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Helmut Schütz

2007-Apr-18 12:46 UTC

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

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

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 Sch?tz
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

Charilaos Skiadas

2007-Apr-18 13:19 UTC

head link

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

On Apr 18, 2007, at 8:46 AM, Helmut Sch?tz 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):
[ snip ]
> 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
>
> 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]))
First off, those three could probably be simplified slightly as:
as.numeric(exp(-diff(result$estimate)))
as.numeric(exp(-result$conf.int))

The simplest solution I think is to specify that resp$treatment  
should have the levels ordered in the way you like them using this  
first:

resp$treatment <- ordered(resp$treatment, levels=rev(levels(resp 
$treatment)))

Then the t.test will show things in the order you want them.
> Best regards,
> Helmut
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College

Douglas Bates

2007-Apr-18 13:19 UTC

head link

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

On 4/18/07, Helmut Sch?tz <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 Sch?tz
> 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
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Dimitris Rizopoulos

2007-Apr-18 13:32 UTC

head link

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

take a look at

?relevel()


Best,
Dimitris

----
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
     http://www.student.kuleuven.be/~m0390867/dimitris.htm


----- Original Message ----- 
From: "Helmut Sch?tz" <helmut.schuetz at bebac.at>
To: <r-help at stat.math.ethz.ch>
Sent: Wednesday, April 18, 2007 2:46 PM
Subject: [R] Two sample t.test, order of comparions


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

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 Sch?tz
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

______________________________________________
R-help at stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

Helmut Schütz

2007-Apr-18 14:17 UTC

head link

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

Dear Charilaos!

Charilaos Skiadas wrote:>>
>> 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]))
>
> First off, those three could probably be simplified slightly as:
> as.numeric(exp(-diff(result$estimate)))
> as.numeric(exp(-result$conf.int))
>
> The simplest solution I think is to specify that resp$treatment should 
> have the levels ordered in the way you like them using this first:
>
> resp$treatment <- ordered(resp$treatment, 
> levels=rev(levels(resp$treatment)))
>
> Then the t.test will show things in the order you want them.I applied relevel() as suggested by Douglas and Dimitri:

 > relevel(resp$treatment, ref = "Reference")
 > result <- t.test(logAUC ~ treatment, data = resp, subset = (period == 
1), var.equal = FALSE, conf.level = 0.90)
 > result

yielding

        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

So right now the confidence interval in the log-domain is of the correct 
order.

Your first suggestion is working (sign changed due to reversed level)

 > as.numeric(exp(diff(result$estimate)))
 > [1] 0.8365723

But still I have to apply

 > as.numeric(exp(-result$conf.int[2]))
[1] 0.634936
 > as.numeric(exp(-result$conf.int[1]))
[1] 1.102242

because
 > as.numeric(exp(-result$conf.int))
[1] 1.102242 0.634936

in order to get the correct CI in the untransformed domain I had to sort 
the list:
 > sort(as.numeric(exp(-result$conf.int)))
[1] 0.634936 1.102242

Best regards,
Helmut

-- 
Ing. Helmut Sch?tz
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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