Re: [R] Finicky factor comparison operators

2012-02-20 Thread johnmark
MIchael - Thanks for your insight. I think I see where you're going with this. To make '==' comparisons for subsetting against an ordered factor, I've had to create a lookup table for all possible values I'd ever want to compare against (all dates covered by the quarters in question, in this

Re: [R] ggplot rank stack bar automatically.

2012-02-20 Thread vd3000
df - structure(c(106487, 495681, 1597442, 2452577, 2065141, 2271925, 4735484, 3555352, 8056040, 4321887, 2463194, 347566, 621147, 1325727, 1123492, 800368, 761550, 1359737, 1073726, 36, 53, 141, 41538, 64759, 124160, 69942, 74862, 323543, 247236, 112059, 16595,

[R] Basic advice for a poLCA newbie

2012-02-20 Thread Suranga Kasthurirathne
Hi everyone / poLCA gurus, I'm facing a problem regarding conditional dependence and poLCA. Using a few data sets composed of only 1's and 2's, i'm able to do a latent class analysis for independent data columns using poLCA. The commands I use to do this are something like, bcs =

Re: [R] Non-parametric test for repeated measures and post-hoc single comparisons in R?

2012-02-20 Thread saschaview
Thanks, I got it! (And I think I should have googled what replicated means!) However, then Bortz, Lienert, Boehnke are imprecise, if not wrong: Der Friedman-Test setzt voraus, dass die N Individuen wechselseitig unabhängig sind, dass also nicht etwa ein und dasselbe Individuum zweimal oder

[R] Run function several times changing only one argument - without a loop

2012-02-20 Thread Marion Wenty
Dear people, I created a plot which looks like this: Ee1-matrix(c(88,86,74,62,41),ncol=5) colnames(Ee1)-c(Lehrer,Lehrerinnen,Klassenkollegen,Klassenkolleginnen,Geschwister) par(las=1) par(mar=c(5,13,4,2)) barplot(Ee1,horiz=T,col=grey85,border=NA,xlim=c(0,100),axes=F) axis(2,pos=10, tick=T,

[R] Help on lattice barchart ploting

2012-02-20 Thread MLSC
Hi friends, I have following data and would like to plot this with barchart() availble with lattice package. RsID Freqs Genotype AAA 63.636 1/1 AAA 32.727 1/2 AAA 3.636 2/2 BBB 85.965 2/2 BBB 14.035 2/1 CCC 63.158 1/1 CCC 21.053 1/2 CCC 15.789 2/2

Re: [R] Run function several times changing only one argument - without a loop

2012-02-20 Thread Enrico Schumann
Hi Marion, is all you want the white vertical lines? Then try abline(v = seq(10, 90, by = 10), col = white) instead of your axis commands. Regards, Enrico Am 20.02.2012 11:04, schrieb Marion Wenty: Dear people, I created a plot which looks like this: Ee1-matrix(c(88,86,74,62,41),ncol=5)

[R] overlay of two sets of boxplots

2012-02-20 Thread Mirjam Appel
Hello, I am new to R and currently have the following problem: I have successfully loaded my data in R which consists of two numeric columns (LI_F and female) and one character column (Strain). So far I can plot two different set of boxplots for each of the numeric columns plotted by the groups

[R] Sorting strings

2012-02-20 Thread statquant2
Hi all, I am having difficulties to understand how R sort strings: If I do R) sort(c(X.,X0B)) [1] X. X0B So for me, as far as lexicographic order is concerned I can add whatever to the end, the order will remain the same, but : R) sort(c(X.Z,X0B.Z)) [1] X0B.Z X.Z Can somebody give me a trick

[R] apply with as function ifelse with 2 logical conditions

2012-02-20 Thread Nerak
Hi all, I have a question concerning using several conditions in an ifelse function used as the function in apply. I want to create a new value with the function ifelse ‘ object which can be coerced to logical mode “test[n,] 1 test[n-1,]==0” With n I mean the row. I don’t know how I could

Re: [R] Run function several times changing only one argument - without a loop

2012-02-20 Thread Eik Vettorazzi
Hi Marion, you can either use any of the *apply-functions or vectorize your function (which internally uses mapply): par(las=1) par(mar=c(5,13,4,2)) barplot(Ee1,horiz=T,col=grey85,border=NA,xlim=c(0,100),axes=F) #using sapply invisible(sapply((1:9)*10,function(x)axis(2,pos=x,tick=T, tcl=F,

Re: [R] Sorting strings

2012-02-20 Thread Petr Savicky
On Mon, Feb 20, 2012 at 02:18:42AM -0800, statquant2 wrote: Hi all, I am having difficulties to understand how R sort strings: If I do R) sort(c(X.,X0B)) [1] X. X0B So for me, as far as lexicographic order is concerned I can add whatever to the end, the order will remain the same, but :

[R] chisq.test vs manual calculation - why are different results produced?

