[R] Kernlab: problem with small datasets

2005-07-07 Thread pablo . granitto
Hi, I found a small problem with kernlab. The problem, I think, is that the 3-fold cross-validation performed to estimate probabilities is not class-balanced, so the classifier could find empty classes. The following example (maybe a little forced) show the error: data(glass) set.seed(1)

[R] tcltk package

2005-07-07 Thread Kurt Sys
Hi all, I have a package depending on the tcltk-package. However, I see that this package has been disappeared... Is there a reason why package 'tcltk' is not available anymore? Or is it replaced by another one? thx, Kurt. __

Re: [R] Tables: Invitation to make a collective package

2005-07-07 Thread Gabor Grothendieck
If the functionality you are thinking of already exists across multiple packages an alternative to creating a new package would be to create a task view as in: http://cran.r-project.org/src/contrib/Views/ as explained in the ctv package and the article in R News 5/1. On 7/7/05, Jose Claudio

Re: [R] tcltk package

2005-07-07 Thread Liaw, Andy
It's included in the base R distribution, I believe. Andy From: Kurt Sys Hi all, I have a package depending on the tcltk-package. However, I see that this package has been disappeared... Is there a reason why package 'tcltk' is not available anymore? Or is it replaced by another one?

Re: 答复: 答复: [R] fail in add ing library in new version.

2005-07-07 Thread Gabor Grothendieck
On 7/7/05, Uwe Ligges [EMAIL PROTECTED] wrote: Ivy_Li wrote: Dear all, I have done every step as the previous mail. 1. unpack tools.zip into c:\cygwin 2. install Active perl in c:\Perl 3. install the mingw32 in c:\mingwin 4. add c:\cygwin; c:\mingwin\bin in Control Panel -

Re: [R] tcltk package

2005-07-07 Thread Roger D. Peng
How do you know that it has disappeared? -roger Kurt Sys wrote: Hi all, I have a package depending on the tcltk-package. However, I see that this package has been disappeared... Is there a reason why package 'tcltk' is not available anymore? Or is it replaced by another one? thx,

Re: 答复: 答复: [R] fail in adding librar y in new version.

2005-07-07 Thread Uwe Ligges
Gabor Grothendieck wrote: On 7/7/05, Uwe Ligges [EMAIL PROTECTED] wrote: Ivy_Li wrote: Dear all, I have done every step as the previous mail. 1. unpack tools.zip into c:\cygwin 2. install Active perl in c:\Perl 3. install the mingw32 in c:\mingwin 4. add c:\cygwin; c:\mingwin\bin in

Re: [R] Kernlab: problem with small datasets

2005-07-07 Thread Uwe Ligges
[EMAIL PROTECTED] wrote: Hi, I found a small problem with kernlab. The problem, I think, is that the 3-fold cross-validation performed to estimate probabilities is not class-balanced, so the classifier could find empty classes. The following example (maybe a little forced) show the error:

Re: [R] Making Package, Chm error, Html Help Workshop

2005-07-07 Thread Uwe Ligges
TEMPL Matthias wrote: Hello, When building my package (R CMD check) following error message occurs: ... varinf.plot text html latex example xtext html latex example make[2]: *** No rule to make target `disclosure.chm`. Stop. cp: cannot stat

Re: 答复: 答复: [R] fail in add ing library in new version.

2005-07-07 Thread Gabor Grothendieck
On 7/7/05, Uwe Ligges [EMAIL PROTECTED] wrote: Gabor Grothendieck wrote: On 7/7/05, Uwe Ligges [EMAIL PROTECTED] wrote: Ivy_Li wrote: Dear all, I have done every step as the previous mail. 1. unpack tools.zip into c:\cygwin 2. install Active perl in c:\Perl 3. install the

Re: [R] tcltk package [SOLVED]

2005-07-07 Thread Kurt Sys
I had R 2.0.1... It's not included in that distribution of R. It's ok in distribution 2.1.1. thx (to all that've been replying that it's included in the base distribution), Kurt. Liaw, Andy wrote: It's included in the base R distribution, I believe. Andy From: Kurt Sys Hi all, I

[R] R crashes when spherical autocorrelation specified in nlme

2005-07-07 Thread Dan Bebber
Dear list: R crashes when I specify spatial autocorrelation in nlme: sp3 - corSpher(c(30,0.75),~x+y|Site, nugget = T) cs3 - Initialize(sp3, data = sav) sav.nlme1-nlme(vc.asin ~ SSasymp(canopy, Asym, R0, lrc),data = sav, fixed = Asym + R0 + lrc ~ 1, random = R0 + lrc ~ 1|Site, start = list(fixed =

Re: [R] Java and R help

2005-07-07 Thread John Wang
Im doing an aplication in Java and i have a program made in R what i want to launch with Java. I have the following instructions: Runtime r = Runtime.getRuntime(); try { System.out.println (Llamada a R...); p = r.exec(sRutaR); } catch (IOException e)

[R] What method I should to use for these data?

