Re: [R] Ridge for logistic regression
On Fri, 3 Nov 2006, Zheng Yuan wrote: Dear all experts, Does anyone know if there is a R function which can perform Ridge regression for logistic models? multinom and nnet in the package of that name. -- 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-help@stat.math.ethz.ch 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] R package/function for ridge logistic regression
Hi, Is there a R function/package which could do ridge regression for logistic regression? Thank you. -- Zheng __ R-help@stat.math.ethz.ch 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] Error when using cobs library
Dear R-Users, I have problems with the cobs library. When doing the cobs example, I get the folling error message: example(cobs) cobs x - seq(-1, 3, , 150) cobs y - (f.true - pnorm(2 * x)) + rnorm(150)/10 cobs con - rbind(c(1, min(x), 0), c(-1, max(x), 1), c(0, 0, 0.5)) cobs Rbs - cobs(x, y, constraint = increase, pointwise = con) qbsks2(): Performing general knot selection ... Error in as.matrix.csr(new(matrix.coo, ra = c(z1$design), ia = i1, ja = j1, : unable to find a non-generic version of function as.matrix.csr Any suggestions how to fix this problem? Thank you for your help. Jaci -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error when using cobs library
jacinthe == jacinthe [EMAIL PROTECTED] on Sat, 04 Nov 2006 10:06:10 +0100 writes: jacinthe Dear R-Users, I have problems with the cobs jacinthe library. ^^^ It's package! It's package! . [say it load five times, so you re-train your brain ] jacinthe When doing the cobs example, I get the jacinthe folling error message: jacinthe example(cobs) cobs x - seq(-1, 3, , 150) cobs y - (f.true - pnorm(2 * x)) + rnorm(150)/10 cobs con - rbind(c(1, min(x), 0), c(-1, max(x), 1), c(0, jacinthe 0, 0.5)) cobs Rbs - cobs(x, y, constraint = increase, pointwise = con) cobs qbsks2(): Performing general knot selection ... jacinthe Error in as.matrix.csr(new(matrix.coo, ra = jacinthe c(z1$design), ia = i1, ja = j1, : unable to find a jacinthe non-generic version of function as.matrix.csr Of course, the above works typically, since otherwise the package would not be on CRAN. jacinthe Any suggestions how to fix this problem? It's not easy to help you, since you didn't give any details about your setup. Please do so, e.g. by showing the result of sessionInfo(). I guess a mismatch of versions of the packages involved, notably your version of SparseM maybe outdated. jacinthe Thank you for your help. you're welcome. Martin Maechler, ETH Zurich __ R-help@stat.math.ethz.ch 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.
Re: [R] plotting residuals
Jeff == Jeff Miller [EMAIL PROTECTED]
on Fri, 3 Nov 2006 19:16:20 -0500 writes:
Jeff Does anyone know how to obtain a plot of residuals by
Jeff predicted values for a main-effects aov?
You didn't give a reproducible example, but plot()
[via plot.lm()] will do this {and more by default} :
E.g
example(aov, echo = FALSE )
summary(npkM - update(npk.aov, . ~ N+P+K))
Df Sum Sq Mean Sq F value Pr(F)
N1 189.28 189.28 6.4880 0.01919 *
P1 8.408.40 0.2880 0.59743
K1 95.20 95.20 3.2632 0.08592 .
Residuals 20 583.48 29.17
---
Signif. codes: 0 $,1rx(B***$,1ry(B 0.001 $,1rx(B**$,1ry(B 0.01
$,1rx(B*$,1ry(B 0.05 $,1rx(B.$,1ry(B 0.1 $,1rx(B $,1ry(B 1
plot(npkM) ## the first plot is yours
plot(npkM, which=1) # does only your plot
The plot is called Tukey-Anscombe plot, and there's also a
bell-and-whistle version of it, TA.plot() in package 'sfsmisc'
(with a longer history than R's plot.lm() !)
Jeff I want to check that the residuals are distributed
Jeff equally across treatment means.
Jeff Thanks,
Jeff Jeff
Jeff [[alternative HTML version deleted]]
^
wouldn't have appeared had you followed the
posting guide
Jeff __
Jeff R-help@stat.math.ethz.ch mailing list
Jeff https://stat.ethz.ch/mailman/listinfo/r-help
Jeff PLEASE do read the posting guide
Jeff http://www.R-project.org/posting-guide.html and
Jeff provide commented, minimal, self-contained,
Jeff reproducible code.
