Re: [R] KalmanLike: missing exogenous factor?

2004-10-12 Thread Prof Brian Ripley
On Mon, 11 Oct 2004, Heng Sun wrote: From the help document on KalmanLike, KalmanRun, etc., I see the linear Gaussian state space model is a - T a + R e y = Z' a + eta following the book of Durbin and Koopman. In practice, it is useful to run Kalman filtering/smoothing/forecasting

Re: [R] plotting directly to the printer

2004-10-12 Thread Prof Brian Ripley
On Mon, 11 Oct 2004, T. Murlidharan Nair wrote: How do I send the plots directly to the printer ? On what operating system? On Windows, see the rw-FAQ Q2.9. On Linux/Unix, see ?dev.print and the print.it argument in ?postscript. Please do read the posting guide and supply enough information

[R] Statistical analysis of a large database

2004-10-12 Thread Victoria Landsman
Deall all, We need to perform a statistical analysis of a large database (40,000 entries with approximately 500 fields in each entry) currently handled in Oracle. The data contains categorical variables only. At the current stage we suggest classification and clustering analysis. We are

Re: [R] plotting with multiple files

2004-10-12 Thread Prof Brian Ripley
On Mon, 11 Oct 2004, T. Murlidharan Nair wrote: I need to generate plots from several multiple file and I am doing this I presume you are making plots from *data* in those files rather than R scripts, but you did not say. by reading it as a list using c(file1, file2.). Since I need to

RE: [R] dot density maps

2004-10-12 Thread Johannes SCHNITZLER
Dear Roger, Thank you very much for the reply. And now I have to a apologize for my late response. I was quite a while out of the office. This is exactly what I was looking for. I think it will be of great help to have this implemented in a package. Johannes -Original Message-

[R] Statistical analysis of a large database

2004-10-12 Thread Vito Ricci
Hi, for your analysis use the package: ROracle Oracle database interface for R http://microarrays.unife.it/CRAN/src/contrib/Descriptions/ROracle.html see also: Diego Kuonen, Introduction au data mining avec R : vers la reconquête du `knowledge discovery in databases' par les statisticiens.

Re: [R] Statistical analysis of a large database

2004-10-12 Thread Prof Brian Ripley
I believe this is a reply to a posting -- since this is by no means the first time this has happened, please - use the Reply function of your mailer, or at least use Re: in the subject line and include the relevant part of the original posting, and - send the reply to the questioner, as well as

[R] lm#contrasts#one level in factor: bug or feature

2004-10-12 Thread Ritter, Christian C MCIL-CTANL/S
(R.1.9.1; win2000) Since it's about the tenth time I had to write an if around this to catch the error ... Let's look at the line myfit-lm(res~groupvar,data=Data) Here res is of numeric type and groupvar is a factor. On first sight, it would be logical that if groupvar had only one

Re: [R] 64-bit R on Intel Xeon EM64T running fine

2004-10-12 Thread Roger D. Peng
This is good news. As far as I know R has built for quite some time now on a number of 64 bit platforms (Linux on AMD Opteron/Athlon64, Solaris/Sparc) but I can't recall seeing a build on Intel with the 64 bit extensions. By the way, did you happen to run `make check' just for kicks? -roger

Re: [R] Diagnosing trouble with R-2.0, Fedora Core 2, and Rcmdf

2004-10-12 Thread John Fox
Dear Paul, I'm currently out of town, limiting a bit my ability to answer these questions definitively, but I'll give it a shot (hoping that my memory isn't faulty): On Mon, 11 Oct 2004 13:08:39 -0500 Paul Johnson [EMAIL PROTECTED] wrote: Greetings, R-help! On 2 Fedora Core 2 Linux systems,

Re: [R] 64-bit R on Intel Xeon EM64T running fine

2004-10-12 Thread Prof Brian Ripley
On Tue, 12 Oct 2004, Roger D. Peng wrote: This is good news. As far as I know R has built for quite some time now on a number of 64 bit platforms (Linux on AMD Opteron/Athlon64, Solaris/Sparc and Alpha and Irix and HP-UX and AIX as far as I understand. ) but I can't recall seeing a build

