RE: [R] Protocol for answering basic questions
I'm a recent subscriber to the list. I was very impressed by the quality of people subscribing to the list, including the authors of all the books on R thateither I own or are present in my local uni library. However, I was astonished by the volume of messages. I have set up a folder for R messages, route the messages there automatically, and browse it at times of low panic levels. Personally, I think this list would be much better served by a standard bulletin board. The list could be broken down into a number of topics (e.g. Newbie questions, etc. etc.), the messages would be stored under threads so that people could choose to read or not read based on the topic. 'Sticky' threads could be left at the top so that new subscriberts would see them, and people who only want to follow a very few threads could tick the box for email alerts. Finally, there could be a search box enabling people to search out past answers (I know that this is possible now). An example board is: http://www.linuxquestions.org/questions/index.php Comments? Cheers, Ross-c __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Label data points in scatterplot matrices
Tom Mulholland wrote:
This does job, but it reveals that I don't really understand panels.
What I would like to know is how do you get the same result but without
the warnings.
This is essentially taken from the ?pairs help.
data(USJudgeRatings)
# There are 43 observations in this data.frame
z - 1:43
panel.text - function(x,y,z, ...)
{
text(x,y,z)
}
panel.hist - function(x, ...)
{
usr - par(usr); on.exit(par(usr))
par(usr = c(usr[1:2], 0, 1.5) )
h - hist(x, plot = FALSE)
breaks - h$breaks; nB - length(breaks)
y - h$counts; y - y/max(y)
rect(breaks[-nB], 0, breaks[-1], y, col=cyan, ...)
}
pairs(USJudgeRatings[1:5], panel=panel.text,z=z,,
cex = 1.5, pch = 24, bg=light blue,
diag.panel=panel.hist, cex.labels = 2, font.labels=2)
Well, in principle you cannot easily (it's a warning, not an errror, BTW).
But you can fake a little bit by, e.g., renaming z to pch:
data(USJudgeRatings)
# There are 43 observations in this data.frame
z - 1:43
panel.text - function(x,y,pch, ...)
{
text(x,y,pch)
}
panel.hist - function(x, ...)
{
usr - par(usr); on.exit(par(usr))
par(usr = c(usr[1:2], 0, 1.5) )
h - hist(x, plot = FALSE)
breaks - h$breaks; nB - length(breaks)
y - h$counts; y - y/max(y)
rect(breaks[-nB], 0, breaks[-1], y, col=cyan, ...)
}
pairs(USJudgeRatings[1:5], panel=panel.text,
cex = 1.5, pch = z, bg=light blue,
diag.panel=panel.hist, cex.labels = 2, font.labels=2)
Uwe Ligges
Mauricio Esguerra wrote:
Hello,
I am new to R and would like to know how to label data points in the
matrices of scatterplots made by the pairs() command.
To be more specific, I want to assign a number to each data point,
instead
of the small circumference that appears as a data point.
If anyone here knows if its possible to do this with R, I would greatly
appreciate your help.
Thank you,
Mauricio Esguerra
PhD candidate
Chemistry and Chemical Biology Department
Rutgers, the State University of New Jersey
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Re: [R] How to wrap or split labels on plot
Marc Schwartz wrote: On Fri, 2004-12-03 at 15:00 -0500, Heather J. Branton wrote: Dear R gurus, I want to wrap labels that are too long for a plot. I have looked at strsplit(), substr(), nchar(), and strwrap(). I think it's some combination but I'm having difficulty trying to figure out the right combo. I think I need to create some new matrix containing the labels already split, though I'm not sure if maybe there is a quick and dirty way to address this without my wandering around the block. I am using R 1.9.1, Windows XP. (Note: we are currently in the midst of a big project and probably won't upgrade to R 2.0.1 for another couple of weeks -- *unless* that's what I need to do to address these issues.) Here is my script with two label options at the bottom that are not working. # Settings win.graph(width=8, height=8, pointsize=10) # Read in data test - matrix(data=c(2.52,9.5,3.07,2.5,1.99,8.95), nrow = 6, byrow=TRUE) # Read in and attach labels (names) to data rownames(test) - c(Mount Pleasant,Jordan,Oil City,Pleasant Valley,Village of Lake Isabella,Rosebush) # Set plot limits: xmax - nrow(test) nvec - ncol(test) ymax - ceiling(max(test)) yinc - 1 # Generate Pareto order test - test[order(test[,1],decreasing=TRUE),] # Set color palette MyCols - rep(c(lightcyan,cornsilk,lavender), each = xmax) # Adjust the margins par(mar = c(7, 5, 6, 3)) # Bar graph mp - barplot(test, beside = TRUE, col = MyCols, axisnames = FALSE, names.arg = rep(names(test),nvec), las = 2, cex.names = 0.75, ylab = IXYV, ylim = c(0,ymax), yaxt = n) # Set up the y axis tick marks and labels ifelse (ymax=10,decpt - 2,decpt - 0) ticks - seq(0, ymax, yinc) axis(2, at = ticks, las = 1, labels = formatC(ticks, format = f, digits = decpt)) # Draw a box around the whole thing box() # Draw the x axis labels mtext(side = 1, at = rowMeans(mp)-.2, line = .5, las=2, text = strsplit(names(test), )) mtext(side = 1, at = rowMeans(mp), line = .5, las=2, text = strwrap(names(test),7)) mtext(side = 1, line = 5.5, text = Division) # Draw titles title(main=Central, outer=F, font.main=4, line=4) title(main=IXYV by Division, outer=F, font.main=2, line=2.5) Heather, There is likely to be more than one approach, but the one that I generally use is to explicitly put a newline character \n into the plot labels where required. So, in this case, you could do something like: names(test) - c(Mount\nPleasant,Jordan,Oil City, Pleasant\nValley, Village of\nLake Isabella, Rosebush) ... or automatically by combining strwrap() and paste(): names(test) - sapply(lapply(names(test), strwrap, 15), paste, collapse = \n) Uwe Ligges Also, there are some confusing things in your code, which I suspect may tie back to your test data versus the actual data you are using. If I am missing something here, you might want to clarify that, since things like your colors and other things don't entirely make sense. Here is something of a simplified approach using the test data as you have it: # Test can be a vector test - c(2.52, 9.5, 3.07, 2.5, 1.99, 8.95) names(test) - c(Mount\nPleasant,Jordan,Oil City, Pleasant\nValley, Village of\nLake Isabella, Rosebush) # Use sort here test - sort(test, decreasing = TRUE) ymax - ceiling(max(test)) par(mar = c(7, 5, 6, 3)) # Note that you can use the names here for names.arg # As a result of the \n, the titles will print on two lines mp - barplot(test, names.arg = names(test), cex.names = 0.8, ylab = IXYV, yaxt = n, ylim = c(0, ymax)) ticks - seq(0, ymax, 1) axis(2, at = ticks, las = 1, labels = formatC(ticks, format = f, digits = ifelse(ymax = 10, 2, 0))) box() mtext(side = 1, line = 3.5, text = Division) # you can combine the two title() calls into one mtext() call mtext(side = 3, text = c(Central, IXYV by Division), font = c(4, 2), line = c(4, 2.5)) If your actual data is a more complex matrix, adjust the above accordingly. HTH, Marc Schwartz __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Odd underflow(?) error
