Re: [Rd] Rsquared bug lm() (PR#10516)
Basically, I used the without intercept to get an estimate for each of my factor levels instead of using a reference class. So I use a kind of hidden intercept. I should have noticed that the behavior was documented in ?summary.lm. Sorry for the inconvenience. Lieven Duncan Murdoch-2 wrote: On 12/14/2007 8:10 AM, [EMAIL PROTECTED] wrote: Full_Name: lieven clement Version: R version 2.4.0 Patched (2006-11-25 r39997) OS: i486-pc-linux-gnu Submission from: (NULL) (157.193.193.180) summary.lm() does not calculate R² accurately for models without intercepts if one of the predictor variables is a factor. In order to avoid one of the factor levels to be considered as a reference class you can use the -1 option in a formula. When you use this, R² is not correctly calculated. This is not a bug. A model without an intercept should be using y=0 as a reference. Duncan Murdoch x1-rnorm(100) x2-c(rep(0,25),rep(10,25),rep(20,25),rep(30,25)) y-10*x1+x2+rnorm(100,0,4) x2-as.factor(x2) lmtest-lm(y~-1+x1+x2) summary(lmtest)$r.sq [1] 0.9650201 1-sum(lmtest$res^2)/sum((y-mean(y))^2) [1] 0.9342672 The R squared by summary is calculated as 1-sum(lmtest$res^2)/sum((y)^2) [1] 0.9650201 apparently because lm.summary assumes the mean of y to be zero. In case of an intercept model everything seems ok lmtest-lm(y~x1+x2) summary(lmtest)$r.sq [1] 0.9342672 1-sum(lmtest$res^2)/sum((y-mean(y))^2) [1] 0.9342672 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- View this message in context: http://www.nabble.com/Rsquared-bug-lm%28%29-%28PR-10516%29-tp14335791p14370172.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] help files for load and related functions
I recently had a discussion with a user about loading and attaching in R. I was surprised that the help files don't provide a very clear picture. From my point of view 'load' and 'attach' are very similar operations, the difference being that 'attach' creates a new database on the search list while 'load' puts all the objects into the global environment. The help file for 'load' is inexplicit that this is what happens. The 'load' and 'attach' help files neither refer to the other in their See Also. Furthermore, the 'library' help file talks about loading packages. I would suggest that it should use attaching as that is the analogous operation. None of these three help files (nor that of 'save') has a Side Effects section. Personally I think that all help files should have a Side Effects section (to make it clear to new users what side effects are and that they are not a good thing for most functions to have). I can understand there could be another point of view on that. However, I definitely think that there should be a Side Effects section in the help files of functions whose whole point is a side effect. Patrick Burns [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] help files for load and related functions
On 12/17/2007 6:00 AM, Patrick Burns wrote: I recently had a discussion with a user about loading and attaching in R. I was surprised that the help files don't provide a very clear picture. From my point of view 'load' and 'attach' are very similar operations, the difference being that 'attach' creates a new database on the search list while 'load' puts all the objects into the global environment. The help file for 'load' is inexplicit that this is what happens. The 'load' and 'attach' help files neither refer to the other in their See Also. Furthermore, the 'library' help file talks about loading packages. I would suggest that it should use attaching as that is the analogous operation. None of these three help files (nor that of 'save') has a Side Effects section. Personally I think that all help files should have a Side Effects section (to make it clear to new users what side effects are and that they are not a good thing for most functions to have). I can understand there could be another point of view on that. However, I definitely think that there should be a Side Effects section in the help files of functions whose whole point is a side effect. I think you make good points. Care to submit patches? The source for those man pages are in https://svn.R-project.org/R/trunk/src/library/base/man/attach.Rd https://svn.R-project.org/R/trunk/src/library/base/man/library.Rd https://svn.R-project.org/R/trunk/src/library/base/man/load.Rd https://svn.R-project.org/R/trunk/src/library/base/man/save.Rd If you send them to me before Thursday or after Jan 2, I'll take a look. (If you send them to me during the Xmas break there's a good chance they'll get lost.) Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] help files for load and related functions
