[R] p values from GLM

[peter dalgaard]

> On 03 Apr 2016, at 01:00 , Heinz Tuechler <tuechler at gmx.at> wrote:
> 
> 
> Bert Gunter wrote on 01.04.2016 23:46:
>> ... of course, whether one **should** get them is questionable...
>> 
>> http://www.nature.com/news/statisticians-issue-warning-over-misuse-of-p-values-1.19503#/ref-link-1
>> 
> This paper repeats the common place statement that a small p-value does not necessarily indicate an important finding. Agreed, but maybe I overlooked examples of important findings with large p-values.
> If there are some, I would be happy to get to know some of them. Otherwise a small p-value is no guarantee of importance, but a prerequisite.

This is getting seriously off-topic, but lots of underdimensioned studies would qualify. However, the effects found are almost indistiguishable from Type I errors. Later, larger, studies would be required to confirm that the effect is really there. (Like, halving or doubling the risk of some cancer is hardly unimportant, but knowing that that is often the detection limit in medium-scaled epidemiological studies may make you a bit jaded when hearing such reports.)

-pd

> 
> best regards,
> 
> Heinz
> 
>> 
>> Cheers,
>> Bert
>> 
>> 
>> 
>> Bert Gunter
>> 
>> "The trouble with having an open mind is that people keep coming along
>> and sticking things into it."
>> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>> 
>> 
>> On Fri, Apr 1, 2016 at 3:26 PM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
>>> On 01/04/2016 6:14 PM, John Sorkin wrote:
>>>> How can I get the p values from a glm ? I want to get the p values so I
>>>> can add them to a custom report
>>>> 
>>>> 
>>>>   fitwean<-
>>>> glm(data[,"JWean"]~data[,"Group"],data=data,family=binomial(link ="logit"))
>>>>   summary(fitwean)             # This lists the coefficeints, SEs, z and p
>>>> values, but I can't isolate the pvalues.
>>>>   names(summary(fitwean))  # I see the coefficients, but not the p values
>>>>   names(fitmens)                  # p values are not found here.
>>> 
>>> Doesn't summary(fitwean) give a matrix? Then it's
>>> colnames(summary(fitwean)$coefficients) you want, not names(fitwean).
>>> 
>>> Duncan Murdoch
>>> 
>>> P.S. If you had given a reproducible example, I'd try it myself.
>>> 
>>> 
>>> 
>>>> 
>>>> Thank you!
>>>> John
>>>> 
>>>> John David Sorkin M.D., Ph.D.
>>>> Professor of Medicine
>>>> Chief, Biostatistics and Informatics
>>>> University of Maryland School of Medicine Division of Gerontology and
>>>> Geriatric Medicine
>>>> Baltimore VA Medical Center
>>>> 10 North Greene Street
>>>> GRECC (BT/18/GR)
>>>> Baltimore, MD 21201-1524
>>>> (Phone) 410-605-7119
>>>> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
>>>> 
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>> 
>> ______________________________________________
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>> and provide commented, minimal, self-contained, reproducible code.
> 
> ______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/r-help
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-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
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