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

[Charilaos Skiadas]

On Apr 18, 2007, at 8:46 AM, Helmut Schütz 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