Re: [R] Problem with as.data.frame when an extra attribute is present

On Fri, 10 Nov 2006, Frank E Harrell Jr wrote: > Prof Brian Ripley wrote: >> It's quite intentional, as it is the documented behaviour of data.frame: >> >> Objects passed to 'data.frame' should have the same number of >> rows, but atomic vectors, factors and character vectors protected >

Re: [R] Speed Optimization: Faster Way of Accessing data.frame in a Loop?

I don't see how this code can work at all. '[<-.data.frame' does not accept three arguments, e.g. > women[1,2,3] <- 17 Error in `[<-.data.frame`(`*tmp*`, 1, 2, 3, value = 17) : unused argument(s) (3) If df is in fact a three-dimensional array you can do df[1:20, 1:30, 20] <- df[1:20, 1

Re: [R] predict.lda is missing ?

i think you should use lda_res <- lda(over_win ~ t1_scrd_a + t1_alwd_a, data=train, CV=F) loo should be disabled for predicting purpose. On 11/10/06, Larry White <[EMAIL PROTECTED]> wrote: > I'm trying to classify some observations using lda and I'm getting a > strange error. I loaded the MASS p

[R] predict.lda is missing ?

I'm trying to classify some observations using lda and I'm getting a strange error. I loaded the MASS package and created a model like so: >train <- mod1[mod1$rand < 1.7,] >classify <- mod1[mod1$rand >= 1.7,] >lda_res <- lda(over_win ~ t1_scrd_a + t1_alwd_a, data=train, CV=TRUE) That works, and

Re: [R] missing symbols for mathplot

Try this: plot(0, main = quote(P(X ~ "|" ~ A ~ intersect(B On 11/10/06, stortignauz <[EMAIL PROTECTED]> wrote: > > Hi all, > > I'm trying to write an axis label > that sounds P( X | K and Xb ) (probability of X given K and Xb ) > but I need the intersection symbol > (the "\cap" in latex) > A

Re: [R] count data with nested mixed effects

Hi Deborah, A very good source for hands-on information on mixed models in S is: "Mixed-effects models in S and S-PLUS" by Pinheiro and Bates Incidentally, it's available in your university's library http://toroprod.library.utoronto.ca/uhtbin/cgisirsi/2XfWcMI0Ns/ROBARTS/140640080/2/1000 I beli

[R] count data with nested mixed effects

Dear R-Pros, I have count data in which 6-10 points are nested within 17 larger units (which are nested within 3 larger-still units) plus a number of covariates. It could be nested ANCOVA but for poisson family. Could someone kindly advise me 1) if lmer is the correct function for the analysis? a

Re: [R] Selective subsetting

"Davendra Sohal" <[EMAIL PROTECTED]> writes: > Hi all, > Here's an interesting (for me, at least!) problem I came across: > I have a correlation matrix, let's say with 6 variables, A to F, as column > headings and the same 6 as row headings. > The matrix is filled with correlation coefficients. Th

Re: [R] Selective subsetting

Look at the functions tril() and triu() in the Matrix package Regards Francisco Davendra Sohal wrote: > Hi all, > Here's an interesting (for me, at least!) problem I came across: > I have a correlation matrix, let's say with 6 variables, A to F, as column > headings and the same 6 as row headin

Re: [R] Selective subsetting

try this: cor.mat <- cor(iris[1:4]) cor.mat[lower.tri(cor.mat)] I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/3

Re: [R] Selective subsetting

A=matrix(1:9,3) A[lower.tri(A)] b On Nov 10, 2006, at 4:50 PM, Davendra Sohal wrote: > Hi all, > Here's an interesting (for me, at least!) problem I came across: > I have a correlation matrix, let's say with 6 variables, A to F, as > column > headings and the same 6 as row headings. > The matr

[R] Position as professor of statistics availabe

Dear R community, The Department of Statistics, Umeå University, Sweden, is searching for a Professor of Statistics (deadline December 7, 2006). We would appreciate applications from people on this list! More information is available at http://www.stat.umu.se/index_eng.shtml Welcome with your app