TL == Thomas Lumley [EMAIL PROTECTED] on Fri, 3 Dec 2004 15:22:07 -0800 (PST) writes: TL On Fri, 3 Dec 2004, William Faulk wrote: I'm still trying to install R on my Irix machine. Now I have a new problem that crops up during the checks. I've found the root cause, and it's that R is returning zero for certain things for reasons I don't understand. 2.225073859e-308, entered directly into R, responds 2.225074e-308. 2.225073858e-308 responds 0. Their negative values respond similarly, so it would appear that somewhere in there is the smallest absolute value that that installation of R will hold. TL Yes. .Machine$double.xmin tells you the smallest number representable to TL full precision, which is 2.225074e-308 (I think on all machines where R TL works) On another machine where the checks passed, both responses are correct, not just the first one. The underflow there is significantly lower, with much less accuracy, as opposed to what seems to be good accuracy on what looks like the broken one. The values there are: 2.4703282293e-324 gives 4.940656e-324 2.4703282292e-324 gives 0 TL Machines can differ in what they do with numbers smaller than TL .Machine$double.xmin. They can report zero, or they can add leading zeros TL and so lose precision. Suppose you had a 4-digit base 10 machine with 2 TL digits of exponent. The smallest number representable to full accuracy TL would be TL 1.000e-99 TL but by allowing the leading digits to be zero you could represent TL 0.001e-99 TL ie, 1e-102, to one digit accuracy (these are called denormalized TL numbers). TL My Mac laptop denormalizes, and agrees with your other computer, giving TL the smallest representable number as 4.940656e-324. It is TL .Machine$double.xmin/2^52. This number has very few bits left to TL represent values, so for example (a/2^52)*1.3==(a/2^52) TL [1] TRUE TL where a is .Machine$double.xmin (very nice explanation, thanks Thomas!) TL Both your machines should be correct. I don't think we deliberately TL require denormalized numbers to work anywhere. yes, indeed. I can imagine that some of regression tests (aka validation !) implicitly use some property -- but as Thomas said, that's not deliberate (and a buglet in our tests). William, could you move this topic from R-help to R-devel and give more specifics about what is failing for your installation? Martin __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How about a mascot for R?
DScottNZ == David Scott [EMAIL PROTECTED] on Fri, 3 Dec 2004 15:04:52 +1300 (NZDT) writes: DScottNZ As to an animal mascot, I think a New Zealand DScottNZ mascot is a must, well, thinking that must is bit strong, I agree that I have had the same idea (NZ animal) before your post. I first thought of the obvious Kiwi, but hoping for something more beautiful had been googling around for New Zealand animals, then had been side tracted by the Kakapo which I found nice, intriguing, but in his fight against extinction didn't seem to fit to my notion of R.. DScottNZ and suggestions of Australian DScottNZ ones would not be warmly received by New DScottNZ Zealanders. (To clarify, despite the address, I am DScottNZ Australian.) DScottNZ My suggestion is the Kea: inquisitive and intelligent. See: DScottNZ http://www.doc.govt.nz/Conservation/001~Plants-and-Animals/001~Native-Animals/Kea.asp Yesterday, when I posed the question at our group's coffee break, someone also immediately mentioned the Kea. Given all the things I've read in the mean time, I did like the R-madillo from it's name, but then, from an aesthetic point of view, I'd also vote for the Kea. OTOH, before getting into more, I'd also like to hear from R R -- particularly about the must part... Another thought that I think hasn't been raise: The mascot should typically also be representable as a monochrome line drawing (such as the O'Reilly book covers), and also be somewhat easily identifiable from a relatively small (eg. 32 x 32 ?) icons, since presumably it would eventually replace the current R logo, at least in some places. Also, is anyone willing to put up a web site collecting the proposals and maybe also allowing to collect votes? Though, I'm not at all sure we will reach that state. Martin Maechler, ETH Zurich __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Excel *.xls files, RODBC
I gather from reading the back-issues of r-help that it should be possible (modulo a number of caveats) to read an excel (yuck!) file into R using RODBC. I have obtained and installed ODBC and the RODBC package, but cannot for the life of me figure out how to go about it. Can anyone give me a simple recipe? I have an excel file on cdrom, say: /mnt/cdrom/melvin.xls I have started R and loaded the RODBC package. I want to create a data frame ``melvin'' by reading in /mnt/cdrom/melvin.xls. What (in monosyllables --- step by step) do I do next? cheers, Rolf Turner [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] A possible way to reduce basic questions
What about starting a database? I know it is a lot of work but one of the difficulties one encounter with R is taht i can be diffcult to know where to look for answers...I do agree that a basic list will tend to be a write only list! (and I take the opportunity here tp thank all of you for your patient answers !) Anne - Original Message - From: Tim Cutts [EMAIL PROTECTED] To: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED] Sent: Thursday, December 02, 2004 6:17 PM Subject: Re: [R] A possible way to reduce basic questions On 2 Dec 2004, at 1:23 am, Gabor Grothendieck wrote: Jim Lemon bitwrit at ozemail.com.au writes: I have been thinking about how to reduce the number of basic questions that elicit the ...ahem... robust debate that has occurred about how to answer The traffic on r-help could be reduced by creating a second list where more elementary questions are asked. But how many people here would read it, and help the novices (like me) out? There is always the danger that novice lists just become write-only lists. Tim -- Dr Tim Cutts Informatics Systems Group, Wellcome Trust Sanger Institute GPG: 1024D/E3134233 FE3D 6C73 BBD6 726A A3F5 860B 3CDD 3F56 E313 4233 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Getting R to emit an image file as a pipe or Base64 stream: Mac OSX 10.3 - R 2.0.1
