Re: [R] R environment

2005-08-31 Thread Henrik Bengtsson
Unfortunately Duncan's suggestion to restart is probably the only way to go here. I've done similar thing myself too. What I've learned was that it is clever to include a so called hot-patch mechanism in your code, which will load R source code found in a certain directory, say, "hot/", once

[R] Dataset size in R

2005-08-31 Thread Peter.Watkins
Dear listers, I would like to know whether a maximum size is set for data sets in R. I'm planning on analysing data sets which have 33 points for a sample. The response is from GCxGC output. Also, with data analysis, is there a time-cost saving by performing the analysis in Linux as ag

Re: [R] basic anova and t-test question

2005-08-31 Thread Spencer Graves
Does the following answer your question: > set.seed(1) > z0 <- rnorm(100) > p.z <- 2*pnorm(-abs(z0)) > sum(p.z<0.05) [1] 5 > pchisq(sum(z0^2), 100, lower=FALSE) [1] 0.917285 Some of the 100 (in this case) normal random deviates seem statistically significant, even though

Re: [R] Linux Standalone Server Suggestions for R

2005-08-31 Thread Whit Armstrong
you can test out a live PPC 64 bit system here: http://www.openpowerproject.org/us/signup.php I have successfully built R in my home dir and compiled a few packages for it. Here are the machines available: Universität AugsburgPeking University Server O

[R] Data Mining Conference Program Announced

2005-08-31 Thread Lisa Solomon
DATA MINING 2006 CONFERENCE sponsored by Salford Systems San Diego, California: March 29 - March 31, 2006 The Conference will offer Real-World Case Study Presentations including Cutting Edge Topics: Crime Prevention * Anti-Terrorism * Gambling * Sports * Video Games * Food & Water Science * Die

[R] Linux Standalone Server Suggestions for R

2005-08-31 Thread Jia-Shing So
Hi All, My group is looking for any suggestions on what to purchase to achieve the most powerful number crunching system that $50k can buy. The main application that will be used is R so input on what hardware benefits R most will be appreciated. The requirements are that it be a single

[R] Question

2005-08-31 Thread Mahmoud Torabi
Dear Sir/Madam I would be pleased if anybody can help me. I'm using linear mixed model (lme) function.I'm doing some simulation in my research and need to be assigned variance components values during of my program. Specifically, when I use lme function, I can get some information by use summary()

Re: [R] R environment

2005-08-31 Thread Duncan Murdoch
Jean Eid wrote: > This is probably a weird question but I need to know if there is a way... > > I run an R batch job without saving the variables at each step to the > disk. Is there a way to invoke another session of R and link it to the > same environment for read only. > > The problem is tha

Re: [R] label *on the side* in conditional lattice plots?

2005-08-31 Thread Maciej Kalisiak
On 8/31/05, Maciej Kalisiak <[EMAIL PROTECTED]> wrote: > I take it you mean to switch the layout so that the conditioned > bwplots are side by side, narrow but tall, with horizontal=TRUE, and Oops, I obviously meant horizontal=FALSE... -- Maciej Kalisiak <[EMAIL PROTECTED]> http://www.dgp.toront

[R] Block-diagonal matrix

2005-08-31 Thread Caio Lucidius Naberezny Azevedo
Dear R-users, Does anybody know how to construct a block-diagonal matrix (with the blocks being different matrixs, concerning the dimension and the values), without use loops ? Thanks all, Caio - [[alternative HTML version delet

Re: [R] label *on the side* in conditional lattice plots?