[R] Selective subsetting

Hi all, Here's an interesting (for me, at least!) problem I came across: I have a correlation matrix, let's say with 6 variables, A to F, as column headings and the same 6 as row headings. The matrix is filled with correlation coefficients. Therefore, the diagonal is all 1's, and each of the two tr

[R] history in Mac

Hi, my "history" in Mac for R does not work. I found the solution is GNU readline and re-installation from source. is there any other way to solve this? i really do not want to re-install: which means I need to install many packages, blabla... i used to use JGR (which solved that problem) but fou

Re: [R] lattice: histogram of factor variable

On 11/10/06, Albrecht, Dr. Stefan (AZ Private Equity Partner) <[EMAIL PROTECTED]> wrote: > Dear all, > > I am encountering a problem with lattice in the current version 0.14-13 > with R version 2.4.0 on a Windows XP system. > For example, > > histogram(~voice.part, singer) > > is not labeling the x

Re: [R] Meta-regression with lmer() ? If so, how ?

Wolfgang Vietchbauer wrote : > The dependent variable to be used with the mima function can be any > measure for which we have a known sampling variance (or approximately > so) and that is (approximately) normally distributed. So, the > dependent variable could be log odds ratios, log risk ratios,

[R] Variable limit in nlm?

Admittedly I am using an old version 1.7.1, but can anyone tell if this is or was a problem. I can only get nlm (nonlinear minimization) to adjust the first three components of function variable. No gradient or hessian is supplied. E.G.; fnoise function(y) { y[5]/(y[4]*sp2) * exp(-((x[,3]-y[1]-

Re: [R] Making a case for using R in Academia

I am just joining this thread. Regarding a tendency of journals to lock out the use of particular packages, there are rumours that SAS proc mixed has to be used for particular things. I wonder if whether R might displace SAS or proc mixed in such a role could depend on wether there the QA

Re: [R] Making a case for using R in Academia

As a student, I'll throw my two cents into this discussion. To preface my opinion, I am in a Joint Ph.D. program in Quantitative Psychology and Computer Science; I have a significant programming background and use R (or custom-built software that relies on R in some way) for the majority o

Re: [R] Making a case for using R in Academia

On Wed, Nov 08, 2006 at 09:24:38PM -0500, Charilaos Skiadas wrote: Hi Charilaos, > I would particularly like to hear from people who were not "hard-core > programmers" before taking up R, so perhaps had originally some > difficulties with it. How hard was it, and how quickly did it start >

Re: [R] Rpad

Tom, I've just downloaded Rpad_1.1.1.tar.gz file from CRAN and I can assure you that those files are ** ALL** missing in it . Ciao Vittorio Alle 16:35, venerdì 10 novembre 2006, tshort ha scritto: > Vittorio, > > Those files being missing is what's causing the errors. Try recopying them > to y

Re: [R] Problem with as.data.frame when an extra attribute is present

Prof Brian Ripley wrote: > It's quite intentional, as it is the documented behaviour of data.frame: > > Objects passed to 'data.frame' should have the same number of > rows, but atomic vectors, factors and character vectors protected > by 'I' will be recycled a whole number of times

Re: [R] Simplifying Sweave graphics

On Fri, 10 Nov 2006, ONKELINX, Thierry wrote: > Dear all, > > > > I was wondering if it's possible to simplify graphs created with Sweave. > I'm using in a document several plots with each about 4000 points > (qqnorm(rnorm(4000))). It looks likes the information of each points is > maintained in t

Re: [R] Problems with plot and X11 in ubuntu

That is, of course, an option. I didn't know his level of familiarity with those things so I answered his question simply. Regards, Mon On 11/10/06, Scionforbai <[EMAIL PROTECTED]> wrote: > > > Change those occurrences in the config file, reboot and that should fix > it. > > Why reboot? Rebuildin

