Re: [R] question about glm vs. loglin()

2011-09-16 Thread Rolf Turner
On 17/09/11 01:19, Michael Friendly wrote: Trying to interpret associations in complex loglinear models from tables of parameter estimates is like trying to extract sunlight from a cucumber. You have to squeeze very hard, and then are usually unhappy with the quality of the sunlight. For

Re: [R] Move the x label to the top of an lattice plot

2011-09-16 Thread David Winsemius
On Sep 16, 2011, at 7:47 PM, markm0705 wrote: Dear R helpers With some help from R-help I've moved the x-scale to the top of a lattice plot using...'alternating' scales = list(x = list(log = 10),alternating=2), but now I cannot seem to find a way to move the x-axis label t

Re: [R] Question about permutation test

2011-09-16 Thread csrabak
Hope you don't find this a rethorical question, but why did you prefer to "google" the function instead of reading the fine manual? Em 16/9/2011 16:07, song_gpqg escreveu: Hi! I am doing a permutation test on 7 data randomly selected into two groups, one has 4 and the other 3. The purpose is t

Re: [R] Problem with memory consuming algorithm

2011-09-16 Thread jim holtman
The first thing I would do, especially before letting it run for 48 hours, is to take a small subset of the data and run it with the profiler (Rprof) enable to see where time is being spent. I would also put some print statements in the main loop to periodically output the amount of CPU and memory

Re: [R] R shell line width

2011-09-16 Thread Joshua Wiley
Hi Mike, Look at ?options particularly something like: options(width = 120) 80 is the default, I believe. On 1920 pixels I can comfortably get around 220 (depending on the overhead of the program, full screen, etc.). I imagine it would also be possible to run into limitations from the termina

Re: [R] R shell line width

2011-09-16 Thread Justin Haynes
you want options(width= ) you can edit your .Rprofile file and the .First function in there to set it when you start R or in the console interactively On Fri, Sep 16, 2011 at 12:48 PM, Mike P wrote: > Hi, > > I want to apologize in advance if this has already been asked. I > wasn't able to fin

[R] Move the x label to the top of an lattice plot

2011-09-16 Thread markm0705
Dear R helpers With some help from R-help I've moved the x-scale to the top of a lattice plot using...'alternating' scales = list(x = list(log = 10),alternating=2), but now I cannot seem to find a way to move the x-axis label to the top ? Thanks -- View this message in contex

[R] Problem with memory consuming algorithm

2011-09-16 Thread Simon Zehnder
Hi guyz, I have serious problems with an algorithm I let run on a supercomputer: You find the functions under the following URLs: simuFunctionCaller: http://pastebin.com/6gw2fJFb calls Function simuFunctionNBM (http://pastebin.com/QeJDUnqx) after reading a csv-file ordered like the following:

[R] SVM model_combination of different vairables issues

2011-09-16 Thread yadav
I am trying to build a classifier using SVM and I have 23 independent variables and 1 response. I want to check the classification ac curacies of each independent variables. I did this without any problem. Now, I want to check the all possible combinations for any two variables using following sc

[R] How to find regions enclosed by edges within a TIF image

2011-09-16 Thread Waichler, Scott R
I am processing grayscale TIF images that represent X-rays of a sand- and gravel-filled tube. Each image represents a plane through the porous medium, and I need to classify each pixel in the image as void or solid. For the most part, voids are dark and solids are bright, but there are many gr

[R] Question about permutation test

2011-09-16 Thread song_gpqg
Hi! I am doing a permutation test on 7 data randomly selected into two groups, one has 4 and the other 3. The purpose is to list all the 35 possible outcomes and calculate p-value. I googled the function perm.test() and not sure if my usage is correct. So I set a=c(7 data), b=(1,1,1,1,2,2,2) which

Re: [R] R functions

2011-09-16 Thread sujitha
Hi, Thanks for your reply. I converted using your idea and since I have big file I thought reading as a table would help. This is just snippet of my data. I have around 150 samples so wrting s in that form would be tedious. >m<-read.table("test.txt",sep='\t',header=TRUE,colClasses=c('character','in

Re: [R] loaded Rcmdr but BiodiversityRGUI () not recognizing it

2011-09-16 Thread SG
Below is the message from the R workspace. I have installed the BiodiversityR and rmcdr How do I get to BiodiversityR GUI ? Thanks, Shreya [Missouri S&T] Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > loca

[R] R shell line width

2011-09-16 Thread Mike P
Hi, I want to apologize in advance if this has already been asked. I wasn't able to find any information, either on google or from local list search. I'm running an R shell from a linux command line, in an xterm window. Whenever I print a data frame, only the first couple of columns are printed s