2012-02-20 Thread Louise Mair
Hello, I am trying to fit gamma, negative exponential and inverse power functions to a dataset, and then test whether the fit of each curve is good. To do this I have been advised to calculate predicted values for bins of data (I have grouped a continuous range of distances into 1km bins), and

Re: [R] installing the package Rcplex

2012-02-20 Thread Uwe Ligges
On 20.02.2012 01:54, David Winsemius wrote: On Feb 19, 2012, at 7:45 PM, zheng wei wrote: I did not know this before. I installed it as you suggested. what to do next? Read the Installation Manual? And don't forget this is a source package for which no CRAN Windows binary exists,

Re: [R] GTK+

2012-02-20 Thread Uwe Ligges
On 19.02.2012 18:58, Idielle Walters wrote: Hi I am struggling to install GTK+ for Windows 7. RGtk2 needs this package to load. Does anybody know of a installation file that works? See the ReadMe for Windows binary packages. For the current R-reelase this is

Re: [R] Sorting strings

2012-02-20 Thread Keith Jewell
Petr Savicky savi...@cs.cas.cz wrote in message news:20120220105153.gc21...@cs.cas.cz... On Mon, Feb 20, 2012 at 02:18:42AM -0800, statquant2 wrote: Hi all, I am having difficulties to understand how R sort strings: If I do R) sort(c(X.,X0B)) [1] X. X0B So for me, as far as

[R] Problems with installation of lsa package

2012-02-20 Thread A J
Hi everybody! First of all, I would like to point that I am newebie in using R. The issue is that I need to install lsa package in R. In theory, I have downloaded and installed all necessary packages to run lsa library, but when I am going to load it I get this message: library(lsa)Loading

Re: [R] GTK

2012-02-20 Thread Yvonnick Noel
I am struggling to install GTK+ for Windows 7. RGtk2 needs this package to load. Does anybody know of a installation file that works? GTK+ is automatically installed when you install the RGtk2 package (you'll be asked about it during installation). As of R-2.14.1, it is installed under

Re: [R] apply with as function ifelse with 2 logical conditions

2012-02-20 Thread Berend Hasselman
On 20-02-2012, at 10:40, Nerak wrote: Hi all, I have a question concerning using several conditions in an ifelse function used as the function in apply. I want to create a new value with the function ifelse ‘ object which can be coerced to logical mode “test[n,] 1 test[n-1,]==0”

Re: [R] Sorting strings

2012-02-20 Thread Enrico Schumann
See ?Comparison, which holds some warnings about what to expect when sorting strings. Am 20.02.2012 11:51, schrieb Petr Savicky: On Mon, Feb 20, 2012 at 02:18:42AM -0800, statquant2 wrote: Hi all, I am having difficulties to understand how R sort strings: If I do R) sort(c(X.,X0B)) [1] X.

Re: [R] Sorting strings

2012-02-20 Thread statquant2
Ok so it changed from 2.12.2 to 2.14.1 ?? Can somebody tell me how to modify my sort or whatever to get the save resilt that I would get in 2.14.1 ? Cheers -- View this message in context: http://r.789695.n4.nabble.com/Sorting-strings-tp4403696p4403858.html Sent from the R help mailing list

[R] How to determine a subset of a binary strings?

2012-02-20 Thread jing tang
Hi, I need some neat ways of determing a subset of binary strings. For example, x=c(0,0,1), y=c(0,1,1), z=c(0,1,0). So x is a subset of y and z is also a subset of y, but x is not a subset of z. I tried to search R functions and packages but no hits. Any ideas? Best, Jing -- Jing Tang,

[R] How to inset a cell into a matrix?

2012-02-20 Thread xushaw
hi i'm facing a problem How to inset a cell into a matrix? for example i have a matrix: 332 244 332244 665 332 665332 785 785 785665 i want to covert the matrix like this: 02440244 332 332

[R] Time taken to process a file after a socket connection was made

2012-02-20 Thread Aniruddha Mukherjee
Hello R people, I have created a '.csv' file of 100 rows by 20 columns whose each cell contains a random numbers between 0 1, thru a Java program. Once that is created a signal (just a letter) is send to the port of a socket connection at localhost, which was earlier started by an R session.