That's right, Thanks for your replies. The reason why I started X11.app first is because Mac OS 10.3.5 doesn't launch X on startup, and instead uses its own Aqua/Quartz gui to render most windows until you specifically ask for X. The issue we're looking at is how to get R to emit the file as base64, or to somehow hand me a pipe. Is there a way to redirect the file in jpeg() to stdout? still hacking. Jin Kee From: Yuandan Zhang If you want to call R from perl, why don't you do a simple system call like: $callR=/usr/loca/bin/R CMD BATCH plotscript.R; system ($callR); It is not necessary to start X display if anything can be done in background But the problem is jpeg()/png() are not available unless an X display is available to the R process (one of the FAQs). Andy On Fri, 3 Dec 2004 12:07:24 +1100 (EST) Thuan-Jin Kee [EMAIL PROTECTED] wrote: Hi All, Anybody know how to make R emit base64 encoded text in some way that perl can grab it, instead of planting a file on your harddrive when calling JPEG or PNG? I've managed to get these scripts to work and put a file on the harddisk #!/usr/bin/perl -Wall # by jin kee. a simple script to demonstrate # the needed steps to get R to emit a jpeg. use strict; my($callR, $callRold); # need to start X if is isn't already started. `open /Applications/Utilities/X11.app`; #need to get let the R program know where to look #for the display immediately before calling #the R executible. $callR =MARKER; DISPLAY=:0.0; export DISPLAY; /usr/bin/R --vanilla plotscript.R; MARKER system($callR); # end script #!/usr/bin/R peg(~/Desktop/test.jpg); plot(rnorm(100)); dev.off(); q(save = no); My sysadmin says that the apache user can't write to the disk due to security policy, so he wants to know if I can emit the jpeg as a base64 stream and embedd it into the dynamically generated tag using a DATA tag to inline the image. http://www.elf.org/essay/inline-image.html http://www.faqs.org/rfcs/rfc2397.html i've tried searching the R-project.org site and help.search() and no luck. Yours Jin __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- -- Yuandan Zhang, PhD Animal Genetics and Breeding Unit The University of New England Armidale, NSW, Australia, 2351 E-mail: [EMAIL PROTECTED] Phone:(61) 02 6773 3786 Fax: (61) 02 6773 3266 http://agbu.une.edu.au AGBU is a joint venture of NSW Primary Industries and The University of New England to undertake genetic RD for Australia's Livestock Industries __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How about a mascot for R?
hi, some weka guys use kea (..with the same intenion to the bird in nz!) for a automatic keyphrase extraction tool (java). http://www.nzdl.org/Kea/ regards, christian Martin Maechler wrote: DScottNZ == David Scott [EMAIL PROTECTED] on Fri, 3 Dec 2004 15:04:52 +1300 (NZDT) writes: DScottNZ As to an animal mascot, I think a New Zealand DScottNZ mascot is a must, well, thinking that must is bit strong, I agree that I have had the same idea (NZ animal) before your post. I first thought of the obvious Kiwi, but hoping for something more beautiful had been googling around for New Zealand animals, then had been side tracted by the Kakapo which I found nice, intriguing, but in his fight against extinction didn't seem to fit to my notion of R.. DScottNZ and suggestions of Australian DScottNZ ones would not be warmly received by New DScottNZ Zealanders. (To clarify, despite the address, I am DScottNZ Australian.) DScottNZ My suggestion is the Kea: inquisitive and intelligent. See: DScottNZ http://www.doc.govt.nz/Conservation/001~Plants-and-Animals/001~Native-Animals/Kea.asp Yesterday, when I posed the question at our group's coffee break, someone also immediately mentioned the Kea. Given all the things I've read in the mean time, I did like the R-madillo from it's name, but then, from an aesthetic point of view, I'd also vote for the Kea. OTOH, before getting into more, I'd also like to hear from R R -- particularly about the must part... Another thought that I think hasn't been raise: The mascot should typically also be representable as a monochrome line drawing (such as the O'Reilly book covers), and also be somewhat easily identifiable from a relatively small (eg. 32 x 32 ?) icons, since presumably it would eventually replace the current R logo, at least in some places. Also, is anyone willing to put up a web site collecting the proposals and maybe also allowing to collect votes? Though, I'm not at all sure we will reach that state. Martin Maechler, ETH Zurich __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Getting R to emit an image file as a pipe or Base64 stream: Mac OSX 10.3 - R 2.0.1
Thuan-Jin Kee [EMAIL PROTECTED] writes: That's right, Thanks for your replies. The reason why I started X11.app first is because Mac OS 10.3.5 doesn't launch X on startup, and instead uses its own Aqua/Quartz gui to render most windows until you specifically ask for X. The issue we're looking at is how to get R to emit the file as base64, or to somehow hand me a pipe. Is there a way to redirect the file in jpeg() to stdout? This is really nasty, but on linuxen, you can do things like bitmap(file=/proc/self/fd/1,type=png256);plot(0);dev.off() which gives you several screenfulls of junk, the first characters of which is PNG... A cleaner way would be if the file argument to bitmap() could be a connection, but it can't (and it is nontrivial to change). still hacking. Jin Kee -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Excel *.xls files, RODBC
library(RODBC) z - odbcConnectExcel(c:/myfolder/mydata.xls) myframe - sqlFetch(z, Sheet1) close(z) I found the reading of whole sheets somewhat unsafe, so I always create a named range (here: data) including header and do the following. Never had problems with this. channel = odbcConnectExcel(macronutrients.xls) ac = sqlQuery(channel,select * from data) odbcClose(channel) Dieter __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Re: Protocol for answering basic questions
Perhaps something like the following paragraph should be added to the start of the Posting Guide (as a new paragraph right after the existing first paragraph): Note that R-help is *not* intended for questions that are easily answered by consulting one of the FAQs or other introductory material (see Do your homework before posting below).Such questions are actively discouraged and are likely to evoke a brusque response. Questions about seemingly simple matters that are mentioned in the FAQs or other introductory material *are welcomed* on R-help *when the questioner obviously has done their homework and the question is accompanied by an explanation* like FAQ 7.2.1 seems to be relevant to this but I couldn't understand/apply the answer because Something like this would make it very clear up front what type of questions are not appropriate. (I'm not trying at all to dictate the policy, but as far as I can tell, the above summaries the attitude of the majority of very knowledgeable helpers that respond to questions on R-help.) Also, I think that John Maindonald's idea of a I am new to R, where do I start? page, with a link from the posting guide, is an excellent idea. I'm aware that some feel that the posting guide is already too long, but my feeling is that if users don't read a very easily accessible posting guide AND post inappropriate questions AND become offended