Re: [R] Interrupt R?

On Sun, 11 Jul 2010, Spencer Graves wrote: Hi, Richard and Duncan: Thank you both very much. You provided different but workable solutions. 1. With Rgui 2.11.1 on Vista x64, the escape worked, but neither ctrl-c nor ctrl-C worked for me. Why did you expect them too? C

Re: [R] cbind in for loops

Hi, Assuming that you have read the files into R, and that their names (in R) are held in some object (e.g., 'file2'), then this works do.call(what = cbind, args = mget(x = file2, envir = .GlobalEnv) Here is a reproducible example: x1 <- data.frame(x = 1:10) x2 <- data.frame(y = 1:10) file.name

Re: [R] boxplot on all the columns

Actually, boxplot (bhtest1) Should do what you want... Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (Eng

Re: [R] Is there a "Mixed effect model" for regression/classification trees?

Hello Achim, Thank you very much, this looks exactly like what I was looking for. (p.s: Their presentation here Is most helpful) Best, Tal Contact Details:--- C

Re: [R] problem with comparisons for vectors

This is also mentioned in FAQ 7.31 http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f Also if you search the R-help archives for 'precision' you can find a lot of threads discussing the issue in further depth. On Sun, Jul 11, 2010 at 9:02 PM, Wu Gon

[R] boxplot on all the columns

how to use boxplot on all the columns from he date frame instead of manually entering the columns like below bhtest1 <- read.table("bhtest1.txt", header=TRUE) boxplot (bhtest1[,2], bhtest1[,3], bhtest1[, 4], bhtest1[,5], bhtest1[,6], bhtest1[,7]) please help, Thanks, -- View this mes

Re: [R] make an model object (e.g. nlme) available in a user defined function (xyplot related)

On Mon, Jul 12, 2010 at 2:51 AM, Jun Shen wrote: > Dear all, > > When I construct an nlme model object by calling nlme(...)->mod.nlme, > this object can be used in xyplot(). Something like > > xyplot(x,y,.. > .. > ind.predict<-predict(mod.nlme) > .. > ) is working fine in console envir

[R] cbind in for loops

I have 30 files in the current directories, i would like to perform the cbind(fil1,file2,file3,file4file30) how could i do this in a for loop: such as: file2 <- list.files(pattern=".out3$") for (j in file2) { cbind(j)...how to implement cbind here } Thanks.

[R] long to wide on larger data set

I have a data set that has 4 columns and 53860858 rows. I was able to read this into R with: cc <- rep("character",4) myData <- read.table("myData.csv",header=FALSE,skip=1,colClasses=cc,nrow=53860858,sep=",") I need to reshape this data from long to wide. On a small data set the following lines

Re: [R] RSQLite install R x86_64 fail

On Sun, Jul 11, 2010 at 4:25 PM, David Ruau wrote: > Hi Seth, > > Thanks for the answer. > I have install R using macport (since many years now). It compile R from > source using gcc 4.4 by default. But I don't think this is the problem > because I manage to install many other package that do no

[R] Marking the tail of a distribution (was (no subject))

Here is a way: ### x <- sort(c(seq(-4, 4, length=100), 1.96)) hx <- dnorm(x) par(pty="s") plot(x, hx, type="l", xlab="z value", ylab="Density", main="density of N(0,1)") abline(v=1.96, col="red") abline(h = 0) top <- x >= 1.96 tail <- rbind(cbind(x[top], hx[top]), c(4, 0), c(1.96, 0)) polygon(t

Re: [R] problem with comparisons for vectors

I don't know the real reason, but help("==") gives some clues. For numerical and complex values, remember == and != do not allow for the finite representation of fractions, nor for rounding error. Using all.equal with identical is almost always preferable. See the examples. x1 <- 0.5 - 0.3 x2

Re: [R] (no subject)

You need three more lines of code abline(h=0) xx <- seq(1.96, 4, length=25) polygon(x=c(xx[1],xx,xx[25]), y=c(0,dnorm(xx),0), col='red') Please see the normal.and.t.dist function in the HH package for more detailed control of the graph. ## install.packages("HH") ## if you don't have it yet

Re: [R] (no subject)