Re: [R] Run function several times changing only one argument - without a loop

2012-02-20 Thread Marion Wenty
Hi Enrico, Yes, you were right, I just wanted to draw white vertical lines and with your command it's much simpler. Thanks a lot! Hi Eik, I learned a lot from your tips about sapply and Vectorize! I had only used apply, lapply and mapply but not yet sapply. I find the Vectorize function very

Re: [R] proto: make a parameter persist

2012-02-20 Thread Ben quant
I like it better. Thanks! Ben On Fri, Feb 17, 2012 at 11:38 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Sat, Feb 18, 2012 at 12:44 AM, Ben quant ccqu...@gmail.com wrote: The code below works as expected but: Using the proto package, is this the best way to 1) make a parameter

[R] Triangular Test

2012-02-20 Thread kende jan
Hello, I would like to perform triangular test for clinical trial with R. can you help me please ? Jan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the

Re: [R] How to determine a subset of a binary strings?

2012-02-20 Thread Berend Hasselman
On 20-02-2012, at 14:15, jing tang wrote: Hi, I need some neat ways of determing a subset of binary strings. For example, x=c(0,0,1), y=c(0,1,1), z=c(0,1,0). So x is a subset of y and z is also a subset of y, but x is not a subset of z. I tried to search R functions and packages but no

Re: [R] coxme: model simplification using LR-test?

2012-02-20 Thread Terry Therneau
Summary of the query: update does not work on a coxme object I ran into this bug myself 2 days ago -- I rarely use update() so hadn't encountered it before. The problem is that coxme breaks the formula into fixed and random portions, and this confuses the default method for formula. Solution:

Re: [R] Finicky factor comparison operators

2012-02-20 Thread David Winsemius
On Feb 20, 2012, at 1:45 AM, johnmark wrote: MIchael - Thanks for your insight. I think I see where you're going with this. To make '==' comparisons for subsetting against an ordered factor, I've had to create a lookup table for all possible values I'd ever want to compare against (all

Re: [R] Help on lattice barchart ploting

2012-02-20 Thread David Winsemius
On Feb 20, 2012, at 5:34 AM, MLSC wrote: Hi friends, I have following data and would like to plot this with barchart() availble with lattice package. RsID Freqs Genotype AAA 63.636 1/1 AAA 32.727 1/2 AAA 3.636 2/2 BBB 85.965 2/2 BBB 14.035 2/1 CCC 63.158

Re: [R] How to determine a subset of a binary strings?

2012-02-20 Thread Enrico Schumann
Hi Jing, I am not sure I got your definition of a subset right, but maybe this helps. Regards, Enrico x - c(0,0,1) y - c(0,1,1) z - c(0,1,0) ## is x a 'subset' of y? isSubset - function(x, y) { x - as.logical(x) y - as.logical(y) all(y[x] == TRUE) } isSubset(x, y) isSubset(z,

Re: [R] Run function several times changing only one argument - without a loop

2012-02-20 Thread David Winsemius
On Feb 20, 2012, at 5:04 AM, Marion Wenty wrote: Dear people, I created a plot which looks like this: Ee1-matrix(c(88,86,74,62,41),ncol=5) colnames(Ee1)- c (Lehrer ,Lehrerinnen,Klassenkollegen,Klassenkolleginnen,Geschwister) par(las=1) par(mar=c(5,13,4,2))

Re: [R] chisq.test vs manual calculation - why are different results produced?

2012-02-20 Thread David Winsemius
On Feb 20, 2012, at 5:57 AM, Louise Mair wrote: Hello, I am trying to fit gamma, negative exponential and inverse power functions to a dataset, and then test whether the fit of each curve is good. To do this I have been advised to calculate predicted values for bins of data (I have

Re: [R] Sorting strings

2012-02-20 Thread statquant2
I did, but this does not give the answer to my question... Anybody knows how to tweack the behaviour of sort or how to do ? -- View this message in context: http://r.789695.n4.nabble.com/Sorting-strings-tp4403696p4404091.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Reporting Kaplan-Meier / Cox-Proportional Hazard Standard Error, km.coxph.plot, survfit.object

2012-02-20 Thread Frank Harrell
The 10% rule does not provide a unique answer. Should it apply to the cumulative probability, its logarithm, or log-log (log hazard scale)? Many studies are too small to achieve 10% at any time point. I think it is more traditional (but not without bias) to stop where fewer than 10 subjects are

