[R] Two sample t.test, order of comparions

[Douglas Bates]

On 4/18/07, Helmut Schütz <helmut.schuetz at bebac.at> wrote:
> Dear group members,
>
> I want to compare response variables ("logAUC") of two groups (treatment
> "Test", "Reference") of a subset ("period == 1") in dataframe "resp"
> (below):
>
>    sequence subject period treatment  AUC   logAUC
> 1        RT       1      1 Reference 44.1 3.786460
> 2        RT       1      2      Test 39.1 3.666122
> 3        RT       2      1 Reference 33.6 3.514526
> 4        RT       2      2      Test 23.8 3.169686
> 5        RT       3      1 Reference 45.5 3.817712
> 6        RT       3      2      Test 40.8 3.708682
> 7        TR       4      1      Test 19.5 2.970414
> 8        TR       4      2 Reference 21.1 3.049273
> 9        TR       5      1      Test 67.2 4.207673
> 10       TR       5      2 Reference 51.5 3.941582
> 11       TR       6      1      Test 25.7 3.246491
> 12       TR       6      2 Reference 30.1 3.404525
> 13       RT       7      1 Reference 35.3 3.563883
> 14       RT       7      2      Test 26.7 3.284664
> 15       RT       8      1 Reference 26.0 3.258097
> 16       RT       8      2      Test 36.5 3.597312
> 17       RT       9      1 Reference 38.2 3.642836
> 18       RT       9      2      Test 57.8 4.056989
> 19       TR      10      1      Test 33.6 3.514526
> 20       TR      10      2 Reference 32.5 3.481240
> 21       TR      11      1      Test 25.1 3.222868
> 22       TR      11      2 Reference 36.8 3.605498
> 23       TR      12      1      Test 44.1 3.786460
> 24       TR      12      2 Reference 42.9 3.758872
> 25       RT      13      1 Reference 25.6 3.242592
> 26       RT      13      2      Test 20.1 3.000720
> 27       RT      14      1 Reference 58.0 4.060443
> 28       RT      14      2      Test 45.3 3.813307
> 29       RT      15      1 Reference 47.2 3.854394
> 30       RT      15      2      Test 51.8 3.947390
> 31       TR      16      1      Test 16.5 2.803360
> 32       TR      16      2 Reference 21.4 3.063391
> 33       TR      17      1      Test 47.3 3.856510
> 34       TR      17      2 Reference 39.4 3.673766
> 35       TR      18      1      Test 22.6 3.117950
> 36       TR      18      2 Reference 17.3 2.850707
> 37       RT      19      1 Reference 17.5 2.862201
> 38       RT      19      2      Test 30.1 3.404525
> 39       RT      20      1 Reference 51.7 3.945458
> 40       RT      20      2      Test 36.0 3.583519
> 41       RT      21      1 Reference 24.5 3.198673
> 42       RT      21      2      Test 18.2 2.901422
> 43       TR      22      1      Test 36.3 3.591818
> 44       TR      22      2 Reference 27.2 3.303217
> 45       TR      23      1      Test 29.4 3.380995
> 46       TR      23      2 Reference 39.6 3.678829
> 47       TR      24      1      Test 18.3 2.906901
> 48       TR      24      2 Reference 20.7 3.030134
>
> The formula method of t.test
>
>  > result <- t.test(logAUC ~ treatment, data = resp, subset = (period ==
> 1), var.equal = FALSE, conf.level = 0.90)
>  > result
>
> gives
>
>         Welch Two Sample t-test
>
> data:  logAUC by treatment
> t = 1.1123, df = 21.431, p-value = 0.2783
> alternative hypothesis: true difference in means is not equal to 0
> 90 percent confidence interval:
>  -0.0973465  0.4542311
> sample estimates:
> mean in group Reference      mean in group Test
>                3.562273                3.383831
>
> Now I'm interested rather in the confidence interval of "Test" -
> "Reference" rather than "Reference" - "Test" which is given by t.test

You could change the order of the levels of the treatment factor.  See

?relevel

>
> Do you know a more elegant way than the clumsy one I have tried?
>
>  > as.numeric(exp(result$estimate[2]-result$estimate[1]))
>  > as.numeric(exp(-result$conf.int[2]))
>  > as.numeric(exp(-result$conf.int[1]))
>
> Best regards,
> Helmut
>
> --
> Ing. Helmut Schütz
> BEBAC - Consultancy Services for
> Bioequivalence and Bioavailability Studies
> Neubaugasse 36/11
> 1070 Vienna, Austria
> tel/fax +43 1 2311746
> e-mail  helmut.schuetz at bebac.at
> web     http://bebac.at
> forum   http://forum.bebac.at
>
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