by brusque responses, then they are beyond where they can easily be helped. The most important thing is to make it very clear what types of questions are and are not considered appropriate, so that beginning users know what they are getting into. And the following might merit inclusion in the FAQ: Why is R-help not for hand-holding beginner questions? R-help is a high traffic list and the general sentiment is that too many very simple questions will overwhelm everyone and most importantly result in the knowledgeable helpers ceasing to participate. The reason that there is no R-help-me-quickly-I-dont-want-to-read-the-documentation list is that no-one has felt that it would work well -- it is unlikely that many knowledgeable users of R would be willing to participate. Without such users participating, it is likely that sometimes bad advice would be offered and stand uncorrected, because R is a complex language with many ways of doing things, some markedly inferior to others. For these reasons, some feel it would be a very bad idea to create such a list. (However, anyone who believes otherwise and wishes to start and maintain such a list or other similar service is free to do so.) One reason for this overall state of affairs is that R is free software and consequently there is no revenue stream to support a hand-holding support service with paid employees. So although the actual software is free, some investment in terms of time spent reading documentation is required in order to use it. Furthermore, many of the frequent helpers on R-help have written introductory documents intended to help beginners with many aspects of learning and using R (e.g., An Introduction to R, and the various FAQs). Consequently they sometimes get fed up getting asked again and again the same question they have already written a document to explain. Nonetheless, the general sentiment on R-help is very helpful -- a quote summarizes it well: It's OK if you need some spoonfeeding (I need that quite often myself), but at least show how you have tried to use the spoon yourself, instead of just showing us your open mouth. [Attribution to Andy Liaw, or remain anonymous?] As some feel that sufficient time and bandwidth has already been spent on this issue, if anyone has any comments on this particular matter of an addition to the posting guide (or FAQ), feel free to choose to respond to me privately, and I will summarize as appropriate. -- Tony Plate __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Excel *.xls files, RODBC
Chuck Cleland wrote: The following works for me under WinXP Pro to create myframe as a data frame: library(RODBC) z - odbcConnectExcel(c:/myfolder/mydata.xls) myframe - sqlFetch(z, Sheet1) close(z) I tried that and got the error message: Error: couldn't find function odbcConnectExcel Are you indicating the name of the worksheet you want within the *.xls file? I suspect there could be additional issues on a non-Windows OS that I don't know about. On which Brian Ripley commented: Most notably the absence of an Excel ODBC driver. I guess that's the problem. In my initial message I forgot to indicate that I am working on a Linux box. Sorry; mea culpa. It would appear then, that there is NO WAY to read Excel files into R save by transporting them to a Windoze system, saving them as .csv files and then transporting these back reading them into R. A bit unsatisfactory, but it ***is*** a workaround. Thanks to all who contributed advice/comments. cheers, Rolf Turner [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How about a mascot for R?
When I think of New Zealand I think Rabbit :) How 'bout something like the Monty Python rabbit from the Holy Grail (nasty pointy teeth..., look at the bones!) Doug __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Excel *.xls files, RODBC
On Sat, 2004-12-04 at 14:32 -0400, Rolf Turner wrote: Chuck Cleland wrote: The following works for me under WinXP Pro to create myframe as a data frame: library(RODBC) z - odbcConnectExcel(c:/myfolder/mydata.xls) myframe - sqlFetch(z, Sheet1) close(z) It would appear then, that there is NO WAY to read Excel files into R save by transporting them to a Windoze system, saving them as .csv files and then transporting these back reading them into R. A bit unsatisfactory, but it ***is*** a workaround. To stay on Linux one possibility would be to use perl: http://www-106.ibm.com/developerworks/linux/library/l-pexcel/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Excel *.xls files, RODBC
On Sat, 4 Dec 2004 14:32:24 -0400 (AST) Rolf Turner [EMAIL PROTECTED] wrote: Chuck Cleland wrote: The following works for me under WinXP Pro to create myframe as a data frame: library(RODBC) z - odbcConnectExcel(c:/myfolder/mydata.xls) myframe - sqlFetch(z, Sheet1) close(z) I tried that and got the error message: Error: couldn't find function odbcConnectExcel Are you indicating the name of the worksheet you want within the *.xls file? I suspect there could be additional issues on a non-Windows OS that I don't know about. On which Brian Ripley commented: Most notably the absence of an Excel ODBC driver. I guess that's the problem. In my initial message I forgot to indicate that I am working on a Linux box. Sorry; mea culpa. It would appear then, that there is NO WAY to read Excel files into R save by transporting them to a Windoze system, saving them as .csv files and then transporting these back reading them into R. A bit unsatisfactory, but it ***is*** a workaround. library(gdata) ?read.xls HTH, Tobias __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Excel *.xls files, RODBC
Success! Tobias Verbeke's kind suggestion of read.xls from the gdata package (from the gregmisc bundle) works like a charm. It's perl based, so no problema on Linux. The R community is wonderful! cheers, Rolf Turner __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re[2]: [R] How about a mascot for R?
Hello, I have a dataset with three numerical variables, and two factor
variables, one of which is shown:
deel1[,1:4]
median ucl lcl coupon.period
1 10.894672NA 14.255623 fixed0-1
5 12.536729 11.658164 13.341038 fixed1-5
9 10.616561 9.979676 11.039264 fixed5-7
13 8.457571 8.048390 8.723679 fixed7-10
17 7.537831 7.274149 7.895592fixed10-15
21 4.392874 4.279858 4.586663 fixed15more
Think of the data as six regression coefficients, with an upper and lower
confidence limit. I would like to make a lattice plot, with the factor
(fixed0-1,fixed1-5, etc) on the vertical axis, and the median on the
horizontal axis. This is simple:
xyplot(coupon.period ~ median,data=prepayment,
panel=function(x,y,...){
panel.xyplot(x,y)
}
)
does the trick. Now I want to have a line extending from the dots
representing the median, that run from the median to upper/lower confidence
limit. How do pass the information of deel1$ucl and deel1$lcl to the panel
function, and how do I make segments within the panel function?