Re: [R] Help on lattice barchart ploting

2012-02-20 Thread Richard M. Heiberger
I do not see the restricted range that you report. There is probably some masking as David pointed out. Try again in a fresh R session with --vanilla. You probably want three additional arguments. update(.Last.value, xlim=c(0, 100), between=list(x=1, y=1), origin = 0) to the barchart function

Re: [R] Sorting strings

2012-02-20 Thread R. Michael Weylandt
I don't *think* it's version specific, but rather it depends on your (still unstated) locale, as the documentation goes to great lengths to point out. Change that and you might see different behaviors. Michael On Mon, Feb 20, 2012 at 8:55 AM, statquant2 statqu...@gmail.com wrote: I did, but

[R] Confused: Inconsistent result?

2012-02-20 Thread Ajay Askoolum
This is copy paste from my session: xyz-as.vector(c(ls(),as.matrix(lapply(ls(),class dim(xyz)-c(length(xyz)/2,2) allobj-function(){ + xyz-as.vector(c(ls(),as.matrix(lapply(ls(),class; + dim(xyz)-c(length(xyz)/2,2); + return(xyz) + } xyz   [,1]  [,2]    [1,] a   

[R] stats on transitions from one state to another

2012-02-20 Thread Murali.Menon
Folks, I'm trying to get stats from a matrix for each transition from one state to another. I have a matrix x as below. structure(c(0, 2, 2, 2, 0, 0, 0, 1, 1, 1, 1, 2, 2, 1, 1, 1, 0, 0, 2, 2, 0.21, -0.57, -0.59, 0.16, -1.62, 0.18, -0.81, -0.19, -0.76, 0.74, -1.51, 2.79, 0.41, 1.63, -0.86,

Re: [R] Confused: Inconsistent result?

2012-02-20 Thread David Winsemius
On Feb 20, 2012, at 10:07 AM, Ajay Askoolum wrote: This is copy paste from my session: xyz-as.vector(c(ls(),as.matrix(lapply(ls(),class dim(xyz)-c(length(xyz)/2,2) allobj-function(){ + xyz-as.vector(c(ls(),as.matrix(lapply(ls(),class; + dim(xyz)-c(length(xyz)/2,2); + return(xyz) +

Re: [R] Confused: Inconsistent result?

2012-02-20 Thread R. Michael Weylandt
Sorry, just checked it and you need to add .GlobalEnv to both ls() calls. Michael On Mon, Feb 20, 2012 at 10:17 AM, R. Michael Weylandt michael.weyla...@gmail.com wrote: Short answer, environments -- ls() looks (by default) in its current environment, which is not the same as the global

Re: [R] Confused: Inconsistent result?

2012-02-20 Thread R. Michael Weylandt
Short answer, environments -- ls() looks (by default) in its current environment, which is not the same as the global environment when being called inside a function. This would (I think) give the same answer but I haven't checked it. : allobj-function(){ +

[R] Computing plot size in Sweave

2012-02-20 Thread BXC (Bendix Carstensen)
Sometimes you want to compute the physical size of a plot based on data. In R itself this is no problem. But is there a way to compute the values of height and width in S-weave, say: graph,fig=TRUE,height=xx,width=yy= where xx and yy are computed and not physically written in the document?

Re: [R] Confused: Inconsistent result?

2012-02-20 Thread Petr PIKAL
Hi This is copy paste from my session: xyz-as.vector(c(ls(),as.matrix(lapply(ls(),class dim(xyz)-c(length(xyz)/2,2) allobj-function(){ + xyz-as.vector(c(ls(),as.matrix(lapply(ls(),class; + dim(xyz)-c(length(xyz)/2,2); + return(xyz) + } xyz [,1] [,2]

Re: [R] stats on transitions from one state to another

2012-02-20 Thread David Winsemius
On Feb 20, 2012, at 10:11 AM, murali.me...@avivainvestors.com wrote: Folks, I'm trying to get stats from a matrix for each transition from one state to another. I have a matrix x as below. structure(c(0, 2, 2, 2, 0, 0, 0, 1, 1, 1, 1, 2, 2, 1, 1, 1, 0, 0, 2, 2, 0.21, -0.57, -0.59, 0.16,

Re: [R] How to resample matrices to test for the robustness of their correlation

2012-02-20 Thread camilleislande
Thank you Chuck, Here is the head of my data set (tjornres): Fish.1 Fish.2 MORPHO DIET 1 1 20.03768 0.1559250 2 1 30.05609 0.7897060 3 1 40.03934 0.4638010 4 1 50.03363

Re: [R] How to determine a subset of a binary strings?

