p values from GLM

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p values from GLM

John Sorkin
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.
 
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)

Confidentiality Statement:
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
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Re: p values from GLM

Duncan Murdoch-2
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)
 >
 > Confidentiality Statement:
 > This email message, including any attachments, is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. Any unauthorized use, disclosure or distribution is
prohibited. If you are not the intended recipient, please contact the
sender by reply email and destroy all copies of the original message.
 > ______________________________________________
 > [hidden email] mailing list -- To UNSUBSCRIBE and more, see
 > 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.
 >

______________________________________________
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Re: p values from GLM

Bert Gunter-2
... 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


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 <[hidden email]> 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)
>>
>> Confidentiality Statement:
>> This email message, including any attachments, is for the sole use of the
>> intended recipient(s) and may contain confidential and privileged
>> information. Any unauthorized use, disclosure or distribution is prohibited.
>> If you are not the intended recipient, please contact the sender by reply
>> email and destroy all copies of the original message.
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> 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.
>>
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> 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.

______________________________________________
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Re: p values from GLM

Duncan Murdoch-2
On 01/04/2016 6:46 PM, Bert Gunter wrote:
> ... of course, whether one **should** get them is questionable...

They're just statistics.  How could it hurt to look at them?

Duncan Murdoch

>
> http://www.nature.com/news/statisticians-issue-warning-over-misuse-of-p-values-1.19503#/ref-link-1
>
>
> 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 <[hidden email]> 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)
>>>
>>> Confidentiality Statement:
>>> This email message, including any attachments, is for the sole use of the
>>> intended recipient(s) and may contain confidential and privileged
>>> information. Any unauthorized use, disclosure or distribution is prohibited.
>>> If you are not the intended recipient, please contact the sender by reply
>>> email and destroy all copies of the original message.
>>> ______________________________________________
>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>> 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.
>>>
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> 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.

______________________________________________
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Re: [FORGED] Re: p values from GLM

Rolf Turner
On 02/04/16 13:01, Duncan Murdoch wrote:
> On 01/04/2016 6:46 PM, Bert Gunter wrote:
>> ... of course, whether one **should** get them is questionable...
>
> They're just statistics.  How could it hurt to look at them?

Fortune nomination.

cheers,

Rolf

--
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

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Re: p values from GLM

Jeff Newmiller
In reply to this post by Duncan Murdoch-2
Because they are Medusa statistics?
--
Sent from my phone. Please excuse my brevity.

On April 1, 2016 5:01:12 PM PDT, Duncan Murdoch <[hidden email]> wrote:

>On 01/04/2016 6:46 PM, Bert Gunter wrote:
>> ... of course, whether one **should** get them is questionable...
>
>They're just statistics.  How could it hurt to look at them?
>
>Duncan Murdoch
>
>>
>>
>http://www.nature.com/news/statisticians-issue-warning-over-misuse-of-p-values-1.19503#/ref-link-1
>>
>>
>> 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
><[hidden email]> 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)
>>>>
>>>> Confidentiality Statement:
>>>> This email message, including any attachments, is for the sole use
>of the
>>>> intended recipient(s) and may contain confidential and privileged
>>>> information. Any unauthorized use, disclosure or distribution is
>prohibited.
>>>> If you are not the intended recipient, please contact the sender by
>reply
>>>> email and destroy all copies of the original message.
>>>> ______________________________________________
>>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>>> 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.
>>>>
>>>
>>> ______________________________________________
>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>> 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.
>
>______________________________________________
>[hidden email] mailing list -- To UNSUBSCRIBE and more, see
>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.

        [[alternative HTML version deleted]]

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Re: p values from GLM

David Winsemius
In reply to this post by Duncan Murdoch-2

> On Apr 1, 2016, at 5:01 PM, Duncan Murdoch <[hidden email]> wrote:
>
> On 01/04/2016 6:46 PM, Bert Gunter wrote:
>> ... of course, whether one **should** get them is questionable...
>
> They're just statistics.  How could it hurt to look at them?

Like Rolf, I thought that this utterance on April 1 deserved fortune enshrinement. It reminded me of one of my favorite articles: "P-Values are Random Variables".

Unfortunately a legal copy of that paper is still behind a corporate firewall for which you would need to fork over USD 50.00, but a google search for "P-Values are Random Variables The American Statistician" should yield options for the less squeamish. (My copy was obtained when I did have legal access.)

--
David.