Dear Patrick, Firstly, and most importantly, I do not think that your post qualified for Rd! Please use the correct mail list for such things: R-help. I do not think anybody on Rd wants mailboxes clogged with irrelevant messages. Back to your question: it is not clear if you are confused, or your 'user' is confused, but all three help pages look pretty clear and straight forward to me. Moreover, I do not see any connection between attach and library, which you find logical: - load - the general use of this one is to load external data sets, e.g. load serialised R object(s) (as the example shows). Until you load, you cannot use the object as it has no relation to the R session and can be e.g. a file sitting somewhere on a network - attach - the general use of this one would be to access elements of a data set directly, without the data set name specifier and the accessor operator, such as $, thus as the help page states - it is used to add the data set to the search path (as the example shows). If you look at the example, you do not have to call attach to be able to use data, data could have existed there before and what you effectively get with attach is a more convenient way of dealing with the data - library - is used to load *and* attach an R package, which is not exactly the same as a serialised R object(s), but a full set of other functionality. Attaching packages is just a part of the loading process, which occurs basically when the package becomes visible to the user. Same as with load, you cannot use the package until you load it. There is not a hint of similarity between loading a package and attaching a data set as I see it. Regards, Oleg On Mon, 2007-12-17 at 11:00 +, Patrick Burns wrote: I recently had a discussion with a user about loading and attaching in R. I was surprised that the help files don't provide a very clear picture. From my point of view 'load' and 'attach' are very similar operations, the difference being that 'attach' creates a new database on the search list while 'load' puts all the objects into the global environment. The help file for 'load' is inexplicit that this is what happens. The 'load' and 'attach' help files neither refer to the other in their See Also. Furthermore, the 'library' help file talks about loading packages. I would suggest that it should use attaching as that is the analogous operation. None of these three help files (nor that of 'save') has a Side Effects section. Personally I think that all help files should have a Side Effects section (to make it clear to new users what side effects are and that they are not a good thing for most functions to have). I can understand there could be another point of view on that. However, I definitely think that there should be a Side Effects section in the help files of functions whose whole point is a side effect. Patrick Burns [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Dr Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-494466 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] help files for load and related functions
On Mon, 2007-12-17 at 14:06 +, Oleg Sklyar wrote: Dear Patrick, Firstly, and most importantly, I do not think that your post qualified for Rd! Please use the correct mail list for such things: R-help. I do not think anybody on Rd wants mailboxes clogged with irrelevant messages. No. R Devel *is* the correct place for this discussion, as it pertains to the development of R. Patrick is reporting that he found the current help for load(), attach() etc lacking explicit statements about what R actually does when you call them, and how the functions differ in their side effects, especially from the point of view of a new user. The reason for your comment above is perhaps related to the one below my text; Patrick _isn't_ looking for help, just pointing out an infelicity in the current documentation as identified by the user, and, I suspect, welcoming comment on his suggestions for changes. G Back to your question: it is not clear if you are confused, or your 'user' is confused, but all three help pages look pretty clear and straight forward to me. Moreover, I do not see any connection between attach and library, which you find logical: - load - the general use of this one is to load external data sets, e.g. load serialised R object(s) (as the example shows). Until you load, you cannot use the object as it has no relation to the R session and can be e.g. a file sitting somewhere on a network - attach - the general use of this one would be to access elements of a data set directly, without the data set name specifier and the accessor operator, such as $, thus as the help page states - it is used to add the data set to the search path (as the example shows). If you look at the example, you do not have to call attach to be able to use data, data could have existed there before and what you effectively get with attach is a more convenient way of dealing with the data - library - is used to load *and* attach an R package, which is not exactly the same as a