2005-08-31 Thread Maciej Kalisiak
On 8/31/05, Wiener, Matthew <[EMAIL PROTECTED]> wrote: > I think you might be able to use the "horizontal" argument to lattice to > rotate all your plots and squish them in the other dimension. (Though I > don't know whether you consider that a good outcome ...) I take it you mean to switch the l

[R] R binaries, platform independent and Design of Experiments

2005-08-31 Thread Nam-Ky Nguyen
Dear Rexpert, I would like to thank those who spend time answering my email on the burning of a CD with all R binary files for Windows and Linux. I have tried a couple of suggestions but have not been successful. I will pass these suggestions to our system administrator and I am sure that he can

[R] R environment

2005-08-31 Thread Jean Eid
This is probably a weird question but I need to know if there is a way... I run an R batch job without saving the variables at each step to the disk. Is there a way to invoke another session of R and link it to the same environment for read only. The problem is that I am running optim with ever

Re: [R] loop

2005-08-31 Thread Jean Eid
just one more thing. Why are you defining the function over and over again... On Wed, 31 Aug 2005, Hathaikan Chootrakool wrote: > I was wondering why this loop doesn't work! > > for (i in 1:k) > fnTr[i] <- function (p) 0.5* sum ( n*log(2*pi) - log(sd(i)^2) > +(logitp(i)

Re: [R] "best" c++ matrix library?

2005-08-31 Thread Dirk Eddelbuettel
Ott Toomet ut.ee> writes: > I am planning to write some more time-consuming matrix manipulations > in c++. What is the experience with the existing c++ matrix > libraries? Do you have some recommendations? Are some libraries more > compatible with R than the others? A lng time ago, I used

[R] eigen-decomposition of symmetric BCCB matrices

2005-08-31 Thread Globe Trotter
Hi, Can anyone please point to how to decompose BCCB (Block-Circulant-Circulant-Block) matrices? I am interested in the derivations: I do know that this can be numerically done using 2-dimensional FFTs. Many thanks and best wishes! __ R-help@stat.math.

[R] Imputation using Pan in R

2005-08-31 Thread Yi-Fu Chen
Hi, I've tried to run the multiple imputation for longitudinal data using Pan in R. The trimmed data consist 10 individuals across 4 time points. Following the example in panex.R, I imputated the model with one y variable and only random intercept. It worked well. The next step for me is to impu

Re: [R] label *on the side* in conditional lattice plots?

2005-08-31 Thread Wiener, Matthew
I think you might be able to use the "horizontal" argument to lattice to rotate all your plots and squish them in the other dimension. (Though I don't know whether you consider that a good outcome ...) Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAI

Re: [R] "best" c++ matrix library?

2005-08-31 Thread Rafael Laboissiere
* Ott Toomet <[EMAIL PROTECTED]> [2005-08-31 19:53]: > I am planning to write some more time-consuming matrix manipulations > in c++. What is the experience with the existing c++ matrix > libraries? Do you have some recommendations? Are some libraries more > compatible with R than the others?

[R] label *on the side* in conditional lattice plots?

2005-08-31 Thread Maciej Kalisiak
I'm doing bwplot(x ~ y | z, ...) with lattice, but would like the z-labels to appear to the *side* of each bwplot, rather than on top... is this possible? The main reason is that my bwplots are horizontal, and as such can be nicely squished in the vertical axis (big space-saver when including in p

[R] b1 function in ch 12 scripts of MASS

2005-08-31 Thread Jordi
Dear list, I have been trying to reproduce the scripts of the MASS library and I have found a problem when trying to reproduce the code in 12.4, with the use of neural networks and the function b1: b1 <- function(Z, ...) { zp <- Z[,3] - pmax(Z[,2], Z[,1]) contour(xp/log(10), yp/log

Re: [R] Advice about system for installing & updating all R packa ge in a Linux Lab?

2005-08-31 Thread Warnes, Gregory R
If you have several different versions of R installed, you might want to use a script like this one, which should work on (at least) 1.9.1 and newer. #!/bin/sh echo "##" echo "## This script will attempt to install all available R packages" echo "## from the package repositories:" e

Re: [R] Block-Diagonal Matrix and Multivariate Skew Normal

2005-08-31 Thread Liaw, Andy
For your first question, here's a function originally posted by Ben Bolker, with modification by Rich Raubertas: blockdiag <- function (x, ...) { if (!is.list(x)) x <- list(x) args <- list(...) if (length(args) > 0) args <- c(x, args) else args <- x idx <- wh

Re: [R] sinput for Windows

2005-08-31 Thread Duncan Murdoch
On 8/31/2005 12:57 PM, Isotta Felli wrote: > Hi, I'm trying to latex part of my R- code and don't know where to find the > sinput package to include in my version of miktex (I have the LINUX version > handy, but need also the Windows one) Any idea? (sorry it is not really a R > question) If yo

Re: [R] "best" c++ matrix library?