On Sun, 11 Jul 2010, li li wrote: Hi all, I want to add the red color under the standard normal curve to the right of 1.96. Can anyone give me a hand? Please see the code below. Thank you. x <- seq(-4, 4, length=100) hx <- dnorm(x) par(pty="s") plot(x, hx, type="l", xlab="z value", ylab="

Re: [R] The formula interface of SVM

Hi, On Sun, Jul 11, 2010 at 7:11 PM, Amy Hessen wrote: > > Hi > Could you please explain the line that I got from the documentation of R? > does it mean that there is a difference between using  and not using the > formula interface with SVM ?: > If the predictor variables include factors, the

[R] (no subject)

Hi all, I want to add the red color under the standard normal curve to the right of 1.96. Can anyone give me a hand? Please see the code below. Thank you. x <- seq(-4, 4, length=100) hx <- dnorm(x) par(pty="s") plot(x, hx, type="l", xlab="z value", ylab="Density", main="density of N(0,1)"

[R] The formula interface of SVM

Hi Could you please explain the line that I got from the documentation of R? does it mean that there is a difference between using and not using the formula interface with SVM ?: If the predictor variables include factors, the formula interface must be used to get a correct model matrix.

Re: [R] Not nice behaviour of nlminb (windows 32 bit, version 2.11.1)

I guess it is ok, but then a warning should be added, when describing the `abs.tol' parameter in the help file to state that changing it may result in premature stopping when f(x*) = 0. Regards, Ravi. Ravi Varadhan, Ph.D. A

Re: [R] RSQLite install R x86_64 fail

Hi Seth, Thanks for the answer. I have install R using macport (since many years now). It compile R from source using gcc 4.4 by default. But I don't think this is the problem because I manage to install many other package that do not need RSQLite. The configure options for the macport port are

Re: [R] Compress string memCompress/Decompress

On Sun, Jul 11, 2010 at 11:31 AM, Matt Shotwell wrote: > On Fri, 2010-07-09 at 20:02 -0400, Erik Wright wrote: >> Hi Matt, >> >> This works great, thanks! >> >> At first I got an error message saying BLOB is not implemented in RSQLite.   >> When I updated to the latest version it worked. > > SQLit

Re: [R] RSQLite install R x86_64 fail

Hi David, On Sun, Jul 11, 2010 at 12:27 PM, David Ruau wrote: > On a fresh install of R on mac os x 10.6.4 (snow leopard) RSQLite > did not install while running biocLite() How did you install R? > $ R > biocLite("RSQLite") > Using R version 2.11.1, biocinstall version 2.6.7. > Installing Bioc

Re: [R] Not nice behaviour of nlminb (windows 32 bit, version 2.11.1)

On 11/07/2010 10:22 AM, Ravi Varadhan wrote: Hi, I am ok with setting abs.tol=0. Here is an nlminb.patch that has this. There is just one line of code that has been added: control$abs.tol <- 0 I have commented where this change happens. I am sorry if I was not being clear. I just wante

Re: [R] Is there a "Mixed effect model" for regression/classification trees?

On Sun, 11 Jul 2010, Tal Galili wrote: Hello all, This is more a statistical question then an R question, but I am sure it will have an R interpretation to it. If I wish to predict an outcome based on some potential features, I could (in some cases) use either regression or regression-tree. Ho

[R] make an model object (e.g. nlme) available in a user defined function (xyplot related)

Dear all, When I construct an nlme model object by calling nlme(...)->mod.nlme, this object can be used in xyplot(). Something like xyplot(x,y,.. .. ind.predict<-predict(mod.nlme) .. ) is working fine in console environment. But the same structure is not working in a user defined fun

[R] Is there a "Mixed effect model" for regression/classification trees?

Hello all, This is more a statistical question then an R question, but I am sure it will have an R interpretation to it. If I wish to predict an outcome based on some potential features, I could (in some cases) use either regression or regression-tree. However, if my observations are divided to g

Re: [R] Interrupt R?

Hi, Richard and Duncan: Thank you both very much. You provided different but workable solutions. 1. With Rgui 2.11.1 on Vista x64, the escape worked, but neither ctrl-c nor ctrl-C worked for me. 2. The TCLTK version works but seems to require either more

Re: [R] data export HELP!