[R] tclk, tcltk

2004-10-12 Thread Jean Eid
I have been having problems with these two 'libraries' since I installed 2.0.0. I have built a package with couple of functions so that I can load it at startup every time R is booted. The problem is that I have the following error every time I call the library Loading required package: tclk

[R] Sweave and xtable

2004-10-12 Thread Doran, Harold
Dear List: I have some coded embedded within a LaTeX document where I subset a dataframe and use xtable to place it in my appendix. However, one of the tables is rather large and seems to extend beyond the page length. Is there a nice way to use Sweave to continue this table onto the next page?

Re: [R] tclk, tcltk

2004-10-12 Thread Prof Brian Ripley
What is package `tclk'? I think you have a typo somewhere in your code. At a guess you have Depends: tclk in a DESCRIPTION file for one of your packages. On Tue, 12 Oct 2004, Jean Eid wrote: I have been having problems with these two 'libraries' since I installed 2.0.0. I have built a

Re: [R] tclk, tcltk

2004-10-12 Thread Jean Eid
Thanks to Brian. I was looking everywhere except the typo. I guess the previous build (1.9.1) ignored the dependece error. Thanks again, jean On Tue, 12 Oct 2004, Prof Brian Ripley wrote: What is package `tclk'? I think you have a typo somewhere in your code. At a guess you have Depends:

Re: [R] Sweave and xtable

2004-10-12 Thread Frank E Harrell Jr
Doran, Harold wrote: Dear List: I have some coded embedded within a LaTeX document where I subset a dataframe and use xtable to place it in my appendix. However, one of the tables is rather large and seems to extend beyond the page length. Is there a nice way to use Sweave to continue this table

Re: [R] plot hclust - canberra dist + median linkage

2004-10-12 Thread Martin Maechler
Dan == Dan Bolser [EMAIL PROTECTED] on Mon, 11 Oct 2004 16:21:53 +0100 (BST) writes: Dan Gives strange results. Dan I get 'weird' dendrograms with canberra / binary distance metric and Dan median / centroid cluster methods. it doesn't depend on the metric: Both 'median' and

[R] A question in R

2004-10-12 Thread Yayira har
I started to learn the R language, but I didn't suceed to use an external file. Let say that I have an excel file called test1.xls in the directory C:/program files/R/rw2000/external_files that looks like that: name mark yair 80 yosi 70 ... In the appropriate directory I

Re: [R] A question in R

2004-10-12 Thread Kevin Bartz
Yayira har wrote: I started to learn the R language, but I didn't suceed to use an external file. Let say that I have an excel file called test1.xls in the directory C:/program files/R/rw2000/external_files that looks like that: name mark yair 80 yosi 70 ... In the

Re: [R] A question in R

2004-10-12 Thread Sundar Dorai-Raj
Yayira har wrote: I started to learn the R language, but I didn't suceed to use an external file. Let say that I have an excel file called test1.xls in the directory C:/program files/R/rw2000/external_files that looks like that: name mark yair 80 yosi 70 ... In the

Re: [R] A question in R

2004-10-12 Thread Prof Brian Ripley
Take a look at the `R Data Import/Export' manual. Hint: if test1.xls is an Excel worksheet, it is not a tab-delimited file. On Tue, 12 Oct 2004, Yayira har wrote: I started to learn the R language, but I didn't suceed to use an external file. Let say that I have an excel file called

Re: [R] A question in R

2004-10-12 Thread Yves Magliulo
hi, check R-data import/export document at this link cran.r-project.org/doc/manuals/R-data.pdf let me give you an advice for further questions : it's easiest to find answer to your question searching directly with google -- -- Yves Magliulo [EMAIL PROTECTED] RD Engineer, CLIMPACT Tel.

