[R] R_HOME not found

Hi, I have a problem with R 1.9.1. I installed it on my mac (os 10.2.8), and then tried to start it from the terminal. I got the following error message: R_HOME ('/Applications/StartR.app/RAqua.app/Contents') not found It also won't let me start the GUI version. Any comments or suggestions

Re: [R] Population simulation.

[EMAIL PROTECTED] wrote: Hello, can anyone tell me if R has any special function for simulating the structure of human populations? Something like the genetic algorithm? I need to simulate a sample of a population with a specific structure. Is there something on R that can help me? As

[R] Read SPSS data (*.sav) in R 1.8.0 (ok) and R1.9.1(error)

Hallo! I read SPSS data in the following way: library(Hmisc) library(foreign) dat-spss.get(surv_abb.sav) In R1.9.1 I got the message: Error in all(arg == choices) : Object typeDate not found In R1.8.0 the same script works fine. Does anybody know a possibilty to read a SPSS file under R1.9.1?

[R] computing sum of indicator variables

My problem is as follows: i is a list of integers of variable length. Now I want to compute a new vector/array that contains 1's at the positions indicated in i. For example: c(2, 4) - c(0, 1, 0, 1) Using something like i = i - c(0, i[2:length(i) - 1]); sapply(i, function(x) c(rep(0, x - 1),

Re: [R] computing sum of indicator variables

Stefan Böhringer wrote: My problem is as follows: i is a list Do you mean a vector? of integers of variable length. Now I want to compute a new vector/array A vector or an array (which dimensions?)? that contains 1's at the positions indicated in i. For example: c(2, 4) - c(0, 1, 0, 1) How long

Re: [R] computing sum of indicator variables

Hi Stefan, you could try something like, x - c(2,4,7) as.numeric(!is.na(match(seq(1, max(x)), x))) I hope this helps. Best, Dimitris Dimitris Rizopoulos Doctoral Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven,

RE: [R] computing sum of indicator variables

What about x - c(2,4,7) out-rep(0,max(x)) out[x]-1 Regards Wayne -Original Message- From: Stefan Böhringer [mailto:[EMAIL PROTECTED] Sent: 26 July 2004 09:46 To: R Help Subject: [R] computing sum of indicator variables My problem is as follows: i is a list of integers of variable

Re: [R] fisher.test FEXACT error 7

Thanks Sundar, That changes the behaviour of R, but only in so far as it waits longer before giving the same error: fisher.test(testDataTwoColumns, workspace = 2e8) Error in fisher.test(testDataTwoColumns, workspace = 2e+08) : FEXACT error 7. LDSTP is too small for this problem. Try

Re: [R] Read SPSS data (*.sav) in R 1.8.0 (ok) and R1.9.1(error)

On 07/26/04 10:36, Karl Knoblick wrote: Hallo! I read SPSS data in the following way: library(Hmisc) library(foreign) dat-spss.get(surv_abb.sav) In R1.9.1 I got the message: Error in all(arg == choices) : Object typeDate not found In R1.8.0 the same script works fine. Does anybody know a

Re: [R] Eclipse plugin for R or perhaps S-plus.

Richard Piper wrote: Does any one know of an eclipse (http://eclipse.org) plugin for R/S. thanks RIchard Hi, You can download a small Eclipse plug-in for R from my homepage: http://www.walware.de/rplugin.zip . Simply unzip the file into the Eclipse directory. The plug-in requires

[R] Econometrics Packages On R

Dear Allan, I still use R principally in ts analysis. Tha main packages I employ are: ts, tseries, ast (it supplies some helpfull functions and can be downloaded from CRAN) and lmtest. Just in this period I preparing a summary of functions involved in ts analysis grouped by goal. I would send

[R] X11 device problem on linux: 100% cpu usage

Hi, I'm using R 1.9.1 (patched, 5th July) on linux (Mandrake 9.2) and am having a problem with the X11() device. Trying to plot(1:10) results in my CPU going to 100% and I have to terminate the process. Using postscript() with the same plot is fine. Everything else on my system seems to work

[R] covariate selection in cox model (counting process)

Hello everyone, I am searching for a covariate selection procedure in a cox model formulated as a counting process. I use intervals, my formula looks like coxph(Surv(start,stop,status)~ x1+x2+...+cluster(id),robust=T) where id is a country code (I study occurence of civil wars from 1962 to 1997).

