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# st: bug in -anova-

 From "Airey, David C" To Statalist Subject st: bug in -anova- Date Sat, 12 Dec 2009 20:59:50 -0600

```I think I am noticing a bug in -anova- in Stata 11 in relation to automatic handling of categorical variables. Notice how if I don't tell -anova- a variable is categorical, it misses a level when noconstant is used.

. anova htr pretreat##strain // normal result

Number of obs =      36     R-squared     =  0.8933
Root MSE      = 7.77827     Adj R-squared =  0.8755

Source |  Partial SS    df       MS           F     Prob > F
----------------+----------------------------------------------------
Model |  15189.5106     5  3037.90212      50.21     0.0000
|
pretreat |   11977.163     2  5988.58148      98.98     0.0000
strain |  1953.15158     1  1953.15158      32.28     0.0000
pretreat#strain |  1259.19604     2  629.598022      10.41     0.0004
|
Residual |  1815.04618    30  60.5015394
----------------+----------------------------------------------------
Total |  17004.5568    35  485.844479

.
. egen c = group(pretreat strain) // make variable for cell means model

. table pretreat strain, c(mean c) // show cell means grouping variable

------------------------------
|       strain
pretreat | C57BL/6J    DBA/2J
----------+-------------------
SB206553 |        1         2
SB242084 |        3         4
Saline |        5         6
------------------------------

. anova htr ibn.c, noconstant // run cell means model ***CORRECT with 6 df***

Number of obs =      36     R-squared     =  0.9624
Root MSE      = 7.77827     Adj R-squared =  0.9548

Source |  Partial SS    df       MS           F     Prob > F
-----------+----------------------------------------------------
Model |  46410.4313     6  7735.07188     127.85     0.0000
|
c |  46410.4313     6  7735.07188     127.85     0.0000
|
Residual |  1815.04618    30  60.5015394
-----------+----------------------------------------------------
Total |  48225.4775    36   1339.5966

. anova htr c, noconstant // run cell means model ***WRONG with 5 df***

Number of obs =      36     R-squared     =  0.9496
Root MSE      = 8.85083     Adj R-squared =  0.9415

Source |  Partial SS    df       MS           F     Prob > F
-----------+----------------------------------------------------
Model |  45797.0261     5  9159.40521     116.92     0.0000
|
c |  45797.0261     5  9159.40521     116.92     0.0000
|
Residual |  2428.45141    31  78.3371423
-----------+----------------------------------------------------
Total |  48225.4775    36   1339.5966

. regress

Source |       SS       df       MS              Number of obs =      36
-------------+------------------------------           F(  5,    31) =  116.92
Model |  45797.0261     5  9159.40521           Prob > F      =  0.0000
Residual |  2428.45141    31  78.3371423           R-squared     =  0.9496
-------------+------------------------------           Adj R-squared =  0.9415
Total |  48225.4775    36   1339.5966           Root MSE      =  8.8508

------------------------------------------------------------------------------
htr |      Coef.   Std. Err.      t    P>|t|     [95% Conf. Interval]
-------------+----------------------------------------------------------------
c |
2  |   14.16667   3.613335     3.92   0.000     6.797221    21.53611
3  |   17.08333   3.613335     4.73   0.000     9.713888    24.45278
4  |         26   3.613335     7.20   0.000     18.63055    33.36945
5  |   39.05555   3.613335    10.81   0.000      31.6861      46.425
6  |   70.27778   3.613335    19.45   0.000     62.90834    77.64723
------------------------------------------------------------------------------

. test, showorder

Order of columns in the design matrix
1: (c==1)
2: (c==2)
3: (c==3)
4: (c==4)
5: (c==5)
6: (c==6)

I know that at <http://www.stata.com/support/faqs/stat/test1.html> the ibn.c notation is used, but this should be fixed if I'm not missing anything.

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```

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