[R] need help on GAM

2004-10-12 Thread Liu Song
Get some question about the function gam. Suppose I have a semiparametric model, Y~x1+x2+s(z1). Using gam, how could I get the estimates for the parametric part and nonparametric part respectively? And another question: we could find the coefficients for both parametric term and nonparametric

Re: [R] need help on GAM

2004-10-12 Thread Prof Brian Ripley
Please read the posting guide and do give sufficient details for your questions to be answered. On Tue, 12 Oct 2004, Liu Song wrote: Get some question about the function gam. There are at least two functions gam() available for R, but none in standard R. Which package are you talking about?

Re: [R] need help on GAM

2004-10-12 Thread Gabor Grothendieck
Prof Brian Ripley ripley at stats.ox.ac.uk writes: : And another question: we could find the coefficients for both : parametric term and nonparametric term, what do these coefficients : for the nonparametric term stand for, the coefficients for the base : functions? : : By definition,

[R] locfit confidence intervals

2004-10-12 Thread Suresh Krishna
hi, after m=locfit(y~x,..., family=binomial) plot(m,band=local) gives me a plot of locfit's result with a confidence interval around it. i would like to get the actual values that are being used to plot the lines in this figure. i tried using predict, but the standard error it returns

Re: [R] need help on GAM

2004-10-12 Thread Simon Wood
Get some question about the function gam. Suppose I have a semiparametric model, Y~x1+x2+s(z1). Using gam, how could I get the estimates for the parametric part and nonparametric part respectively? For a gam object (called, b,say) fitted using the mgcv `gam' then coef(b) will extract the

[R] constrained optimization using nlm/optim?

2004-10-12 Thread Jeff D. Hamann
I'm looking for an example of a simple R script that impliments a contrained nonlinear function using nlm or optim. I'm not exactly sure how to impliment the constraints within the objective function that is passed to nlm/optim. obj.func - function( p ) { x(p) - unconstrained obj function

Re: [R] locfit confidence intervals

2004-10-12 Thread Prof Brian Ripley
Why not use predict(se=TRUE, band=local)? That's what plot.locfit does, via preplot.locfit. I'm afraid the only real way to answer questions like this is to read the sources. On Tue, 12 Oct 2004, Suresh Krishna wrote: hi, after m=locfit(y~x,..., family=binomial)

[R] problem with lapack.so under Debian Sid

2004-10-12 Thread Christian Fiebach
Dear list, I am sorry to bother you with this. I just upgraded yesterday to R 2.0.0 (using apt-get under Debian Sid), and now have problems running e.g., summary(lm(...)) the lm is calculated, but the summary statement gives me the following error: Error in La.chol2inv(x, size) : lapack routines

[R] graph question

2004-10-12 Thread Dean Sonneborn
I would like to produce a graph which plots a log scale variable on the y-axis but have the tick marks on the y-axis be the non log transformed values that are round like .5, 1, 2, 3, 4 etc. Has anyone done something like this in the past? How did you implement it in the code? Thanks, Dean

[R] Course***R/S-plus Fundamentals and Programming Techniques In New York and Chicago

2004-10-12 Thread elvis
XLSolutions Corporation (www.xlsolutions-corp.com) is proud to announce 2-day R/S-plus Fundamentals and Programming Techniques. New York, NY --- November 18th-19th Chicago, IL -- November 11th-12th Reserve your seat now at the early bird

Re: [R] constrained optimization using nlm/optim?

2004-10-12 Thread Patrick Burns
You want the penalty for the constraint to depend on how much the constraint is broken -- unlike your sample code. Page 336 of S Poetry has an example. 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

Re: [R] problem with lapack.so under Debian Sid

2004-10-12 Thread Prof Brian Ripley
On Tue, 12 Oct 2004, Christian Fiebach wrote: Dear list, I am sorry to bother you with this. I just upgraded yesterday to R 2.0.0 (using apt-get under Debian Sid), and now have problems running e.g., summary(lm(...)) the lm is calculated, but the summary statement gives me the

Re: [R] constrained optimization using nlm/optim?