Re: [R] Help writing basic loop

2011-09-16 Thread MacQueen, Don
Just a minor aside; I would have done my.slopes <- numeric(100) Note that: > class(numeric(5)) [1] "numeric" -Don -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062 On 9/16/11 12:37 PM, "Luke Miller" wrote: >Create an output

Re: [R] Problematic If-Else statement

2011-09-16 Thread MacQueen, Don
It's probably not a sensible thing to do, but I'm going to guess. With a name like "days_to_tumor_recurrence", I might expect numeric (integer) values. But "null" and numeric don't mix. as.numeric(c('24','null',23')) will return 24, NA, 23. There may have been such a conversion in the preparatio

Re: [R] Returning the name of an object passed directly or from a list by lapply

2011-09-16 Thread Peter Ehlers
On 2011-09-16 16:27, andrewH wrote: Dear Bill-- Wow. This is very clever and I learned a lot from it. I've never seen the ...() trick before, and on a Google code search, I could not find anyone else who had used it. And I've never used the "..." feature, which, BTW, though mentioned in every int

Re: [R] Returning the name of an object passed directly or from a list by lapply

2011-09-16 Thread andrewH
Dear Bill-- Wow. This is very clever and I learned a lot from it. I've never seen the ...() trick before, and on a Google code search, I could not find anyone else who had used it. And I've never used the "..." feature, which, BTW, though mentioned in every intro to R text, has no help page I can f

Re: [R] Help writing basic loop

2011-09-16 Thread R. Michael Weylandt
You can also do the regressions "in parallel" as follows: x = -25:25 y = 0.05*x^2 + 2* x - 4 y1 = y + rcauchy(51) y2 = y + rcauchy(51)^2 y3 = y/10 - 5 + rnorm(51) Y = cbind(y, y1, y2, y3) m = lm(Y~x) print(coef(m)) Hope this helps, Michael On Fri, Sep 16, 2011 at 3:37 PM, Luke Miller wrote:

Re: [R] parsing error when using R CMD check

2011-09-16 Thread Duncan Murdoch
On 11-09-16 4:48 PM, Tarca, Adi wrote: Hi all, I am trying to run R CMD check on a package which passes R CMD INSTALL. The check stops because of a parsing problem in the example of a given function at this line: return(res[res$ID %in% list$targetGeneSets,]) The code is ok, since it runs if I

Re: [R] download files using ftp: avoid error

2011-09-16 Thread Mary Kindall
wget worked for me. Thanks Willian and Rainer. -M On Fri, Sep 16, 2011 at 4:18 PM, William Dunlap wrote: > Wrap the call that may abort with try() or tryCatch(). > > Bill Dunlap > Spotfire, TIBCO Software > wdunlap tibco.com > > > -Original Message- > > From: r-help-boun...@r-project.or

[R] parsing error when using R CMD check

2011-09-16 Thread Tarca, Adi
Hi all, I am trying to run R CMD check on a package which passes R CMD INSTALL. The check stops because of a parsing problem in the example of a given function at this line: return(res[res$ID %in% list$targetGeneSets,]) The code is ok, since it runs if I paste it in R. Is this a known parsing i

Re: [R] download files using ftp: avoid error

2011-09-16 Thread William Dunlap
Wrap the call that may abort with try() or tryCatch(). Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On > Behalf Of Rainer > Schuermann > Sent: Friday, September 16, 2011 1:09 PM > T

Re: [R] download files using ftp: avoid error

2011-09-16 Thread Rainer Schuermann
I haven't tested it thoroughly but what worked here is replacing > download.file(url, destfile, quiet = FALSE) with sys_call <- paste( "wget", url, ">", destfile, sep=" " ) system( sys_call ) Program execution continues, whether or not the download from url was successful. However, wget is, I be

Re: [R] cannot load rjags package on Mac

2011-09-16 Thread David Winsemius
Already answered on the Mac mailing list. You are asked not to cross- post. On Sep 16, 2011, at 1:57 PM, Wei Wang wrote: Dear list, I ran into problem trying to load rjags on my Macbook Air running OS X 10.7.1. snip [[alternative HTML version deleted]] and you are asked to post in

Re: [R] Help writing basic loop

2011-09-16 Thread Luke Miller
Create an output vector to hold your slopes before starting the loop, then use your index i to place each new slope in the appropriate position in your vector. y1<-rnorm(100, mean=0.01, sd=0.001) y2<-rnorm(100, mean=0.1, sd=0.01) x<-(c(10,400)) my.slopes = vector("numeric",100) # initialize a

[R] Help writing basic loop

2011-09-16 Thread Beaulieu . Jake
Hello, I would like to write a loop to 1) run 100 linear regressions, and 2) compile the slopes of all regression into one vector. Sample input data are: y1<-rnorm(100, mean=0.01, sd=0.001) y2<-rnorm(100, mean=0.1, sd=0.01) x<-(c(10,400)) #I have gotten this far with the loop for (i in 1:10

