... 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 <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) >> >> 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. >> ______________________________________________ >> R-help at r-project.org 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. >> > > ______________________________________________ > R-help at r-project.org 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.
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 <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) >>> >>> 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. >>> ______________________________________________ >>> R-help at r-project.org 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. >>> >> >> ______________________________________________ >> R-help at r-project.org 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.
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
Because they are Medusa statistics? -- Sent from my phone. Please excuse my brevity. On April 1, 2016 5:01:12 PM PDT, Duncan Murdoch <murdoch.duncan at gmail.com> 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 ><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) >>>> >>>> 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. >>>> ______________________________________________ >>>> R-help at r-project.org 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. >>>> >>> >>> ______________________________________________ >>> R-help at r-project.org 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. > >______________________________________________ >R-help at r-project.org 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]]
> On Apr 1, 2016, at 5:01 PM, Duncan Murdoch <murdoch.duncan at gmail.com> 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 <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) >>>> >>>> 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. >>>> ______________________________________________ >>>> R-help at r-project.org 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. >>>> >>> >>> ______________________________________________ >>> R-help at r-project.org 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. > > ______________________________________________ > R-help at r-project.org 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
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 <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) >>> >>> 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. >>> ______________________________________________ >>> R-help at r-project.org 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. >>> >> >> ______________________________________________ >> R-help at r-project.org 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. > > ______________________________________________ > R-help at r-project.org 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.
> 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) >>>> >>>> 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. >>>> ______________________________________________ >>>> R-help at r-project.org 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. >>>> >>> >>> ______________________________________________ >>> R-help at r-project.org 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. >> >> ______________________________________________ >> R-help at r-project.org 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. > > ______________________________________________ > R-help at r-project.org 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: pd.mes at cbs.dk Priv: PDalgd at gmail.com