2005-08-31 Thread Vehbi Sinan Tunalioglu
Hi, I used Meschach: http://www.math.uiowa.edu/~dstewart/meschach/ However, it is written in C. The API is strong. I used the same API and trimmed down the functionality, as well. Both worked for me. IBM Developworks has an article on the subject "Matrix libraries for C and C++": http://www-128.i

[R] Reading numeric data in Excel as character data in R using RODBC

2005-08-31 Thread White, Charles E WRAIR-Wash DC
The Excel 'database' I am pulling from mixes multiple character indicators for different kinds of non-numeric results in the same column as the numeric values. A simple sqlFetch turns all of the character indicators into NAs. I would like to pull in all of the Excel data as character so that I can

[R] En: Block-Diagonal Matrix and Multivariate Skew Normal

2005-08-31 Thread Caio Lucidius Naberezny Azevedo
Dear R-users, Does anybody know how to construct a block-diagonal matrix (with the blocks being different matrixs, concerning the dimension and the values) ? I would like to know also if there is any package that generates values from a multivariate skew normal distribution. Thanks all,

[R] Block-Diagonal Matrix and Multivariate Skew Normal

2005-08-31 Thread Caio Lucidius Naberezny Azevedo
Dear R-users, Does anybody know how to construct a block-diagonal matrix (with the blocks being different matrixs, concerning the dimension and the values) ? I would like to know also if there is any package that generates values from a multivariate skew normal distribution. Thanks all,

[R] sinput for Windows

2005-08-31 Thread Isotta Felli
Hi, I'm trying to latex part of my R- code and don't know where to find the sinput package to include in my version of miktex (I have the LINUX version handy, but need also the Windows one) Any idea? (sorry it is not really a R question) Thanks Isotta

[R] "best" c++ matrix library?

2005-08-31 Thread Ott Toomet
Hi folks, I am planning to write some more time-consuming matrix manipulations in c++. What is the experience with the existing c++ matrix libraries? Do you have some recommendations? Are some libraries more compatible with R than the others? All suggestions welcome! Best, Ott __

Re: [R] extrating BLUP values from linear mixed models

2005-08-31 Thread Doran, Harold
Use the ranef() command ranef(fm1, level=1) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Matt Robinson Sent: Wednesday, August 31, 2005 12:26 PM To: r-help@stat.math.ethz.ch Subject: [R] extrating BLUP values from linear mixed models Hello, I wish t

[R] extrating BLUP values from linear mixed models

2005-08-31 Thread Matt Robinson
Hello, I wish to learn how to extract best linear unbiased predictor values from a linear mixed model of repeated measures on individuals which has a random error structure (random =~ 1|individual). Thanks for your time, Kind regards Matt -- Matt Robinson Institute of Evolutionary Biology Univer

Re: [R] loop

2005-08-31 Thread ernesto
Hathaikan Chootrakool wrote: >I was wondering why this loop doesn't work! > >for (i in 1:k) >fnTr[i] <- function (p) 0.5* sum ( n*log(2*pi) - log(sd(i)^2) > +(logitp(i)-p)^2/sd(i)^2 ) >outTr[i]<- nlm (fnTr[i],p=c(10),hessian=TRUE) >minimumTr[i] <- outTr[i]$minimum >valueTr

[R] loop

2005-08-31 Thread Hathaikan Chootrakool
I was wondering why this loop doesn't work! for (i in 1:k) fnTr[i] <- function (p) 0.5* sum ( n*log(2*pi) - log(sd(i)^2) +(logitp(i)-p)^2/sd(i)^2 ) outTr[i]<- nlm (fnTr[i],p=c(10),hessian=TRUE) minimumTr[i] <- outTr[i]$minimum valueTr[i] <- outTr[i]$estimate list (minimum

Re: [R] xtable

2005-08-31 Thread Don MacQueen
You do have to load optional packages in each R session. See ?require But you can automate the loading; see ?Startup -Don At 6:46 PM +0200 8/30/05, Mag. Ferri Leberl wrote: >I have installed package xtable with > >su -c 'R CMD INSTALL xtable' > >and got this promising feedback: > >* Inst

Re: [R] Bioconductor and R-devel

2005-08-31 Thread Seth Falcon
Hi Jennifer, I'm moving this over to the bioconductor mail list since we are discussing Bioconductor packages, that would be the best place for the discussion at this point. Please subscribe and reply there. A couple quick comments: 1. You do realize BioC 1.7 is the current devel version, right

[R] Cases as Variables in Principal Component Analysis?