Re: [R] problems to report indexes when I have two min value

2011-09-16 Thread Jeff Newmiller
Yes, you are confusing, because that is exactly what your original message had in it. --- Jeff Newmiller The . . Go Live... DCN: Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/B

[R] download files using ftp: avoid error

2011-09-16 Thread Mary Kindall
I am planning to download a large number of files from some website. I am using the following script. files2down = c('aaa', 'bbb', ) for (i in 1: len) { print(paste('downloading file', i, ' of total ', len)); url = paste(urlPrefix, files2down[i], sep='') destfile = paste (dest, 'in

[R] cannot load rjags package on Mac

2011-09-16 Thread Wei Wang
Dear list, I ran into problem trying to load rjags on my Macbook Air running OS X 10.7.1. I installed JAGS 3.1.0 through binary and it seems OK. $ jags Welcome to JAGS 3.1.0 on Fri Sep 16 13:27:03 2011 JAGS is free software and comes with ABSOLUTELY NO WARRANTY Loading module: basemod: ok L

Re: [R] substitute games with randomForest::partialPlot

2011-09-16 Thread Stephen Milborrow
Johann Hibschman wrote: I'm having trouble calling randomForest::partialPlot programmatically. It tries to use name of the (R) variable as the data column name. You may want to consider looking at plotmo (in the plotmo package) which doesn't have the above issue. library(randomForest) library

Re: [R] writing data from several matrices in R into one excel-file with several sheets

2011-09-16 Thread David Winsemius
On Sep 16, 2011, at 11:18 AM, Marion Wenty wrote: hello, does anyone know how I can write several matrices from R into one exel-file using different sheets for the different matrices? You should describe what sort of searching efforts you have attempted. When I use what I think are the

Re: [R] writing data from several matrices in R into one excel-file with several sheets

2011-09-16 Thread Greg Snow
Look at the XLConnect package. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of Marion Wenty > Sent: Friday, S

Re: [R] writing data from several matrices in R into one excel-file with several sheets

2011-09-16 Thread jim holtman
Try the XLConnect package. On Fri, Sep 16, 2011 at 11:18 AM, Marion Wenty wrote: > hello, > > does anyone know how I can write several matrices from R into one exel-file > using different sheets for the different matrices? > > thank you very much in advance for your help. > > Marion > >        [[

Re: [R] problems to report indexes when I have two min value

2011-09-16 Thread marlene marchena
Thanks Jim, That is exactly what I was looking for. Marlene 2011/9/16 jim holtman > Will this work for you: > > > dat <- > + > matrix(c(5.4,4.8,5.6,4.8,NA,4.4,4.6,3.4,NA,NA,4,2.4,NA,NA,NA,2),byrow=TRUE,ncol=4) > > k <- apply(dat, 1, function(x) which(x == min(x, na.rm = TRUE))) > > k > [[1]

Re: [R] problems to report indexes when I have two min value

2011-09-16 Thread jim holtman
Will this work for you: > dat <- + matrix(c(5.4,4.8,5.6,4.8,NA,4.4,4.6,3.4,NA,NA,4,2.4,NA,NA,NA,2),byrow=TRUE,ncol=4) > k <- apply(dat, 1, function(x) which(x == min(x, na.rm = TRUE))) > k [[1]] [1] 2 4 [[2]] [1] 4 [[3]] [1] 4 [[4]] [1] 4 > sapply(k, paste, collapse = ', ') [1] "2, 4" "4"

[R] Scheirer-Ray-Hare

2011-09-16 Thread garciap
Hello to all the people in the forum, I'm trying to perform a Scheirer-Ray-Hare test in R, and despite I've found some posts talking about this test, there no one in which I can found how to do so. Can anyone explain me how to do the test? Thanks Pablo -- View this message in context: http:/

[R] Call for Papers Special Sessions ICPRAM 2012

2011-09-16 Thread Pedro Latorre Carmona
Dear R-members, My name is Pedro Latorre Carmona, program co-chair of the 2012 "International Conference on Pattern Recognition Applications and Methods" (ICPRAM 2012) http://www.icpram.org Please let me send you below the text version of the "Open Call for papers for Special Sessions" in

[R] help with mediate() and medsens()

2011-09-16 Thread Chris
I'm having trouble with the mediate() and medsens() functions from the mediation package. My treatment, mediator and outcomes variables are all continuous and scaled to the 0-1 interval. The data is observational not experimental. I am thus using lm() for the initial outcome and mediation regressi

[R] writing data from several matrices in R into one excel-file with several sheets