2005-07-07 Thread luan_sheng
Dear R user: I am studying the allele data of two populations. the following is the data: a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 pop10.0217 0. 0.0109 0.0435 0.0435 0. 0.0109 0.0543

[R] What method I should to use for these data?

2005-07-07 Thread luan_sheng
Dear R user: I am studying the allele data of two populations. the following is the data: a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 pop10.0217 0. 0.0109 0.0435 0.0435 0. 0.0109 0.0543

Re: [R] plotting on a reverse log scale

2005-07-07 Thread Gabor Grothendieck
There is an enhanced pretty function called nice in the Epi package that also works with log data. Not sure if this could lead to any simplifications in this problem? On 7/6/05, Marc Schwartz [EMAIL PROTECTED] wrote: I thought that I would take a stab at this. I should note however that my

Re: [R] Lack of independence in anova()

2005-07-07 Thread Göran Broström
On Thu, Jul 07, 2005 at 11:18:09AM +0100, Ted Harding wrote: My first reaction to Duncan's example was Touché -- with apologies to Göran for suspecting on over-trivial example! No need to apologize; that was of course my first reaction to Thomas' statement. I had not thought long enough

[R] What method I should to use for these data?

2005-07-07 Thread luan_sheng
-Original Message- From: luan_sheng [mailto:[EMAIL PROTECTED] Sent: Thursday, July 07, 2005 9:46 PM To: (r-help@stat.math.ethz.ch) Cc: ([EMAIL PROTECTED]) Subject: What method I should to use for these data? Dear R user: I am studying the allele data of two populations. the following

Re: [R] About ade4 and overlaying points

2005-07-07 Thread Renaud Lancelot
Jacques VESLOT a écrit : Dear R-users, Is there an easy way to avoid points one upon another when ploting rows and columns of 'dudi' objects ? Maybe there is a function in ade4 or in an other package, or maybe someone has his or her own function to do this (for example to automatically

[R] function par(mfrow....)

2005-07-07 Thread Navarre Sabine
Hi, I have made 3 barplots differents in the some window plot with the function par(mfrow), but is it possible to give different dimension to this 3 parts. for example, I want the first part smaller than the others. I have attached my plot! thanks Sabine

Re: [R] timezone problems

2005-07-07 Thread Don MacQueen
?POSIXt says: 'POSIXlt' objects will often have an attribute 'tzone', a character vector of length 3 giving the timezone name from the 'TZ' environment variable and the names of the base timezone and the alternate (daylight-saving) timezone. Sometimes this may just

Re: [R] function par(mfrow....)

2005-07-07 Thread Chuck Cleland
Navarre Sabine wrote: Hi, I have made 3 barplots differents in the some window plot with the function par(mfrow), but is it possible to give different dimension to this 3 parts. for example, I want the first part smaller than the others. ... Here is one approach using

[R] Fwd: Plotting confidence intervals for lme

2005-07-07 Thread Ghislain Vieilledent
-- Forwarded message -- From: Ghislain Vieilledent [EMAIL PROTECTED] Date: 7 juil. 2005 11:38 Subject: Re: [R] Plotting confidence intervals for lme To: Spencer Graves [EMAIL PROTECTED] That's what I was looking for. Thanks a lot! That's true units are mixing and that values of

Re: [R] function par(mfrow....)

2005-07-07 Thread TEMPL Matthias
Hi, Is layout the function you will need? ?layout E.g.: l - matrix(c(rep(1,4), rep(2,8),rep(3,8)), ncol=5) layout(l) layout.show(3) plot(1,1) plot(1:25,pch=1:25) plot(2,5) Best regards, Matthias Hi, I have made 3 barplots differents in the some window plot with the function

Re: [R] How to get the minimum ?