Thanks for any help, Ruud
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[R] lattice graph with segments (erroneously posted earlier)
Hello, I have a dataset with three numerical variables, and two factor
variables, one of which is shown:
deel1[,1:4]
median ucl lcl coupon.period
1 10.894672NA 14.255623 fixed0-1
5 12.536729 11.658164 13.341038 fixed1-5
9 10.616561 9.979676 11.039264 fixed5-7
13 8.457571 8.048390 8.723679 fixed7-10
17 7.537831 7.274149 7.895592fixed10-15
21 4.392874 4.279858 4.586663 fixed15more
Think of the data as six regression coefficients, with an upper and lower
confidence limit. I would like to make a lattice plot, with the factor
(fixed0-1,fixed1-5, etc) on the vertical axis, and the median on the
horizontal axis. This is simple:
xyplot(coupon.period ~ median,data=prepayment,
panel=function(x,y,...){
panel.xyplot(x,y)
}
)
does the trick. Now I want to have a line extending from the dots
representing the median, that run from the median to upper/lower confidence
limit. How do pass the information of deel1$ucl and deel1$lcl to the panel
function, and how do I make segments within the panel function?
Thanks for any help, Ruud
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Re: [R] How about a mascot for R?
Ruud,
try something like the following (not debugged, no coffee yet):
xyplot(coupon.period ~ median, data=prepayment,
subscripts=T,
panel=function(x,y,subscripts,...){
panel.xyplot(x,y)
panel.segments(deel1$lcl[subscripts], deel$ucl[subscripts])
}
)
I hope that this helps,
Andrew
On Sat, Dec 04, 2004 at 08:43:47PM +0100, Ruud H. Koning wrote:
Hello, I have a dataset with three numerical variables, and two factor
variables, one of which is shown:
deel1[,1:4]
median ucl lcl coupon.period
1 10.894672NA 14.255623 fixed0-1
5 12.536729 11.658164 13.341038 fixed1-5
9 10.616561 9.979676 11.039264 fixed5-7
13 8.457571 8.048390 8.723679 fixed7-10
17 7.537831 7.274149 7.895592fixed10-15
21 4.392874 4.279858 4.586663 fixed15more
Think of the data as six regression coefficients, with an upper and lower
confidence limit. I would like to make a lattice plot, with the factor
(fixed0-1,fixed1-5, etc) on the vertical axis, and the median on the
horizontal axis. This is simple:
xyplot(coupon.period ~ median,data=prepayment,
panel=function(x,y,...){
panel.xyplot(x,y)
}
)
does the trick. Now I want to have a line extending from the dots
representing the median, that run from the median to upper/lower confidence
limit. How do pass the information of deel1$ucl and deel1$lcl to the panel
function, and how do I make segments within the panel function?
Thanks for any help, Ruud
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--
Andrew Robinson Ph: 208 885 7115
Department of Forest Resources Fa: 208 885 6226
University of Idaho E : [EMAIL PROTECTED]
PO Box 441133W : http://www.uidaho.edu/~andrewr
Moscow ID 83843 Or: http://www.biometrics.uidaho.edu
No statement above necessarily represents my employer's opinion.
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[R] D-V-D-Moviez for d-o-w-n-l-o-a-d-i-n-g
http://24.130.27.91:8180/dvp/ 9492 741 12746 842 103420 8005 731 32937 864 375550 1444 547 07897 844 268552 2486 852 31255 690 170959 Leave me alone! http://24.130.27.91:8180/dvp/[EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Lattice graph with segments
Andrew Robinson wrote:
Ruud,
try something like the following (not debugged, no coffee yet):
xyplot(coupon.period ~ median, data=prepayment,
subscripts=T,
panel=function(x,y,subscripts,...){
panel.xyplot(x,y)
panel.segments(deel1$lcl[subscripts], deel$ucl[subscripts])
}
)
Andrew Robinson wrote:
Ruud,
try something like the following (not debugged, no coffee yet):
xyplot(coupon.period ~ median, data=prepayment,
subscripts=T,
panel=function(x,y,subscripts,...){
panel.xyplot(x,y)
panel.segments(deel1$lcl[subscripts], deel$ucl[subscripts])
}
)
Not quite:
library(lattice)
prepayment - data.frame(median=c(10.89,12.54,10.62,8.46,7.54,4.39),
ucl=c(NA,11.66,9.98,8.05,7.27,4.28),
lcl=c(14.26,13.34,11.04,8.72,7.90,4.59),
coupon.period=c('a','b','c','d','e','f'))
xyplot(coupon.period ~ median, data=prepayment,
subscripts=T,
panel=function(x,y,subscripts,...){
panel.xyplot(x,y)
panel.segments(prepayment$lcl[subscripts], prepayment$ucl[subscripts])
}
)
throws the error:
Error in max(length(x0), length(x1), length(y0), length(y1)) :
Argument x1 is missing, with no default
Tim C
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[R] R plus SAS
Is it possible use SAS/DDE to communicate with R? Sorry for offending useR. ^_^ Thanks a lot. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Lattice graph with segments
On Saturday 04 December 2004 14:40, Tim Churches wrote:
Andrew Robinson wrote:
Ruud,
try something like the following (not debugged, no coffee yet):
xyplot(coupon.period ~ median, data=prepayment,
subscripts=T,
panel=function(x,y,subscripts,...){
panel.xyplot(x,y)
panel.segments(deel1$lcl[subscripts], deel$ucl[subscripts])
}
)
Not quite:
library(lattice)
prepayment - data.frame(median=c(10.89,12.54,10.62,8.46,7.54,4.39),
ucl=c(NA,11.66,9.98,8.05,7.27,4.28),
lcl=c(14.26,13.34,11.04,8.72,7.90,4.59),
coupon.period=c('a','b','c','d','e','f'))
xyplot(coupon.period ~ median, data=prepayment,
subscripts=T,
panel=function(x,y,subscripts,...){
panel.xyplot(x,y)
panel.segments(prepayment$lcl[subscripts],
prepayment$ucl[subscripts]) }
)
throws the error:
Error in max(length(x0), length(x1), length(y0), length(y1)) :
Argument x1 is missing, with no default
Right. Also, to make the resulting object self-contained (i.e. not
dependent on having a particular data frame in the scope), I would do
something similar to (either one of):
with(prepayment,
xyplot(coupon.period ~ median,
lcl = lcl, ucl = ucl,
panel=function(x, y, subscripts, lcl, ucl, ...) {
panel.xyplot(x, y, ...)
panel.segments(lcl[subscripts], as.numeric(y),
ucl[subscripts], as.numeric(y), ...)
}))
xyplot(coupon.period ~ median, data = prepayment,
lcl = prepayment$lcl, ucl = prepayment$ucl,
panel=function(x, y, subscripts, lcl, ucl, ...) {
panel.xyplot(x, y, ...)
panel.segments(lcl[subscripts], as.numeric(y),
ucl[subscripts], as.numeric(y), ...)