__
R-help@stat.math.ethz.ch 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] package version error
Dear List when trying to run the library(smida) I get the following error: Error in package_version(vers): invalid version specification Is there any way to rectify this? Thank you! Friederike __ R-help@stat.math.ethz.ch 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.
Re: [R] read.fwf and header
FrPi == François Pinard [EMAIL PROTECTED] on Wed, 1 Nov 2006 20:21:11 -0500 writes: FrPi [Martin Maechler] In my (and probably R-core's) view, read.fwf() should only have to be used for ``legacy data files'' (those times when people used *no* separators in order to save disk space), since nowadays, such data files should automatically have correct separators. FrPi In my day-to-day experience, the main virtue for fixed width format FrPi files is basic, humble legibility, much more than disk space savings. Good point. For this reason, I often prefer tab-delimited data files which are human readable too (and don't need quoting of strings, typically). But also, the read.table() default white space-separated files are very well humanly readable if the column starts are aligned. You do need to quote (..) strings with embedded white space then, but that is very well human-readable if you have a smart editor (such as Emacs ;-) which then automatically colorizes strings differently than the rest of the file entries. However, I think this (human-readibility) only applies to relatively small files. FrPi The FWF files I see have delimiters between fields, FrPi but also embedded space within fields, or at end of FrPi fields, without extraneous quotes. XML markup, CSVs, FrPi quoted fields, etc. are devices meant for helping FrPi machines much more than for helping humans. They FrPi significantly decrease legibility. Humans not only FrPi know better, they decipher fixed width format easily FrPi enough for not really needing hairier devices in FrPi general. FrPi FWF files may be archaic, they are not obsolescent. FrPi They will resist the fashion of the day for FrPi complexity, and survive in the long run. I cannot really oppose this statement, but am not as sure as you seem ;-) Thanks anyway for the thought provoking reply. With regards, Martin __ R-help@stat.math.ethz.ch 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] question about your photo
I've accidently found [1]your photo at a flickr and i'm very interested in it. Can you tell me what place i can see in the background of it? --- wbr, Barbara References 1. file://localhost/home/cmf3/tasks/keeper_au_new/0lXwcx/http://www.hunting.pl/flickr.html [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] User-friendly selective variable-loading function
This is probably somewhere in the archives but I couldn't find it: What's the R equivalent function to the Stata command: Use v1 v3 v5 v7 v2 using fileX.dat Where vn are variables named within the headed file fileX.dat I know I could do this crudely by just loading the file then creating a subset, but the file is pretty huge. The Import/Export Manual gives some examples of how to perform some low level operations using scan() but I'd rather use something more prosaic. Cheers, Jon Minton [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] tcltk difficulties
Friends: I have a tcltk widget for inputting constants and other values that are needed by subsequent R functions. My widget works well. I have an OnOK function that does what I had hoped it would. Among other input items the widget also uses 6 radio buttons to select one of 6 choices. It functions as it should. Here is the problem: I would like one of the buttons to be the default and to be switched on when the widget is created so that the user will have some guidance. (Currently all 6 buttons are blank until one is selected.) I can't handle the job. I have Welch and Jones _Practical Programming in Tcl and Tk_ but would appreciate any help from fellow R users. Many thanks. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com __ R-help@stat.math.ethz.ch 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.
Re: [R] tcltk difficulties
Charles Annis, P.E. [EMAIL PROTECTED] writes: Friends: I have a tcltk widget for inputting constants and other values that are needed by subsequent R functions. My widget works well. I have an OnOK function that does what I had hoped it would. Among other input items the widget also uses 6 radio buttons to select one of 6 choices. It functions as it should. Here is the problem: I would like one of the buttons to be the default and to be switched on when the widget is created so that the user will have some guidance. (Currently all 6 buttons are blank until one is selected.) I can't handle the job. I have Welch and Jones _Practical Programming in Tcl and Tk_ but would appreciate any help from fellow R users. library(tcltk) demo(tkdensity) # possibly: # options(pager=tkpager) file.show(system.file(demo/tkdensity.R,package=tcltk)) -- 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-help@stat.math.ethz.ch 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.