Re: [R] Making a case for using R in Academia

On Fri, 10 Nov 2006, Jim Lemon wrote: > Charilaos Skiadas wrote: >> Not having a background in SPSS would put these students at a >> disadvantage." >> >> Is this really the case? Does anyone have any such statistics? >> > Unfortunately not statistics, but my experience in nearly every > (psycholog

Re: [R] Problems with plot and X11 in ubuntu

> Change those occurrences in the config file, reboot and that should fix it. Why reboot? Rebuilding the font-cache and restart X is *largely* enough! Marco __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

[R] lattice: histogram of factor variable

Dear all, I am encountering a problem with lattice in the current version 0.14-13 with R version 2.4.0 on a Windows XP system. For example, histogram(~voice.part, singer) is not labeling the x labels according to the factor levels of voice.part, which it should do (and has done in former vers

Re: [R] Question about error message - or is it a bug?

Carmen Meier said the following on 11/10/2006 9:46 AM: > Hi to all ... the same code, but another question. > > I changed only the type='n' to type='l' and debugged the function xy.coords. > with type = 'l' : > there are the correct values of x and y inside the function xy.coords > but the y valu

Re: [R] Problems with plot and X11 in ubuntu

Davide, It looks to be an issue in the /etc/X11/xorg.conf file of Edgy. The paths to the X11 fonts are wrong, you've got to change them to the right one. I'm not in my Ubuntu box, but I think the part of the Font paths should have been /usr/share/fonts/X11 and it was /usr/share/X11/fonts in the co

Re: [R] axis command and excel time format

You should look at ?plot.default ?times You need to supply an x vector (time) along with a y value vector of the same length. Your error message tells you that you vectors were not of equal length. You are repeatedly supplying different length vectors. times() takes a text vector and translate

Re: [R] Rpad

Vittorio, Those files being missing is what's causing the errors. Try recopying them to your server home location. Those files should be under Rpad/basehtml/gui/* in your R library installation. If not, try reinstalling or extract the necessary files right out of the Rpad_1.1.1.tar.gz file. - T

Re: [R] Problems with plot and X11 in ubuntu

A few questions before I may help. Is this a NEW installation or an upgrade? If an upgrade, what version are you upgrading from? Regards, Oscar >From: Bagatti Davide <[EMAIL PROTECTED]> >Date: 2006/11/10 Fri AM 09:22:24 CST >To: r-help@stat.math.ethz.ch >Subject: [R] Problems with plot and X1

[R] Can plot(augPred()) be used with objects that are not groupedData?

Dear Friends, Is there a workaround to this problem or must the object plotted by plot(augPred(object, ...)) be a grouped object? score <- c(108, 103, 96, 84, 118, 110, 129, 90, 84, 96, 105, 113, 96, 117, 107, 85, 125, 107, 128, 84, 104, 100, 114, 117, 110, 127, 106, 92, 125, 96, 123,

Re: [R] Which genetic optimization package allows customized crossover and mutation operation

On 10 November 2006 at 16:19, sun wrote: | No, I am not familiar with that project, actually never heard it before your | reply.:) | | Anyway, I found some code later on from "Claudio Agostinelli" who developed | this code for his teaching, I think. Unfortornuitly, his code does not work | on

Re: [R] Confidence interval for relative risk

Hello, A common way to calculate the CI for a relative risk is the following. Given a 2x2 table of the form: a b c d the log of the risk ratio is given by: lrr = log[ a/(a+b) / ( c/(c+d) ) ] which is asymptotically normal with variance: vlrr = 1/a - 1/(a+b) + 1/c - 1/(c+d). So an approximat

[R] Speed Optimization: Faster Way of Accessing data.frame in a Loop?

Hello, currently I am using code, which basically works like this: | | for (i in 1:20) { | for (j in 1:30) { | df[i, j, 20] <- df[i,j,27] + df[i,j,30] | } | } df is: `data.frame: 360 obs. of 30 variables' Do you have any ideas whether I could get this code any faster? Regards, Sven

[R] Question about error message - or is it a bug?