2012-02-20 Thread Petr Savicky
On Mon, Feb 20, 2012 at 03:15:53PM +0200, jing tang wrote: Hi, I need some neat ways of determing a subset of binary strings. For example, x=c(0,0,1), y=c(0,1,1), z=c(0,1,0). So x is a subset of y and z is also a subset of y, but x is not a subset of z. I tried to search R functions and

Re: [R] Sorting strings

2012-02-20 Thread Petr Savicky
On Mon, Feb 20, 2012 at 05:55:30AM -0800, statquant2 wrote: I did, but this does not give the answer to my question... Anybody knows how to tweack the behaviour of sort or how to do ? Hi. Try this Sys.setlocale(LC_COLLATE, C) This comes from ?locale and reads there

Re: [R] Sorting strings

2012-02-20 Thread Rui Barradas
Hello, statquant2 wrote Ok so it changed from 2.12.2 to 2.14.1 ?? Can somebody tell me how to modify my sort or whatever to get the save resilt that I would get in 2.14.1 ? Cheers I don't know about 2.12.2 but for 2.12.0 I get: R.version _

[R] Metafor: Moderator variables for each study arm

2012-02-20 Thread Faiz Ahmad Khan
Hello, I am trying to do a meta-analysis where each study has two arms, similar to the BCG data set. However, follow-up duration was different for each study arm, so I would like to fit a model that uses the length of follow-up in each arm as a moderator. Is this possible? For example, if

[R] Column wise matrix multiplication

2012-02-20 Thread Graziano Mirata
Hi all, I am trying to multiply each column of a matrix such to have a unique resulting vector with length equal to the number of rows of the original matrix. In short I would like to do what prod(.) function in Matlab does, i.e. A -matrix(c(1:10),5,2) V = A[,1]*A[,2] Thank you Graziano

Re: [R] Sorting strings

2012-02-20 Thread statquant2
Ok I have : R) str(R.Version()) List of 13 $ platform : chr x86_64-unknown-linux-gnu $ arch : chr x86_64 $ os: chr linux-gnu $ system: chr x86_64, linux-gnu $ status: chr $ major : chr 2 $ minor : chr 12.2 $ year : chr

[R] FW: Problems with R

2012-02-20 Thread Thorsten Pöllinger
Dears, I am a new R user and I am trying to analyze my data sets, R gives me a default when I type in the regression formula as following: fit1=gamlss(tot_remun_revenue$tot_remun.y~tot_remun_revenue$revenue.x,family=NO) Fehler in model.frame.default(formula =

Re: [R] Column wise matrix multiplication

2012-02-20 Thread Dimitris Rizopoulos
Try apply(A, 1, prod) I hope it helps. Best, Dimitris On 2/20/2012 4:21 PM, Graziano Mirata wrote: Hi all, I am trying to multiply each column of a matrix such to have a unique resulting vector with length equal to the number of rows of the original matrix. In short I would like to do

Re: [R] stats on transitions from one state to another

2012-02-20 Thread Berend Hasselman
On 20-02-2012, at 16:11, murali.me...@avivainvestors.com murali.me...@avivainvestors.com wrote: Folks, I'm trying to get stats from a matrix for each transition from one state to another. I have a matrix x as below. structure(c(0, 2, 2, 2, 0, 0, 0, 1, 1, 1, 1, 2, 2, 1, 1, 1, 0, 0,

Re: [R] Sorting strings

2012-02-20 Thread De-Jian Zhao
It seems OS-dependent. I got different results when trying it on windows xp and Redhat linux. R.version _ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 9.1 year

Re: [R] Sorting strings

2012-02-20 Thread Petr Savicky
On Mon, Feb 20, 2012 at 04:56:21PM +0100, Petr Savicky wrote: On Mon, Feb 20, 2012 at 05:55:30AM -0800, statquant2 wrote: I did, but this does not give the answer to my question... Anybody knows how to tweack the behaviour of sort or how to do ? Hi. Try this

Re: [R] Sorting strings

2012-02-20 Thread De-Jian Zhao
Sorry, just made a mistake. This is the result from windows xp. sort(c(X.,X0B)) [1] X. X0B sort(c(X.Z,X0B.Z)) [1] X.Z X0B.Z R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor

Re: [R] FW: Problems with R

2012-02-20 Thread David Winsemius
On Feb 20, 2012, at 10:26 AM, Thorsten Pöllinger wrote: Dears, I am a new R user and I am trying to analyze my data sets, R gives me a default when I type in the regression formula as following: fit1=gamlss(tot_remun_revenue$tot_remun.y~tot_remun_revenue $revenue.x,family=NO) Most

Re: [R] Non-parametric test for repeated measures and post-hoc single comparisons in R?