Re: [R] tcltk difficulties
Thank you, Peter. The code provides a great example of packing the widget nicely too. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Peter Dalgaard Sent: Saturday, November 04, 2006 8:12 AM To: [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Subject: Re: [R] tcltk difficulties Charles Annis, P.E. [EMAIL PROTECTED] writes: Friends: I have a tcltk widget for inputting constants and other values that are needed by subsequent R functions. My widget works well. I have an OnOK function that does what I had hoped it would. Among other input items the widget also uses 6 radio buttons to select one of 6 choices. It functions as it should. Here is the problem: I would like one of the buttons to be the default and to be switched on when the widget is created so that the user will have some guidance. (Currently all 6 buttons are blank until one is selected.) I can't handle the job. I have Welch and Jones _Practical Programming in Tcl and Tk_ but would appreciate any help from fellow R users. library(tcltk) demo(tkdensity) # possibly: # options(pager=tkpager) file.show(system.file(demo/tkdensity.R,package=tcltk)) -- 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-help@stat.math.ethz.ch 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.
Re: [R] multiple plots in the same graph
Li, What type of plot? A profile plot would be interaction.plot(factor1,factor2,y) Jeff -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Li Zhang Sent: Friday, November 03, 2006 9:55 PM To: R-help@stat.math.ethz.ch Subject: [R] multiple plots in the same graph I'd like to plot y vs x according to the third variable group which has three levels. I am wondering how can I put the three plots in one graph? Thank you (http://groups.yahoo.com) __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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.
Re: [R] Install RMySQL with R 2.4.0
I am having trouble as well with the new version of R 2.4. I downloaded the gz file from the cran website, followed the instructions in the README.win file and installed RMySQL. I have mysql installed under c:\mysql not the program files directory which is the only difference. I get the following error when I attempt to connect to the MySQL Db ## open a connection to a MySQL database con - dbConnect(dbDriver(MySQL),host='localhost', + username='',dbname = 'StorageSims'); Error in function (classes, fdef, mtable) : unable to find an inherited method for function dbConnect, for signature MySQLDriver Any help will be appreciated. I would like to note that there are no problems with RMySQL on my linux system, only on XP's. Thank you Joe Frank McCown wrote: I just installed RMySQL 0.5-9 with R 2.4.0 on Windows XP and got the following error message when trying to run a script with RMySQL: Error in library(RMySQL) : 'RMySQL' is not a valid package -- installed 2.0.0? Any ideas? Thanks, Frank __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] Equivalent to Stata command
Hi: Do any of you know if there's an equivalent function to the Stata command: Use v1 v3 v5 v2 v7 using file.dat In R? (i.e. something that just selectively loads certain variables from a file and not others)? Thanks Jon Minton [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
Re: [R] Equivalent to Stata command
On Sat, 2006-11-04 at 15:57 +, Jon Minton wrote: Hi: Do any of you know if there's an equivalent function to the Stata command: Use v1 v3 v5 v2 v7 using file.dat In R? (i.e. something that just selectively loads certain variables from a file and not others)? See ?read.table and note the 'colClasses' argument, which allows you to set a NULL value to columns that should be skipped. Alternatively, you can do a post import column selection using ?subset. The appropriate solution may be dependent upon whether you are RAM constrained and/or whether the columns to be skipped are easier to define than the columns to be selected. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch 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.
Re: [R] Equivalent to Stata command
On Nov 4, 2006, at 10:57 AM, Jon Minton wrote: Do any of you know if there's an equivalent function to the Stata command: Use v1 v3 v5 v2 v7 using file.dat In R? (i.e. something that just selectively loads certain variables from a file and not others)? How about (assuming that columns in 'file.dat' are separated by white space) data - read.table(file.dat, header = T, sep = ) # reads in the whole file data - data[, c(1, 3, 5, 2, 7)] # keeps the columns you need For more, see http://finzi.psych.upenn.edu/R/doc/manual/R-data.html _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch 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.