2005-07-07 Thread Christoph Buser
Dear Philipe You can use optimize (see ?optimize), e.g. : funToMin - function(x, data, a = 1, b = 1) { sum((data[data[,group]==A,y] - x)^2) + sum((data[data[,group]==B,y] - a*x - b)^2) } dat - data.frame(y = rnorm(100), group = rep(c(A,B), each = 50)) (m - optimize(function(x)

Re: [R] timezone problems

2005-07-07 Thread Martin Keller-Ressel
I cannot reproduce Don's results below on my system. However I do not know if timezone names can be expected to be compatible across systems/country settings/etc... I get: Sys.putenv(TZ='US/Pacific') z - as.POSIXlt(Sys.time()) attributes(z)$tzone [1] \001S/Pacific US/ Pac

[R] Plotting Character Variable

2005-07-07 Thread ohalawa
Any ideas about the following problem: I have a matrix (A) that looks like this: gene_names values hsa-mir-124 0.3 hsa-mir-234 0.1 hsa-mir-344 0.4 hsa-mir-333 0.7 . ... (This is a 2 by 22283 matrix: quite

[R] plotcp

2005-07-07 Thread Alvarez Pedro
win2000/R 2.0.1/rpart-version: 3.1-23 I use the plotcp-function of the rpart-package and it works very well. however, plotcp plots the cv-estimated relative errors only until the minimum of the curve. How can I plot the values after the minimum? Choosing the size-option for generating the tree

Re: [R] Tempfile error

2005-07-07 Thread Doran, Harold
We just explored the issue a little further here and here is what we have found. If we look in the temp directory we noticed that the last temp file name is rf32767. This number coincides with 2^16 with a 16 bit signed integer. Is there a way to modify the temp file settings to use an unsigned or

Re: [R] tcltk package [SOLVED]

2005-07-07 Thread Martin Maechler
Kurt == Kurt Sys [EMAIL PROTECTED] on Thu, 07 Jul 2005 15:07:52 +0200 writes: Kurt I had R 2.0.1... It's not included in that distribution of R. That's not correct. The tcltk package has been part of R for a very long time. The question is where you got the version of 'R 2.0.1' from

Re: [R] Plotting Character Variable

2005-07-07 Thread Marc Schwartz (via MN)
On Thu, 2005-07-07 at 11:47 -0400, [EMAIL PROTECTED] wrote: Any ideas about the following problem: I have a matrix (A) that looks like this: gene_names values hsa-mir-124 0.3 hsa-mir-234 0.1 hsa-mir-344 0.4 hsa-mir-333 0.7

[R] Segmentation fault on exit

2005-07-07 Thread Omar Lakkis
q() Segmentation fault I wrote a library and whenever this library is loaded R sigfaults on exit. This is not hurting the running of my application since it happens on exit but does anyone have an idea why might this happen? The library is a collection of R scripts and has no C or FORTRAN code

[R] Failing to install Hmisc on Mac OS 10.3.9, R Version 2.1.0 Patched (2005-05-12)

2005-07-07 Thread Michael Kubovy
Kindly cc me when replying to the list. trying URL 'http://www.biometrics.mtu.edu/CRAN/src/contrib/Hmisc_3.0-6.tar.gz' Content type 'application/x-gzip' length 462535 bytes opened URL == downloaded 451Kb * Installing *source* package 'Hmisc' ...

[R] xmat[1, 2:3] - NULL

2005-07-07 Thread Mikkel Grum
I have a situation where I'm filling out a dataframe from a database. Sometimes the database query doesn't get anything, so I end up trying to place NULL in the dataframe like below. temp - NULL xmat - as.data.frame(matrix(NA, 2, 3)) xmat[1, 2:3] - temp Error in if (m n * p (n * p)%%m)

Re: [R] xmat[1, 2:3] - NULL

2005-07-07 Thread Marc Schwartz (via MN)
On Thu, 2005-07-07 at 10:20 -0700, Mikkel Grum wrote: I have a situation where I'm filling out a dataframe from a database. Sometimes the database query doesn't get anything, so I end up trying to place NULL in the dataframe like below. temp - NULL xmat - as.data.frame(matrix(NA, 2, 3))

Re: [R] Segmentation fault on exit

2005-07-07 Thread Uwe Ligges
Omar Lakkis wrote: q() Segmentation fault I wrote a library and whenever this library is loaded R sigfaults on exit. This is not hurting the running of my application since it happens on exit but does anyone have an idea why might this happen? The library is a collection of R scripts and

