmBengt O. Muthen6
Error message11-07-10  9:35 amLinda K. Muthen2
Missingness by design? 7-30-13  10:14 amLinda K. Muthen4
PSI matrix NPD in imputation6-18-13  11:23 amBengt O. Muthen8
Export multiple imputation11-29-10  5:56 amLinda K. Muthen4
Multiple Imputation1-07-15  5:49 pmBengt O. Muthen22
Multiple imputation with categorical covariates12-02-10  9:57 amLinda K. Muthen2
PA with missing data, binary dependent vars12-05-10  5:21 pmKathryn Degnan3
Can I ask Mplus to read Multiple inputation data?2-14-11  8:08 amWen-Hsu Lin4
MI of incidental truncated variables3-09-11  6:22 pmBengt O. Muthen5
Bootstrapped Confidence Intervals for Correlations5-25-11  11:00 pmLevente Littvay5
SRMR with missing, continuous data4-05-11  9:37 amLinda K. Muthen2
Missing data regression question4-22-11  3:49 pmBengt O. Muthen2
Propensity of missingness 5-21-11  9:56 amBengt O. Muthen6
Multiple imputation with survival data5-13-11  6:09 amLinda K. Muthen2
MAR vs. MCAR6-22-11  9:42 amLinda K. Muthen15
Generating missing data6-09-11  6:48 amLinda K. Muthen2
Missing Data with Categorical Variables10-21-16  12:56 pmBengt O. Muthen11
Multilevel imputation9-05-16  9:38 amBonamy Oliver32
Ordinal data6-28-11  9:21 amTihomir Asparouhov11
WLSMV with missing data6-19-11  7:56 pmLinda K. Muthen2
Observations removed because of missing values7-05-11  7:50 amLinda K. Muthen2
Missing data using logistic regression9-24-15  5:18 pmLinda K. Muthen4
Nested model comparisons with imputed data4-05-17  4:02 pmBengt O. Muthen13
How to delete a particular observation #?10-20-16  2:01 pmLinda K. Muthen6
Zero covariance coverage9-08-11  3:17 pmTihomir Asparouhov4
Multiple Imputation with count data6-19-12  3:58 pmBengt O. Muthen7
Missing original variables in imputed dataset9-30-11  6:31 amLinda K. Muthen2
Imputation and WEIGHT option2-18-16  10:44 amLinda K. Muthen13
Missing observations in LCA5-15-15  5:40 pmBengt O. Muthen8
Loglikelihood ratio test with MI data11-07-11  1:13 pmTihomir Asparouhov2
Ordinal independent variables11-14-11  6:23 amLinda K. Muthen2
MLM11-19-11  5:34 amLinda K. Muthen2
Extracting fit statistics from MI output7-12-13  7:19 amMichael Hallquist7
Mean display12-16-11  2:05 pmLinda K. Muthen2
Significance of path analysis versus t-test12-22-11  10:51 amLinda K. Muthen2
LGM with a large fraction of missing data1-20-12  9:34 amAlan Johnson3
Non-ignorable, non-monotone missing data6-09-16  6:29 pmBengt O. Muthen4
# observations lower than # cases1-26-12  2:18 pmLinda K. Muthen2
Integration=montecarlo6-17-16  1:23 pmBengt O. Muthen5
Multiple imputation with complex survey data2-27-17  6:49 pmBengt O. Muthen30
Multiple Imputation and imputed values2-18-12  8:36 amLinda K. Muthen2
Monte carlo for logistic regression2-21-12  1:51 pmLinda K. Muthen2
Error Message on Missing Data Estimator2-21-12  6:30 pmBengt O. Muthen2
Arbitrary missing X & Y in complex survey data3-06-12  7:21 pmKevin K. Makino8
H1 imputation with multiple groups5-31-12  3:40 pmLinda K. Muthen11
How many decimals is MPlus using?3-03-15  12:09 pmBengt O. Muthen14
Latent Variable Mixture Ignoring Missing6-21-12  3:06 pmLinda K. Muthen6
WLSMV with missing data8-27-14  4:46 pmBengt O. Muthen7
Technical appendices6-22-12  8:40 pmBengt O. Muthen2
Mplus and the "usevariables" list6-27-12  9:04 pmBengt O. Muthen2
Fix index under WLSMV with multiple imputed data9-08-14  11:20 amLinda K. Muthen10
Missingness partly due to non-observed variables8-24-12  2:30 pmLinda K. Muthen8