Re: [R] Error when using cobs library
Martin == Martin Maechler [EMAIL PROTECTED] on Sat, 4 Nov 2006 10:59:16 +0100 writes: jacinthe == jacinthe [EMAIL PROTECTED] on Sat, 04 Nov 2006 10:06:10 +0100 writes: jacinthe Dear R-Users, I have problems with the cobs jacinthe library. Martin ^^^ Martin It's package! Martin It's package! Martin . Martin [say it load five times, so you re-train your brain ] to which Peter Dalgaard appropriately responded PD It's loud! PD It's loud! PD ... PD PD;-) jacinthe When doing the cobs example, I get the jacinthe folling error message: [] Martin Of course, the above works typically, since otherwise the Martin package would not be on CRAN. jacinthe Any suggestions how to fix this problem? Martin It's not easy to help you, since you didn't give any details Martin about your setup. Martin Please do so, e.g. by showing the result of sessionInfo(). In the mean time jacinthe sent me Jaci sessionInfo() Jaci Version 2.3.1 (2006-06-01) Jaci i386-pc-mingw32 Jaci attached base packages: Jaci [1] splines methods stats graphics grDevices utils datasets base Jaci other attached packages: Jaci cobs quantreg SparseM fMultivar fSeries . Jaci 1.1-3.54.01 0.68 221.10065 221.10065 .. which I think explains things: Your version of SparseM is probably too old and or may not have been for R 2.3.1. Do the following 1) Get R 2.4.0 (or even R-2.4.0-patched) 2) upgrade.packages() where you should get newer versions of SparseM (and quantreg) [you can also try to do 2) alone; and that will be much quicker; but note that S4 class/methods handling has been wastly improved for R 2.4.0 and later, and SparseM does use them] Martin I guess a mismatch of versions of the packages involved, Martin notably your version of SparseM maybe outdated. jacinthe Thank you for your help. Martin you're welcome. Martin Martin Maechler, ETH Zurich __ R-help@stat.math.ethz.ch 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.
Re: [R] Equivalent to Stata command
Thanks, that's the kind of hint I was looking for: the types of data I'm using (survey responses) generally contain hundreds of variables, of which I'm typically only looking to extract about 5 or so (hence the 'load everything then subset' approach being less than ideal...) Jon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Marc Schwartz Sent: 04 November 2006 16:22 To: Jon Minton Cc: R-help@stat.math.ethz.ch Subject: Re: [R] Equivalent to Stata command On Sat, 2006-11-04 at 15:57 +, Jon Minton wrote: Hi: Do any of you know if there's an equivalent function to the Stata command: Use v1 v3 v5 v2 v7 using file.dat In R? (i.e. something that just selectively loads certain variables from a file and not others)? See ?read.table and note the 'colClasses' argument, which allows you to set a NULL value to columns that should be skipped. Alternatively, you can do a post import column selection using ?subset. The appropriate solution may be dependent upon whether you are RAM constrained and/or whether the columns to be skipped are easier to define than the columns to be selected. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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.
Re: [R] Error when using cobs library
On Sat, Nov 04, 2006 at 05:29:00PM +0100, Martin Maechler wrote: Your version of SparseM is probably too old and or may not have been for R 2.3.1. Do the following 1) Get R 2.4.0 (or even R-2.4.0-patched) 2) upgrade.packages() ^^^ perhaps you meant update.packages()? Tamas __ R-help@stat.math.ethz.ch 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.
Re: [R] Error when using cobs library
Martin Maechler wrote: Martin == Martin Maechler [EMAIL PROTECTED] on Sat, 4 Nov 2006 10:59:16 +0100 writes: jacinthe == jacinthe [EMAIL PROTECTED] on Sat, 04 Nov 2006 10:06:10 +0100 writes: jacinthe Dear R-Users, I have problems with the cobs jacinthe library. Martin ^^^ Martin It's package! Martin It's package! Martin . Martin [say it load five times, so you re-train your brain ] to which Peter Dalgaard appropriately responded PD It's loud! PD It's loud! PD ... PD PD;-) jacinthe When doing the cobs example, I get the jacinthe folling error message: [] Martin Of course, the above works typically, since otherwise the Martin package would not be on CRAN. jacinthe Any suggestions how to fix this problem? Martin It's not easy to help you, since you didn't give any details Martin about your setup. Martin Please do so, e.g. by showing the result of sessionInfo(). In the mean time jacinthe sent me Jaci sessionInfo() Jaci Version 2.3.1 (2006-06-01) Jaci i386-pc-mingw32 Jaci attached base packages: Jaci [1] splines methods stats graphics grDevices utils datasets base Jaci other attached packages: Jaci cobs quantreg SparseM fMultivar fSeries . Jaci 1.1-3.54.01 0.68 221.10065 221.10065 .. which I think explains things: Your version of SparseM is probably too old and or may not have been for R 2.3.1. Do the following 1) Get R 2.4.0 (or even R-2.4.0-patched) 2) upgrade.packages() Let me jump in: It's update.packages()! It's update.packages()! ... (and use argument checkBuilt = TRUE) ;-) where you should get newer versions of SparseM (and quantreg) [you can also try to do 2) alone; and that will be much quicker; but note that S4 class/methods handling has been wastly improved for R 2.4.0 and later, and SparseM does use them] Martin I guess a mismatch of versions of the packages involved, Martin notably your version of SparseM maybe outdated. jacinthe Thank you for your help. Martin you're welcome. Martin Martin Maechler, ETH Zurich __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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] can update.packages Debian package files?
