[R] Fisher test problem

[markleeds at verizon.net]

  by definition, the one tailed p-value has to be <= 0.5 so there is 
still something wrong with your OpenEpi calc. Most likely it's 
calculating the
2 tailed p-value  and then mistakenly multiplying by 2. For example:

A) Suppose you are testing

                                Ho: u = u_0
                                H1 u > u_0

and your t-stat was  -0.3 Then prob( T > t_0) = 0.62  so your pvalue 
would be 0.62.


B) Instead, suppose you are testing

                                Ho: u = u_0
                                H1 u != u_0

and your t-stat was -0.3. Then, one calculates, prob(T  < t_0 = -.3) = 
.31 and then multiplies by 2 ( because the test is 2 sided ) so the 
pvalue is still 0.62.

So, it's probably doing the first case andf them multiplying it by 2 
which is incorrect. Also, no offense intended but it's dangerous to use 
these things
unless the understanding is there. In fact, it can be dangerous to use 
them even when the understanding is there !!!!!!! Peter Daalgard's book
or John Verzani's book  are probably decent recommendations to read for 
the above kind of thing but an introduction to statistical testing 
textbook is probably most useful. I can't think of a title at the 
moment.









On Sat, Mar 21, 2009 at  9:07 PM, C.H. wrote:

> I tried the OpenEpi, the p-value of 1.25 is due to the fact that the
> one tailed p-value is 0.62. The two tailed p-value then is 0.62 * 2 =
> 1.25. OpenEpi is not clever enough to ceiling the p-value to 1.
>
> CH
>
> On Sun, Mar 22, 2009 at 3:43 AM, David Winsemius 
> <dwinsemius at comcast.net> wrote:
>> Let me ask you: What degree of credibility should be accorded a WWW
>> application that delivers a p-value of 1.25?
>>
>> If the answer is not immediately and glaringly obvious, then tell us, 
>> what
>> sort of axioms of probability are you working with?
>>
>> --
>> David Winsemius
>> On Mar 21, 2009, at 3:17 PM, Viju Moses wrote:
>>
>>> Hi, I noted a discrepancy between R and openepi when I ran a fisher 
>>> test
>>> with the same matrix. In R:
>>>
>>>> a=matrix(c(1,2,6,17), nrow=2)
>>>> a
>>>   [,1] [,2]
>>> [1,]    1    6
>>> [2,]    2   17
>>>> fisher.test(a, conf.int=T)
>>>
>>>      Fisher's Exact Test for Count Data
>>>
>>> data:  a
>>> p-value = 1
>>> alternative hypothesis: true odds ratio is not equal to 1
>>> 95 percent confidence interval:
>>> 0.02061498 31.73691924
>>> sample estimates:
>>> odds ratio
>>> 1.396646
>>>
>>> But in openepi the P value is 1.25. (In another instance too for 
>>> other
>>> sets of data, I had got a p value of 1 in 3 instances for a 
>>> prop.test when I
>>> got 3 other answers on a friend's stata software with the same data. 
>>> )
>>>
>>> I'm using R on Ubuntu Intrepid. Is there anything I'm doing wrong? 
>>> Any
>>> other packages I have to install?
>>>
>>> Thanks in advance
>>>
>>> Viju Moses
>>>
>>> ______________________________________________
>>> R-help at r-project.org 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.
>>
>> David Winsemius, MD
>> Heritage Laboratories
>> West Hartford, CT
>>
>> ______________________________________________
>> R-help at r-project.org 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.
>>
>
>
>
> -- 
> CH Chan
> Research Assistant - KWH
> http://www.macgrass.com
>
> ______________________________________________
> R-help at r-project.org 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.