# F-test differences Stata and R

I have a question about what the difference is in how Stata and R compute ANOVAs. I have run exactly the same ANOVA in both softwares, but curiously get a different F-statistics for one of the predictors. I´m not too familiar with Stata, but as far as I understood it, I do a Type 2 SS ANOVA for both.

To understand my output, this is my model:
Outcome variable is a continuous variable called vertrauen (=trust)
predictor 1 is a 2-level factor called trustee in R and Goodguy in Stata
predictor 2 is also a 2 level factor called Group in R and uw in Stata.

This is the R output:


>m2-lm(vertrauen~trustee*Group,data=RTG.UWD.short.50)
> Anova(m2,type="2")
>Anova Table (Type II tests)

>Response: vertrauen
>              Sum Sq Df F value    Pr(>F)
>trustee       2.4928  1 24.5497    1.367e-05 ***
>Group         0.0030  1  0.0292    0.8651
>trustee:Group 0.1137  1  1.1200    0.2963
>Residuals     4.0617 40
>
>Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>


This is the Stata output:

. anova vertrauen uw Goodguy uw#Goodguy

Number of obs =         44    R-squared     =  0.3912
Root MSE      =    .318658    Adj R-squared =  0.3455

Source | Partial SS         df         MS        F    Prob>F
-----------+----------------------------------------------------
Model |  2.6095358          3   .86984526      8.57  0.0002
|
uw |  .00296733          1   .00296733      0.03  0.8651
Goodguy |  1.2981586          1   1.2981586     12.78  0.0009
uw#Goodguy |  .11373073          1   .11373073      1.12  0.2963
|
Residual |  4.0617062         40   .10154266
-----------+----------------------------------------------------
Total |   6.671242         43   .15514516


As you can see, the F-statistics for the Group (UW) main effect and for the Group (UW) x trustee (Goodguy) interaction are the same, but for the trustee (Goodguy) main effect they differ. In R it´s almost twice as high as in Stata. I tried to change the order of the predictor and the reference levels, but that didn´t change my R output.

Does anyone know what causes the difference in the F-statistic here? I´m really puzzled about it. I expected it to be the same.

Here is the Stata output without the interaction:

. anova vertrauen uw Goodguy

Number of obs =         44    R-squared     =  0.3741
Root MSE      =    .319124    Adj R-squared =  0.3436

Source | Partial SS         df         MS        F    Prob>F
-----------+----------------------------------------------------
Model |   2.495805          2   1.2479025     12.25  0.0001
|
uw |  .00296733          1   .00296733      0.03  0.8653
Goodguy |  2.4928377          1   2.4928377     24.48  0.0000
|
Residual |   4.175437         41   .10183993
-----------+----------------------------------------------------
Total |   6.671242         43   .15514516


And here is the R output without the interaction:

> m2.4-lm(vertrauen~trustee+Group,data=RTG.UWD.short.50)
> Anova(m2.4)
Anova Table (Type II tests)

Response: vertrauen
Sum Sq Df F value    Pr(>F)
trustee   2.4928  1 24.4780 1.328e-05 ***
Group     0.0030  1  0.0291    0.8653
Residuals 4.1754 41
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>


It´s the same, thus it has to do something with how the two softwares incorporate the interaction term.

I also tried to manually compute the interaction term and found something interesting:

Here is the R output:

RTG.UWD.short.50$interaction-as.numeric(RTG.UWD.short.50$trustee)*as.numeric(RTG.UWD.short.50$Group) > m2.7 Anova(m2.7) Anova Table (Type II tests) Response: vertrauen Sum Sq Df F value Pr(>F) trustee 1.2982 1 12.7844 0.0009316 *** Group 0.0030 1 0.0292 0.8651282 interaction 0.1137 1 1.1200 0.2962617 Residuals 4.0617 40 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 >  And here is the Stata output: . gen interaction=uw*Goodguy . anova vertrauen uw Goodguy interaction Number of obs = 44 R-squared = 0.3912 Root MSE = .318658 Adj R-squared = 0.3455 Source | Partial SS df MS F Prob>F ------------+---------------------------------------------------- Model | 2.6095358 3 .86984526 8.57 0.0002 | uw | .0399785 1 .0399785 0.39 0.5339 Goodguy | 2.3984067 1 2.3984067 23.62 0.0000 interaction | .11373073 1 .11373073 1.12 0.2963 | Residual | 4.0617062 40 .10154266 ------------+---------------------------------------------------- Total | 6.671242 43 .15514516  Thus it seems that there is a difference in how R/ Stata computes the interactions. The R output of the manually computed interaction matches the automatically computed interaction output in Stata. And finally the descriptives from R: > describe(RTG.UWD.short.50$vertrauen)
RTG.UWD.short.50$vertrauen n missing unique Info Mean 44 0 43 1 0.5046 > describe(RTG.UWD.short.50$Group)
RTG.UWD.short.50$Group n missing unique 44 0 2 1 (34, 77%), 2 (10, 23%) > describe(RTG.UWD.short.50$trustee)
RTG.UWD.short.50\$trustee
n missing  unique
44       0       2

bad (22, 50%), good (22, 50%)


and from Stata:

. sum vertrauen uw Goodguy

Variable |        Obs        Mean    Std. Dev.       Min        Max
-------------+---------------------------------------------------------
vertrauen |         44    .5045969    .3938847    .000998          1
uw |         44    .2272727    .4239151          0          1
Goodguy |         44          .5    .5057805          0          1

• There is no equivalent of if vertrauen>-.0001 in your R syntax so far as I can see. Show us the results of summarize uw Goodguy in Stata. Can you get the same results if you omit the interaction term in each case? May 11 '16 at 16:48
• Thanks for looking into this! Missing values of the vertrauen variable were coded as -.0001 in Stata, but I excluded them so that the Stata dataset matches exactly the R dataset. May 12 '16 at 15:00
• I included the outputs without the interaction term and they are identical. However if I manually compute the interaction terms, the R output matches the automatically computed interaction term output from Stata. But if I manually compute the interaction term in Stata, the output doesn´t match the R output. Any idea why that is? May 12 '16 at 15:08