Hi, I have searched the archive for the solution of this question, but couldn't find anything, so I thought I would ask here. I am using R on a Debian (testing) system. Many of the R packages I use are installed as .deb packages, those which are not available in this format I install using install.packages. When calling update.packages, sometimes the R repository version is more recent than the Debian package, and update.packages offers to update it which I don't want because the new debianized version will be out soon. Is it possible to have update.packages recognize that these are systemwide packages and ignore them when updating? Or is manual selection of what to update the only option? Thanks, Tamas __ R-help@stat.math.ethz.ch 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.
Re: [R] Error when using cobs library
Uwe Ligges [EMAIL PROTECTED] writes: Martin Maechler wrote: Martin == Martin Maechler [EMAIL PROTECTED] on Sat, 4 Nov 2006 10:59:16 +0100 writes: jacinthe == jacinthe [EMAIL PROTECTED] on Sat, 04 Nov 2006 10:06:10 +0100 writes: jacinthe Dear R-Users, I have problems with the cobs jacinthe library. Martin ^^^ Martin It's package! Martin It's package! Martin . Martin [say it load five times, so you re-train your brain ] to which Peter Dalgaard appropriately responded PD It's loud! PD It's loud! PD ... PD PD;-) 2) upgrade.packages() Let me jump in: It's update.packages()! It's update.packages()! ... (and use argument checkBuilt = TRUE) ;-) Before anyone else joins the fun, I actually should have said aloud... -- 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-help@stat.math.ethz.ch 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.
Re: [R] Install RMySQL with R 2.4.0
Joe W. Byers [EMAIL PROTECTED] writes: I am having trouble as well with the new version of R 2.4. I downloaded the gz file from the cran website, followed the instructions in the README.win file and installed RMySQL. I have mysql installed under c:\mysql not the program files directory which is the only difference. I get the following error when I attempt to connect to the MySQL Db ## open a connection to a MySQL database con - dbConnect(dbDriver(MySQL),host='localhost', + username='',dbname = 'StorageSims'); Error in function (classes, fdef, mtable) : unable to find an inherited method for function dbConnect, for signature MySQLDriver Any help will be appreciated. I would like to note that there are no problems with RMySQL on my linux system, only on XP's. Just to make sure: Before trying the code you posted, you did library(RMySQL), right? Also, what versions of DBI and RMySQL are you using? __ R-help@stat.math.ethz.ch 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.