serialised R object(s), but a full set of other functionality. Attaching packages is just a part of the loading process, which occurs basically when the package becomes visible to the user. Same as with load, you cannot use the package until you load it. There is not a hint of similarity between loading a package and attaching a data set as I see it. Regards, Oleg On Mon, 2007-12-17 at 11:00 +, Patrick Burns wrote: I recently had a discussion with a user about loading and attaching in R. I was surprised that the help files don't provide a very clear picture. From my point of view 'load' and 'attach' are very similar operations, the difference being that 'attach' creates a new database on the search list while 'load' puts all the objects into the global environment. The help file for 'load' is inexplicit that this is what happens. The 'load' and 'attach' help files neither refer to the other in their See Also. Furthermore, the 'library' help file talks about loading packages. I would suggest that it should use attaching as that is the analogous operation. None of these three help files (nor that of 'save') has a Side Effects section. Personally I think that all help files should have a Side Effects section (to make it clear to new users what side effects are and that they are not a good thing for most functions to have). I can understand there could be another point of view on that. However, I definitely think that there should be a Side Effects section in the help files of functions whose whole point is a side effect. Patrick Burns [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Installation of RGtk2 (PR#10519)
Full_Name: Caroline Keef Version: 2.6.1 OS: Windows XP Submission from: (NULL) (195.171.203.131) I have tried to install the package rggobi which if I'm right requires the package RGtk2 If I install RGtk2 using the install.packages (I used the UK (Bristol) mirror, I haven't tried any other mirror) within R and then use library(RGtk2) I get the following message box This application has failed to start because libtak-1.0-0.dll was not found. Re-installing the application may fix this problem. I click ok and the following is printed to the R console. Error in dyn.load(file, ...) : unable to load shared library 'C:/PROGRA~1/R/R-26~1.1/library/RGtk2/libs/RGtk2.dll': LoadLibrary failure: The specified module could not be found. [1] PLEASE RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN Error in .C(R_gtkInit, length(args), x = args, PACKAGE = RGtk2) : C symbol name R_gtkInit not in DLL for package RGtk2 In addition: Warning message: In fun(...) : Failed to load RGtk2 dynamic library:Error in dyn.load(file, ...) : unable to load shared library 'C:/PROGRA~1/R/R-26~1.1/library/RGtk2/libs/RGtk2.dll': LoadLibrary failure: The specified module could not be found. Error : .onLoad failed in 'loadNamespace' for 'RGtk2' Error: package/namespace load failed for 'RGtk2' I've re-started R again and the same happened. I've also tried downloading the RGtk2 zip files from the CRAN website and installing from a local zip file option which gave the same results. I haven't tried re-installing R to get around this problem. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] help files for load and related functions
Patches to the help files sound like a good idea. However, it isn't something I'm likely to get to immediately. I'm hoping that some other nice person will volunteer. Pat Duncan Murdoch wrote: On 12/17/2007 6:00 AM, Patrick Burns wrote: I recently had a discussion with a user about loading and attaching in R. I was surprised that the help files don't provide a very clear picture. From my point of view 'load' and 'attach' are very similar operations, the difference being that 'attach' creates a new database on the search list while 'load' puts all the objects into the global environment. The help file for 'load' is inexplicit that this is what happens. The 'load' and 'attach' help files neither refer to the other in their See Also. Furthermore, the 'library' help file talks about loading packages. I would suggest that it should use attaching as that is the analogous operation. None of these three help files (nor that of 'save') has a Side Effects section. Personally I think that all help files should have a Side Effects section (to make it clear to new users what side effects are and that they are not a good thing for most functions to have). I can understand there could be another point of view on that. However, I definitely think that there should be a Side Effects section in the help files of functions whose whole point is a side effect. I think you make good points. Care to submit patches? The source for those man pages are in https://svn.R-project.org/R/trunk/src/library/base/man/attach.Rd https://svn.R-project.org/R/trunk/src/library/base/man/library.Rd https://svn.R-project.org/R/trunk/src/library/base/man/load.Rd https://svn.R-project.org/R/trunk/src/library/base/man/save.Rd If you send them to me before Thursday or after Jan 2, I'll take a look. (If you send them to me during the Xmas break there's a good chance they'll get lost.) Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] help files for load and related functions
