Mplus Data Analysis Examples
Multinomial Logistic Regression

Version info: Code for this page was tested in Mplus version 6.12.

Multinomial logistic regression is used to model nominal outcome variables, in which the log odds of the outcomes are modeled as a linear combination of the predictor variables.

Please note: The purpose of this page is to show how to use various data analysis commands. It does not cover all aspects of the research process which researchers are expected to do. In particular, it does not cover data cleaning and checking, verification of assumptions, model diagnostics and potential follow-up analyses.

Examples of multinomial logistic regression

Example 1. People's occupational choices might be influenced by their parents' occupations and their own education level. We can study the relationship of one's occupation choice with education level and father's occupation.  The occupational choices will be the outcome variable which consists of categories of occupations.

Example 2. A biologist may be interested in food choices that alligators make. Adult alligators might have different preferences from young ones. The outcome variable here will be the types of food, and the predictor variables might be size of the alligators and other environmental variables.

Example 3. Entering high school students make program choices among general program, vocational program and academic program. Their choice might be modeled using their writing score and their social economic status. 

Description of the data

For our data analysis example, we will expand our third example with a hypothetical data set. The data set contains variables on 200 students. The outcome variable is prog, program type, where program type 1 is general, type 2 is academic, and type 3 is vocational. The predictor variables are social economic status, ses, a three-level categorical variable and writing score, write, a continuous variable. Let's start with getting some descriptive statistics of the variables of interest. You can download the data set here.

Data:
  File is D:\hsbdemo.dat ;
Variable:
  Names are 
     id female ses schtyp prog read write math science socst honors awards
     cid;
  Missing are all (-9999) ; 
Analysis: 
  Type = basic;
Plot:
    type = plot1;



RESULTS FOR BASIC ANALYSIS


     ESTIMATED SAMPLE STATISTICS


           Means
              ID            FEMALE        SES           SCHTYP        PROG
              ________      ________      ________      ________      ________
      1       100.500         0.545         2.055         1.160         2.025


           Means
              READ          WRITE         MATH          SCIENCE       SOCST
              ________      ________      ________      ________      ________
      1        52.230        52.775        52.645        51.850        52.405


           Means
              HONORS        AWARDS        CID
              ________      ________      ________
      1         0.265         1.670        10.430


           Covariances
              ID            FEMALE        SES           SCHTYP        PROG
              ________      ________      ________      ________      ________
 ID          3333.250
 FEMALE        -2.507         0.248
 SES            8.797        -0.045         0.522
 SCHTYP        10.210         0.003         0.036         0.134
 PROG          -2.308         0.001         0.009        -0.024         0.474
 READ          87.755        -0.270         2.167         0.323        -0.951
 WRITE        101.907         1.208         1.417         0.441        -1.179
 MATH         118.283        -0.137         1.840         0.337        -0.966
 SCIENCE      183.260        -0.628         2.018         0.234        -1.291
 SOCST        113.333         0.279         2.568         0.380        -1.440
 HONORS         1.148         0.031         0.060        -0.002        -0.012
 AWARDS        10.490         0.160         0.318         0.038        -0.152
 CID           89.335         0.031         1.336         0.236        -0.766


           Covariances
              READ          WRITE         MATH          SCIENCE       SOCST
              ________      ________      ________      ________      ________
 READ         104.597
 WRITE         57.707        89.394
 MATH          63.297        54.555        87.329
 SCIENCE       63.649        53.266        58.212        97.538
 SOCST         68.067        61.236        54.489        49.191       114.681
 HONORS         2.209         2.820         2.234         1.820         1.833
 AWARDS        10.421        14.616        10.168         9.021        10.129
 CID           50.576        44.807        46.073        47.645        40.461


           Covariances
              HONORS        AWARDS        CID
              ________      ________      ________
 HONORS         0.195
 AWARDS         0.652         3.291
 CID            1.611         7.832        33.485


           Correlations
              ID            FEMALE        SES           SCHTYP        PROG
              ________      ________      ________      ________      ________
 ID             1.000
 FEMALE        -0.087         1.000
 SES            0.211        -0.125         1.000
 SCHTYP         0.482         0.015         0.137         1.000
 PROG          -0.058         0.004         0.017        -0.095         1.000
 READ           0.149        -0.053         0.293         0.086        -0.135
 WRITE          0.187         0.256         0.207         0.127        -0.181
 MATH           0.219        -0.029         0.272         0.098        -0.150
 SCIENCE        0.321        -0.128         0.283         0.065        -0.190
 SOCST          0.183         0.052         0.332         0.097        -0.195
 HONORS         0.045         0.139         0.190        -0.015        -0.038
 AWARDS         0.100         0.177         0.243         0.057        -0.121
 CID            0.267         0.011         0.320         0.111        -0.192