2012-02-20 Thread Meyners, Michael
No, the authors are correct: the individuals (i.e. the 17 individuals) you have need to be independent (i.e. no correlation between them, let alone any individual running through your temporal experiment more than once, as indicated in the citation), while the *observations* are of course

Re: [R] coxme: model simplification using LR-test?

2012-02-20 Thread Simon Tragust
Many thanks for the suggestion. I tried it already, but as I've never wrote a function, I had no luck. If it's not asked too much, maybe you or somebody else could help me getting the code for the function right. Regards Simon Am 20/02/2012 14:52, schrieb Terry Therneau: Summary of the

Re: [R] Sorting strings

2012-02-20 Thread De-Jian Zhao
On 2012-2-20 23:15, Rui Barradas wrote: Could it be OS related? Yes, it seems. I tried it on my local windows xp and redhat linux server, and got different results. Hope it will be fixed in the future versions. Maybe we should keep alert to check whether the results are consistent when

Re: [R] overlay of two sets of boxplots

2012-02-20 Thread John Kane
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. At a rough guess you may want to have a look at the mfrow in ?par but without some sample data and a bit more information about what you need it is

Re: [R] Sorting strings

2012-02-20 Thread Ted Harding
On 20-Feb-2012 Petr Savicky wrote: On Mon, Feb 20, 2012 at 05:55:30AM -0800, statquant2 wrote: I did, but this does not give the answer to my question... Anybody knows how to tweack the behaviour of sort or how to do ? Hi. Try this Sys.setlocale(LC_COLLATE, C) This comes from

Re: [R] ggplot rank stack bar automatically.

2012-02-20 Thread Ista Zahn
Hi, That is not what I get. After running your code I get levels(df.m$Period) [1] 1991-00 1901-10 1981-90 2001-06 1911-20 1881-90 1971-80 [8] 1921-30 1891-00 1961-70 1871-80 1851-60 1951-60 1861-70 [15] 1841-50 1941-50 1831-40 1931-40 1820-30 this is my version info: sessionInfo() R version

Re: [R] help updating package rJava (on ubuntu)

2012-02-20 Thread Karl Brand
Simon, Thanks alot for the further clarification. As i said some where in my lengthy explanation - i don't what of the myriad steps were needed, only that they were performed and i now have an up-to-date rJava. Next time (actually coming up soon) i'll certainly be following the couple

Re: [R] coxme: model simplification using LR-test?

2012-02-20 Thread David Winsemius
On Feb 20, 2012, at 11:41 AM, Simon Tragust wrote: Many thanks for the suggestion. I tried it already, it means .. what exactly? but as I've never wrote a function, I had no luck. no luck means ... what? If it's not asked too much, maybe you or somebody else could help me getting the

Re: [R] Computing plot size in Sweave

2012-02-20 Thread Yihui Xie
I guess that is not possible with Sweave, but it is possible in the knitr package (an alternative to Sweave). You can set opts_knit$set(eval.opts = c('fig.height', 'fig.width')) so that these two options will be evaluated as R expressions (e.g. fig.height=x means it takes value from a variable

Re: [R] Column wise matrix multiplication

2012-02-20 Thread Ted Harding
On 20-Feb-2012 Graziano Mirata wrote: Hi all, I am trying to multiply each column of a matrix such to have a unique resulting vector with length equal to the number of rows of the original matrix. In short I would like to do what prod(.) function in Matlab does, i.e. A -matrix(c(1:10),5,2)

[R] How to change the objective function of quantile regression?

2012-02-20 Thread Nathalie Sanches
Dear all, I need to run a quantile regression but considering a different objective function to be minimized: instead of finding the parameters that minimize rho(t) = u*(t - I(u0)), I need to find the parameters beta that minimize a sum of two rho functions rho(t1) = u1*(t1 - I(u10)) and

[R] Disabling shell access through system() possible?

2012-02-20 Thread lists
Hi! I'm deploying R behind a web-app on a linux-server and I don't want to grant the users shell access through the system() function for security reasons. Is there any safe way to deny a user access to the function? I tried a) alter the function in the R-Sources before compiling them.

