Re: [R] FW: R Version Problem in using write.foreign+SAS

2006-12-21 Thread Stephen D. Weigand
Shubha, On Dec 20, 2006, at 10:54 PM, Shubha Vishwanath Karanth wrote: Could I find a solution for this? Please please please... How can I change the built in code of foreign:::writeForeignSAS for the format? I tend not to change originals if I can help it, so I would create my own version

Re: [R] RuleFit quantreg: partial dependence plots; showing an effect

2006-12-21 Thread Mark Difford
Dear Professors Koenker and Varadhan, Thank you for your detailed and engaging replies. The (very) muddy waters clear slowly, but only if I keep moving my hands! Kind regards, Mark Difford. Mark Difford Ph.D. candidate, Botany Department, Nelson Mandela Metropolitan University, Port

Re: [R] call by reference

2006-12-21 Thread Gabor Grothendieck
You can do this: fb - function(bS, env = parent.frame()) { bS - deparse(substitute(bS)) assign(bS, 3, env = env) } fb(bS) bS rm(bS) # or corresponding to your code fb(bS, env = .GlobalEnv) Of course when typed in both give the same result since the global

Re: [R] \Sexpr in MikTex

2006-12-21 Thread Doran, Harold
I don't run the program this way so I don't know. But it makes me wonder if the problem is with \Sexpr{} or the way she is trying to run Sweave and compile. So, is it possible that code chunks are working but not \Sexpr{}? If you have something like = R code here @ Do you get that output?

Re: [R] Rotating a distribution plot by 90 degrees

2006-12-21 Thread Benjamin Otto
I forgot one thing: Gregs example results in what I seek. However he has roteted the data in his mind and in the data submitted to the plot command. What I would like to know is whether I can use the plot command to make some normal plot and add some second command which rotates the data for

Re: [R] Rotating a distribution plot by 90 degrees

2006-12-21 Thread Benjamin Otto
Hi Knut, hi Greg, Thanks for the quick help! @Greg: Yes THATÂ’S exactly what I meant. Thanks for the example. @Knut: Thanks for the hint. However my problem was that the combination of plot and grid wasn't working. But probably it isn't supposed to. Regards Benjamin

[R] Add line to plot. The line falls outside the current plot.

2006-12-21 Thread fjmolina
Hi, I have plotted the graph of x^2 and I would like to add to it a line that is currently outside of the plot ( the points of the line fall outside of the plot ). When I use the function 'lines' the graphics window does not became larger to show this line. Is there any way I can fix this?

Re: [R] Add line to plot. The line falls outside the current plot.

2006-12-21 Thread Jonne Zutt
Use xlim and ylim to your call to plot (see ?plot and ?par). So, plot(..your.parameters.., xlim=c(minx, maxx), ylim=c(miny,maxy)) Replace minx,maxx,miny,maxy by numbers. Usually, the function range() comes in very handy here, see ?range Jonne. On Thu, 2006-12-21 at 04:38 -0800, [EMAIL

Re: [R] Memory problem on a linux cluster using a large data set [Broadcast]

2006-12-21 Thread Iris Kolder
Thank you all for your help! So with all your suggestions we will try to run it on a computer with a 64 bits proccesor. But i've been told that the new R versions all work on a 32bits processor. I read in other posts that only the old R versions were capable of larger data sets and were

Re: [R] \Sexpr in MikTex

2006-12-21 Thread Duncan Murdoch
Wow, that's a lot of errors in my post. Sorry about that. You should probably just ignore it completely. Duncan Murdoch On 12/20/2006 10:05 PM, Duncan Murdoch wrote: On 12/20/2006 6:26 PM, Blanchard, Suzette wrote: Greetings, \Sexpr{} has worked on MikTex with earlier versions of R, I can

[R] where is the source code of bca.ci?

2006-12-21 Thread Meinhard Ploner
i was searching for the source of bca.ci, a function of the package boot. I tried require(boot, keep.source=TRUE) but again the source was not viewable. How should i do? Best regards Meinhard Ploner PS version _ platform i386-apple-darwin8.8.1 arch

Re: [R] where is the source code of bca.ci?

2006-12-21 Thread Chuck Cleland
Meinhard Ploner wrote: i was searching for the source of bca.ci, a function of the package boot. I tried require(boot, keep.source=TRUE) but again the source was not viewable. How should i do? If you download the source package

Re: [R] how to replace some objects?

2006-12-21 Thread Adrian Dusa
On Tuesday 19 December 2006 13:49, Michael Kubovy wrote: On Dec 19, 2006, at 3:05 AM, Zhang Jian wrote: I want to replace some objects in one row or column.For example, One colume: a,b,a,c,b,b,a,a,c. I want to replace a with 1, b with 2, and c with 3. Like this: 1,2,1,3,2,2,1,1,3. let -

Re: [R] where is the source code of bca.ci?