           Correlations
              READ          WRITE         MATH          SCIENCE       SOCST
              ________      ________      ________      ________      ________
 READ           1.000
 WRITE          0.597         1.000
 MATH           0.662         0.617         1.000
 SCIENCE        0.630         0.570         0.631         1.000
 SOCST          0.621         0.605         0.544         0.465         1.000
 HONORS         0.489         0.676         0.542         0.418         0.388
 AWARDS         0.562         0.852         0.600         0.503         0.521
 CID            0.855         0.819         0.852         0.834         0.653


           Correlations
              HONORS        AWARDS        CID
              ________      ________      ________
 HONORS         1.000
 AWARDS         0.815         1.000
 CID            0.631         0.746         1.000

Analysis methods you might consider

• Multinomial logistic regression: the focus of this page.
• Multinomial probit regression: similar to multinomial logistic regression but with independent normal error terms.
• Multiple-group discriminant function analysis: A multivariate method for multinomial outcome variables
• Multiple logistic regression analyses, one for each pair of outcomes: One problem with this approach is that each analysis is potentially run on a different sample. The other problem is that without constraining the logistic models, we can end up with the probability of choosing all possible outcome categories greater than 1. 
• Collapsing number of categories to two and then doing a logistic regression: This approach suffers from loss of information and changes the original research questions to very different ones.
• Ordinal logistic regression: If the outcome variable is truly ordered and if it also satisfies the assumption of proportional odds, then switching to ordinal logistic regression will make the model more parsimonious. 
• Alternative-specific multinomial probit regression: allows different error structures therefore allows to relax the independence of irrelevant alternatives (IIA, see below "Things to Consider") assumption. This requires that the data structure be choice-specific.
• Nested logit model: also relaxes the IIA assumption, also requires the data structure be choice-specific.

Multinomial logistic regression

Below we show how to regress prog on ses and write in a multinomial logit model in Mplus.  We specify that the dependent variable, prog, is an unordered categorical variable using the Nominal option.  Mplus will not automatically dummy-code categorical variables for you, so in order to get separate coefficients for ses groups 1 and 2 relative to ses group 3, we must create dummy variables using the Define command. We include our newly created dummy variables, ses1 and ses2, in both the Usevariables option and the Model command. In the multinomial logit model, one outcome group is used as the "reference group" (also called a base category), and the coefficients for all other outcome groups describe how the independent variables are related to the probability of being in that outcome group versus the reference group. Mplus automatically uses the last category of the dependent variable as the base category or comparison group, which in this case is the vocational category. Looking at the syntax below, in the model statement we have entered "prog#1 prog#2 on ses1 ses2 write." Mplus uses a variable name followed by a pound sign and a number to refer to the categories of the nominal dependent variable, except the final category, which is the reference group and cannot be referred to in the model statement (if you try, Mplus will issue an error message). Thus the line included in our model statement indicates that we want to regress both levels of prog on ses(as dummy variables) and write.  Additionally, by default for multinomial logistic regression, Mplus calculates robust standard errors.

Data:
  File is C:\Users\alin\Documents\mplus_andy\hsbdemo.dat ;
Variable:
  Names are 
     id female ses schtyp prog read write math science socst honors awards
     cid;
  Missing are all (-9999) ;
  Usevariables are prog write ses1 ses2;
  Nominal is prog;
Define:
  ses1 = ses == 1;
  ses2 = ses == 2; 
Model:
    prog#1 prog#2 on ses1 ses2 write;

MODEL FIT INFORMATION

Number of Free Parameters                        8

Loglikelihood

          H0 Value                        -179.982
          H0 Scaling Correction Factor       1.016
            for MLR

Information Criteria

          Akaike (AIC)                     375.963
          Bayesian (BIC)                   402.350
          Sample-Size Adjusted BIC         377.005
            (n* = (n + 2) / 24)



MODEL RESULTS

                                                    Two-Tailed
                    Estimate       S.E.  Est./S.E.    P-Value

 PROG#1     ON
    SES1               0.180      0.651      0.277      0.782
    SES2              -0.645      0.602     -1.071      0.284
    WRITE              0.056      0.024      2.276      0.023