})
Deepayan
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[R] (sin asunto)
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[R] Kalman Filtering
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RE: [R] Testing for S4 objects (redux)
Dear John,
I've encountered the following problem:
x - rnorm(100)
y - sample(2, 100, replace=TRUE)
res - by(x, y, mean)
res
INDICES: 1
[1] 0.1129494
INDICES: 2
[1] -0.2066684
isS4object - function(object)(length(attr(object, class))==1
+ !is.null(getClass(class(object
isS4object(res)
Error in getClass(class(object)) : by is not a defined class
For a simple question, this has gotten rather complicated. Any suggestions
would be appreciated.
Regards,
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: John Chambers [mailto:[EMAIL PROTECTED]
Sent: Tuesday, November 30, 2004 9:40 AM
To: John Fox
Cc: Martin Maechler; [EMAIL PROTECTED]
Subject: Re: [R] Testing for S4 objects
Let me suggest a different test, because slotNames was
written to work differently when given a string or a class
definition. With your definition,
R x - classRepresentation
R isS4object(x)
[1] TRUE
which I assume is not what you wanted. (Given a single string,
slotNames() tries to look up the class definition of that name.)
How about the following? The logic is that an S4 object must
have an actual class attribute of length 1 (that rules out
basic data types, where class(x) is a string but there is no
actual attribute, and also rules out some S3 objects). Then
if that's true, try to look up the class definition. If it
is non-null, seems like an S4 object.
R isS4object - function(object)(length(attr(object, class))==1
+ !is.null(getClass(class(object
R isS4object(x)
[1] FALSE
R isS4object(getClass(class(x)))
[1] TRUE
This definition seems to work, at least on the examples I
could think of right away. Notice though, that some classes,
such as ts, that have been around for a long while are
nevertheless legitimate S4 classes, so:
R t1 = ts(1:12)
R isS4object(t1)
[1] TRUE
(this applies to either version of isS4object).
There are a couple of details, more appropriate for the r-devel list.
Seems a good candidate for a function to add to R.
On Sat, 27 Nov 2004 17:48:30 -0500, John Fox [EMAIL PROTECTED] wrote:
Dear Martin,
As it turns out, the test that I proposed (i.e., testing for NULL
slotNames) sometimes fails. For example:
library(car)
data(Prestige)
sum - summary(lm(prestige ~ income + education, data=Prestige))
slotNames(sum)
character(0)
The following, however, seems to work (at least as far as I've been
able to
ascertain):
isS4object - function(object) length(slotNames(object)) != 0
I hope that this is a more robust test.
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: Martin Maechler [mailto:[EMAIL PROTECTED]
Sent: Friday, November 26, 2004 3:18 AM
To: John Fox
Cc: [EMAIL PROTECTED]
Subject: Re: [R] Testing for S4 objects
JohnF == John Fox [EMAIL PROTECTED]
on Thu, 25 Nov 2004 22:28:50 -0500 writes:
JohnF Dear r-help list members, Is there a way to test
JohnF whether an object is an S4 object? The best that I've
JohnF been able to come up with is
JohnFisS4object - function(object)
!(is.null(slotNames(object)))
you can drop one pair of (..) to give
isS4object - function(object) !is.null(slotNames(object))
JohnF which assumes that an S4 object has at least one
JohnF slot. I think this is safe, but perhaps I'm missing
JohnF something.
The question is a very good one -- that I have posed to R-core a
while ago myself.
Inside utils:::str.default {which doesn't show the many
commments
in the *source* of str.default()}, I have wanted a way that even
works when the 'methods' package is not attached and use the more
obscure
#NOT yet:if(has.class - !is.null(cl - class(object)))
if(has.class - !is.null(cl - attr(object, class)))#
S3 or S4 class
S4 - !is.null(attr(cl, package))## 'kludge' FIXME!
##or length(methods::getSlots(cl)) 0
For the time being, I'd keep your function, but I don't
think we'd
guarantee that it will remain the appropriate test in all
future.
But till then many things will have happened (if not all of them
;-).
Martin Maechler, ETH Zurich
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[R] What is the most useful way to detect nonlinearity in logistic regression?
It is easy to spot response nonlinearity in normal linear models using plot(something.lm). However plot(something.glm) produces artifactual peculiarities since the diagnostic residuals are constrained by the fact that y can only take values 0 or 1. What do R users find most useful in checking the linearity assumption of logistic regression (i.e. log-odds =a+bx)? Patrick Foley [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How about a mascot for R?
On 4 Dec 2004, at 16:19, Martin Maechler wrote: DScottNZ == David Scott [EMAIL PROTECTED] on Fri, 3 Dec 2004 15:04:52 +1300 (NZDT) writes: DScottNZ As to an animal mascot, I think a New Zealand DScottNZ mascot is a must, well, thinking that must is bit strong, I agree that I have had the same idea (NZ animal) before your post. I first thought of the obvious Kiwi, but hoping for something more beautiful had been googling around for New Zealand animals, then had been side tracted by the Kakapo which I found nice, intriguing, but in his fight against extinction didn't seem to fit to my notion of R.. Firstly, Kiwi is a rip snorter for a bird. Secondly, there are other kind of kiwis than the kiwi bird. I'm living about as far a away from NZ as is it is possible (you're getting closer if you try to get away), but even I've heard of 'kiwi fruit', 'kiwi bear' (brushtail possum) and 'kiwi' as people. So it could be something 'kiwi'. I do think that a kiwi bird would be mascotty like a creature: cuddly and round and easiesh to draw. One parallel story brought about here is the penguin as a Linux mascot. Actually, this is a not-so-pleasant story: Linus Torvalds told somewhere that a penguin (hardly gentoo but some other species) tried to bite off his finger in a zoo, which made him to like those animals (he's a Swedish speaking Finn which helps to explain this attitude). With this attitude, you could pick a gray, mouse-like nocturnal bird as a mascot. Naturally, this is none of my business, so you should not let this message influence your opinion (it wouldn't anyway). cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Testing for S4 objects (redux)
Which version of R?
I just replicated it in R 2.0.0patched. I know that 2.0.1 is now
available, but I haven't found time to upgrade yet.
By the way, I can replicate the error message with only one line:
getClass(by)
Error in getClass(by) : by is not a defined class
hope this helps. spencer graves
John Fox wrote:
Dear John,
I've encountered the following problem:
x - rnorm(100)
y - sample(2, 100, replace=TRUE)
res - by(x, y, mean)
res
INDICES: 1
[1] 0.1129494
INDICES: 2
[1] -0.2066684
isS4object - function(object)(length(attr(object, class))==1
+ !is.null(getClass(class(object
isS4object(res)
Error in getClass(class(object)) : by is not a defined class
For a simple question, this has gotten rather complicated. Any suggestions
would be appreciated.