Hi to all ... the same code, but another question. I changed only the type='n' to type='l' and debugged the function xy.coords. with type = 'l' : there are the correct values of x and y inside the function xy.coords but the y value is filled with NA seems that the length is matching now because o

[R] Announcement: sciplot (includes functions for graphs w/ error bars)

The package "sciplot" is now available for download from CRAN. This package includes a collection of functions that create graphs with error bars for data collected from one-way or higher factorial designs, as well as a function to plot bifurcation diagrams resulting from analysis with XPPAUTO. The

[R] Problems with plot and X11 in ubuntu

Hello, I am an italian student, who is trying to use R 2.3.1 with Ubuntu 6.10 (last version). When I try to use the plot command, I get the error: "could not find any X11 fonts Check that the Font Path is correct" How can I solve this problem? Thank you very much Davide [[alternative

Re: [R] Which genetic optimization package allows customized crossover and mutation operation

No, I am not familiar with that project, actually never heard it before your reply.:) Anyway, I found some code later on from "Claudio Agostinelli" who developed this code for his teaching, I think. Unfortornuitly, his code does not work on my settings. And I do not want to send much time on th

[R] Confidence interval for relative risk

The concrete problem is that I am refereeing a paper where a confidence interval is presented for the risk ratio and I do not find it credible. I show below my attempts to do this in R. The example is slightly changed from the authors'. I can obtain a confidence interval for the odds ratio from fi

[R] Rpad

I've just compiled and installed Rpad from the sources under *nix (freeBSD 6.1) and R 2.4.0, and followed the suggested procedure to setup an Rpad server step by step. Now when I try to execute whatever .Rpad example file the IE browser hangs endlessly with a "loading page" pop-up and the fol

[R] help with nlme function

Hello. I am trying to fit a nonlinear mixed model involving 3 parameters. I have successfully made a self-starting function. getInitial() correctly outputs the initial estimates. I can also use the nlsList with this function to get the separate nonlinear fits by group. However, I get an error m

Re: [R] Problem with as.data.frame when an extra attribute is present

It's quite intentional, as it is the documented behaviour of data.frame: Objects passed to 'data.frame' should have the same number of rows, but atomic vectors, factors and character vectors protected by 'I' will be recycled a whole number of times if necessary. > data.frame(a =

Re: [R] Making a case for using R in Academia

More impressions -- > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of > Charilaos Skiadas > Sent: Thursday, November 09, 2006 11:45 PM > To: r-help@stat.math.ethz.ch > Subject: Re: [R] Making a case for using R in Academia > > John (and everyone els

Re: [R] Combining factors

Rainer M Krug <[EMAIL PROTECTED]> writes: > Hi > > I know this is a basic question and I know I have done it before but I > can't find the answer any more. > > I have a data set, say: > > F1, F2, Value > > F1 and F2 are Factors. > > I would like to plot > > plot(TheCombinationOf(F1, F2), Va

Re: [R] Combining factors

Peter Dalgaard wrote: > Rainer M Krug <[EMAIL PROTECTED]> writes: > >> Hi >> >> I know this is a basic question and I know I have done it before but I >> can't find the answer any more. >> >> I have a data set, say: >> >> F1, F2, Value >> >> F1 and F2 are Factors. >> >> I would like to plot >> >>

Re: [R] Simplifying Sweave graphics

Hi. One guy of my team (Thibaut Jombart) wrote a driver to sweave in png (see http://tolstoy.newcastle.edu.au/R/devel/06/03/4599.html). The driver works very nice and is very useful for plots with many points, raster images... I thought that Friedrich Leisch would include it in the Sweave distr

[R] missing symbols for mathplot

Hi all, I'm trying to write an axis label that sounds P( X | K and Xb ) (probability of X given K and Xb ) but I need the intersection symbol (the "\cap" in latex) Actually I did'nt find any "cap" symbol in plotmath, the only one is intersect(A[i],i==1,n) but is not my case because subscript