 PROG#2     ON
    SES1              -0.983      0.612     -1.604      0.109
    SES2              -1.274      0.524     -2.430      0.015
    WRITE              0.114      0.022      5.208      0.000

 Intercepts
    PROG#1            -2.546      1.331     -1.914      0.056
    PROG#2            -4.236      1.206     -3.511      0.000


LOGISTIC REGRESSION ODDS RATIO RESULTS

 PROG#1     ON
    SES1               1.197
    SES2               0.525
    WRITE              1.057

 PROG#2     ON
    SES1               0.374
    SES2               0.280
    WRITE              1.120

• In the output above we see the final log likelihood (-179.982), which can be used in comparisons of nested models.
• Under the heading "Information Criteria" we see the Akaike and Bayesian information criterion values. Both the AIC and the BIC are measures of fit with some correction for the complexity of the model, but the BIC has a stronger correction for parsimony. In both cases, lower values indicate better fit of the model.
• The output above has two parts, labeled with the categories of the outcome variable prog. They correspond to the two equations below:
  \[ln\left(\frac{P(prog=general)}{P(prog=vocational)}\right) = b_{10} + b_{11}(ses=1) + b_{12}(ses=2) + b_{13}write\]

  \[ln\left(\frac{P(prog=academic)}{P(prog=vocational)}\right) = b_{20} + b_{21}(ses=1) + b_{22}(ses=2) + b_{23}write\]

  where \(b\)'s are the regression coefficients.

  • A one-unit increase in the variable write is associated with a 0.056 increase in the relative log odds of being in general program vs. vocational program .
  • A one-unit increase in the variable write is associated with a 0.114 decrease in the relative log odds of being in academic program vs. vocational program.
  • The relative log odds of being in general program vs. in vocational program will decrease by 0.645 if moving from the highest level of ses (ses==3) to the middle level of ses (ses==2).

The ratio of the probability of choosing one outcome category over the probability of choosing the baseline category is often referred to as relative risk (and it is also sometimes referred to as odds as we have just used to described the regression parameters above).  Relative risk can be obtained by exponentiating the linear equations above, yielding regression coefficients that are relative risk ratios for a unit change in the predictor variable. These relative risk ratios can be found in the Logistic Regression Odds Ratio Results section of the output.

• The relative risk ratio for a one-unit increase in the variable write is 1.057 (exp(0.056) from the Model Results output) for being in general program vs. vocational program.
• The relative risk ratio switching from ses = 3 to 1 is 1.197(exp(0.180) from the Model Results output) for being in general program vs. vocational program. In other words, the expected risk of staying in the general program is higher for subjects who are low in ses.

Things to consider

• The Independence of Irrelevant Alternatives (IIA) assumption: roughly, the IIA assumption means that adding or deleting alternative outcome categories does not affect the odds among the remaining outcomes.
• Diagnostics and model fit: unlike logistic regression where there are many statistics for performing model diagnostics, it is not as straightforward to do diagnostics with multinomial logistic regression models.  For the purpose of detecting outliers or influential data points, one can run separate logit models and use the diagnostics tools on each model.
• Pseudo-R-Squared: the R-squared offered in the output is basically the change in terms of log-likelihood from the intercept-only model to the current model. It does not convey the same information as the R-square for linear regression, even though it is still "the higher, the better".
• Sample size: multinomial regression uses a maximum likelihood estimation method, it requires a large sample size. It also uses multiple equations. This implies that it requires an even larger sample size than ordinal or binary logistic regression.
• Complete or quasi-complete separation: Complete separation implies that the outcome variable separates a predictor variable completely, leading to perfect prediction by the predictor variable.  Perfect prediction means that only one value of a predictor variable is associated with only one value of the response variable.  You can do a two-way tabulation of the outcome variable with the problematic variable to look for separation, and if detected, rerun the model without the problematic variable.
• Empty cells or small cells:  You should check for empty or small cells by doing a cross-tabulation between categorical predictors and the outcome variable.  If a cell has very few cases (a small cell), the model may become unstable or it might not even run at all.

See also

• Beyond Binary Logistic Regression with Stata with movies
• Annotated output for the mlogit command

References

• Long, J. S. and Freese, J. (2006) Regression Models for Categorical and Limited Dependent Variables Using Stata, Second Edition. College Station, Texas: Stata Press.
• Hosmer, D. and Lemeshow, S. (2000) Applied Logistic Regression (Second Edition). New York: John Wiley & Sons, Inc..
• Agresti, A. (1996) An Introduction to Categorical Data Analysis. New York: John Wiley & Sons, Inc.