Missing Data Modeling  
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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 data4-22-14  1:33 pmLorena Llosa506
Fit indexes1-28-14  3:11 pmTihomir Asparouhov25
Data with structural missingness6-21-11  10:26 amLinda K. Muthen11
Missing by design3-20-14  3:21 pmBengt O. Muthen92
Interpreting 'estimated sample statistics'3-07-12  9:13 amLisa M. Yarnell9
Sample statistics in latent growth modeling with missing data9-30-02  2:36 pmLinda K. Muthen2
Significance of correlations in LGM modeling with missing data2-28-14  4:25 pmLinda K. Muthen14
Significance of correlations in LGM modeling with missing data10-03-02  4:25 pmAnonymous1
Missing data in binary outcomes4-03-12  4:11 pmLinda K. Muthen20
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 imputation4-09-14  10:58 amLinda K. Muthen411
Dummy interpretation12-21-13  2:53 amhassan zeb1
Test for MCAR12-09-08  8:30 amLinda K. Muthen15
Missing data modeling3-25-14  3:57 pmAndrea Barrocas Gott35
Missing at Random and Not7-21-08  2:47 pmLinda K. Muthen13
Monte Carlo simulations with missing data10-27-09  4:04 pmLinda K. Muthen26
Missing in EFA/CFA2-16-14  11:17 amLinda K. Muthen36
Missing Data, Complex Samples, and Categorical Data9-16-13  11:17 amLinda K. Muthen21
Sample size3-06-06  10:51 ampoker casino6107
Two part growth model12-02-05  10:33 amtnguyen8
Multiple Group MIMIC model with censored data and MI9-25-08  10:22 amLinda K. Muthen4
Growth model with missing time points4-02-05  8:55 pmLinda K. Muthen2
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 imputation3-02-12  4:30 pmLinda K. Muthen21
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 data8-15-13  8:49 amLinda K. Muthen21
Does Mplus impute missing data/ role of EM?11-19-12  12:06 pmLinda K. Muthen25
Implications of type = missing2-21-06  3:41 pmJoseph7
Dont want deletion in logistic regression2-29-12  8:54 amBengt O. Muthen21
Robust standard errors under MAR3-24-06  6:07 amLinda K. Muthen6
Wrong mean estimates with FIML?6-18-13  5:54 amLinda K. Muthen15
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 Datasets1-24-13  2:50 pmOxnard Montalvo27
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 model4-17-10  6:31 amMyong Hwa Lee5
Missing on Y variables only4-05-07  9:28 amDaniel Rodriguez5
Maximum number of missing data patterns?5-14-07  11:11 amLinda K. Muthen2
FQL Estimation6-04-07  10:47 amLinda K. Muthen2
Multiple mediation, FIML, and bootstrap5-06-10  9:14 amLinda K. Muthen6
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 MI10-12-13  9:45 amLinda K. Muthen35
Nonignorable Missing Data4-20-12  8:35 pmBengt O. Muthen13
Joint-Modeling Survival and Repeated Measure 1-12-12  9:46 amLinda K. Muthen9
MI Datasets Generated Outside of Mplus9-25-07  1:34 pmLinda K. Muthen6
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 case3-17-14  9:44 amLinda K. Muthen9
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 data3-05-14  10:34 amBengt O. Muthen31
Missing on x-variable - solution?4-21-14  6:26 amLinda K. Muthen24
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 variance9-08-13  6:47 amLinda K. Muthen8
Missing data in analysis with count outcomes3-17-10  2:54 pmLinda K. Muthen8
Correlations and covariances6-19-09  9:53 amLinda K. Muthen2
Errors for replication8-08-12  5:58 pmLinda K. Muthen7
Missing on x-variables 2-25-14  1:25 pmLinda K. Muthen16
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 studies5-18-10  1:29 amJon Heron14
Probabilistic latent semantic analysis3-29-10  2:44 pmLinda K. Muthen2
Multivariate normality7-16-10  3:24 pmTom Fisseha7
Multiple Imputation in Mplus 66-27-13  6:05 amAlvin Wee11
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 Analysis1-16-14  9:34 amLinda K. Muthen5
Individual and aggregated results for imputation7-21-10  10:12 amLinda K. Muthen2
Plausible value7-10-13  12:28 pmLinda K. Muthen24
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?10-20-10  6:15 pmBengt O. Muthen4
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 Imputation2-18-14  6:08 pmBengt O. Muthen18
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 Variables6-09-11  7:11 pmLinda K. Muthen2
Multilevel imputation4-04-12  1:47 pmLinda K. Muthen16
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 regression7-05-11  7:48 amLinda K. Muthen2
Nested model comparisons with imputed data8-15-13  10:15 amLinda K. Muthen9
How to delete a particular observation #?8-03-11  11:49 amLinda K. Muthen4
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 option1-22-14  10:13 amLinda K. Muthen11
Missing observations in LCA4-04-12  6:30 amLinda K. Muthen6
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 data1-25-12  9:57 amBengt O. Muthen2
# observations lower than # cases1-26-12  2:18 pmLinda K. Muthen2
Integration=montecarlo1-30-12  8:03 pmJune Zhou3
Multiple imputation with complex survey data3-26-14  6:49 amChristoph Weber24
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?12-06-13  4:08 pmAndriana Rapti12
Latent Variable Mixture Ignoring Missing6-21-12  3:06 pmLinda K. Muthen6
WLSMV with missing data7-05-12  10:38 amLinda K. Muthen5
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 data7-14-12  10:38 amLinda K. Muthen4
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 data9-19-13  11:04 amJohn Plake9
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 FIML2-13-13  4:01 pmLinda K. Muthen3
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 4-13-13  1:57 pmLinda K. Muthen2
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 scale6-18-13  5:05 pmBengt O. Muthen6
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 estimator9-19-13  9:33 amEwan Carr8
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 Data1-22-14  6:22 amLinda K. Muthen4
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
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