Re: [R] X11 device problem on linux: 100% cpu usage

David Whiting wrote: I'm using R 1.9.1 (patched, 5th July) on linux (Mandrake 9.2) and am having a problem with the X11() device. Trying to plot(1:10) results in my CPU going to 100% I'm not sure where to start with identifying the cause. Can someone suggest some things that I should look at?

Re: [R] interpreting profiling output

On Sun, 25 Jul 2004, Peter Dalgaard wrote: Kasper Daniel Hansen [EMAIL PROTECTED] writes: I have some trouble interpreting the output from profiling. I have read the help pages Rprof, summaryRprof and consult the R extensions manual, but I still have problems understanding the output.

[R] Re: smooth non cumulative baseline hazard in Cox model

Hello everyone, I am searching for a covariate selection procedure in a cox model formulated as a counting process. I use intervals, my formula looks like coxph(Surv(start,stop,status)~ x1+x2+...+cluster(id),robust=T) where id is a country code (I study occurence of civil wars from 1962 to 1997).

[R] aggregate function

Hi all, I have the folowing frame(there are more columns than shown), 1 2 34 5 Year Total TusWhi Norw 1994 1.00 1830 0 355 1995 1.00 0 00 1995 1.00 0

Re: [R] R on AMD64 (Opteron)

We are using Fedora Core 2 and some version(s) of SuSe Linux on various dual Opteron servers. We also have a copy of RHEL, but AFAIK are not currently using it. I've been using a dual Opteron 248 under FC2 I don't know that Windows XP 64-Bit Edition is actually released yet (although there

Re: [R] aggregate function

Hi, # x ... your frame attach(x) sum(Total[Year==1997 Tus 0]) I hope this helps Best, Matthias -Ursprüngliche Nachricht- Von: Luis Rideau Cruz [mailto:[EMAIL PROTECTED] Gesendet: Montag, 26. Juli 2004 14:52 An: [EMAIL PROTECTED] Betreff: [R] aggregate function Hi all, I

Re: [R] aggregate function

Hi, # x ... your frame attach(x) sum(Total[Year==1997 Tus 0]) I hope this helps Best, Matthias Templ -Ursprüngliche Nachricht- Von: Luis Rideau Cruz [mailto:[EMAIL PROTECTED] Gesendet: Montag, 26. Juli 2004 14:52 An: [EMAIL PROTECTED] Betreff: [R] aggregate function

RE: [R] aggregate function

I would try something like: lapply(frame[3:5], function(i) tapply(frame$Total[i0], frame$Year[i0], sum)) $Tus 1994 1995 1997 1999 1121 $Whi 1995 1997 1999 1.00 4.00 2.04 $Norw 1994 1995 1997 1998 1999 11512 HTH, Andy From: Luis Rideau Cruz Hi

RE: [R] R on AMD64 (Opteron)

Just one more thing for folks intending to try Opterons with 1 cpu: You'll probably want to use a NUMA kernel, rather than a SMP one. Cheers, Andy From: Prof Brian Ripley We are using Fedora Core 2 and some version(s) of SuSe Linux on various dual Opteron servers. We also have a copy of

Re: [R] R on AMD64 (Opteron)

- Original Message - From: Liaw, Andy [EMAIL PROTECTED] To: 'Prof Brian Ripley' [EMAIL PROTECTED]; Jose Quesada [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Sent: Monday, July 26, 2004 9:18 AM Subject: RE: [R] R on AMD64 (Opteron) Just one more thing for folks intending to try Opterons with

Re: [R] covariate selection in cox model (counting process)

On Mon, 26 Jul 2004, Mayeul KAUFFMANN wrote: Hello everyone, I am searching for a covariate selection procedure in a cox model formulated as a counting process. I use intervals, my formula looks like coxph(Surv(start,stop,status)~ x1+x2+...+cluster(id),robust=T) where id is a country code

Re: [R] Read SPSS data (*.sav) in R 1.8.0 (ok) and R1.9.1(error)

On Mon, 26 Jul 2004, [iso-8859-1] Karl Knoblick wrote: Hallo! I read SPSS data in the following way: library(Hmisc) library(foreign) dat-spss.get(surv_abb.sav) In R1.9.1 I got the message: Error in all(arg == choices) : Object typeDate not found In R1.8.0 the same script works fine.