2011-09-16 Thread Marion Wenty
hello, does anyone know how I can write several matrices from R into one exel-file using different sheets for the different matrices? thank you very much in advance for your help. Marion [[alternative HTML version deleted]] __ R-help@r-projec

Re: [R] automatic selection of object without loop

2011-09-16 Thread Marion Wenty
hello jim, thank you for your reply. Do you know a solution without having to use a loop? Marion 2011/9/16 jim holtman > for (i in names(kinderrechte)){ >q1 <- kinderrechte[, i] >i 1 <- get(i) > } > > On Fri, Sep 16, 2011 at 4:47 AM, Marion Wenty > wrote: > > Hello, > > > > does anyo

Re: [R] Mystified - comparing chron times

2011-09-16 Thread MacQueen, Don
Not that anything more needs to be said ... it doesn't, not really ... But I think that in cases like this it is helpful to use the digits arg to print(). It probably would have shown in a simple way that the two numeric versions aren't really equal -- and demonstrated a little about R's default p

Re: [R] "rounding" to a number that is LOWER than my number

2011-09-16 Thread Dimitri Liakhovitski
Thanks a lot, guys - very helpful! On Fri, Sep 16, 2011 at 12:52 PM, Bert Gunter wrote: > This is easy to do (e.g. divide by the appropriate power of 10, use floor, > multiply the power of 10), but you are going about it in the wrong way. > > See the "xaxs"  component of the ?par  argument list f

Re: [R] "rounding" to a number that is LOWER than my number

2011-09-16 Thread Bert Gunter
This is easy to do (e.g. divide by the appropriate power of 10, use floor, multiply the power of 10), but you are going about it in the wrong way. See the "xaxs" component of the ?par argument list for the right way. -- Bert On Fri, Sep 16, 2011 at 9:28 AM, Dimitri Liakhovitski < dimitri.liakh

Re: [R] Can't get installing a package source (.tar.gz) from a web page to work...

2011-09-16 Thread Uwe Ligges
On 16.09.2011 18:27, Martin Morgan wrote: On 09/16/2011 04:21 AM, Søren Højsgaard wrote: Thanks Uwe, The problem, however, is not solved. If I do: download.file("http://gbi.agrsci.dk/statistics/courses/2011-ISMLS-course/data/LiSciData_0.0-03.tar.gz";, tempdir()) Error in download.file("http

Re: [R] "rounding" to a number that is LOWER than my number

2011-09-16 Thread Sarah Goslee
Just for fun: roundDown <- function(x, digits = 2) { currplaces <- nchar(as.character((floor(x x <- x * 10 ^ (digits - currplaces) x <- floor(x) x <- x / (10 ^ (digits - currplaces)) x } > roundDown(1.98, 2) [1] 1.9 > roundDown(1.98, 1) [1] 1 > roundDown(1.98, 3) [1] 1.98 > > > roundDown(2

Re: [R] "rounding" to a number that is LOWER than my number

2011-09-16 Thread Dimitri Liakhovitski
In other words, I am looking for something like floor, but more flexible - as it should allow me to: turn 1.98 into 1.9 or turn 298 into 290, etc. Dimitri On Fri, Sep 16, 2011 at 12:28 PM, Dimitri Liakhovitski wrote: > Hello! > > What function would allow me to "round" down, rather than up? > For

Re: [R] Mystified - comparing chron times

2011-09-16 Thread Sarah Goslee
I'll freely admit that I know little about chron and didn't have a computer with R in front of me at the time. But the original querent converted the chron times to numeric and then used ==, and thus it became a 7.31 issue. Converting to character is a different way to approach the problem; which

Re: [R] Can't get installing a package source (.tar.gz) from a web page to work...

2011-09-16 Thread Martin Morgan
On 09/16/2011 04:21 AM, Søren Højsgaard wrote: Thanks Uwe, The problem, however, is not solved. If I do: download.file("http://gbi.agrsci.dk/statistics/courses/2011-ISMLS-course/data/LiSciData_0.0-03.tar.gz";, tempdir()) Error in download.file("http://gbi.agrsci.dk/statistics/courses/2011-ISMLS

[R] "rounding" to a number that is LOWER than my number

2011-09-16 Thread Dimitri Liakhovitski
Hello! What function would allow me to "round" down, rather than up? For example, x<-1.98 I'd like to get 1.9 - rather than 2.0. Reason - I am creating a minimum for an axis for a plot, and I need it to be lower than x (which, in turn, is the lowest number already). Thank you! -- Dimitri Liakho

Re: [R] problems to report indexes when I have two min value

2011-09-16 Thread marlene marchena
Sorry, maybe I was not clear in what I want. I need the two indexes. k 2 4 4 4 4 Marlene 2011/9/16 Jean-Christophe BOUËTTÉ > Hi there, > Assuming you would prefer to have only one min per row: > > apply(dat,1,which.min) > > there is a link to this function in the help page for ?min. > JC > > 2