Not necessarily the best way if your dataframe will get large, but it should work: parameters <- NULL # where you will collect the result for(j in 1:dim(r)[2]){ indiv=r[,j][which(r[,j]>-1)] #removes -1 growth data age.1=age[1:length(indiv)] length.ind=data.frame(age.1,indiv,

Re: [R] eval and assign in loop problem

On Fri, 09-Jul-2010 at 08:25AM -0700, S.Nicholas wrote: |> deaR useRs, |> |> I am trying to assign different values to different objects in a for loop. |> The following is a toy example of the part that has been giving me a hard |> time. |> |> The first "for loop" generates four objects, b0, b1,

[R] data export HELP!

Hello! So, this is going to seem like a very simple question - I am quite new to R and am having some trouble figuring out little nuances: I am running a loop that goes through my data and performs a nls parameter estimation on each data set. At the end of the loop, I would like to collect the p

[R] RSQLite install R x86_64 fail

Hi, On a fresh install of R on mac os x 10.6.4 (snow leopard) RSQLite did not install while running biocLite() $ R R version 2.11.1 (2010-05-31) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 [...] Loading required package: utils BioC_mirror = http://www.biocond

Re: [R] Interrupt R?

On 11/07/2010 2:29 PM, Spencer Graves wrote: How can one interrupt the following gracefully: while(TRUE){ Sys.sleep(1) } In R2.11.1 under Emacs+ESS, some sequence of ctrl-g, ctrl-c eventually worked for me. Under Rgui 2.11.1, the only way I've found was to kill R.

Re: [R] Interrupt R?

Use the timer in tcl. See this email from Phillipe Grosjean with details. https://stat.ethz.ch/pipermail/r-help/2009-July/203151.html Rich [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/

Re: [R] Fast string comparison

Ralf B wrote: > > What is the fastest way to compare two strings in R? > > Ralf > Which way is not fast enough? In other words, are you asking this question because profiling showed one of R's string comparison operations is causing a massive bottleneck in your code? If so, which one and how

Re: [R] F# vs. R

Sergey Goriatchev wrote: > > Hello, Marc > > No, I do not want to validate Cox PH. :-) > I do use R daily, though right now I do not use the statistical part that > much. > > I just generally wonder if any R-user tried F# and his/her opinions. > > Regards, > Sergey > In my work as a program

Re: [R] Compress string memCompress/Decompress

On Fri, 2010-07-09 at 20:02 -0400, Erik Wright wrote: > Hi Matt, > > This works great, thanks! > > At first I got an error message saying BLOB is not implemented in RSQLite. > When I updated to the latest version it worked. SQLite began to support BLOBs from version 3.0. > > Is there any rea

[R] Interrupt R?

How can one interrupt the following gracefully: while(TRUE){ Sys.sleep(1) } In R2.11.1 under Emacs+ESS, some sequence of ctrl-g, ctrl-c eventually worked for me. Under Rgui 2.11.1, the only way I've found was to kill R. Suggestions on something more graceful?

Re: [R] Durban Watson statistics

On Sun, 11 Jul 2010, Leigh E. Lommen wrote: I would like to do the Durban-Watson test on a time series of log returns. 2 questions: 1) If I am just trying to find out if there is serial correlation, what do I do for the residuals? there is no model, so do I just use the log retu

Re: [R] Inserting an image into a PDF file

On Jul 11, 2010, at 10:51 AM, David Winsemius wrote: > > On Jul 11, 2010, at 11:06 AM, Dennis Fisher wrote: > >> Colleagues, >> >> I am creating a PDF document from R using pdf(), the document contains text >> / images created with R. I also have an image in either PDF / TIFF / JPEG >> forma

Re: [R] F# vs. R

On Wed, 07 Jul 2010 14:34:05 -0300 Bernardo Rangel Tura wrote: > F# is public, but is not open source. > > F# run in windows but run in AIX, linux, MAC, UNIX etc? > > Compiled code should run faster than R, but is precise? > > Compiled code should run faster than R, but is reliable? > > Comp

Re: [R] Inserting an image into a PDF file

On Jul 11, 2010, at 11:06 AM, Dennis Fisher wrote: Colleagues, I am creating a PDF document from R using pdf(), the document contains text / images created with R. I also have an image in either PDF / TIFF / JPEG format (in this case, a scanned image saved as a file). I would like to