2004-10-12 Thread Roger D. Peng
My guess is that approach will not work particularly well with nlm(), which expects the objective function to be smooth. You might have better luck using the Nelder-Mead method in optim(). -roger Jeff D. Hamann wrote: I'm looking for an example of a simple R script that impliments a contrained

Re: [R] graph question

2004-10-12 Thread Prof Brian Ripley
On Tue, 12 Oct 2004, Dean Sonneborn wrote: I would like to produce a graph which plots a log scale variable on the y-axis but have the tick marks on the y-axis be the non log transformed values that are round like .5, 1, 2, 3, 4 etc. Has anyone done something like this in the past? How

Re: [R] 64-bit R on Intel Xeon EM64T running fine

2004-10-12 Thread Murad Nayal
Roger D. Peng wrote: This is good news. As far as I know R has built for quite some time now on a number of 64 bit platforms (Linux on AMD Opteron/Athlon64, Solaris/Sparc) Ill add SGI/IRIX 64 bit platform to the list. I've been running a 64 bit-compiled R on an SGI octane 2 for over a

[R] bandwidths for bivariate density estimation

2004-10-12 Thread Emili Tortosa-Ausina
Hi, I am using the KernSmooth package to estimate nonparametrically bivariate density functions. However, it seems that the bandwidths (one for each co-ordinate direction) have to be selected manually. This does not apply for the univariate case, for which dpik (included in KernSmooth) uses

[R] bandwidths for bivariate density estimation

2004-10-12 Thread Emili Tortosa-Ausina
Hi, I am using the KernSmooth package to estimate nonparametrically bivariate density functions. However, it seems that the bandwidths (one for each co-ordinate direction) have to be selected manually. This does not apply for the univariate case, for which dpik (included in KernSmooth) uses

Re: [R] plot hclust - canberra dist + median linkage

2004-10-12 Thread Dan Bolser
On Tue, 12 Oct 2004, Martin Maechler wrote: Dan == Dan Bolser [EMAIL PROTECTED] on Mon, 11 Oct 2004 16:21:53 +0100 (BST) writes: Dan Gives strange results. Dan I get 'weird' dendrograms with canberra / binary distance metric and Dan median / centroid cluster methods. it

Re: [R] problem with lapack.so under Debian Sid

2004-10-12 Thread Dirk Eddelbuettel
On Tue, Oct 12, 2004 at 10:46:09AM -0700, Christian Fiebach wrote: Dear list, I am sorry to bother you with this. I just upgraded yesterday to R 2.0.0 (using apt-get under Debian Sid), and now have problems running e.g., summary(lm(...)) the lm is calculated, but the summary statement

Re: [R] lm#contrasts#one level in factor: bug or feature

2004-10-12 Thread Thomas Lumley
On Tue, 12 Oct 2004, Ritter, Christian C MCIL-CTANL/S wrote: (R.1.9.1; win2000) Since it's about the tenth time I had to write an if around this to catch the error ... Let's look at the line myfit-lm(res~groupvar,data=Data) Here res is of numeric type and groupvar is a factor. On first

[R] covariate selection?

2004-10-12 Thread Ian Fiske
Hello, I am hoping someone can help me with the following multivariate issue: I have a model consisting of about 50 covariates. I would like to reduce this to about 5 covariate for the reduced model by combining cofactors that are strongly correlated. Is there a package or function that

[R] Why I can't retrieve GO identifier correctly?

2004-10-12 Thread szhan
Hello, R experts, I tried to retrieve all biological process GO terms at level 3 starting biological process as level 1 using the code as bellows: 1 library(GO) 2 library(GOstats) 3 level2-getGOChildren(GO:0008150)$GO:0008150$Children 4 for ( i in 1:length(level2)) { 5level3 -

RE: [R] covariate selection?