Re: [R] xmat[1, 2:3] - NULL

2005-07-07 Thread Uwe Ligges
Mikkel Grum wrote: I have a situation where I'm filling out a dataframe from a database. Sometimes the database query doesn't get anything, so I end up trying to place NULL in the dataframe like below. temp - NULL xmat - as.data.frame(matrix(NA, 2, 3)) xmat[1, 2:3] - temp Error in if

Re: [R] xmat[1, 2:3] - NULL

2005-07-07 Thread Patrick Burns
Maybe I have it wrong, but I think you merely want: temp - NA Patrick Burns Burns Statistics [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) Mikkel Grum wrote: I have a situation where I'm filling out a dataframe from a

Re: [R] plotting on a reverse log scale

2005-07-07 Thread Michael Friendly
Thanks to all who replied, particularly Duncan Murdoch, whose solution I adopted. It thought it might be of interest to some to see the results and compare these ways of representing the distribution of historical events over time. The events are the items I record on my site, Milestones in the

Re: [R] plotting on a reverse log scale

2005-07-07 Thread Sundar Dorai-Raj
Michael Friendly wrote: Thanks to all who replied, particularly Duncan Murdoch, whose solution I adopted. It thought it might be of interest to some to see the results and compare these ways of representing the distribution of historical events over time. The events are the items I

Re: [R] plotting on a reverse log scale

2005-07-07 Thread Sundar Dorai-Raj
Michael Friendly wrote: Thanks to all who replied, particularly Duncan Murdoch, whose solution I adopted. It thought it might be of interest to some to see the results and compare these ways of representing the distribution of historical events over time. The events are the items I

Re: [R] What method I should to use for these data?

2005-07-07 Thread Spencer Graves
I'm sorry, but I do not understand your question well enough to comment. Are you familiar with www.bioconductor.org? They have their own list serve and might be better equipped to help you. Beyond this, I suggest you read the posting guide,

[R] randomForest

2005-07-07 Thread Weiwei Shi
Hi there: I have a question on random foresst: recently i helped a friend with her random forest and i came with this problem: her dataset has 6 classes and since the sample size is pretty small: 264 and the class distr is like this (Diag is the response variable) sample.size - lapply(1:6,

[R] look for help on nlm in R

2005-07-07 Thread Zhu, Maggie
Hi, I had a hard time in learning nlm in R and appreciate any help. I encounted the following error message from time to time when I tried different starting parameter values (three parameter values in this case) in nlm(f=SS.fun,p=c(0.1/40,0.1,2),hessian =

[R] Orthogonal Distance Regressions

2005-07-07 Thread Peter J. Hernes
Hi, I work with environmental data and want to determine correlations between variables that either have no dependent/independent relationship or the relationship is unknown. Therefore I prefer to use orthogonal distance regression (orthogonal linear regression, perpendicular sum of squares,

Re: [R] randomForest

2005-07-07 Thread Duncan Murdoch
On 7/7/2005 3:38 PM, Weiwei Shi wrote: Hi there: I have a question on random foresst: recently i helped a friend with her random forest and i came with this problem: her dataset has 6 classes and since the sample size is pretty small: 264 and the class distr is like this (Diag is the

Re: [R] randomForest

2005-07-07 Thread Weiwei Shi
it works. thanks, but: (just curious) why i tried previously and i got is.vector(sample.size) [1] TRUE i also tried as.vector(sample.size) and assigned it to sampsz,it still does not work. On 7/7/05, Duncan Murdoch [EMAIL PROTECTED] wrote: On 7/7/2005 3:38 PM, Weiwei Shi wrote: Hi there:

[R] manupulating a data frame column

2005-07-07 Thread Steven T.
Could someone tell me how to fix the following error? It looks like that the reason is that df$x is of the class factor. Thanks! x1-LETTERS[1:8]; x2-letters[1:8]; x1[2]-NA; x1[4]-NA; df-data.frame(x1=x1, x2=x2) idx-which(is.na(df$x1)) df[idx,1]-df[idx,2] Warning message: invalid factor level,

Re: [R] randomForest

2005-07-07 Thread Liaw, Andy
From: Weiwei Shi it works. thanks, but: (just curious) why i tried previously and i got is.vector(sample.size) [1] TRUE Because a list is also a vector: a - c(list(1), list(2)) a [[1]] [1] 1 [[2]] [1] 2 is.vector(a) [1] TRUE is.numeric(a) [1] FALSE Actually, the way I

Re: [R] randomForest

2005-07-07 Thread Duncan Murdoch
On 7/7/2005 3:47 PM, Weiwei Shi wrote: it works. thanks, but: (just curious) why i tried previously and i got is.vector(sample.size) [1] TRUE i also tried as.vector(sample.size) and assigned it to sampsz,it still does not work. Sorry, I used vector incorrectly. Lists are vectors.