Re: [R] Sorting strings

2012-02-20 Thread statquant2
NICE DDE It solves my problem ! Awesome stuff -- View this message in context: http://r.789695.n4.nabble.com/Sorting-strings-tp4403696p4404424.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list

[R] how to How to compare the concordance index between two nomograms with R

2012-02-20 Thread lijundfgd
I have got two kinds of nomogram for the same data set analyzed by Cox regression. My question is how to compare the concordance index between these two nomograms with R? -- View this message in context:

[R] Time Series - Trend Line

2012-02-20 Thread anaraster
How can I had a trend line to my plot? My data looks like this: Date=seq(as.Date(1910/1/1), as.Date(1920/1/1), day) Values=runif(length(Date), min=-5, max=5) dataset=data.frame(Values,as.Date(Date)) I just want to add a linear trend line to this plot(dataset,col=rgb(1,0,0,1/8),cex=0.5,pch=19)

Re: [R] overlay of two sets of boxplots

2012-02-20 Thread Mirjam Appel
Hello John, Thanks for your fast answer. I will try to be clearer and more detailed this time. At the moment I am importing a dataframe like below as a '.csv file'. I want to generate a boxplot for M and F values grouped by X whereby boxplots for M and F should be above or very close to each

Re: [R] overlay of two sets of boxplots

2012-02-20 Thread David Winsemius
On Feb 20, 2012, at 1:59 PM, Mirjam Appel wrote: Hello John, Thanks for your fast answer. I will try to be clearer and more detailed this time. At the moment I am importing a dataframe like below as a '.csv file'. I want to generate a boxplot for M and F values grouped by X whereby

Re: [R] Disabling shell access through system() possible?

2012-02-20 Thread Petr Savicky
On Mon, Feb 20, 2012 at 06:17:23PM +0100, li...@mwoywod.de wrote: Hi! I'm deploying R behind a web-app on a linux-server and I don't want to grant the users shell access through the system() function for security reasons. Is there any safe way to deny a user access to the function? Hi.

Re: [R] JGR Segmentation fault

2012-02-20 Thread dberringer
The http://mxcl.github.com/homebrew/ Homebrew package manager is an exelent way to manage packages like R on osx. I highly recommend it to any developer. I am hoping there are others in the R community that are interested in getting this working too. Does anyone else run a Homebrew install of

[R] error with persp()- increasing 'x' and 'y' values expected

2012-02-20 Thread adick
I want to use persp to graph my data and it keeps giving me the error increasing 'x' and 'y' values expected, even though my data is in increasing order with respect to x and y. Here is the code I'm currently using: bob= scan (SBA3dataTaxonB.txt,what=char) labels = bob[1:3] bob=bob[-c(1,2,3)]

Re: [R] overlay of two sets of boxplots

2012-02-20 Thread John Kane
Does something like the code below give you want you want? It requires the ggplot2 package so you will likely have to install it. John Kane Kingston ON Canada # sample data converted using dput xx - structure(list(X = c(Exp1, Exp1, Exp1,

Re: [R] error with persp()- increasing 'x' and 'y' values expected

2012-02-20 Thread David Winsemius
On Feb 20, 2012, at 2:15 PM, adick wrote: I want to use persp to graph my data and it keeps giving me the error increasing 'x' and 'y' values expected, even though my data is in increasing order with respect to x and y. Do you have missing entries? (Running your data fragment through

Re: [R] Computing plot size in Sweave

2012-02-20 Thread Marc Schwartz
On Feb 20, 2012, at 9:15 AM, BXC (Bendix Carstensen) wrote: Sometimes you want to compute the physical size of a plot based on data. In R itself this is no problem. But is there a way to compute the values of height and width in S-weave, say: graph,fig=TRUE,height=xx,width=yy= where xx

Re: [R] Column wise matrix multiplication

2012-02-20 Thread Ted Harding
[See at end] On 20-Feb-2012 Ted Harding wrote: On 20-Feb-2012 Graziano Mirata wrote: Hi all, I am trying to multiply each column of a matrix such to have a unique resulting vector with length equal to the number of rows of the original matrix. In short I would like to do what prod(.)

Re: [R] Time Series - Trend Line

2012-02-20 Thread R. Michael Weylandt
This isn't being plotted with any special time series methods (because it's not a time-based object here) so ?abline will work. Michael On Mon, Feb 20, 2012 at 12:14 PM, anaraster rrast...@gmail.com wrote: How can I had a trend line to my plot? My data looks like this:

[R] counting characters starting point

2012-02-20 Thread Juliet Ndukum
I have three character strings represented below as seq1, seq2, and seq3. Each string has a reference character different from the other. Thus, for seq1, the reference character is U, seq2, S (3rd S from left where A is leftmost character) and for seq3 Y. seq1 = PQRTUWXYseq2 = AQSDSSDHRSseq3 =

[R] slope in curves - how to compare?