[R] Combining factors

Hi I know this is a basic question and I know I have done it before but I can't find the answer any more. I have a data set, say: F1, F2, Value F1 and F2 are Factors. I would like to plot plot(TheCombinationOf(F1, F2), Value) I remember there was a function for TheCombinationOf() but I don'

Re: [R] Making a case for using R in Academia

Our first-year graduate statistics course (in psychology) is taught by Prof. Paul Rosenbaum, in the statistics department. Last year (according to my students), he discouraged students from using R for their homework. He told them it was too hard. Now he is again teaching the course, recommending

[R] Simplifying Sweave graphics

Dear all, I was wondering if it's possible to simplify graphs created with Sweave. I'm using in a document several plots with each about 4000 points (qqnorm(rnorm(4000))). It looks likes the information of each points is maintained in the graph. As a result of that the pdf filesize get's quite

Re: [R] axis command and excel time format

> > > Carmen, > > Gabor has already given you the detail you ask for, but might try the > following plot to see what is going wrong: > > plot(times(tt), x, type='l') > > This does not give you the EXACT control of the axis you asked for, > but this simple plot command gives you a fairly nice resu

Re: [R] Making a case for using R in Academia

Charilaos Skiadas wrote: > As a addendum to all this, this is one of the responses I got from > one of my colleagues: > > "The problem with R is that our students in many social science > fields, are expected to know SPSS when they go to graduate school. > Not having a background in SPSS wo

Re: [R] Command Line Prompt Symbol

On 11/10/2006 1:46 AM, [EMAIL PROTECTED] wrote: > The simplest way to do this is to put > > options(prompt = "R> ") > > in your .Rprofile file. If you don't have an .Rprofile file, > then persuading Windows to let you call a file by that name can > be frustrating. The easiest way is probabl

Re: [R] Meta-regression with lmer() ? If so, how ?

I guess I'll chip in, since I wrote that function (which is going to be updated thoroughly in the near future -- I will probably expand it to an entire package). > > Have a look at "MiMa" at Wolfgang Viechtbauer's page. Is that what > > you are looking for? > > > >

Re: [R] About using the boot function

Joaquim, you have to write your own function that takes the data and the index, which is passed to it by boot(). try this ... x2 <- c(2, 3, 4, 5, 6, 5, 4, 5, 6, 5, 4, 5, 6, 5, 7, 2, 3, 4, 3, 4, 3, 5, 6, 7, 5) mean.boot <- function(x, i) mean(x[i]) b1 <-boot(x2, mean.boot, 999) b1

[R] About using the boot function

Dear All, I tried to use the boot function, provided in the boot package, in such a simple task as to create a bootstrap distribution of the mean of a vector x. I wrote: b <- boot(x, mean, R=200) Well, it doesn't work. I suspect it has something to do with what is called "second argument" of the

[R] Value at Risk historical simulation

Hi Has someone got a package/script at hand to do a historical simulation to calculate the Value at Risk? If your not sure what Historical Simulation is: In simple terms, Historical Simulation (HS) is just taking sample percentiles over a moving sample. Suppose we want to use HS to predict a port

Re: [R] PCA reconstruction funtion

Also new values can be easy calculated from prcomp object: Data <- scale(iris[,1:4],center=TRUE,scale=TRUE) iris.pc <- prcomp(Data) # Explained variation (iris.pc$sdev^2/sum(iris.pc$sdev^2))*100 # Loadings iric.pc$rotation #Scores iris.pc$x #Fitted Values for each PC # Xfit = T*P^t PCfit <-

Re: [R] dissimilarity matrices

On Thu, 2006-11-09 at 17:50 +, Kris Lockyear wrote: > Dear All, > > I have a dissimilarity matrix which I happily convert to a distance object > by running: > > X <- as.dist(Y) > > and I can happily now run either hclust(X) or agnes(X). > > So that the various bits of output are labelled c