Re: [R] randomForest

2005-07-07 Thread Weiwei Shi
thanks. but can you suggest some ways for the classification problems since for some specific class, there are too few observations. the following is from adding sample.size : najie.rf.2 - randomForest(Diag~., data=one.df[ind==1,4:ncol(one.df)], importance=T, sampsize=unlist(sample.size))

[R] Question

2005-07-07 Thread mjs sad
Hi I am statistician and now I am starting to work with R. I have a question ,I want to see more than 1 figure in working directory and I can't do this. for example when I run plot(...) ,I see a plot ,if I run another plot(...) the first plot change to second plot and first plot disappear .

[R] Main Title for multiple charts

2005-07-07 Thread Laura Holt
Hi R ! I have the following set up: par(mfrow=c(2,2)) curve(dexp,from=0,to=5) hist(z1,main=Size 5) hist(z2,main=Size 15) hist(z3,main=Size 30) I would like to put a title at the very top of the page that ties the theme of all the charts together. How would this be done, please? Thanks

Re: [R] Main Title for multiple charts

2005-07-07 Thread Sundar Dorai-Raj
Laura Holt wrote: Hi R ! I have the following set up: par(mfrow=c(2,2)) curve(dexp,from=0,to=5) hist(z1,main=Size 5) hist(z2,main=Size 15) hist(z3,main=Size 30) I would like to put a title at the very top of the page that ties the theme of all the charts together. How would

Re: [R] xmat[1, 2:3] - NULL

2005-07-07 Thread Mikkel Grum
Thanks a lot!! This was really a big help. The following solves my problem: xmat - as.data.frame(matrix(NA, 2, 3)) temp - dbGetQuery(...) if (!is.null(temp)) {xmat[i, 2:3] - temp} I'm adding data to only some columns of a larger matrix, on a row-by-row basis. Best wishes, Mikkel --- Marc

Re: [R] Orthogonal Distance Regressions

2005-07-07 Thread Berton Gunter
I think you want principal components analysis. Google on this and ?prcomp in R for more details. -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA The business of the statistician is to catalyze the scientific learning process. - George E. P. Box -Original

Re: [R] Main Title for multiple charts

2005-07-07 Thread Peter Dalgaard
Sundar Dorai-Raj [EMAIL PROTECTED] writes: I would like to put a title at the very top of the page that ties the theme of all the charts together. How would this be done, please? How about this: z1 - rexp(100) z2 - rexp(100) z3 - rexp(100) par(mfrow=c(2,2),oma = c(0, 0, 3,

Re: [R] Question

2005-07-07 Thread Uwe Ligges
mjs sad wrote: Hi I am statistician and now I am starting to work with R. I have a question ,I want to see more than 1 figure in working directory and I can't do this. for example when I run plot(...) ,I see a plot ,if I run another plot(...) the first plot change to second plot and

Re: [R] randomForest

2005-07-07 Thread Liaw, Andy
With small sample sizes the variability for estimate of test set error will be large. Instead of splitting the data once, you should consider cross-validation or bootstrap for estimating performance. AFAIK gbm as is won't handle more than two classes. You will need to do quite a bit of work to

Re: [R] manupulating a data frame column

2005-07-07 Thread Uwe Ligges
Steven T. wrote: Could someone tell me how to fix the following error? It looks like that the reason is that df$x is of the class factor. Thanks! You are right. Either don't make it a factor, if you don't want, or try something like the following in order to add the relevant levels to df$x1:

Re: [R] What method I should to use for these data?