2005-08-31 Thread Yukihiro Ishii
Dear R users, I have a data set of 25 cases with 150-160 explanatory variables(the number of which depends on what I choose from 200 odd digitalized spectrum strength numbers) and one dependent variable(a sensory test result). My natural choice is to work on a principal component analysis using th

Re: [R] tcl/tk return problem

2005-08-31 Thread Philippe Grosjean
Duncan Murdoch wrote: > On 8/31/2005 8:57 AM, Prof Brian Ripley wrote: > >> On Wed, 31 Aug 2005, Duncan Murdoch wrote: >> >>> Prof Brian Ripley wrote: >>> > On Wed, 31 Aug 2005, Philippe Grosjean wrote: >>> > >>> > >>> >>deggle wrote: >>> >> >>> >>>Hello, >>> >>> >>> >>>I'm very new in working wit

[R] Bioconductor and R-devel

2005-08-31 Thread Jennifer Lai
Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required pack

Re: [R] problem with certain data sets when using randomForest

2005-08-31 Thread Liaw, Andy
I've been trying to play catch-up on R-help since DSC2005. This one must have slipped through... This is what I'd do: iris.sub <- subset(iris, Species %in% c("setosa", "virginica")) iris.sub$Species <- factor(iris.sub$Species) That last line drops the empty level in the factor. You can then ru

Re: [R] tcl/tk return problem

2005-08-31 Thread Duncan Murdoch
On 8/31/2005 8:57 AM, Prof Brian Ripley wrote: > On Wed, 31 Aug 2005, Duncan Murdoch wrote: > >> Prof Brian Ripley wrote: >> > On Wed, 31 Aug 2005, Philippe Grosjean wrote: >> > >> > >> >>deggle wrote: >> >> >> >>>Hello, >> >>> >> >>>I'm very new in working with tcl/tk in R and have a problem whic

Re: [R] tcl/tk return problem

2005-08-31 Thread Prof Brian Ripley
On Wed, 31 Aug 2005, Duncan Murdoch wrote: > Prof Brian Ripley wrote: > > On Wed, 31 Aug 2005, Philippe Grosjean wrote: > > > > > >>deggle wrote: > >> > >>>Hello, > >>> > >>>I'm very new in working with tcl/tk in R and have a problem which will > >>>probably > >>>sound silly to most of you. > >>>H

Re: [R] tcl/tk return problem

2005-08-31 Thread Duncan Murdoch
Prof Brian Ripley wrote: > On Wed, 31 Aug 2005, Philippe Grosjean wrote: > > >>deggle wrote: >> >>>Hello, >>> >>>I'm very new in working with tcl/tk in R and have a problem which will >>>probably >>>sound silly to most of you. >>>Here is the code I have problems with: >>> >>>readcelfiles <- funct

Re: [R] Gamma for ordinal trends

2005-08-31 Thread Wuming Gong
Is it possible to use delta method to evaluate the standard error of Goodman-Kruskal gamma and then Wald test to evaluate the significance of association? Wuming On 31 Aug 2005 13:42:27 +0200, Peter Dalgaard <[EMAIL PROTECTED]> wrote: > Jonathan Baron <[EMAIL PROTECTED]> writes: > > > On 08/31/

Re: [R] Gamma for ordinal trends

2005-08-31 Thread Peter Dalgaard
Jonathan Baron <[EMAIL PROTECTED]> writes: > On 08/31/05 17:46, Wuming Gong wrote: > > Dear list, > > > > Are there any functions for calculating gamma (and its standard > > error), which measures the association of ordinal factors in I x J > > contingency table. I did a RSiteSearch but did not f