List file9-18-12  5:49 amLinda K. Muthen11
FIML vs. multiple imputation10-30-13  10:18 amLinda K. Muthen4
MLR to handle both missing and non-normal data3-10-17  6:19 pmBengt O. Muthen19
Large amount of missing on predictor11-10-12  8:13 amLinda K. Muthen4
Missings in version 5.21 vs. version 711-21-12  4:13 pmBengt O. Muthen2
Problem with missing data estimation11-29-12  6:52 amBengt O. Muthen2
New to mplus1-15-13  9:13 pmShraddha Kashyap3
Missingness by design and FIML2-17-15  3:28 pmAimee Maxwell8
Missing Data with Log Reg - Error Message 3-10-13  3:47 pmLinda K. Muthen9
Longitudinal missing by design3-22-13  5:08 pmLinda K. Muthen4
Handling missing data: Bayesian vs. MLR 3-12-17  5:33 pmBengt O. Muthen4
Multiple imputation-increase iterations4-14-13  1:05 amKyle2
User's Guide Ex 11.45-10-13  6:03 pmLinda K. Muthen2
Missing item vs missing entire scale10-11-16  12:03 pmBengt O. Muthen14
Three-level multiple imputation8-09-13  9:35 amLinda K. Muthen2
Factorial Invariance & missing data3-02-14  6:52 amLinda K. Muthen4
Program with no outcome9-10-13  6:23 amLinda K. Muthen2
H0 imputation with Bayes estimator10-09-15  10:11 amBengt O. Muthen11
EFA, external imputation, complex survey design9-13-13  3:39 pmLinda K. Muthen4
The appropriate use of integration10-07-13  11:31 amLinda K. Muthen10
Missing data and case deletion11-21-13  11:14 amLinda K. Muthen4
Analysis variables missing, auxiliary present10-11-13  10:23 amLinda K. Muthen2
GCM with missing data imputed in stata10-14-13  9:44 amLinda K. Muthen5
Missing data_covariates11-26-13  9:20 amLinda K. Muthen2
Missing data & multiple group analysis1-14-14  6:28 amLinda K. Muthen2
Missing Categorical Predictors in Multilevel Model1-22-14  10:08 amLinda K. Muthen6
Imputation of Multilevel Data6-23-15  6:33 pmAlan Taylor9
Implist not generating?1-27-14  11:54 amLinda K. Muthen2
DEFINE command with Multiple Imputation data2-06-14  6:34 amLinda K. Muthen4
Why I can't see output?2-16-14  6:33 amLinda K. Muthen2
Discrepancies with ALGORITHM=INTEGRATION2-20-14  10:18 amLinda K. Muthen3
Imputed dummy variable 2-26-14  4:30 pmLinda K. Muthen4
Assessing dropout in a longitudinal study3-03-14  12:57 pmJ Dennis3
Limitations of Maximum Likelihood Estimation8-30-14  10:02 amLinda K. Muthen4
Model Not Running6-06-14  8:30 amLinda K. Muthen2
Multiple Imputation: dat file spacing6-06-14  5:19 pmLinda K. Muthen2
Covariate missing by design8-15-14  4:36 pmBengt O. Muthen10
Joint LCA and Continuous time Survival9-04-14  5:09 pmOxnard Montalvo3
Muthen-Roy PMM: SDs/SEs for Timepoint Means9-02-14  3:24 pmBengt O. Muthen6
Confirmatory factor analysis with NMAR data9-10-14  11:42 pmJukka Matias Marjane7
Two level multiple imputation12-11-14  8:35 amLinda K. Muthen7
FIML in a two level model with covariates2-17-16  9:09 amZeynep Türktorun11
Mplus excludes values that are non-missing3-08-15  1:41 pmLinda K. Muthen4
H0 imputation and type = random10-23-14  11:41 pmJon Heron6
Multiple Imputation clustering and iterations11-24-14  8:12 pmBengt O. Muthen12
Ssd Chemical for cleaning black Dollars, euros,12-05-14  2:07 amJackson0
Latent Class H0 model12-10-14  1:15 amJon Heron7
Random slopes analysis and FIML12-20-14  12:54 pmLinda K. Muthen6
Missing data for a twolevel model1-14-15  10:46 amBengt O. Muthen2
MCAR Chi Square Value1-14-15  4:02 pmLinda K. Muthen2
Wanted missings in longitudinal model1-21-15  9:23 amBengt O. Muthen2