2005-07-07 Thread Kjetil Brinchmann Halvorsen
luan_sheng wrote: -Original Message- From: luan_sheng [mailto:[EMAIL PROTECTED] Sent: Thursday, July 07, 2005 9:46 PM To: (r-help@stat.math.ethz.ch) Cc: ([EMAIL PROTECTED]) Subject: What method I should to use for these data? Dear R user: I am studying the allele data of two

[R] spurious regression in R

2005-07-07 Thread yyan liu
Hi: I am trying to do a spurious regression in R but I can not find the function. Anybody used it before? The problem I have is try to do a regression with several time series. An alternative is to use the GLS function to fit the linear regression with the correlation structure AR(3) for the

[R] multivariate regression using R

2005-07-07 Thread Lusk, Jeffrey J
Does anyone know if there is a way to run multivariate linear regression in R? I tried using the lm function (e.g., lm(dv1, dv2~iv1+iv2+iv3), but got error messages. Is my syntax wrong, or do I need a particular package? Thanks, Jeff--

[R] q() == Segmentation fault

2005-07-07 Thread Omar Lakkis
I created the simple library, attached. When I terminate an R session where the library has been loaded with q() a segmentation fault is thrown. Is there any cleaning that I should be doing? From R session: q() Segmentation fault or from shell: $ R CMD BATCH r.in /usr/lib/R/bin/BATCH: line 55:

Re: [R] multivariate regression using R

2005-07-07 Thread Peter Dalgaard
Lusk, Jeffrey J [EMAIL PROTECTED] writes: Does anyone know if there is a way to run multivariate linear regression in R? I tried using the lm function (e.g., lm(dv1, dv2~iv1+iv2+iv3), but got error messages. Is my syntax wrong, or do I need a particular package? You need a matrix response:

[R] How do you sort a data frame on a selection of columns?

2005-07-07 Thread Briggs, Meredith M
This is what to start with: Data Frame A BC D c1 4 y 5 c3 6 d 7 c1 5 t 6 Now sort on A then C This is what to end with: Data Frame A B C D

Re: [R] How do you sort a data frame on a selection of columns?

2005-07-07 Thread Peter Dalgaard
Briggs, Meredith M [EMAIL PROTECTED] writes: This is what to start with: Data Frame A B C D c1 4 y 5 c3 6 d 7 c1 5 t 6 Now sort on A then C This is what to end with:

Re: [R] How do you sort a data frame on a selection of columns?

2005-07-07 Thread Gabor Grothendieck
On 7/7/05, Briggs, Meredith M [EMAIL PROTECTED] wrote: This is what to start with: Data Frame A BC D c1 4 y 5 c3 6 d 7 c1 5 t 6 Now sort on A then C This is what to

[R] Problem compiling R 2.1.* on SUSE 9.2

2005-07-07 Thread J Dougherty
I have been unable to compile either R 2.1.0 or 2.1.1 under SUSE 9.2. The system simply hangs as far as I can tell. All key board and mouse service dies. I have had no problem compiling earlier versions of R through 2.0.1, aside from remembering to include readline in the configuration.

Re: [R] How do you sort a data frame on a selection of columns?

2005-07-07 Thread Spencer Graves
Does order do what you want? spencer graves Briggs, Meredith M wrote: This is what to start with: Data Frame A B C D c1 4 y 5 c3 6 d 7 c1 5 t 6 Now sort on A then C

Re: [R] spurious regression in R

2005-07-07 Thread Spencer Graves
R has extensive time series capabilities within base R and especially add-on packages like the dse bundle and the several packages associated with www.rmetrics.org. I'm still a novice in this area. The source I've found most useful so far is the time series chapter in Venables and

[R] pairs() uses col argument for axes coloring

2005-07-07 Thread Olaf Mersmann
Hi list, not sure if this is the wanted behavior, but running the following code: version platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor1.1 year 2005 month06 day 20 language R n - 500 d - 4 m -

Re: [R] Problems with nlme: Quinidine example

2005-07-07 Thread Spencer Graves
Since I've seen no reply to this so far, I will venture a few questions / suggestions. I have not used nlme (nor nln for Maggie Zhu), so I can not comment on the specifics. I have two general procedures for debugging when I get a cryptic error message. First, in R, I can

Re: [R] fail in adding library in new version.

2005-07-07 Thread Ivy_Li
Dear all, I really appreciate your help. I think I have a little advancement. ^_^ When I enter the Dos environment, at first, into the D:\, I type the following code: cd Program Files\R\rw2011\ bin\R CMD install /example example is in the d:\, which include the R folder

Re: [R] fail in adding library in new version.