2004-10-12 Thread Martínez Ovando Juan Carlos
Hello Ian, ?princomp If your covariates are scalars, and the following documents: http://www.jstatsoft.org/v07/i01/drdoc.pdf http://www.bioconductor.org/workshops/Milan/PDF/Lab12.pdf Best wishes. Saludos, Juan Carlos Martínez Ovando Banco de México Av. 5 de Mayo No. 18 Piso 5 Sección D

Re: [R] A question in R

2004-10-12 Thread Kevin Wang
Hi, On Tue, 12 Oct 2004, Kevin Bartz wrote: R looks less than fondly on Excel files. The easiest solution for you will be to export your Excel file to a tab-delimited text format (Save - (.txt) Tab-delimited Text), and then use read.delim as you did. Does that make sense? The alternative

Re: [R] Why I can't retrieve GO identifier correctly?

2004-10-12 Thread Peter Dalgaard
[EMAIL PROTECTED] writes: Hello, R experts, I tried to retrieve all biological process GO terms at level 3 starting biological process as level 1 using the code as bellows: 1 library(GO) 2 library(GOstats) 3 level2-getGOChildren(GO:0008150)$GO:0008150$Children 4 for ( i in

Re: [R] covariate selection?

2004-10-12 Thread Ian Fiske
Thanks Juan. I thought that was what I was looking for, but really, I want to know which of the original covariates could best be used to take advantage of their colinearity without creating new variables. I think PCA creates new variables. SAS and SPSS can do what I'm talking about, but I

Re: [R] problem with lapack.so under Debian Sid

2004-10-12 Thread Douglas Bates
On Tue, 12 Oct 2004, Christian Fiebach wrote: Dear list, I am sorry to bother you with this. I just upgraded yesterday to R 2.0.0 (using apt-get under Debian Sid), and now have problems running e.g., summary(lm(...)) the lm is calculated, but the summary statement gives me the following error:

Re: [R] covariate selection?

2004-10-12 Thread Spencer Graves
Have you considered stepwise regression, e.g., step or stepAIC in library(MASS)? The documentation for both contain examples. hope this helps. spencer graves Ian Fiske wrote: Hello, I am hoping someone can help me with the following multivariate issue: I have a model

RE: [R] covariate selection?

2004-10-12 Thread Martínez Ovando Juan Carlos
Hello Ian, Sorry. I don't really understand your problem, which is of model selection. That's right? You could use some criteria based in likelihood. For instante Akaike (AIC) or Schwarz criteria (BIC), see: ?AIC ?mle.aic (The best model is determined minimizing AIC or BIC). I hope this

RE: [R] covariate selection?

2004-10-12 Thread Christian Mora
Hi Ian Have you tried help.search(pca)? Christian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Martínez Ovando Juan Carlos Sent: Tuesday, October 12, 2004 7:56 PM To: Ian Fiske Cc: [EMAIL PROTECTED] Subject: RE: [R] covariate selection? Hello Ian,

Re: [R] read 4-jan-02 as date

2004-10-12 Thread bogdan romocea
Thank you everyone. Indeed, I had read the data via read.csv and the date column was a factor. Everything works fine if I convert to character first. Regards, b. --- Sundar Dorai-Raj [EMAIL PROTECTED] wrote: bogdan romocea wrote: Dear R users, I have a column with dates

RE: [R] 64-bit R on Intel Xeon EM64T running fine

2004-10-12 Thread Liaw, Andy
This article might be of interest to some: http://www.linux-mag.com/2004-07/athlon_01.html Regarding 64-bit build of R, I can confirm Irix, Alpha and AIX, although some w/o readline/jpeg/png/X support, partially because of difficulties linking against 64-bit version of those libraries. Best,

RE: [R] Diagnosing trouble with R-2.0, Fedora Core 2, and Rcmdf

2004-10-12 Thread John Fox
Dear Paul, I've now had a chance to check into these problems further: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Johnson Sent: Monday, October 11, 2004 1:09 PM To: r help Subject: [R] Diagnosing trouble with R-2.0, Fedora Core 2, and

Re: [R] covariate selection?