Re: [R] Measurements of 3000 criminals
On 31-Oct-06 Martin Maechler wrote: Jean == Jean lobry [EMAIL PROTECTED] on Sat, 28 Oct 2006 13:07:04 +0200 writes: Hallo everyone, excuse me if this is not a genuine R question but I do not know where to ask else. Referring to e.g. https://stat.ethz.ch/pipermail/r-help/2004-December/062114.html I wonder if these measurements of 3000 criminals (raw data) are available anywhere. [...] Jean Dietrich, Jean I'm not sure, but this is perhaps what you want: Jean crim - Jean read.table(http://pbil.univ-lyon1.fr/R/donnees/criminals1902.txt;) Jean [...] Jean, this is really very nice, and given the historic importance of the data, I'd like to add this to the official R 'datasets' (the standard data set package), with tribute to you and Anne-Béatrice, and the references. [...] A further historical note. No doubt many R-helpreaders will have recently received (e.g. via allstat) the announcement: RSS Highlands local group meeting, December 5: 100 years of statistics in Aberdeen Dear all! This is a first announcement for a special meeting of the Highlands local group of the RSS celebrating the centenary of the first lecturer in Statistics at the University of Aberdeen (Dr William Robert Macdonell), one of the first in the UK. The same W. R. Macdonell as published the data in question. Being a centenary takes it back to 1906. Such biographic information as I have been able to find says: W. R. MACDONELL. Born October 16, 1852. Died May 15, 1916 KER Biometrika.1917; 11: 281-283 So he was well into his 50s when so honoured, and had only few years to go. Somewhat to my surpise, the excellent Index of Biographies of mathematicians and statisticians at the University of St Andrews: http://www-groups.dcs.st-and.ac.uk/~history/BiogIndex.html has nothing for him, despite his being a First for Scotland! Best wishes to all, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 04-Nov-06 Time: 19:32:50 -- XFMail -- __ R-help@stat.math.ethz.ch 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] Placing of legends
Hello, placings of legends is sometimes tricky. For placing outside the plot region I found locator to be useful. Unfortunately, the click defines the upper left corner. Is there a way to change this corner (say lower right corner)? Thanks, Christian __ R-help@stat.math.ethz.ch 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.
Re: [R] can update.packages Debian package files?
Tamas, Great question. On 4 November 2006 at 11:55, Tamas K Papp wrote: | I have searched the archive for the solution of this question, but | couldn't find anything, so I thought I would ask here. It has been discussed not that long ago on r-sig-debian, feel free to subscribe there as you may find the list useful for all matters Debian and R. | I am using R on a Debian (testing) system. Many of the R packages I | use are installed as .deb packages, those which are not available in | this format I install using install.packages. | | When calling update.packages, sometimes the R repository version is | more recent than the Debian package, and update.packages offers to | update it which I don't want because the new debianized version will | be out soon. Is it possible to have update.packages recognize that | these are systemwide packages and ignore them when updating? Or is | manual selection of what to update the only option? Let's recall that we have three locations for R packages under Debian (and hence also Ubuntu et al): i) /usr/lib/R/library used *exclusively* by r-base-core (and e.g. not even by r-recommended such as r-cran-vr, r-cran-boot, ...) ii) /usr/lib/R/site-library used *exclusively* by Debian (or Ubuntu) supplied packages that you can updated with apt-get et al (provided the maintainer stays current) iii) /usr/local/lib/R/site-library used for the rest The key is that these are non-overlapping which you can employ with update.packages() provided you tell update.packages() to limit itself to the directory in iii). Which is as simple as saying update.packages(lib.loc=/usr/local/lib/R/site-library) Now, for added bonus, the script 'update.r' in the littler package (version 0.0.8 or later) does all that for you. So after an initial $ sudo apt-get install littler all you need is $ sudo /usr/share/doc/littler/examples/update.r Cheers, Dirk -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison __ R-help@stat.math.ethz.ch 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.
Re: [R] Placing of legends
On Nov 4, 2006, at 1:47 PM, Thevini Christian Lerch wrote:
Hello,
placings of legends is sometimes tricky.
For placing outside the plot region I found locator to be useful.
Unfortunately, the click defines the upper left corner.
Is there a way to change this corner (say lower right corner)?
Thanks,
Christian
You could take advantage of the fact that legend() returns the height
and width of the legend box and calculate where the top left should be
given the bottom right. Here's something maybe you can build off of:
mylegend - function(x.right, y.bottom = NULL, ...) {
## allowance for input from locator() or
xy - xy.coords(x = x.right, y = y.bottom)
x.right - xy$x
y.bottom - xy$y
L - legend(x = topleft, plot = FALSE, ...)
x - x.right - L$rect$w # shift left by width of box
y - y.bottom + L$rect$h # shift up by height of box
legend(x = x, y = y, ...)