>
> Duncan Murdoch
>
>>
>> http://www.nature.com/news/statisticians-issue-warning-over-misuse-of-p-values-1.19503#/ref-link-1
>>
>>
>> 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 <[hidden email]> 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)
>>>>
>>>> Confidentiality Statement:
>>>> This email message, including any attachments, is for the sole use of the
>>>> intended recipient(s) and may contain confidential and privileged
>>>> information. Any unauthorized use, disclosure or distribution is prohibited.
>>>> If you are not the intended recipient, please contact the sender by reply
>>>> email and destroy all copies of the original message.
>>>> ______________________________________________
>>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>>> 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.
>>>>
>>>
>>> ______________________________________________
>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>> 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.
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> 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
Alameda, CA, USA

______________________________________________
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Re: p values from GLM

Spencer Graves-4


On 4/2/2016 11:07 AM, David Winsemius wrote:
>> On Apr 1, 2016, at 5:01 PM, Duncan Murdoch <[hidden email]> wrote:
>>
>> On 01/04/2016 6:46 PM, Bert Gunter wrote:
>>> ... of course, whether one **should** get them is questionable...
>> They're just statistics.  How could it hurt to look at them?
> Like Rolf, I thought that this utterance on April 1 deserved fortune enshrinement. It reminded me of one of my favorite articles: "P-Values are Random Variables".
>
> Unfortunately a legal copy of that paper is still behind a corporate firewall for which you would need to fork over USD 50.00, but a google search for "P-Values are Random Variables The American Statistician" should yield options for the less squeamish. (My copy was obtained when I did have legal access.)


       How much did money or do the authors of that paper receive in
royalties?


       That's important, because the purpose of US copyright law is, "To
promote the Progress of Science and useful Arts, by securing for limited
Times to Authors and Inventors the exclusive Right to their respective
Writings and Discoveries."  (E.g., Wikipedia, "Copyright law of the
United States",
"https://en.wikipedia.org/wiki/Copyright_law_of_the_United_States") Very
few if any refereed academic papers are written for financial gain:  
Lawrence Lessig said that congressional representatives rarely hear
counterarguments to the garbage they get from corporate lobbyists.  The
Trans Pacific Partnership (TPP, and probably also the Transatlantic
Trade and Investment Partnership) will strengthen the rights of
corporations in this area.  If you think that will limit the progress of
science and the useful arts, as I do, I suggest you contact your elected
representatives and tell them so -- if you are a citizen of a country
with elected representatives.  I think we should also ask the American
Statistical Association how much money they make from that and what it
would take to put all that material in the public domain.  I think
professional organizations should come out strongly against these
provisions of US copyright law and trade agreements that strengthen
rather than weaken the stranglehold that major corporations have on the
intellectual heritage of humanity.


       This relates to R, because R is based on an assumption that the
dissemination of publications, articles and software, for which the
authors are not remunerated from copyright proceeds should not be
limited by pre-internet rules that stifle unnecessarily the distribution
of knowledge and with it improvements in productivity and economic growth.


       Best Wishes,
       Spencer Graves

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: p values from GLM

miguelito
Maybe it's not the article itself for sale.  Sometimes a company will
charge a fee to have access to its knowledge base.  Not because it owns all
of the content, but because the articles, publications, etc have been
tracked down and centralized.  This is also the whole idea behind paying a
company a few dollars to do a semi-extensive background check.


On Sat, Apr 2, 2016 at 11:51 AM, Spencer Graves <
[hidden email]> wrote:

>
>
> On 4/2/2016 11:07 AM, David Winsemius wrote:
>
>> On Apr 1, 2016, at 5:01 PM, Duncan Murdoch <[hidden email]>
>>> wrote:
>>>
>>> On 01/04/2016 6:46 PM, Bert Gunter wrote:
>>>
>>>> ... of course, whether one **should** get them is questionable...
>>>>
>>> They're just statistics.  How could it hurt to look at them?
>>>
>> Like Rolf, I thought that this utterance on April 1 deserved fortune
>> enshrinement. It reminded me of one of my favorite articles: "P-Values are
>> Random Variables".
>>
>> Unfortunately a legal copy of that paper is still behind a corporate
>> firewall for which you would need to fork over USD 50.00, but a google
>> search for "P-Values are Random Variables The American Statistician" should
>> yield options for the less squeamish. (My copy was obtained when I did have
>> legal access.)
>>
>
>
>       How much did money or do the authors of that paper receive in
> royalties?
>
>
>       That's important, because the purpose of US copyright law is, "To
> promote the Progress of Science and useful Arts, by securing for limited
> Times to Authors and Inventors the exclusive Right to their respective
> Writings and Discoveries."  (E.g., Wikipedia, "Copyright law of the United
> States", "https://en.wikipedia.org/wiki/Copyright_law_of_the_United_States")
> Very few if any refereed academic papers are written for financial gain:
> Lawrence Lessig said that congressional representatives rarely hear
> counterarguments to the garbage they get from corporate lobbyists.  The
> Trans Pacific Partnership (TPP, and probably also the Transatlantic Trade
> and Investment Partnership) will strengthen the rights of corporations in
> this area.  If you think that will limit the progress of science and the
> useful arts, as I do, I suggest you contact your elected representatives
> and tell them so -- if you are a citizen of a country with elected
> representatives.  I think we should also ask the American Statistical
> Association how much money they make from that and what it would take to
> put all that material in the public domain.  I think professional
> organizations should come out strongly against these provisions of US
> copyright law and trade agreements that strengthen rather than weaken the
> stranglehold that major corporations have on the intellectual heritage of
> humanity.
>
>
>       This relates to R, because R is based on an assumption that the
> dissemination of publications, articles and software, for which the authors
> are not remunerated from copyright proceeds should not be limited by
> pre-internet rules that stifle unnecessarily the distribution of knowledge
> and with it improvements in productivity and economic growth.
>
>
>       Best Wishes,
>       Spencer Graves
>
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> 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.
>