On 12/17/2007 9:06 AM, Oleg Sklyar wrote: Dear Patrick, Firstly, and most importantly, I do not think that your post qualified for Rd! Please use the correct mail list for such things: R-help. I do not think anybody on Rd wants mailboxes clogged with irrelevant messages. Since Patrick's message was about changes to the documentation, I think it is relevant to this list. Duncan Murdoch Back to your question: it is not clear if you are confused, or your 'user' is confused, but all three help pages look pretty clear and straight forward to me. Moreover, I do not see any connection between attach and library, which you find logical: - load - the general use of this one is to load external data sets, e.g. load serialised R object(s) (as the example shows). Until you load, you cannot use the object as it has no relation to the R session and can be e.g. a file sitting somewhere on a network - attach - the general use of this one would be to access elements of a data set directly, without the data set name specifier and the accessor operator, such as $, thus as the help page states - it is used to add the data set to the search path (as the example shows). If you look at the example, you do not have to call attach to be able to use data, data could have existed there before and what you effectively get with attach is a more convenient way of dealing with the data - library - is used to load *and* attach an R package, which is not exactly the same as a serialised R object(s), but a full set of other functionality. Attaching packages is just a part of the loading process, which occurs basically when the package becomes visible to the user. Same as with load, you cannot use the package until you load it. There is not a hint of similarity between loading a package and attaching a data set as I see it. Regards, Oleg On Mon, 2007-12-17 at 11:00 +, Patrick Burns wrote: I recently had a discussion with a user about loading and attaching in R. I was surprised that the help files don't provide a very clear picture. From my point of view 'load' and 'attach' are very similar operations, the difference being that 'attach' creates a new database on the search list while 'load' puts all the objects into the global environment. The help file for 'load' is inexplicit that this is what happens. The 'load' and 'attach' help files neither refer to the other in their See Also. Furthermore, the 'library' help file talks about loading packages. I would suggest that it should use attaching as that is the analogous operation. None of these three help files (nor that of 'save') has a Side Effects section. Personally I think that all help files should have a Side Effects section (to make it clear to new users what side effects are and that they are not a good thing for most functions to have). I can understand there could be another point of view on that. However, I definitely think that there should be a Side Effects section in the help files of functions whose whole point is a side effect. Patrick Burns [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Installation of RGtk2 (PR#10519)
This isn't an R bug. You should send contributed package problems to the package maintainer, in this case Michael Lawrence. You need to install GTK; it's not included as part of the package. See this page for instructions: http://www.ggobi.org/rgtk2/ It would probably be a good idea for the R package to recognize this omission and print more helpful error messages, but setting that up is tricky. Michael, if you want help, please contact me offline. Duncan Murdoch On 12/17/2007 9:00 AM, [EMAIL PROTECTED] wrote: Full_Name: Caroline Keef Version: 2.6.1 OS: Windows XP Submission from: (NULL) (195.171.203.131) I have tried to install the package rggobi which if I'm right requires the package RGtk2 If I install RGtk2 using the install.packages (I used the UK (Bristol) mirror, I haven't tried any other mirror) within R and then use library(RGtk2) I get the following message box This application has failed to start because libtak-1.0-0.dll was not found. Re-installing the application may fix this problem. I click ok and the following is printed to the R console. Error in dyn.load(file, ...) : unable to load shared library 'C:/PROGRA~1/R/R-26~1.1/library/RGtk2/libs/RGtk2.dll': LoadLibrary failure: The specified module could not be found. [1] PLEASE RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN Error in .C(R_gtkInit, length(args), x = args, PACKAGE = RGtk2) : C symbol name R_gtkInit not in DLL for package RGtk2 In addition: Warning message: In fun(...) : Failed to load RGtk2 dynamic library:Error in dyn.load(file, ...) : unable to load shared library 'C:/PROGRA~1/R/R-26~1.1/library/RGtk2/libs/RGtk2.dll': LoadLibrary failure: The specified module could not be found. Error : .onLoad failed in 'loadNamespace' for 'RGtk2' Error: package/namespace load failed for 'RGtk2' I've re-started R again and the same happened. I've also tried downloading the RGtk2 zip files from the CRAN website and installing from a local zip file option which gave the same results. I haven't tried re-installing R to get around this problem. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Installation of RGtk2 (PR#10519)
