UCLA Academic Technology Services HomeServicesClassesContactJobs
Stat Computing > Stata > FAQ
Help the Stat Consulting Group by giving a gift             
Loading

Stata FAQ
How can I do anova contrasts using the margins command? (Stata 11)

The margins command introduced in Stata 11 provides an easy way to compute contrasts in analysis of variance designs. We will begin by loading the hsbanova dataset and running a factorial anova with read as the response variable. 
use http://www.ats.ucla.edu/stat/data/hsbanova, clear

anova read grp##female

                           Number of obs =     200     R-squared     =  0.2104
                           Root MSE      = 9.27502     Adj R-squared =  0.1817

                  Source |  Partial SS    df       MS           F     Prob > F
              -----------+----------------------------------------------------
                   Model |     4402.42     7  628.917143       7.31     0.0000
                         |
                     grp |   3909.6042     3   1303.2014      15.15     0.0000
                  female |  117.305356     1  117.305356       1.36     0.2444
              grp#female |  427.282493     3  142.427498       1.66     0.1780
                         |
                Residual |       16517   192  86.0260417   
              -----------+----------------------------------------------------
                   Total |    20919.42   199  105.122714
Neither the grp by female interaction nor the female main effect were significant. Prior to the experiment we decided that four comparisons among the grp means would be theoretically interesting and that we would test these if grp was statistically significant. It was and so we will test the following contrasts:

It can also be useful to look at these contrasts in terms of the weights applied to each of the means. The four contrasts above would look something like this: Note that for each of the above contrasts the sum of the weights is zero.

We can now begin our multiple comparisons by running the margins command with the asbalanced and post options. 

margins grp, asbalanced post

Adjusted predictions                              Number of obs   =        200

Expression   : Linear prediction, predict()
at           : grp              (asbalanced)
               female           (asbalanced)

------------------------------------------------------------------------------
             |            Delta-method
             |     Margin   Std. Err.      z    P>|z|     [95% Conf. Interval]
-------------+----------------------------------------------------------------
         grp |
          1  |   46.15942   1.315904    35.08   0.000      43.5803    48.73854
          2  |   49.95536   1.385722    36.05   0.000     47.23939    52.67132
          3  |   54.99107    1.20007    45.82   0.000     52.63898    57.34317
          4  |   57.86032   1.399677    41.34   0.000     55.11701    60.60364
------------------------------------------------------------------------------
The margins command displays the adjusted marginal means (aka lsmeans, aka estimated marginal means) for each of the four levels of grp. We will now proceed to compute each of the one degree of freedom contrasts two ways; first using the test command and then using lincom. The test command produces a chi-square while the lincom command produces a z-test. Squaring the z yields the same value as the chi-square. 
/* contrast 1: grp1 vs grp2 */

test 1.grp - 2.grp = 0

 ( 1)  1bn.grp - 2.grp = 0

           chi2(  1) =    3.95
         Prob > chi2 =    0.0470

lincom 1.grp - 2.grp

 ( 1)  1bn.grp - 2.grp = 0

------------------------------------------------------------------------------
             |      Coef.   Std. Err.      z    P>|z|     [95% Conf. Interval]
-------------+----------------------------------------------------------------
         (1) |  -3.795937   1.910975    -1.99   0.047     -7.54138   -.0504938
------------------------------------------------------------------------------

/* contrast 2: grp3 vs grp4 */

test 3.grp - 4.grp = 0

 ( 1)  3.grp - 4.grp = 0

           chi2(  1) =    2.42
         Prob > chi2 =    0.1197

lincom 3.grp - 4.grp

 ( 1)  3.grp - 4.grp = 0

------------------------------------------------------------------------------
             |      Coef.   Std. Err.      z    P>|z|     [95% Conf. Interval]
-------------+----------------------------------------------------------------
         (1) |  -2.869252   1.843709    -1.56   0.120    -6.482856    .7443509
------------------------------------------------------------------------------

/* contrast 3: (grp1 & grp2) vs (grp3 & grp4) */

test 1.grp + 2.grp - 3.grp - 4.grp = 0

 ( 1)  1bn.grp + 2.grp - 3.grp - 4.grp = 0

           chi2(  1) =   39.73
         Prob > chi2 =    0.0000

lincom 1.grp + 2.grp - 3.grp - 4.grp

 ( 1)  1bn.grp + 2.grp - 3.grp - 4.grp = 0

------------------------------------------------------------------------------
             |      Coef.   Std. Err.      z    P>|z|     [95% Conf. Interval]
-------------+----------------------------------------------------------------
         (1) |  -16.73662   2.655389    -6.30   0.000    -21.94108   -11.53215
------------------------------------------------------------------------------

/* contrast 4: (grp1, grp2 &grp3) vs (grp4) */

test 1/3*1.grp + 1/3*2.grp + 1/3*3.grp - 4.grp = 0

 ( 1)  .3333333*1bn.grp + .3333333*2.grp + .3333333*3.grp - 4.grp = 0

           chi2(  1) =   22.23
         Prob > chi2 =    0.0000

lincom 1/3*1.grp + 1/3*2.grp + 1/3*3.grp - 4.grp

 ( 1)  .3333333*1bn.grp + .3333333*2.grp + .3333333*3.grp - 4.grp = 0

------------------------------------------------------------------------------
             |      Coef.   Std. Err.      z    P>|z|     [95% Conf. Interval]
-------------+----------------------------------------------------------------
         (1) |  -7.491708   1.588985    -4.71   0.000    -10.60606   -4.377355
------------------------------------------------------------------------------
We did the last comparison using the weights (1/3 1/3 1/3 -1). We could get the same chi-square and z using the weights (1 1 1 -3). However, you will note that the coefficient in the lincom will have a different numerical value. 
test 1.grp + 2.grp + 3.grp - 3*4.grp = 0

 ( 1)  1bn.grp + 2.grp + 3.grp - 3*4.grp = 0

           chi2(  1) =   22.23
         Prob > chi2 =    0.0000

lincom 1.grp + 2.grp + 3.grp - 3*4.grp

 ( 1)  1bn.grp + 2.grp + 3.grp - 3*4.grp = 0

------------------------------------------------------------------------------
             |      Coef.   Std. Err.      z    P>|z|     [95% Conf. Interval]
-------------+----------------------------------------------------------------
         (1) |  -22.47512   4.766954    -4.71   0.000    -31.81818   -13.13206
------------------------------------------------------------------------------
At this point we should consider some kind of adjustment for having done four contrasts. The easiest approach would be a Bonferroni adjustment made by dividing our alpha level by the number of comparisons (.05/4 = .0125). Thus, any contrast less then .0125 would be significant, namely contrasts 3 and 4.

Alternatively, we might want to consider using a Scheffé adjustment since two of the contrasts (3 and 4) were non-pairwise contrasts. The critical value for Scheffé can be computed from the following:

Although, the critical value for Scheffé is an F-ratio we can compare it to the chi-square with one degree of freedom from the test commands. Once again only contrasts 3 and 4 were statistically significant.

How to cite this page

Report an error on this page or leave a comment

UCLA Researchers are invited to our Statistical Consulting Services
We recommend others to our list of Other Resources for Statistical Computing Help
These pages are Copyrighted (c) by UCLA Academic Technology Services

The content of this web site should not be construed as an endorsement of any particular web site, book, or software product by the University of California.