Re: [R] problems to report indexes when I have two min value

2011-09-16 Thread Jean-Christophe BOUËTTÉ
Hi there, Assuming you would prefer to have only one min per row: apply(dat,1,which.min) there is a link to this function in the help page for ?min. JC 2011/9/16 marlene marchena : > Hi, > > I need to repor the index of a min value of each row in a matrix, but I > don't know how to do that when

Re: [R] problems to report indexes when I have two min value

2011-09-16 Thread Jeff Newmiller
Your coded answer looks right, and is represented in a syntactically correct manner. Your "desired" answer looks ambiguous, and is certainly not syntactically correct R. If you want ambiguous and vague answers, perhaps you need to keep a human in the loop. ---

Re: [R] Where to put tryCatch or similar in a very big for loop

2011-09-16 Thread Bonnett, Laura
Hi all, I've made some progress today. I've managed to move the set seed part of the function outside of the loop. The only problem I have now is that it says " Error in results[k, ] <- lapply(1:nsim, function(k) { : number of items to replace is not a multiple of replacement length" Give

Re: [R] Problematic If-Else statement

2011-09-16 Thread David Winsemius
On Sep 16, 2011, at 11:49 AM, Ben Ganzfried wrote: > Thanks David. That works perfectly! Although, I'm still not sure I > understand entirely why the input file says the character value > "null" and yet, it actually is NA... Unless you show us the file as it would appear in a text editor, a

[R] problems to report indexes when I have two min value

2011-09-16 Thread marlene marchena
Hi, I need to repor the index of a min value of each row in a matrix, but I don't know how to do that when I have more than one min value. Here is my example > dat <- matrix(c(5.4,4.8,5.6,4.8,NA,4.4,4.6,3.4,NA,NA,4,2.4,NA,NA,NA,2),byrow=TRUE,ncol=4) > dat [,1] [,2] [,3] [,4] [1,] 5.4 4.8

Re: [R] How to save row values from a matrix into one vector?

2011-09-16 Thread Jean-Christophe BOUËTTÉ
This is want you want: op <- as.vector(t(test)) JC 2011/9/16 Chris82 : > Dear R users, > > I guess, I have a quit simple problem, but I'm not getting the solution. > > I create a matrix like this: > > test <- matrix(seq(1,3,1),ncol=5,nrow=3) > > then I want to create one vector, consisting of eve

Re: [R] How to save row values from a matrix into one vector?

2011-09-16 Thread Uwe Ligges
On 16.09.2011 17:43, Chris82 wrote: Dear R users, I guess, I have a quit simple problem, but I'm not getting the solution. I create a matrix like this: test<- matrix(seq(1,3,1),ncol=5,nrow=3) then I want to create one vector, consisting of every row of the matrix. My first idea was to do th

Re: [R] Problematic If-Else statement

2011-09-16 Thread Ben Ganzfried
Thanks David. That works perfectly! Although, I'm still not sure I understand entirely why the input file says the character value "null" and yet, it actually is NA... On Fri, Sep 16, 2011 at 11:35 AM, David Winsemius wrote: > > On Sep 16, 2011, at 11:08 AM, David Winsemius wrote: > > >> On Sep

[R] How to save row values from a matrix into one vector?

2011-09-16 Thread Chris82
Dear R users, I guess, I have a quit simple problem, but I'm not getting the solution. I create a matrix like this: test <- matrix(seq(1,3,1),ncol=5,nrow=3) then I want to create one vector, consisting of every row of the matrix. My first idea was to do this with a for loop. op <- vector() f

Re: [R] Problematic If-Else statement

2011-09-16 Thread David Winsemius
On Sep 16, 2011, at 11:08 AM, David Winsemius wrote: On Sep 16, 2011, at 10:36 AM, Ben Ganzfried wrote: Hi guys, snipped Second, I changed the first line of my code to: tmp <- ifelse(uncurated $days_to_tumor_recurrence==NA,"norecurrence","recurrence") I do not know why your original d

Re: [R] question concerning the acf function

2011-09-16 Thread Jean-Christophe BOUËTTÉ
Hi Samir, to me, autocorrelation is the cross-correlation of a signal with itself. Which is why I don't really understand the meaning of your question. Are you looking for cross-correlation, for example the ccf function documented in the same help page as acf ? JC 2011/9/16 Samir Benzerfa : > Be

Re: [R] automatic selection of object without loop

2011-09-16 Thread jim holtman
You have to give more specifications as to what you want to do with the data that is being processed. You have values being put into 'q1' and 'i1' that don't seem to be used in the loop. Do you just want these values returned? You can easily do it "without a loop" using lapply: result <- lapply