[EMAIL PROTECTED] wrote: Full_Name: Caroline Keef Version: 2.6.1 OS: Windows XP Submission from: (NULL) (195.171.203.131) I have tried to install the package rggobi which if I'm right requires the package RGtk2 If I install RGtk2 using the install.packages (I used the UK (Bristol) mirror, I haven't tried any other mirror) within R and then use library(RGtk2) I get the following message box This application has failed to start because libtak-1.0-0.dll was not found. Re-installing the application may fix this problem. I click ok and the following is printed to the R console. Error in dyn.load(file, ...) : unable to load shared library 'C:/PROGRA~1/R/R-26~1.1/library/RGtk2/libs/RGtk2.dll': LoadLibrary failure: The specified module could not be found. [1] PLEASE RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN Error in .C(R_gtkInit, length(args), x = args, PACKAGE = RGtk2) : C symbol name R_gtkInit not in DLL for package RGtk2 In addition: Warning message: In fun(...) : Failed to load RGtk2 dynamic library:Error in dyn.load(file, ...) : unable to load shared library 'C:/PROGRA~1/R/R-26~1.1/library/RGtk2/libs/RGtk2.dll': LoadLibrary failure: The specified module could not be found. Error : .onLoad failed in 'loadNamespace' for 'RGtk2' Error: package/namespace load failed for 'RGtk2' I've re-started R again and the same happened. I've also tried downloading the RGtk2 zip files from the CRAN website and installing from a local zip file option which gave the same results. I haven't tried re-installing R to get around this problem. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel This is a package problem, not an issue in R itself, hence you should not use the bug report interface. However, the error indicates reliance on an external library, which you presumably haven't got, so retrying is not going to help anything. You probably need to go to http://www.ggobi.org/rgtk2/ and follow the instructions that start with If you're on Windows... -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Installation of RGtk2 (PR#10519)
This is not a bug, and not appropriate to R-bugs as it is about a contributed package. From http://cran.r-project.org/bin/windows/contrib/2.6/ReadMe you will see Package RGtk2 requires an installed version of Gtk2 with version number = 2.10.11. Now, so does GGobi and hence rggobi. 'Installed' includes ensuring they are on your path, so if GGobi works I would expect RGtk2 to. On Mon, 17 Dec 2007, [EMAIL PROTECTED] wrote: Full_Name: Caroline Keef Version: 2.6.1 OS: Windows XP Submission from: (NULL) (195.171.203.131) I have tried to install the package rggobi which if I'm right requires the package RGtk2 If I install RGtk2 using the install.packages (I used the UK (Bristol) mirror, I haven't tried any other mirror) within R and then use library(RGtk2) I get the following message box This application has failed to start because libtak-1.0-0.dll was not found. Re-installing the application may fix this problem. I click ok and the following is printed to the R console. Error in dyn.load(file, ...) : unable to load shared library 'C:/PROGRA~1/R/R-26~1.1/library/RGtk2/libs/RGtk2.dll': LoadLibrary failure: The specified module could not be found. [1] PLEASE RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN Error in .C(R_gtkInit, length(args), x = args, PACKAGE = RGtk2) : C symbol name R_gtkInit not in DLL for package RGtk2 In addition: Warning message: In fun(...) : Failed to load RGtk2 dynamic library:Error in dyn.load(file, ...) : unable to load shared library 'C:/PROGRA~1/R/R-26~1.1/library/RGtk2/libs/RGtk2.dll': LoadLibrary failure: The specified module could not be found. Error : .onLoad failed in 'loadNamespace' for 'RGtk2' Error: package/namespace load failed for 'RGtk2' I've re-started R again and the same happened. I've also tried downloading the RGtk2 zip files from the CRAN website and installing from a local zip file option which gave the same results. I haven't tried re-installing R to get around this problem. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- 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, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