[R] Durban Watson statistics

I would like to do the Durban-Watson test on a time series of log returns. 2 questions: 1) If I am just trying to find out if there is serial correlation, what do I do for the residuals? there is no model, so do I just use the log returns (time series) itself? 2) what is the code in R t

[R] Inserting an image into a PDF file

Colleagues, I am creating a PDF document from R using pdf(), the document contains text / images created with R. I also have an image in either PDF / TIFF / JPEG format (in this case, a scanned image saved as a file). I would like to insert the image into the PDF file. Any ideas on how to

Re: [R] Not nice behaviour of nlminb (windows 32 bit, version 2.11.1)

Hi, I am ok with setting abs.tol=0. Here is an nlminb.patch that has this. There is just one line of code that has been added: control$abs.tol <- 0 I have commented where this change happens. I am sorry if I was not being clear. I just wanted to have the authors to also have a look at t

Re: [R] a very particular plot

Hi Ian, Have a look at the examples in http://had.co.nz/ggplot2/geom_tile.html for some ideas on how to do this with ggplot2. Hadley On Sat, Jul 10, 2010 at 8:10 PM, Ian Bentley wrote: > Hi all, > > Thanks for the really great help I've received on this board in the past. > > I have a very part

Re: [R] Fast string comparison

== ? Hadley On Sun, Jul 11, 2010 at 2:08 PM, Ralf B wrote: > What is the fastest way to compare two strings in R? > > Ralf > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http

[R] Fast string comparison

What is the fastest way to compare two strings in R? Ralf __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self

Re: [R] Not nice behaviour of nlminb (windows 32 bit, version, 2.11.1)

On 10/07/2010 9:48 AM, Prof. John C Nash wrote: I won't add to the quite long discussion about the vagaries of nlminb, but will note that over a long period of software work in this optimization area I've found a number of programs and packages that do strange things when the objective is a func

Re: [R] Not nice behaviour of nlminb (windows 32 bit, version 2.11.1)

On 11/07/2010 5:00 AM, Matthew Killeya wrote: Thanks. Seems to me the easiest sensible fix might be to change the default abs.tol=0 in R and add a warning in the help files? That was exactly my suggestion in the message to which Ravi was replying, but he apparently has doubts. Duncan Murd

Re: [R] Not nice behaviour of nlminb (windows 32 bit, version 2.11.1)

Thanks. Seems to me the easiest sensible fix might be to change the default abs.tol=0 in R and add a warning in the help files? Matt On 11 July 2010 01:41, Duncan Murdoch wrote: > On 10/07/2010 7:32 PM, Ravi Varadhan wrote: > >> Hi, >> >> The best solution would be to identify where the problem

Re: [R] getting data from table command

Thanks very much :). On Sat, Jul 10, 2010 at 10:02 PM, jim holtman wrote: > Is this what you want: > > > x <- c(1,2,2,2,3,3,3,4,4,5) > > z <- table(x) > > z > x > 1 2 3 4 5 > 1 3 3 2 1 > > as.integer(rep(names(z), z)) > [1] 1 2 2 2 3 3 3 4 4 5 > > > > > On Sat, Jul 10, 2010 at 10:55 AM, nn roh

Re: [R] Using Ubuntu as a Server

Hi Leandro, On 07/10/2010 08:46 PM, Leandro Marino wrote: I want to know how can I configure R in a Ubuntu to be a server. I am planning to use R in a Windows machine with Tinn-R, but I want R running at an Ubuntu Lucid machine. How can i do this? One possibility is to use Eclipse/StatET on

Re: [R] simple apply syntax

On Sun, 11 Jul 2010, Robin Jeffries wrote: I know this is a simple question, but I have yet to master the apply statements. Any help would be appreciated. You don't want to use apply() here: rbinom is vectorized. However, you cannot use mat$x on a matrix, and the cbind() gave you a matrix an

Re: [R] simple apply syntax

Hello Robin, I cannot quite figure out what your final goal is (it's late and I'm low on caffeine so if I missed the obvious, bear with me). I think you may mean the rbinom() function rather than the binomial() function (see ?rbinom and ?binomial, respectively). At any rate, this should get you

[R] simple apply syntax

I know this is a simple question, but I have yet to master the apply statements. Any help would be appreciated. I have a column of probabilities and sample sizes, I would like to create a column of binomial random variables using those corresponding probabilities. Eg. mat = as.matrix(cbi