[R] binning a vector

Hello, I was wondering wether there's a function in R that takes two vectors (of same length) as input and computes mean values for bins (intervals) or even a sliding window over these vectros. I've several x/y data set (input/response) that I'd like plot together. Say the x-data for one data

[R] choosing constraints for function optim method=L-BFGS-B when they are in terms of other parameter values

I have a function of several variables which I wish to minimise over four variables, two of the upper bounds for which are defined in terms of other variables in the model over which minimisation will take place. I cannot work out how to code this in such a way as to avoid getting an error message

Re: [R] help(package)-sink()

On Sun, 25 Jul 2004, Thomas Lumley wrote: On Sat, 24 Jul 2004, Spencer Graves wrote: 4. A request for packageInfo.print returned object ... not found. I think someone may have been contaminated by Java or some such. It should be print.packageInfo A request for

[R] installing problems repeated.tgz linux

Hi, i try several possibilities adn looking in the archive, but didn't getting success to install j.lindsey's usefuel library repeated on my linux (suse9.0 with kernel 2.6.7,R.1.9.1) P.S. Windows, works fine Many thanks for help Christian [EMAIL PROTECTED]:/space/downs R CMD INSTALL - l

Re: [R] binning a vector

On Monday 26 July 2004 10:11, [EMAIL PROTECTED] wrote: Hello, I was wondering wether there's a function in R that takes two vectors (of same length) as input and computes mean values for bins (intervals) or even a sliding window over these vectros. I've several x/y data set (input/response)

[R] zsh and R

In the process of evaluating new shells, I've run into a few problems with zsh and the R CMD build, R CMD check scripts. I'd like to ask a few questions off-line if anyone has experience with R and the zsh completion/substitution functionality. Note that bash continues to work as well as

RE: [R] installing problems repeated.tgz linux

From: Christian Schulz Hi, i try several possibilities adn looking in the archive, but didn't getting success to install j.lindsey's usefuel library repeated on my linux (suse9.0 with kernel 2.6.7,R.1.9.1) P.S. Windows, works fine Many thanks for help Christian R CMD

[R] factanal - rotation = oblimin

Hi list. To the best of mylimited understandig currently R (unlike S) does not support oblimin criterion for exploratory factor analysis. Searching through the contributed packages I did not notice any additional package for factor analysis. Does anybody know if such function is present

[R] Building Windows Package

I am using R-1.9.1 with windows 2000 and trying to build a package. However, when I issue the command: RCMD build --binary BSDA I get: Building/Updating help pages for package 'BSDA' Formats: chm hhc: not found cp: cannot stat `C:/R191/R191/JUNK/BSDA/chm/BSDA.chm': No such file or direc

Re: [R] installing problems repeated.tgz linux

On Mon, 2004-07-26 at 09:34, Christian Schulz wrote: Hi, i try several possibilities adn looking in the archive, but didn't getting success to install j.lindsey's usefuel library repeated on my linux (suse9.0 with kernel 2.6.7,R.1.9.1) P.S. Windows, works fine Many thanks for help

[R] ordering of levels.

Hi! Have the following factors with the following levels. tmp$norm [1] rank rank rank rank rank log log log rank sqrt sqrt sqrt log log rank [16] rank rank sqrt sqrt sqrt sqrt log log log log sqrt none none none none [31] none none none none sqrt none Levels: log none rank sqrt I would

RE: [R] installing problems repeated.tgz linux

Sorry, Christian. I have no idea what those error messages in German say. Andy From: [EMAIL PROTECTED] Hello, thanks for your and Marc's hint, but it seems not the probleme!? Is there any probleme with my make? many thanks and regards, christian [EMAIL PROTECTED]:/usr/lib/R

Re: [R] ordering of levels.