Re: [R] demo creating

2011-09-16 Thread Duncan Murdoch
On 16/09/2011 10:53 AM, John Clark wrote: My question was not related to embedding R codes in powerpoint / word, rather I need to execute some of the commands in sequential way in R, so that I do not need to type them. This is similar to what you get when you use the following demo: require(latt

Re: [R] demo creating

2011-09-16 Thread jim holtman
I use NotePad++ and keep the source in there and then can highlight and copy over to the R session by pressing a key. You can easily extend this with the use of AutoHotKey to make it dependent on a mouse click if you wanted. On Fri, Sep 16, 2011 at 10:53 AM, John Clark wrote: > My question was n

Re: [R] demo creating

2011-09-16 Thread Jean-Christophe BOUËTTÉ
looking at the code of example I found that: oldask <- grDevices::devAskNewPage(ask = TRUE) x <- rnorm(1000) hist(x) plot(x) plot(x^2) grDevices::devAskNewPage(oldask) which will do what you want in terms of displaying plots with a pause. 2011/9/16 John Clark : > My question was not related to e

Re: [R] Problematic If-Else statement

2011-09-16 Thread David Winsemius
On Sep 16, 2011, at 10:36 AM, Ben Ganzfried wrote: Hi guys, My code (next 2 lines below) isn't doing what I'm expecting it to: tmp <- ifelse(uncurated $days_to_tumor_recurrence=="null","norecurrence","recurrence") curated$recurrence_status <- tmp I want the column "recurrence_status" in my

Re: [R] Problematic If-Else statement

2011-09-16 Thread R. Michael Weylandt
It seems that your original data has NA values in it (which you should have said in your original post) and that's where they are coming from in tmp. E.g., R> NA == "null" [1] NA To identify them, you need to use is.na() rather than "==NA" E.g., tmp[is.na(tmp)] <- "norecurrence" and similarly

Re: [R] Mystified - comparing chron times

2011-09-16 Thread David Winsemius
On Sep 16, 2011, at 10:08 AM, B77S wrote: I'm sure Sarah's solution works (and she knows more about R than myself), but I ran into a similar problem and used: as.character(start.time)==as.character(expected_start.time) What you did was an implicit rounding of the values to the digits leve

Re: [R] demo creating

2011-09-16 Thread John Clark
My question was not related to embedding R codes in powerpoint / word, rather I need to execute some of the commands in sequential way in R, so that I do not need to type them. This is similar to what you get when you use the following demo: require(lattice); demo(lattice) So I want to put my co

Re: [R] Selecting from matrix and then stacking in array.

2011-09-16 Thread R. Michael Weylandt
I think changing nrow() to NROW() will get around that error. However, this, as you can see, this goes a little astray at the end. Perhaps something like this will work for you: z.ext <- rbind(z,array(0,c(9,3))) z.out <- array(0, c(3,3,9)) for(i in 1:9){ z.out[,,i] <- cbind(z.ext[c(i,i+3,i+6),

Re: [R] Problematic If-Else statement

2011-09-16 Thread Ben Ganzfried
Hi Michael, I mean the character string "null". Thanks, Ben On Fri, Sep 16, 2011 at 10:40 AM, R. Michael Weylandt < michael.weyla...@gmail.com> wrote: > Do you actually mean the character string "null" or do you mean the NULL it > doesn't exist thing? If that's the case, you need to write is.n

Re: [R] Problematic If-Else statement

2011-09-16 Thread R. Michael Weylandt
Do you actually mean the character string "null" or do you mean the NULL it doesn't exist thing? If that's the case, you need to write is.null(), something like is.NA()... Michael Weylandt On Fri, Sep 16, 2011 at 10:36 AM, Ben Ganzfried wrote: > Hi guys, > > My code (next 2 lines below) isn't do

Re: [R] Referring to an object by a variable containing its name: 6 failures

2011-09-16 Thread Eik Vettorazzi
Hi, maybe I did not get the point, but get() does exactly what you want: whatIwant = 2 nomdeplume = "whatIwant" get(nomdeplume) cheers Am 16.09.2011 16:09, schrieb Timothy Bates: > On 16 Sep 2011, at 1:49 AM, andrewH wrote: >>> I'm trying to make a function that takes column names then >>> usin

[R] Problematic If-Else statement

2011-09-16 Thread Ben Ganzfried
Hi guys, My code (next 2 lines below) isn't doing what I'm expecting it to: tmp <- ifelse(uncurated$days_to_tumor_recurrence=="null","norecurrence","recurrence") curated$recurrence_status <- tmp I want the column "recurrence_status" in my output file to have values "recurrence" (if the input val