2006-12-21 Thread Meinhard Ploner
Chuck and Marc, thanks for the good answers! MP On Dec 21, 2006, at 2:48 PM, Chuck Cleland wrote: Meinhard Ploner wrote: i was searching for the source of bca.ci, a function of the package boot. I tried require(boot, keep.source=TRUE) but again the source was not viewable. How should i

[R] Poisson mixed effects model

2006-12-21 Thread Richard Reiss
Hello, I am fitting a Poisson mixed effects model. I have the number of eggs (Eggs) laid by a quail and looking at the effect of dosage of a chemical (Dose) in the study. I have counts of eggs laid by week of the study, so I am including the week number (Week) as a random effect. I'm using

Re: [R] where is the source code of bca.ci?

2006-12-21 Thread Prof Brian Ripley
On Thu, 21 Dec 2006, Meinhard Ploner wrote: i was searching for the source of bca.ci, a function of the package boot. I tried Actually only of the namespace 'boot'. require(boot, keep.source=TRUE) but again the source was not viewable. How should i do? This is discussed in a recent R

Re: [R] where is the source code of bca.ci?

2006-12-21 Thread Marc Schwartz
On Thu, 2006-12-21 at 14:34 +0100, Meinhard Ploner wrote: i was searching for the source of bca.ci, a function of the package boot. I tried require(boot, keep.source=TRUE) but again the source was not viewable. How should i do? Best regards Meinhard Ploner You can see a

Re: [R] Add line to plot. The line falls outside the current plot.

2006-12-21 Thread John Kane
--- [EMAIL PROTECTED] wrote: Also, how can I eliminate the axis from the plot? ?plot.default axes=FALSE ?par xast=n __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] data - data matrix that can be used in regressions

2006-12-21 Thread Ulrich Kaiser
Dear R users, I have spent most of this day figuring out how to read STATA data into R (which eventually worked) and to run a simple OLS regression. It seems that the manuals are written in the most general and abstract way which does not really make it easy to understand what's going on.

Re: [R] data - data matrix that can be used in regressions

2006-12-21 Thread John Kane
--- Ulrich Kaiser [EMAIL PROTECTED] wrote: Dear R users, I have spent most of this day figuring out how to read STATA data into R (which eventually worked) and to run a simple OLS regression. It seems that the manuals are written in the most general and abstract way which does not

[R] Penalized Canonical Variates

2006-12-21 Thread Frank E Harrell Jr
In the excellent paper by Hastie, Buja, and Tibshirani Penalized Discriminant Analysis the authors developed penalized discriminant functions that incorporated shrinkage on the predictor parameters. This is a shrunken version of a canonical correlation analysis in which dummy variables appear

Re: [R] Upgrading

2006-12-21 Thread DEEPANKAR BASU
Thanks for the suggestions; they resolved the problems. First I installed r-base-dev and then started R via sudo R. Now, when I used update.packages(), the process completed without any warning messages. Deepankar - Original Message - From: Ivailo Stoyanov [EMAIL PROTECTED] Date:

Re: [R] data - data matrix that can be used in regressions

2006-12-21 Thread Gabor Grothendieck
Do a google search for cran contributed documentation and at the first hit you will find numerous introductions that may be of use to you. Also read the last line of every post to r-help. On 12/21/06, Ulrich Kaiser [EMAIL PROTECTED] wrote: Dear R users, I have spent most of this day

[R] Online course - Modeling in R

2006-12-21 Thread Peter C. Bruce
Drs. Brian Everitt and Torsten Hothorn will present their online course Modeling in R at statistics.com Jan. 19 - Feb. 16. Participants can ask questions and exchange comments with Drs. Everitt and Hothorn via a private discussion board throughout the period. In this course you learn how to

Re: [R] Rotating a distribution plot by 90 degrees

2006-12-21 Thread Greg Snow
The gridBase package supports the mixing of traditional graphs in grid viewports, that may do what you want (But I am not a grid expert, so can't tell you anything more on that). You could also create a plot, save it as a graphics file, read it back in rotated and add it to a plot, but that

Re: [R] Memory problem on a linux cluster using a large data set [Broadcast]

2006-12-21 Thread Thomas Lumley
On Thu, 21 Dec 2006, Iris Kolder wrote: Thank you all for your help! So with all your suggestions we will try to run it on a computer with a 64 bits proccesor. But i've been told that the new R versions all work on a 32bits processor. I read in other posts that only the old R versions

Re: [R] \Sexpr in MikTex

2006-12-21 Thread Blanchard, Suzette
Thank you for your help. With your fix I was able to get the correct result once but then I would have to close R. If I go back to R-2.3.1 Everything seem to work fine. Best to everyone that helped. Suzette From: Duncan Murdoch [mailto:[EMAIL PROTECTED] Sent:

Re: [R] Memory problem on a linux cluster using a large data set [Broadcast]

