>From a quick look at the code it looks like when you ask for plot number 5 >(included in default when 'which' is not specified), then the deviance >residuals are replaced by the pearson residuals to be used in later >computations. So the difference that you are seeing is that one of the plots >is based on deviance residuals and the other on pearson residuls.
It seems that there is a bug here in that, at a minimum, the label should be changed to indicate which residuals were actually used, or the code changed to continue to use the deviance residuals for plot 3 even when plot 5 is requested. Does anyone else see something that I missed in how the residuals are replaced and used? -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] 801.408.8111 > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > project.org] On Behalf Of Effie Greathouse > Sent: Wednesday, November 12, 2008 11:16 AM > To: r-help@r-project.org > Subject: Re: [R] different results with plot.lm vs. plot.lm(which=c(2)) > > Hi Dr. Ripley--Sorry for the repost everybody. The original message I > sent > never showed up in my inbox, so I thought it didn't get sent to the > list. > > I'm running R 2.8.0, installed from a pre-compiled version, on Windows > XP. > When I type Sys.getlocale() at the R prompt, it returns: > "LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252" > > Here's an example: > bob <- seq(1:100) > bob2 <- rgamma(100, 2, 1)*10+bob > model<-glm(bob2 ~ bob, family=Gamma) > > Then enter: > plot(model, which=c(3)) > to get the Scale-Location graph > > Then compare it to the Scale-Location graph when you run the following > command and page through to the 3rd graph: > plot(model) > > When I do this, I get different results -- some of the high values are > different on each plot. On my real data the difference is more severe > than > in this randomly generated example. I'd be happy to supply my real > data and > R code if this smaller example isn't sufficient. Thank you for any > help!! > > > On Wed, Nov 12, 2008 at 9:43 AM, Prof Brian Ripley > <[EMAIL PROTECTED]>wrote: > > > Instead of re-posting the same message, please study the posting > guide and > > supply the information asked for, including a reproducible example. > There is > > no way we can help you unless you help us to help you. > > > > > > On Wed, 12 Nov 2008, Effie Greathouse wrote: > > > > I am running GLM models using the gamma family. For example: > >> model <-glm(y ~ x, family=Gamma(link="identity")) > >> > >> I am getting different results for the normal Q-Q plot and the > >> Scale-Location plot if I run the diagnostic plots without specifying > the > >> plot vs. if I specify the plot ... e.g., "plot(model)" gives me a > >> different > >> Normal Q-Q graph than "plot(model, which=c(2))". The former gives > data > >> points distributed in a quadratic pattern, while the latter gives > data > >> points more or less along the 1:1 line. Shouldn't these two > commands be > >> giving me the same exact graphs? I have read the documentation on > plot.lm > >> and searched the help archives, but I am still learning GLM's and > I'm not > >> very familiar with understanding diagnostic plots for GLM's, so any > help > >> would be much appreciated! > >> > >> [[alternative HTML version deleted]] > >> > >> ______________________________________________ > >> R-help@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<http://www.r- > project.org/posting-guide.html> > >> and provide commented, minimal, self-contained, reproducible code. > >> > > > > -- > > Brian D. Ripley, [EMAIL PROTECTED] > > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > > University of Oxford, Tel: +44 1865 272861 (self) > > 1 South Parks Road, +44 1865 272866 (PA) > > Oxford OX1 3TG, UK Fax: +44 1865 272595 > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@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. ______________________________________________ R-help@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.