Re: [R] Referring to an object by a variable containing its name: 6 failures

2011-09-16 Thread Timothy Bates
On 16 Sep 2011, at 1:49 AM, andrewH wrote: >> I'm trying to make a function that takes column names then >> using the variable colName, containing the name of >> the column, to refer to the column itself rmail...@justemail.net said > What am I missing about your inquiry: It seems like x[ , colNam

Re: [R] Mystified - comparing chron times

2011-09-16 Thread B77S
I'm sure Sarah's solution works (and she knows more about R than myself), but I ran into a similar problem and used: as.character(start.time)==as.character(expected_start.time) good luck regardless. -BS Sarah Goslee wrote: > > Sounds like a case for FAQ 7.31, or, yet another machine precision

Re: [R] odfWeave: Combining multiple output statements in a function

2011-09-16 Thread Jan van der Laan
Page 7 in my version of formatting.odt (to be sure I have the right version I downloaded the latest odfWeave from CRAN) discusses registering style definitions and "Examples of Changing Styles for Tables, Paragraphs, Bullets and Pages" which has nothing to do with my question (as far as I

Re: [R] question concerning the acf function

2011-09-16 Thread R. Michael Weylandt
Would not something like V = apply(P,2,acf, plot=FALSE) V = sapply(V,`[[`,"acf") work? I'm pretty sure acf() doesn't return any sort of residuals so you'll have to calculate those on your own. Hope this helps, Michael Weylandt On Fri, Sep 16, 2011 at 9:20 AM, Jean-Christophe BOUËTTÉ < jcboue..

Re: [R] Superimposing titles on dotcharts

2011-09-16 Thread Deepayan Sarkar
On Mon, Sep 12, 2011 at 8:54 PM, Mikkel Grum wrote: > I've created a chart with times that employees have entered data on named > tasks as in the following example: > > Employee <- c(rep("Tom", 127), > rep("Dick", 121), > rep("Sally", 130) > ) > Time <- c(seq(as.POSIXct("2011-09-12 07:00:00"), as

Re: [R] odfWeave: Combining multiple output statements in a function

2011-09-16 Thread Max Kuhn
formatting.odf, page 7. The results are in formattingOut.odt On Thu, Sep 15, 2011 at 2:44 PM, Jan van der Laan wrote: > Max, > > Thank you for your answer. I have had another look at the examples (I > already had before mailing the list), but could find the example you > mention. Could you perhap

Re: [R] demo creating

2011-09-16 Thread Duncan Murdoch
On 15/09/2011 10:22 PM, John Clark wrote: R experts: I want to prepare a demo (that will play sequentially in clicks) for a presentation tutorial...Can somebody help me how can I write a demo, suppose the following are steps in the demo.. #start set.seed(1345) x1<- sample(letters[1:10], 5) x1 s

Re: [R] Lattice xyplot log scale labels help!

2011-09-16 Thread Deepayan Sarkar
On Fri, Sep 16, 2011 at 2:17 AM, Cram Rigby wrote: > I have a problem with lattice log scales that I could use some help with. > > I'm trying to print log y-axis scales without exponents in the labels. >  A similar thread with Deepayan' recommendation is here: > http://tolstoy.newcastle.edu.au/R/e

Re: [R] question concerning the acf function

2011-09-16 Thread Jean-Christophe BOUËTTÉ
Hi, you did not supply a reproducible example. We do not know what your data nor your code looks like. Please follow the recommandations found at the bottom of this email! You're more likely to get a quick and meaningful reply. JC 2011/9/16 Samir Benzerfa : > Hi everyone, > > > > I've got a questi

Re: [R] question about glm vs. loglin()

2011-09-16 Thread Michael Friendly
Hi Yana Trying to interpret associations in complex loglinear models from tables of parameter estimates is like trying to extract sunlight from a cucumber. You have to squeeze very hard, and then are usually unhappy with the quality of the sunlight. Instead, you can visualize the association

[R] cutree() and rect.hclust(): different labelling of classes

2011-09-16 Thread Agustin Lobo
I've found that while cutree() and rect.hclust() make the same classes for a given height in the dendrogram, the actual labeling of the classes is different. For example, both produce the same 4 classes but class 1 according to cutree() is class 4 according to rect.hclust(). Would it be possible

Re: [R] demo creating

2011-09-16 Thread Jean-Christophe BOUËTTÉ
Hi, it is not clear to me what your exact request is. If you want to integrate R code in a presentation, using sweave with the beamer class is an option. 2011/9/15 John Clark : > R experts: > > I want to prepare a demo (that will play sequentially in clicks) for a > presentation tutorial...Can some