Wolski wrote: Hi! Have the following factors with the following levels. tmp$norm [1] rank rank rank rank rank log log log rank sqrt sqrt sqrt log log rank [16] rank rank sqrt sqrt sqrt sqrt log log log log sqrt none none none none [31] none none none none sqrt none Levels: log none

RE: [R] aggregate function

[Sorry if this gets posted twice. I have been having some problems with gmane posting.] We can use rowsum like this: rowsum(frame$Total * (frame[,3:5]0), frame$Year) Tus Whi Norw 1994 1 0.00 1 1995 1 1.00 1 1997 2 4.00 5 1998 0 0.00 1

RE: [R] installing problems repeated.tgz linux

I downloaded repeated.tgz and tried it myself on one of our AMD Opterons running SLES8, and it worked (R-1.9.1 compiled as 64-bit). Notice that I do get a couple of warnings from gcc about labels, and from g77 about the use of `sum' function. Andy [EMAIL PROTECTED]:lindsey]% R CMD INSTALL -l

Re: [R] ordering of levels.

Hi! Thanks a lot. Eryk *** REPLY SEPARATOR *** On 7/26/2004 at 2:07 PM Sundar Dorai-Raj wrote: Wolski wrote: Hi! Have the following factors with the following levels. tmp$norm [1] rank rank rank rank rank log log log rank sqrt sqrt sqrt log log rank [16] rank rank

Re: [R] Building Windows Package

You want the directory in your path specification, not the executables. As in .;C:\RStools;C:\MinGW\bin;C:\perl\bin;C:\texmf\miktex\bin; C:\HTMLws;C:\R191\R191\bin;%SystemRoot%\system32; %SystemRoot%;%SystemRoot%\System32\Wbem;C:\Program Files\CommonFiles\AdaptecShared\System; C:\Program

RE: [R] installing problems repeated.tgz linux

I echo Andy's experience on FC2. I was able to install the package here and got the same warning messages. Despite trying to use some web sites to translate the german text, I am unsure of the 'true' meaning. I think it is something pertaining to target patterns not being found, which leads me to

RE: [R] choosing constraints for function optim method=L-BFGS-B whenthey are in terms of other parameter values

Hi Tom, I am not entirely sure what the problem, you haven't been very specific. If you want general linear constraints on your parameters, ie linear combinations of parameters summing to some value, constrOptim may be of help. hth, ingmar Ingmar Visser Developmental Processes Research Group

[R] spec.pgram() possible bug

test=spec.pgram(rnorm(128,0,1), kernel(daniell,1)) test$df [1] 5.374771 df should be 6= 2*(2*m+1) where m=1 in this case ... and so on __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the

[R] Significance Test for Correlation Coefficients

Hello all, I have a set of microarray timeseries (approx. 18000 genes and 7 time points per gene) data that I have correlated with a template (a vector of length 7). I have also correlated random data from a normal distribution with the same mean and standard deviation as my data set with

[R] Problem with a while loop embedded in a function.

Hello all. I have been working on a (fairly simple) function for way too long. I’ve really hit a wall and I was hoping someone might be able to point me in the right direction. I have (attempted) to create a function that has an embedded while loop. The while loop works fine by itself,

Re: [R] spec.pgram() possible bug

Perhaps you could take the trouble to read the references (or the code)? Hint: do you know about tapering and how to work out its effect? On Mon, 26 Jul 2004, David Stoffer wrote: test=spec.pgram(rnorm(128,0,1), kernel(daniell,1)) test$df [1] 5.374771 df should be 6= 2*(2*m+1) where m=1

Re: [R] binning a vector

Also, you can use cut and tapply to calculate means by bins. Andrew - Original Message - From: Deepayan Sarkar [EMAIL PROTECTED] Date: Tuesday, July 27, 2004 3:38 am Subject: Re: [R] binning a vector On Monday 26 July 2004 10:11, [EMAIL PROTECTED] wrote: Hello, I was wondering

Re: [R] Building Windows Package

Thanks. It works great now! Alan Alan T. Arnholt Associate Professor Dept. of Mathematical Sciences Appalachian State University 2003-2004 International Exchange Scholar Universidad Publica de Navarra - Nafarroako Unibertsitate Publikoa Pamplona, Spain TEL : +34 948 169 205 CELL: +34 656 668

RE: [R] R on AMD64 (Opteron)

From: Jerome Asselin From: Liaw, Andy [EMAIL PROTECTED] Just one more thing for folks intending to try Opterons with 1 cpu: You'll probably want to use a NUMA kernel, rather than a SMP one. Cheers, Andy Thanks for the advice, but is there another reason why you write this

[R] qcc package syndromic surveillance (multivar CUSUM?)