        [[alternative HTML version deleted]]

______________________________________________
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Re: p values from GLM

Heinz Tuechler
In reply to this post by Bert Gunter-2

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.

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 <[hidden email]> 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)
>>>
>>> Confidentiality Statement:
>>> This email message, including any attachments, is for the sole use of the
>>> intended recipient(s) and may contain confidential and privileged
>>> information. Any unauthorized use, disclosure or distribution is prohibited.
>>> If you are not the intended recipient, please contact the sender by reply
>>> email and destroy all copies of the original message.
>>> ______________________________________________
>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>> 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.
>>>
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> 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.
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> 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.

______________________________________________
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Re: p values from GLM

Peter Dalgaard-2

> On 03 Apr 2016, at 01:00 , Heinz Tuechler <[hidden email]> 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 <[hidden email]> 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)
>>>>
>>>> Confidentiality Statement:
>>>> This email message, including any attachments, is for the sole use of the
>>>> intended recipient(s) and may contain confidential and privileged
>>>> information. Any unauthorized use, disclosure or distribution is prohibited.
>>>> If you are not the intended recipient, please contact the sender by reply
>>>> email and destroy all copies of the original message.
>>>> ______________________________________________
>>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>>> 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.
>>>>
>>>
>>> ______________________________________________
>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>> 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.
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> 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.
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> 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.

--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: [hidden email]  Priv: [hidden email]

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Re: p values from GLM

John Maindonald
In reply to this post by John Sorkin
How small does a p-value need to be to warrant attention, however?

Witness Fisher’s comment that:
“. . . we may, if we prefer it, draw the line at one in fifty (the 2 per cent point), or one in a hundred (the 1 per cent point). Personally, the writer prefers to set a low standard of significance at the 5 per cent point, and ignore entirely all results which fail to reach this level. A scientific fact should be regarded as experimentally established only if a properly designed experiment rarely fails to give this level of significance.”
[Fisher RA (1926), “The Arrangement of Field Experiments,” Journal of the Ministry of Agriculture of Great Britain, 33, 503-513.]

See the selection of Fisher quotes at http://www.jerrydallal.com/lhsp/p05.htm .

In contexts where a p <= 0.05 becomes more likely under the NULL (not the case if the experiment might just as well have been a random number generator), small P-values shift the weight of evidence.  An alternative that is apriori highly unlikely takes a lot of shifting.


John Maindonald             email: [hidden email]<mailto:[hidden email]>


On 3/04/2016, at 22:00, [hidden email]<mailto:[hidden email]> wrote:

From: Heinz Tuechler <[hidden email]<mailto:[hidden email]>>
Subject: Re: [R] p values from GLM
Date: 3 April 2016 11:00:50 NZST
To: Bert Gunter <[hidden email]<mailto:[hidden email]>>, Duncan Murdoch <[hidden email]<mailto:[hidden email]>>
Cc: r-help <[hidden email]<mailto:[hidden email]>>



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.

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 <[hidden email]<mailto:[hidden email]>> 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)

Confidentiality Statement:
This email message, including any attachments, is for the sole use of the
intended recipient(s) and may contain confidential and privileged
information. Any unauthorized use, disclosure or distribution is prohibited.
If you are not the intended recipient, please contact the sender by reply
email and destroy all copies of the original message.
______________________________________________
[hidden email]<mailto:[hidden email]> mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
and provide commented, minimal, self-contained, reproducible code.


______________________________________________
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______________________________________________
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and provide commented, minimal, self-contained, reproducible code.



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