Re: [R] automatic selection of object without loop

2011-09-16 Thread jim holtman
did not see the "_l" so changes below: On Fri, Sep 16, 2011 at 8:33 AM, jim holtman wrote: > for (i in names(kinderrechte)){ >    q1 <- kinderrechte[, i] >    i 1 <- get(paste(i, "_l", sep = "")) > } > > On Fri, Sep 16, 2011 at 4:47 AM, Marion Wenty wrote: >> Hello, >> >> does anyone know the so

Re: [R] automatic selection of object without loop

2011-09-16 Thread jim holtman
for (i in names(kinderrechte)){ q1 <- kinderrechte[, i] i 1 <- get(i) } On Fri, Sep 16, 2011 at 4:47 AM, Marion Wenty wrote: > Hello, > > does anyone know the solution to this problem: > > I imported a dataframe from Spss into R and saved it as an object called > "kinderrechte". > > I hav

Re: [R] Numeric Characters in String

2011-09-16 Thread jim holtman
try this: > str <- c("14.XYZ", "15.ABCDE", "16.dkieowo", "120.EIDKAI") > x <- gsub("[^0-9]", "", str) > x [1] "14" "15" "16" "120" > as.integer(x) [1] 14 15 16 120 > On Fri, Sep 16, 2011 at 5:13 AM, Karl Weinmayer wrote: > Dear all, > > > > I have a vector, which looks about like this: >

Re: [R] Numeric Characters in String

2011-09-16 Thread Eik Vettorazzi
Hi Karl, both strategies are possible using gsub: gsub("([0-9]*).*","\\1",str) #extract numbers gsub("[^0-9]","",str) #remove all non-numeric characters wrap it nicely in an "as.numeric" call to get numeric values. cheers. Am 16.09.2011 11:13, schrieb Karl Weinmayer: > Dear all, > > > > I h

Re: [R] Mystified - comparing chron times

2011-09-16 Thread Sarah Goslee
Sounds like a case for FAQ 7.31, or, yet another machine precision issue. Try all.equal() instead of == Sarah On Fri, Sep 16, 2011 at 7:36 AM, mebstyne wrote: > I have two local variables: startTime and expectedStartTime.  Both are chron > related objects. > When I look at the class for the obje

[R] lpSolveAPI optimizer treating some of the constraints as soft constraint

2011-09-16 Thread Ashish Kumar
Hello Folks, I am trying to do linear optimization using linear constraints on the decision variables. The problem is it is treating some of the constraints as soft constraints(violating couple of constraints condition), instead of throwing infeasible solution. Is there an option in lpsolveapi

Re: [R] R-help Digest, Vol 103, Issue 15

2011-09-16 Thread mihalicza . peter
Szeptember 12-től 26-ig irodán kívül vagyok, és az emailjeimet nem érem el. Sürgős esetben kérem forduljon Kárpáti Edithez (karpati.e...@gyemszi.hu). Üdvözlettel, Mihalicza Péter I will be out of the office from 12 till 26 September with no access to my emails. In urgent cases please contact

[R] Mystified - comparing chron times

2011-09-16 Thread mebstyne
I have two local variables: startTime and expectedStartTime. Both are chron related objects. When I look at the class for the objects I can see they are of class "times". When I print them to the console, they both read: "09:30:00" When I print them as.numeric(), they both read: 0.3958333 When I t

Re: [R] merging nexus sequence files

2011-09-16 Thread nikki22
Thanks David, I'll give it a go! Cheers Nikki -- View this message in context: http://r.789695.n4.nabble.com/merging-nexus-sequence-files-tp3816907p3817675.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing l

[R] question concerning the acf function

2011-09-16 Thread Samir Benzerfa
Hi everyone, I've got a question concerning the function acf(.) in R for calculating the autocorrelation in my data. I have a table with daily returns of several stocks over time and I would like to calculate the autocorrelation for all the series (not only for one time series). How can I d

[R] Rect.hclust problem - "which=" not working

2011-09-16 Thread Robin Cura
Hi, I'm using ade4 R package to perform some clustering operations. I've got a problem with the representation of my data with rect.hclust Currently, I do a tree plot, and I'd like to add color boxes on it to show where the classes are. As the order of the classes is never the same, I wanted to u

[R] automatic selection of object without loop

2011-09-16 Thread Marion Wenty
Hello, does anyone know the solution to this problem: I imported a dataframe from Spss into R and saved it as an object called "kinderrechte". I have got the following command lines: q1 <- kinderrechte[,"q0007_0001"] l1 <- q0007_0001_l now i would like to be able to change the column name in t

[R] Numeric Characters in String

2011-09-16 Thread Karl Weinmayer
Dear all, I have a vector, which looks about like this: str <- c("14.XYZ", "15.ABCDE", "16.dkieowo", "120.EIDKAI") I need to extract the numerical characters out of the string, so I receive in the end a normal vector containing: vec <- c(14, 15, 16, 120) I need a generic solutio

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