Dear R Community: I am working on a public health early warning system, and I see that the qcc package allows for CUSUM and other statistical quality tests but I am not sure if my project is a good match for qcc functions as written. Any advice you may have is very much appreciated. I have four

[R] bad restore file magic number

I'm running R 1.9.1 and trying to load a macro I've written. It gives the e Error: bad restore file magic number (file may be corrupted)-- no data loaded what does this error mean, and how can I fix this problem. thanks, jordan __ [EMAIL PROTECTED]

Re: [R] bad restore file magic number

I'm running R 1.9.1 and trying to load a macro I've written. It gives the e Error: bad restore file magic number (file may be corrupted)-- no data loaded You probably want to use source() here, if you have the code in a file. The load() command is for use with stuff saved via the save()

[R] covariate selection in cox model (counting process)

Thank you a lot for your time and your answer, Thomas. Like all good answers, it raised new questions for me ;-) In the case of recurrent events coxph() is not using maximum likelihood or even maximum partial likelihood. It is maximising the quantity that (roughly speaking) would be the partial

[R] lattice / pdf bug ?

I've been scrathing my head over this one. Suppose I have a data.frame which maps to a 'n x k' lattice, and that one of those cells is empty. An artificial example is generated by Q-data.frame(x1=sample(c(A,B),10,replace=TRUE), x2=c(C, rep(D,9)), y=rnorm(10)) where by having

Re: [R] binning a vector

?tapply *** REPLY SEPARATOR *** On 7/26/2004 at 5:11 PM [EMAIL PROTECTED] wrote: Hello, I was wondering wether there's a function in R that takes two vectors (of same length) as input and computes mean values for bins (intervals) or even a sliding window over these vectros.

Re: [R] lattice / pdf bug ?

On Monday 26 July 2004 18:17, Dirk Eddelbuettel wrote: I've been scrathing my head over this one. Suppose I have a data.frame which maps to a 'n x k' lattice, and that one of those cells is empty. An artificial example is generated by Q-data.frame(x1=sample(c(A,B),10,replace=TRUE),

Re: [R] qcc package syndromic surveillance (multivar CUSUM?)

What do you think is most plausible: an abrupt jump or a gradual drift? To detect an abrupt jump from a null hypothesis H0 to an alternative H1, the tool of choice seems to be a cumulative sum (CUSUM) of log(likelihood ratio). If H0 and H1 are normal distributions with equal variances,

[R] dumpClass

What do people do in R to get something comparable to the functionality of dumpClass described by Chambers (1998) Programming with Data (Springer)? Thanks, spencer graves __ [EMAIL PROTECTED] mailing list

[R] Reading SPSS file

Hi Karl: a possible solution: require(foreign) mydata - read.spss(somedata.sav, use.value.labels = TRUE, to.data.frame = TRUE) - for more information, try library(foreign) ?read.spss HTH, Arin Message: 21 Date: Mon, 26 Jul 2004 10:36:33 +0200 (CEST) From: Karl Knoblick [EMAIL PROTECTED]

[R] re: help with lattice plot

Dear List, I have been using R to create an xyplot using the panel function within lattice libraries. This plot is based on the data supplied in R named 'Oats'. The graph represents oat yield by nitro level with an overlay of each variety of oats for each nitro level. I have three questions

Re: [R] re: help with lattice plot

On Monday 26 July 2004 21:51, [EMAIL PROTECTED] wrote: Dear List, I have been using R to create an xyplot using the panel function within lattice libraries. This plot is based on the data supplied in R named 'Oats'. The graph represents oat yield by nitro level with an overlay of each