2005-07-07 Thread Gabor Grothendieck
You cannot use an empty DESCRIPTION file. To get more info on the DESCRIPTION file see 1.1.1 of the Writing Extensions manual which you can get to from the Help | Manuals menu entry in the Windows R GUI. There is also an example in that section. Also \Program Files\R\rw2011\library contains one

Re: [R] fail in adding library in new version.

2005-07-07 Thread Gabor Grothendieck
There is also an even larger source of examples at: http://cran.r-project.org/src/contrib/Descriptions/ although the built caveat mentioned below applies here as well. On 7/7/05, Gabor Grothendieck [EMAIL PROTECTED] wrote: You cannot use an empty DESCRIPTION file. To get more info on the

Re: [R] PCA and overlaying points

2005-07-07 Thread Jacques VESLOT
Hi Renaud, Thanks a lot for helping ! Actually, I did think about such a function (jitter), but it didn't really solve the problem, as it may change nothing for some overlaying points and even create new cases of overlaying points. Moreover, it modifies every coordinates, even if it is not

Re: [R] timezone problems

2005-07-07 Thread Martin Keller-Ressel
Thank you Don for your hints. I have checked my environment vairable TZ again. But everything is set correctly. I think the problem is with Sys.timezone(). Maybe it is a conflict between how my system formats the time/date and what Sys.timezone() expects. This is what I get on my system:

Re: [R] rlm/M/MM-estimator questions

2005-07-07 Thread Matthias Kohl
Christian Hennig wrote: Hi list, 1) How can the MM-estimator method=MM in function rlm be tuned to 85% efficiency? It seems that there is a default tuning to 95%. I presume, but am not sure, that the MM-estimator uses phi=phi.bisquare as default and the tuning constant could be set by adding a

[R] r: LOOPING

2005-07-07 Thread Clark Allan
hi all i know that one should try and limit the amount of looping in R programs. i have supplied some code below. i am interested in seeing how the code cold be rewritten if we dont use the loops. a brief overview of what is done in the code. ==

[R] R under suse linux 9.3

2005-07-07 Thread Mahdi Osman
Hi, dear list members, I've been using R under windows XP and I am now changing my system to SUSE LINUX 9.3. I could figure out that there is no precompiled version of R for LINUX. To get me going, I would like your help regarding what I need to setup R under my SUSE LINUX. Which

Re: [R] Tempfile error

2005-07-07 Thread Uwe Ligges
Doran, Harold wrote: Dear List: I am encountering an error that I can't resolve. I'm looping through rows of a dataframe to generate individual tex files using Sweave. At random points along the way, I encounter the following error Error in file() : cannot find unused tempfile name

Re: [R] Discriminant Function Analysis

2005-07-07 Thread michael watson \(IAH-C\)
Thanks for the answers Uwe! So this is a common problem in biology - few number of cases and many, many variables (genes, proteins, metabolites, etc etc)! Under these conditions, is discriminant function analysis not an ideal method to use then? Are there alternatives? 1) First problem, I

Re: [R] Discriminant Function Analysis

2005-07-07 Thread Uwe Ligges
michael watson (IAH-C) wrote: Thanks for the answers Uwe! So this is a common problem in biology - few number of cases and many, many variables (genes, proteins, metabolites, etc etc)! Under these conditions, is discriminant function analysis not an ideal method to use then? Are there

Re: [R] R under suse linux 9.3

2005-07-07 Thread Ernesto Jardim
Mahdi Osman wrote: Hi, dear list members, I've been using R under windows XP and I am now changing my system to SUSE LINUX 9.3. I could figure out that there is no precompiled version of R for LINUX. To get me going, I would like your help regarding what I need to setup R under my

[R] How to get the minimum ?

2005-07-07 Thread Philippe Lamy
Hi, I have a model with differents observations Xi. Each observation belongs to a group, either A or B. I would like to minimize a fonction like : sum( Xi - Z)^2 + sum (Xi - aZ -b)^2 AB The first sum contains all observations from group A and the second all observations from

Re: [R] R under suse linux 9.3

2005-07-07 Thread Peter Dalgaard
Ernesto Jardim [EMAIL PROTECTED] writes: Mahdi Osman wrote: Hi, dear list members, I've been using R under windows XP and I am now changing my system to SUSE LINUX 9.3. I could figure out that there is no precompiled version of R for LINUX. To get me going, I would like

Re: [R] R under suse linux 9.3

2005-07-07 Thread Ernesto Jardim
Peter Dalgaard wrote: Ernesto Jardim [EMAIL PROTECTED] writes: Mahdi Osman wrote: Hi, dear list members, I've been using R under windows XP and I am now changing my system to SUSE LINUX 9.3. I could figure out that there is no precompiled version of R for LINUX. To get me going, I

Re: [R] timezone problems

2005-07-07 Thread Uwe Ligges
Martin Keller-Ressel wrote: Thank you Don for your hints. I have checked my environment vairable TZ again. But everything is set correctly. I think the problem is with Sys.timezone(). Maybe it is a conflict between how my system formats the time/date and what Sys.timezone() expects.