Re: [R] tcl/tk return problem

2005-08-31 Thread Prof Brian Ripley
On Wed, 31 Aug 2005, Philippe Grosjean wrote: > deggle wrote: > > Hello, > > > > I'm very new in working with tcl/tk in R and have a problem which will > > probably > > sound silly to most of you. > > Here is the code I have problems with: > > > > readcelfiles <- function() > > { > >require(tc

Re: [R] tcl/tk return problem

2005-08-31 Thread Philippe Grosjean
deggle wrote: > Hello, > > I'm very new in working with tcl/tk in R and have a problem which will > probably > sound silly to most of you. > Here is the code I have problems with: > > readcelfiles <- function() > { >require(tcltk) >tt <- tktoplevel() >tkgrid(tklabel(tt,text="Choose a

Re: [R] Gamma for ordinal trends

2005-08-31 Thread Jonathan Baron
On 08/31/05 17:46, Wuming Gong wrote: > Dear list, > > Are there any functions for calculating gamma (and its standard > error), which measures the association of ordinal factors in I x J > contingency table. I did a RSiteSearch but did not find any clues... You have to look for Goodman-Kruskal g

[R] tcl/tk return problem

2005-08-31 Thread deggle
Hello, I'm very new in working with tcl/tk in R and have a problem which will probably sound silly to most of you. Here is the code I have problems with: readcelfiles <- function() { require(tcltk) tt <- tktoplevel() tkgrid(tklabel(tt,text="Choose a directory!")) OnOK <- function() {

[R] Gamma for ordinal trends

2005-08-31 Thread Wuming Gong
Dear list, Are there any functions for calculating gamma (and its standard error), which measures the association of ordinal factors in I x J contingency table. I did a RSiteSearch but did not find any clues... Thanks, Wuming __ R-help@stat.math.ethz

Re: [R] PLSR: model notation and reliabilities

2005-08-31 Thread I.Ioannou
On Mon, Aug 29, 2005 at 08:08:53AM +0200, Bj?rn-Helge Mevik wrote: > It seems to me that what you are looking for, is some sort of > structured equation models (? la Lisrel). The pls package implements > partial least squares regression and principal component regression, > which is something di

Re: [R] Installation help

2005-08-31 Thread Prof Brian Ripley
On Tue, 30 Aug 2005, b wrote: > Solved the problem with the 'R' installation! > > One of the processes that loads up on startup was > conflicting with it. It was a program called > "Gameutil.exe" which seems to enhance games by > altering display modes. For some reason a conflict > existed. Anyhow

Re: [R] R binaries

2005-08-31 Thread Thomas Petzoldt
Nam-Ky Nguyen schrieb: > Dear Rexperts, > > I intend to burn some R CDs to colleagues in Vietnam. I want to put all > binary files for base as well as contributed packages (for both Windows > and Linux). It is very time consuming if I download files by files. Is > there a place a can buy a CD wit

[R] Distributional characteristics

2005-08-31 Thread Naji
Hi all I've a continuous variable and I want to test (graphically, plotting observed and theoretical distr, qqplot) whether it follows some formal distribution. (some thing close to Ricci document : Fitting distributions with R, Feb05). The distribution I want to fit is a truncated Gamma at 1 (t

Re: [R] R binaries

2005-08-31 Thread Peter Dalgaard
Berwin A Turlach <[EMAIL PROTECTED]> writes: > Thus, since Nam-Ky works on a Linux box (private e-mail) the commands > should be On a Linux box, I would rather suggest using wget on the appropriate CRAN directories (wget -r --no-parent http://etc.etc.etc/...) - unless of course it is the download

Re: [R] R binaries

2005-08-31 Thread Berwin A Turlach
G'day Brian, > "BDR" == Prof Brian Ripley <[EMAIL PROTECTED]> writes: BDR> On Wed, 31 Aug 2005, Berwin A Turlach wrote: >> available.packages() does not seem to have a type argument >> according to its documentation, so I guess that even if it is >> run under Windows that it r