}
plot(1:10)
### given separate 'x' and 'y'
mylegend(x.right = 10, y.bottom = 2,
legend = c(Alpha, Beta), pch = 1:2, lty = 1:2)
### given locator()-like input
mylegend(list(x=6,y=8), legend = c(Alpha, Beta), pch = 1:2)
Hope this helps,
Stephen
Rochester, Minnesota, USA
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[R] struggling to plot subgroups
Hi Folks, I have data that looks like this: freqgender xBar 1000m 2.32 1000f 3.22 2000m 4.32 2000f 4.53 3000m 3.21 3000f 3.44 4000m 4.11 4000f 3.99 I want to plot two lines (with symbols) for the two groups m and f. I have tried the following: plot(xBar[gender==m]~freq[gender==f]) followed by lines(xBar[gender==m]~freq[gender==f]) with different symbols and lines colors (which I know how to do). However, these initial plots are not giving me the right output. The initial plot command generates the following error. Error in plot.window(xlim, ylim, log, asp, ...) : need finite 'xlim' values In addition: Warning messages: 1: no non-missing arguments to min; returning Inf 2: no non-missing arguments to max; returning -Inf 3: no non-missing arguments to min; returning Inf 4: no non-missing arguments to max; returning -Inf A second issue, I would also like to offset the second set of points along the x-axis so that the error bars will be visible. Any help is appreciated. Regards, Sumit __ R-help@stat.math.ethz.ch 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.
Re: [R] Measuring the effects of history on event probabilities
I haven't seen other replies, so I'll offer a feeble comment: It's not clear to me the events for which you want to estimate probabilities. If you would still like help from this listserve, I suggest you send us a toy example with typical (possibly made up) data consisting of 5-10 observations on 2-4 individuals. Then tell us what you'd like to do in terms of this toy example, possibly including things you've tried and why they didn't seem to give you what you wanted. Hope this helps. Spencer Graves Jon Minton wrote: This is probably very simple but my brain has frozen over. (I'm trying to warm it with coffee) I have observations of around 22000 individuals over 13 successive years: they were either 'interviewed' at time t or 'not interviewed'. What's the most appropriate function/approach to use to find out the extent to which individuals' event outcomes are temporally correlated? Thanks, Jon Minton [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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.
Re: [R] struggling to plot subgroups
On 11/4/06, Sumitrajit Dhar [EMAIL PROTECTED] wrote: Hi Folks, I have data that looks like this: freqgender xBar 1000m 2.32 1000f 3.22 2000m 4.32 2000f 4.53 3000m 3.21 3000f 3.44 4000m 4.11 4000f 3.99 I want to plot two lines (with symbols) for the two groups m and f. I have tried the following: This is pretty easy with ggplot. Something like: install.packages(ggplot) library(ggplot) qplot(freq, xBar, data=my.data.frame, colour=gender, id=gender, type=c(point,line)) should do what you want. Hadley __ R-help@stat.math.ethz.ch 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] Date, date, POSIX question
I have been working with R extensively for several months. I switched from SAS and Matlab to R. My question is Can anyone explain the benefits and detractions of the 'Date' package verses the 'date' package and verses 'POSIX' dates. I have noticed several other packages use one or the other. Rmetrics seems to standardize on POSIX. I can only see differences in default formats, and the starting counting number be it 1 1 1900 or something else. I am trying to standardize code that I write for research and to provide to my students on one date schema. The documentation is very good on using a specific package, but I can not tell the which one provides the broadest coverage across R packages or is just the better one to use. I know all of you have more experience with some of these and I am just soliciting your opinions and comments. Thank you Joe __ R-help@stat.math.ethz.ch 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.
Re: [R] Install RMySQL with R 2.4.0
Seth Falcon wrote: Joe W. Byers [EMAIL PROTECTED] writes: I am having trouble as well with the new version of R 2.4. I downloaded the gz file from the cran website, followed the instructions in the README.win file and installed RMySQL. I have mysql installed under c:\mysql not the program files directory which is the only difference. I get the following error when I attempt to connect to the MySQL Db ## open a connection to a MySQL database con - dbConnect(dbDriver(MySQL),host='localhost', + username='',dbname = 'StorageSims'); Error in function (classes, fdef, mtable) : unable to find an inherited method for function dbConnect, for signature MySQLDriver Any help will be appreciated. I would like to note that there are no problems with RMySQL on my linux system, only on XP's. Just to make sure: Before trying the code you posted, you did library(RMySQL), right? YES Also, what versions of DBI and RMySQL are you using? RMySQL from http://cran.r-project.org/src/contrib/Descriptions/RMySQL.html DBI Version 0.1-10 according to the NEWS file in ../R/library __ R-help@stat.math.ethz.ch 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@stat.math.ethz.ch 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.