Re: [R] R under suse linux 9.3

2005-07-07 Thread michael watson \(IAH-C\)
I've been successfully using R on SuSe linux for the last 2 years and I use the rpm :-) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ernesto Jardim Sent: 07 July 2005 10:48 Cc: r-help@stat.math.ethz.ch Subject: Re: [R] R under suse linux 9.3 Peter

Re: [R] r: LOOPING

2005-07-07 Thread Uwe Ligges
Clark Allan wrote: hi all i know that one should try and limit the amount of looping in R programs. i have supplied some code below. i am interested in seeing how the code cold be rewritten if we dont use the loops. It is not always a good thing to remove loops (without having looked at

答复: 答复: [R] fail in adding library i n new version.

2005-07-07 Thread Ivy_Li
Dear all, I have done every step as the previous mail. 1. unpack tools.zip into c:\cygwin 2. install Active perl in c:\Perl 3. install the mingw32 in c:\mingwin 4. add c:\cygwin; c:\mingwin\bin in Control Panel - System - Advanced - Environment Variables - Path - Variable , and they are

Re: [R] Lack of independence in anova()

2005-07-07 Thread Ted Harding
My first reaction to Duncan's example was Touché -- with apologies to Göran for suspecting on over-trivial example! I had not thought long enough about possible cases. Duncan is right; and maybe it is the same example as Göran was thinking of. Regarding Spencer's argument below, in Duncan's

Re: 答复: 答复: [R] fail in adding librar y in new version.

2005-07-07 Thread Uwe Ligges
Ivy_Li wrote: Dear all, I have done every step as the previous mail. 1. unpack tools.zip into c:\cygwin 2. install Active perl in c:\Perl 3. install the mingw32 in c:\mingwin 4. add c:\cygwin; c:\mingwin\bin in Control Panel - System - Advanced - Environment Variables - Path -

[R] Making Package, Chm error, Html Help Workshop

2005-07-07 Thread TEMPL Matthias
Hello, When building my package (R CMD check) following error message occurs: ... varinf.plot text html latex example xtext html latex example make[2]: *** No rule to make target `disclosure.chm`. Stop. cp: cannot stat

[R] about image() function in R and colors

2005-07-07 Thread javier garcia
Hi! I've got a map in R imported from a GIS (GRASS) as a vector of factors. So I've got 20 different levels in the map and I've created a vector of custom colors of exactly 20 colors in lenght. I'm trying to use image() (really plot.grassmeta() that call image()) to plot the map with those

[R] Problems with nlme: Quinidine example

2005-07-07 Thread rich
This concerns the Clinical Study of Quinidine example on page 380 of the book Mixed-Effects Models in S and S-PLUS by Pinheiro and Bates (2000). I have tried to reproduce the example, but get an error: library(nlme) fm1Quin.nlme - nlme(conc ~ quinModel(Subject, time, conc, dose, interval, lV,

[R] Tables: Invitation to make a collective package

2005-07-07 Thread Jose Claudio Faria
Hi All, I would like to make an invitation to make a collective package with all functions related to TABLES. I know that there are many packages with these functions, the original idea is collect all this functions and to make a single package, because is arduous for the user know all this

[R] About ade4 and overlaying points

2005-07-07 Thread Jacques VESLOT
Dear R-users, Is there an easy way to avoid points one upon another when ploting rows and columns of 'dudi' objects ? Maybe there is a function in ade4 or in an other package, or maybe someone has his or her own function to do this (for example to automatically modify a little the coordinates

Re: [R] about image() function in R and colors

2005-07-07 Thread Tuszynski, Jaroslaw W.
I do not know the solution to your problem, but I had the similar problems with image() function and most of derived functions. It seems that 'image' function was really not meant for displaying image data, instead it was designed to display matrices in the image format. Matlab had the same

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