2006-12-21 Thread Martin Morgan
Section 8 of the Installation and Administration guide says that on 64-bit architectures the 'size of a block of memory allocated is limited to 2^32-1 (8 GB) bytes'. The wording 'a block of memory' here is important, because this sets a limit on a single allocation rather than the memory consumed

[R] : newbie estimating survival curve w/ survfit for coxph

2006-12-21 Thread sj
I am wondering how to estimate the survival curve for a particular case(s) given a coxph model using this example code: #fit a cox proportional hazards model and plot the #predicted survival curve fit - coxph( Surv(futime,fustat)~resid.ds+strata(rx)+ecog.ps+age,data=ovarian[1:23,])

[R] iplots/JGR on OS X 10.4.8

2006-12-21 Thread bobp
iMac Intel Core Duo; OS X 10.4.8; Java 1.5.0_06; R 2.4.1; JGR 1.4-14; rJava 0.4-12; iplots 1.0-5 I'm unable to get JGR or iplots to load using library(JGR) or library(iplots), respectively. This feels like it might be a classpath or Mac look-and-feel issue, but I'm not sure where to go with it

Re: [R] lme4 mcmcsamp matrix not PD

2006-12-21 Thread Martin Henry H. Stevens
Hi folks, A follow up - this problem happens only stochastically. Further, a little trial and error indicates that using mathod=Laplace or method=AGQ reduces the frequency of the problem. Why? I have no idea, and even this could be my own wishful interpretation of my trial and error. -Hank

Re: [R] : newbie estimating survival curve w/ survfit for coxph

2006-12-21 Thread Charles C. Berry
Spencer, It always helps to look at the documentation for the objects you use. ?survfit.object tells you: --- COMPONENTS strata if there are multiple curves, this component gives the number of elements of the time etc. vectors corresponding to

[R] Drawing a 3-D plot for PCA?

2006-12-21 Thread Frank Duan
Hi All, Can anyone point me a hint (package) how to draw a 3D plot using the first 3 components from PCA? Thanks a lot, FD [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list

Re: [R] Drawing a 3-D plot for PCA?

2006-12-21 Thread hadley wickham
Can anyone point me a hint (package) how to draw a 3D plot using the first 3 You might want to have a look at ggobi (http://www.ggobi.org) and rggobi (http://www.ggobi.org/rggobi) which will allow you to look at any number of principle coordinates. (And don't forgot to look at the high ones -

[R] multinom(nnet) analogy for biglm package?

2006-12-21 Thread Yeh, Richard C
I would like to perform a multinomial logistic regression on a large data set, but do not know how. I've only thought of a few possibilities and write to seek advice and guidance on them or deepening or expanding my search. On smaller data sets, I have successfully loaded the data and issued

Re: [R] multinom(nnet) analogy for biglm package?

2006-12-21 Thread Yeh, Richard C
OK, well, seeing Thomas Lumley's post earlier today, I figured out the answer to #4: gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1115191 29.83469679 92.7 13981968 373.4 Vcells 14796791 112.9 79783730 608.8 124640525 951.0 c - rnorm(1e9) Error in rnorm(1e+09) :

Re: [R] multinom(nnet) analogy for biglm package?

2006-12-21 Thread Prof Brian Ripley
Here is the direct way: .Machine$sizeof.pointer [1] 8 on a 64-bit system. You can also figure it out from the size of the Ncells, clearly 28 bytes in your example. You seem to believe a multinomial logistic regression is a GLM: it is not. On Thu, 21 Dec 2006, Yeh, Richard C wrote: OK,

[R] Math expression with object to evaluate

2006-12-21 Thread [EMAIL PROTECTED]
Hello. I have a question that probably has a simple answer. I have a loop where several figures are plotted with each iteration. I calculate some descriptives to put in the title of the figure. When I use expression, since I want to combine math plotting symbols and the descriptives I

[R] odfWeave problem

2006-12-21 Thread Abhijit Dasgupta
Hi, I'm trying to customize some formating for a table using odfWeave. I'm having some trouble getting the formatting to work. I've defined the following format defns: origStyleDefs - getStyleDefs() StyleDefs=origStyleDefs StyleDefs$ArialLeftBold$parentStyleName=''

Re: [R] Math expression with object to evaluate

2006-12-21 Thread Uwe Ligges
You might want to read the R Help Desk: Automation of Mathematical Annotation in Plots in R News 2 (3), 32-34. and you will understand that the following works: plot(x, y, main = substitute(ID is * ID.i * , * italic(R)^2 == r2.i * {, RMSE == error.i}, list(ID.i =

[R] multiline system call

2006-12-21 Thread Nicolas Mazziotta
Hello, I am trying to call sendmail from within R via system(). As sendmail reads from STDIN, I need to pass a multiline input as an argument. E.g. (not working): system('sendmail -f [EMAIL PROTECTED] -t [EMAIL PROTECTED]') I tried a lot of ways to type the EOL characters, but cannot