Regards,
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: John Chambers [mailto:[EMAIL PROTECTED]
Sent: Tuesday, November 30, 2004 9:40 AM
To: John Fox
Cc: Martin Maechler; [EMAIL PROTECTED]
Subject: Re: [R] Testing for S4 objects
Let me suggest a different test, because slotNames was
written to work differently when given a string or a class
definition. With your definition,
R x - classRepresentation
R isS4object(x)
[1] TRUE
which I assume is not what you wanted. (Given a single string,
slotNames() tries to look up the class definition of that name.)
How about the following? The logic is that an S4 object must
have an actual class attribute of length 1 (that rules out
basic data types, where class(x) is a string but there is no
actual attribute, and also rules out some S3 objects). Then
if that's true, try to look up the class definition. If it
is non-null, seems like an S4 object.
R isS4object - function(object)(length(attr(object, class))==1
+ !is.null(getClass(class(object
R isS4object(x)
[1] FALSE
R isS4object(getClass(class(x)))
[1] TRUE
This definition seems to work, at least on the examples I
could think of right away. Notice though, that some classes,
such as ts, that have been around for a long while are
nevertheless legitimate S4 classes, so:
R t1 = ts(1:12)
R isS4object(t1)
[1] TRUE
(this applies to either version of isS4object).
There are a couple of details, more appropriate for the r-devel list.
Seems a good candidate for a function to add to R.
On Sat, 27 Nov 2004 17:48:30 -0500, John Fox [EMAIL PROTECTED] wrote:
Dear Martin,
As it turns out, the test that I proposed (i.e., testing for NULL
slotNames) sometimes fails. For example:
library(car)
data(Prestige)
sum - summary(lm(prestige ~ income + education, data=Prestige))
slotNames(sum)
character(0)
The following, however, seems to work (at least as far as I've been
able to
ascertain):
isS4object - function(object) length(slotNames(object)) != 0
I hope that this is a more robust test.
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: Martin Maechler [mailto:[EMAIL PROTECTED]
Sent: Friday, November 26, 2004 3:18 AM
To: John Fox
Cc: [EMAIL PROTECTED]
Subject: Re: [R] Testing for S4 objects
JohnF == John Fox [EMAIL PROTECTED]
on Thu, 25 Nov 2004 22:28:50 -0500 writes:
JohnF Dear r-help list members, Is there a way to test
JohnF whether an object is an S4 object? The best that I've
JohnF been able to come up with is
JohnFisS4object - function(object)
!(is.null(slotNames(object)))
you can drop one pair of (..) to give
isS4object - function(object) !is.null(slotNames(object))
JohnF which assumes that an S4 object has at least one
JohnF slot. I think this is safe, but perhaps I'm missing
JohnF something.
The question is a very good one -- that I have posed to R-core a
while ago myself.
Inside utils:::str.default {which doesn't show the many
commments
in the *source* of str.default()}, I have wanted a way that even
works when the 'methods' package is not attached and use the more
obscure
#NOT yet:if(has.class - !is.null(cl - class(object)))
if(has.class - !is.null(cl - attr(object, class)))#
S3 or S4 class
S4 - !is.null(attr(cl, package))## 'kludge' FIXME!
##or length(methods::getSlots(cl)) 0
For the time being, I'd keep your function, but I don't
think we'd
guarantee that it will remain the appropriate test in all
future.
But till then many things will have happened (if not all of them
;-).
Martin Maechler, ETH Zurich
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Re: [R] AIC, AICc, and K
I don't know the best way, but the following looks like it will work: tstDF - data.frame(x=1:3, y=c(1,1,2)) fit0 - lm(y~1, tstDF) fitDF - lm(y~x, tstDF) AIC(fitDF,fit0) df AIC fitDF 3 5.842516 fit0 2 8.001399 The function AIC with only 1 argument returns only a single number. However, given nested models, it returns a data.frame with colums df and AIC. At least in this example (and I would think in all other contexts as well), df is the K you want. hope this helps. Spencer Graves Benjamin M. Osborne wrote: How can I extract K (number of parameters) from an AIC calculation, both to report K itself and to calculate AICc? I'm aware of the conversion from AIC - AICc, where AICc = AIC + 2K(K+1)/(n-K-1), but not sure of how K is calculated or how to extract that value from either an AIC or logLik calculation. This is probably more of a basic statistics question than an R question, but I thank you for your help. -Ben Osborne -- Botany Department University of Vermont 109 Carrigan Drive Burlington, VT 05405 [EMAIL PROTECTED] phone: 802-656-0297 fax: 802-656-0440 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Spencer Graves, PhD, Senior Development Engineer O: (408)938-4420; mobile: (408)655-4567 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] boot package
Hi,
I using the boot package 1.2-20 on R 2.0.1.
My statistics function estimates 6 parameters.
In a small percentage of resampled data sets my statistics function
doesn't produce an estimate for one parameter and the boot function
stops with an error.
I can write an ifelse(exists('parameter.estimate'), parameter.estimate,
NA) statement within the statistic function to substitute an NA for the
missing estimate value.
However, the boot.ci function to generate CIs from the boot object
won't accept NAs.
My problem is writing code to impute a numeric value for the missing
estimate. ifelse won't generate a numeric value if the test is mode
logical.
Any suggestions?
Nathan
Nathan Leon Pace, MD, MStat Work:[EMAIL PROTECTED]
Department of AnesthesiologyHome:[EMAIL PROTECTED]
University of Utah Work:801.581.6393
Salt Lake City, UtahHome:801.467.2925
Fax:801.581.4367
Cell:801.558.3987
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Re: [R] What is the most useful way to detect nonlinearity in logistic regression?