Missing covariate data in Cox regression1-26-15  3:52 pmTihomir Asparouhov4
Reading imputed datasets1-28-15  9:09 amLinda K. Muthen2
Missing Items needed to compute total score2-24-15  7:36 amLinda K. Muthen8
Filling in Missing Data and Saving New File2-21-15  9:13 amLinda K. Muthen2
Comparing models with multiple imputation3-12-15  10:04 amTihomir Asparouhov4
Creating new variables and Saving3-04-15  4:10 pmBengt O. Muthen2
Missing correlations in matrix3-20-15  4:08 pmBengt O. Muthen12
Discrepant number of observations imputed (error)3-24-15  8:12 amMichelle Colder Carr4
FIML and warning message4-06-15  10:38 amJames McMahon3
Barcelona v bayern munich live5-06-15  10:48 ammoti mala0
FIML or LISTWISE5-07-15  6:54 pmMarie Alice3
Bayern munich vs barcelona5-12-15  5:44 amjmmlae0
Missing Data Imputation Approach5-20-15  11:51 amBengt O. Muthen2
Single file with multiple imputions5-22-15  7:15 amLinda K. Muthen2
Missing data regression6-02-15  7:03 pmAnthony Mancini3
Juventus vs Barcelona6-06-15  2:15 amjmmlae0
FIML in Large Samples6-12-15  4:54 pmBengt O. Muthen2
Specifying Iterations for Multiple Imputation6-16-15  2:25 amSimon Grund3
Cases with missing DV discarded in MI (H0)6-15-15  2:23 pmTihomir Asparouhov2
Reporting Sample Stats from Imputed Data7-02-15  12:47 pmLinda K. Muthen2
Managing items with two response categories8-12-15  5:11 pmBengt O. Muthen6
Missing Observed Covariates8-12-15  5:13 pmBengt O. Muthen3
Multiple Imputation with MODEL = SEQUENTIAL8-22-15  11:15 amJonathon Little6
Multiple Imputation H1 - estimator choice8-21-15  2:45 pmBengt O. Muthen2
Latent interactions with missing data9-20-15  11:43 amBengt O. Muthen6
Multiple imputation of individual items vs. scale2-01-17  6:23 pmBengt O. Muthen4
Missing data in discrete time survival analysis10-27-15  5:51 pmBengt O. Muthen4
FIML for linear regression4-07-17  12:46 pmAds3
Missing data with estimated intercepts3-14-16  6:20 pmBengt O. Muthen2
Multiple Imputation Saved Files3-23-16  12:40 pmLinda K. Muthen5
Imputing aggregate scores3-22-16  6:20 pmBengt O. Muthen4
Quick MNAR query4-25-16  2:26 amJon Heron3
Missing data and DEFINE5-08-16  11:58 pmAurelie Lange7
Missing Data and Bootstrap6-06-16  10:20 amTihomir Asparouhov2
Single Stochastic Imputation for Missing Data6-20-16  4:35 pmBengt O. Muthen2
Shared parameter model7-21-16  5:28 pmBengt O. Muthen2
Bootstrapping with Non-Normal Data7-29-16  3:14 pmBengt O. Muthen3
Missingness correlated variables8-03-16  10:49 amBengt O. Muthen4
Listwise=OFF8-24-16  1:20 pmLinda K. Muthen4
Missing data in moderated mediation model9-09-16  3:38 pmBengt O. Muthen6
Missing data, moderation, mediation9-17-16  11:28 pmS. Schukajlow13
Multilevel models, imputation and interactions9-12-16  10:59 amBengt O. Muthen4
Multiple Regression with Imputed Data11-23-16  2:42 pmBengt O. Muthen2
Multiple Regression with Imputed Data11-23-16  2:43 pmBengt O. Muthen2
Multiple Regression with Imputed Data11-23-16  2:43 pmBengt O. Muthen2
Fatal error during imputation12-13-16  6:33 pmBengt O. Muthen4
Using imputated data for a twolevel model12-16-16  5:42 pmBengt O. Muthen2
Muthen Roy s and q parameter1-13-17  5:23 pmBengt O. Muthen2
FIML Requirements1-24-17  6:35 amBengt O. Muthen8
Multiple Regression with Imputed Data1-25-17  9:12 amLarissa Gaias1
Missing data: mediation with count outcome4-13-17  4:17 pmBengt O. Muthen2
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