2004-10-12 Thread Kjetil Brinchmann Halvorsen
Ian Fiske wrote: Hello, I am hoping someone can help me with the following multivariate issue: I have a model consisting of about 50 covariates. I would like to reduce this to about 5 covariate for the reduced model by combining cofactors that are strongly correlated. Is there a package or

RE: [R] covariate selection?

2004-10-12 Thread Austin, Matt
I like Kjetil's suggestion of a shrinkage estimator. Perhaps this would be a good time to experiment with Trevor Hastie's 'lars' package. If you have a lot of correlated inputs I might suggest using Andy Liaw's randomforest package. I have found this technique to be very valuable in this

RE: [R] tclk, tcltk

2004-10-12 Thread Liaw, Andy
From NEWS of R-2.0.0: o library() now checks the version dependence (if any) of required packages mentioned in the Depends: field of the DESCRIPTION file. This is not done in R-1.9.1 and prior, I believe (or it wouldn't be in NEWS). Andy From: Jean Eid Thanks to

Re: [R] KalmanLike: missing exogenous factor?

2004-10-12 Thread Heng Sun
Prof Ripley, Thanks for explanation. I now understand where KalmanLike fits. I should not use exogenous factor. It should be called exogenous variable or inputs or known effects. My study on how trading sizes impact on stock prices has trading sizes as this exogenous variable. As you said, this

RE: [R] graph question

2004-10-12 Thread Wiener, Matthew
Dean -- I believe just setting log = y in your plot command should do this. For example: plot(runif(100, 1, 100), runif(100, 1, 100), log = xy) gives me tick marks at 2, 5, 10, 20, 50, and 100. (YMMV because of the random numbers.) Hope this helps, Matt Wiener -Original Message-

[R] diagonal matrix construction

2004-10-12 Thread Chris Ryan
Hi, I have worked long and hard and looked in the manuals and am having a hard time constructing a diagonal matrix. I can get the diagonals out of a matrix but can't construct the matrix with just the diagonals. I have been on the web site and manuals and I think that it says to use: dsj

[R] data(eurodist) and PCA ??

2004-10-12 Thread Dan Bolser
If I perform PCA on the 'eurodist' data, should I get an accurate geographic layout of the cities with biplot? (barring inversions, i.e. their is no way to define north.. but you get the idea...) I have a complex distance matrix, and I am thinking about how to cluster it and how to visualize

Re: [R] diagonal matrix construction

2004-10-12 Thread Gabor Grothendieck
Chris Ryan chrisryan at wvdnr.gov writes: : : Hi, : : I have worked long and hard and looked in the manuals and am having a hard time constructing a diagonal : matrix. I can get the diagonals out of a matrix but can't construct the matrix with just the diagonals. I : have been on the web

Re: [R] diagonal matrix construction

2004-10-12 Thread Spencer Graves
Did you try working the examples in the diag documentation, one of which is as follows: diag(10,3,4) # guess what? [,1] [,2] [,3] [,4] [1,] 10000 [2,]0 1000 [3,]00 100 (R 1.9.1 for Windows). The R syntax expects three in that

[R] debugging non-visible functions

2004-10-12 Thread Murad Nayal
Hi, I would like to step-through a non-visible function. but apparently I don't know enough about namespaces to get that to work: methods(predict) ... deleted lines ... [27] predict.rpart* predict.smooth.spline* [31] predict.survreg.penal* Non-visible functions are

Re: [R] debugging non-visible functions

2004-10-12 Thread Gabor Grothendieck
Murad Nayal mn216 at columbia.edu writes: : : Hi, : : I would like to step-through a non-visible function. but apparently I : don't know enough about namespaces to get that to work: : : methods(predict) : ... deleted lines ... : [27] predict.rpart* predict.smooth.spline* :