Patrick Foley [EMAIL PROTECTED] writes: It is easy to spot response nonlinearity in normal linear models using plot(something.lm). However plot(something.glm) produces artifactual peculiarities since the diagnostic residuals are constrained by the fact that y can only take values 0 or 1. What do R users find most useful in checking the linearity assumption of logistic regression (i.e. log-odds =a+bx)? Well, there's basically - grouping - higher-order terms - smoothed residuals A simple technique is to include a variable _both_ as a continuous term and cut up into a factor (as in ~ age + cut(age,seq(30,70,10))). The model that you are fitting is a bit weird but it gives you a clean test for omitting the grouped term. A somewhat nicer variant of the same theme is to do a linear spline (or a higher order one for that matter) with selected knots. Re. the smoothed residuals, you do need to be careful about the smoother. Some of the robust ones will do precisely the wrong thing in this context: You really are interested in the mean, not some trimmed mean (which can easily amount to throwing away all your cases...). Here's an idea: x - runif(500) y - rbinom(500,size=1,p=plogis(x)) xx - predict(loess(resid(glm(y~x,binomial))~x),se=T) matplot(x,cbind(xx$fit, 2*xx$se.fit, -2*xx$se.fit),pch=20) Not sure my money isn't still on the splines, though. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] A possible way to reduce basic questions
On 12/02/04 21:15, Anne wrote: What about starting a database? Of what? Like the one in the last line of my .sig? -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron R search page: http://finzi.psych.upenn.edu/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Excel *.xls files, RODBC
There is another way to read and write excel files using jakarta POI. Hopefully, I'll have a package available in a week or so. I have a working example of writing a matrix from R to excel, but I haven't finished the read excel portion of the code. If anyone wants to give it a spin, contact me off list and I'll send a copy. http://jakarta.apache.org/poi/index.html Regards, Whit -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Rolf Turner Sent: Saturday, December 04, 2004 2:43 PM To: [EMAIL PROTECTED] Subject: Re: [R] Excel *.xls files, RODBC Success! Tobias Verbeke's kind suggestion of read.xls from the gdata package (from the gregmisc bundle) works like a charm. It's perl based, so no problema on Linux. The R community is wonderful! cheers, Rolf Turner __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Nice christmas presents! Men's Ladies' Watches. Gift Boxes.
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RE: [R] Testing for S4 objects (redux)
Dear Spencer,
-Original Message-
From: Spencer Graves [mailto:[EMAIL PROTECTED]
Sent: Saturday, December 04, 2004 8:00 PM
To: John Fox
Cc: 'John Chambers'; [EMAIL PROTECTED]; 'Martin Maechler'
Subject: Re: [R] Testing for S4 objects (redux)
Which version of R?
Sorry -- this was with R 2.0.1 under Windows.
John
I just replicated it in R 2.0.0patched. I know that
2.0.1 is now available, but I haven't found time to upgrade yet.
By the way, I can replicate the error message with only
one line:
getClass(by)
Error in getClass(by) : by is not a defined class
hope this helps. spencer graves
John Fox wrote:
Dear John,
I've encountered the following problem:
x - rnorm(100)
y - sample(2, 100, replace=TRUE)
res - by(x, y, mean)
res
INDICES: 1
[1] 0.1129494
INDICES: 2
[1] -0.2066684
isS4object - function(object)(length(attr(object, class))==1
+ !is.null(getClass(class(object
isS4object(res)
Error in getClass(class(object)) : by is not a defined class
For a simple question, this has gotten rather complicated. Any
suggestions would be appreciated.
Regards,
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: John Chambers [mailto:[EMAIL PROTECTED]
Sent: Tuesday, November 30, 2004 9:40 AM
To: John Fox
Cc: Martin Maechler; [EMAIL PROTECTED]
Subject: Re: [R] Testing for S4 objects
Let me suggest a different test, because slotNames was
written to work
differently when given a string or a class definition. With your
definition,
R x - classRepresentation
R isS4object(x)
[1] TRUE
which I assume is not what you wanted. (Given a single string,
slotNames() tries to look up the class definition of that name.)
How about the following? The logic is that an S4 object
must have an
actual class attribute of length 1 (that rules out basic
data types,
where class(x) is a string but there is no actual
attribute, and also
rules out some S3 objects). Then if that's true, try to
look up the
class definition. If it is non-null, seems like an S4 object.
R isS4object - function(object)(length(attr(object,
class))==1
+ !is.null(getClass(class(object
R isS4object(x)
[1] FALSE
R isS4object(getClass(class(x)))
[1] TRUE
This definition seems to work, at least on the examples I
could think
of right away. Notice though, that some classes, such as
ts, that
have been around for a long while are nevertheless legitimate S4
classes, so:
R t1 = ts(1:12)
R isS4object(t1)
[1] TRUE
(this applies to either version of isS4object).
There are a couple of details, more appropriate for the
r-devel list.
Seems a good candidate for a function to add to R.
On Sat, 27 Nov 2004 17:48:30 -0500, John Fox
[EMAIL PROTECTED] wrote:
Dear Martin,
As it turns out, the test that I proposed (i.e., testing for NULL
slotNames) sometimes fails. For example:
library(car)
data(Prestige)
sum - summary(lm(prestige ~ income + education, data=Prestige))
slotNames(sum)
character(0)
The following, however, seems to work (at least as far as
I've been
able to
ascertain):
isS4object - function(object) length(slotNames(object)) != 0
I hope that this is a more robust test.
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: Martin Maechler [mailto:[EMAIL PROTECTED]
Sent: Friday, November 26, 2004 3:18 AM
To: John Fox
Cc: [EMAIL PROTECTED]
Subject: Re: [R] Testing for S4 objects
JohnF == John Fox [EMAIL PROTECTED]
on Thu, 25 Nov 2004 22:28:50 -0500 writes:
JohnF Dear r-help list members, Is there a way to test
JohnF whether an object is an S4 object? The best that I've
JohnF been able to come up with is
JohnFisS4object - function(object)
!(is.null(slotNames(object)))
you can drop one pair of (..) to give
isS4object - function(object) !is.null(slotNames(object))
JohnF which assumes that an S4 object has at least one
JohnF slot. I think this is safe, but perhaps I'm missing
JohnF something.
The question is a very good one -- that I have posed to R-core a
while ago myself.
Inside utils:::str.default {which doesn't show the many
commments
in the *source* of str.default()}, I have wanted a way that even
works when the 'methods' package is not attached and use the more
obscure
RE: [R] What is the most useful way to detect nonlinearity in logisticregression?
Dear Patrick, Component+residual plots can be defined for generalized linear models (including logistic regression) as for linear models, but they may require smoothing for interpretation. See, e.g., the cr.plots() functions in the car package, which works with glm objects. I hope this helps, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Patrick Foley Sent: Saturday, December 04, 2004 7:49 PM To: [EMAIL PROTECTED] Subject: [R] What is the most useful way to detect nonlinearity in logisticregression? It is easy to spot response nonlinearity in normal linear models using plot(something.lm). However plot(something.glm) produces artifactual peculiarities since the diagnostic residuals are constrained by the fact that y can only take values 0 or 1. What do R users find most useful in checking the linearity assumption of logistic regression (i.e. log-odds =a+bx)? Patrick Foley [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