2012-02-20 Thread John Kohr
Hello, Is there any formula or way to compare slopes of different functions? If we fit 2 functions in our data, and we have 2 slope parameters, how can we compare these slopes? Plotting y=5x and y=exp(5x) in which slope is equal to 5 in both of them.. doesn't seem that it makes sense to

Re: [R] how to How to compare the concordance index between two nomograms with R

2012-02-20 Thread Frank Harrell
A nomogram is a graphical device for displaying a model. Please try again with your question. If you also wrote me privately earlier today please choose one mode of communication. Thanks Frank lijundfgd wrote I have got two kinds of nomogram for the same data set analyzed by Cox regression.

Re: [R] Computing plot size in Sweave

2012-02-20 Thread Yihui Xie
Yes, with the old good cat() and results=tex, you can do anything. It is just so unnatural. Why must a simple task like setting the size of a plot involve with so much coding work? % complete knitr code setup, include=FALSE= opts_knit$set(eval.opts = c('fig.height', 'fig.width')) my.height = 6;

Re: [R] slope in curves - how to compare?

2012-02-20 Thread Joshua Wiley
Hi John, What do you mean by 'compare'? y = exp(5x) could equally be said: y = exp(x)^5 so no, the slopes of those two lines are not the same or are only equal when you take the natural logarithm of y (log_{e}(y) = log_{e}(5x). They specify _completely_ different relationships between x and y;

[R] prediction for linear mixed model

2012-02-20 Thread array chip
Hi, I am wondering if we can make prediction on a linear mixed model by lmer() from lme4 package? Specifically I am fitting a very simple glmer() with binomial family distribution, and want to see if I can get the predicted probability like that in regular logistic regression?  

[R] Call R from C

2012-02-20 Thread nitin kumar
Dear All, I am new to calling R in C. I want to call sample R function in C. i.e. I want to do a sample equivalent to n - c(1:10) p - seq(0,10,length.out= 10) sample(n,size = 1, prob = p, replace = FALSE) how can I call this function directly in C? any help would be great, thanks, nitin

[R] bigmemory not really parallel

2012-02-20 Thread Lishu Liu
Hi, all, I have a really big matrix that I want to run k-means on. I tried: data - read.big.memory('mydata.csv',type='double',backingfile='mydata.bin',descriptorfile='mydata.desc') I'm using doMC to register multicore. library(doMC) registerDoMC(cores=8) ans-bigkmeans(data,k) In system monitor,

Re: [R] Call R from C

2012-02-20 Thread Steve Lianoglou
Hi, On Mon, Feb 20, 2012 at 6:15 PM, nitin kumar nit...@gmail.com wrote: Dear All, I am new to calling R in C. I want to call sample R function in C. i.e. I want to do a sample equivalent to n - c(1:10) p - seq(0,10,length.out= 10) sample(n,size = 1, prob = p, replace = FALSE) how

[R] question on axis labels

2012-02-20 Thread Gerard Smits
Hi All, I'm trying to label my plot axis with times (HH:MM) that correspond to a numeric index (values 0:6) for my time variable. I'd like to plot 08:00, 12:00, and so on, instead of 0 through 6. I have used the following line of code: axis(1, 0:6, labels=c(08:00, 12:00, 16:00, 20:00,

Re: [R] question on axis labels

2012-02-20 Thread Sarah Goslee
This works for me: plot(0:6, runif(7), xaxt=n) axis(1, at=0:6, labels=c(08:00, 12:00, 16:00, 20:00, 24:00, 04:00, 08:00), cex=0.8) You need the xaxt=n in the plot statement, and the correct form is at=0:6 Sarah On Mon, Feb 20, 2012 at 6:39 PM, Gerard Smits g_sm...@verizon.net wrote: Hi

[R] how to print km square in the form of km2

2012-02-20 Thread Elaine Kuo
Hello, This is Elaine. I am drawing a plot with x-axis label with km square as the unit. Now I want to print km square in the form of km2 and output 2 as the uppercase. Please kindly help suggest command to show the uppercase. Thank you. Elaine [[alternative HTML version deleted]]

Re: [R] question on axis labels

2012-02-20 Thread Gerard Smits
Worked like a charm! Thanks for your help. Gerard On Feb 20, 2012, at 3:52 PM, Sarah Goslee wrote: This works for me: plot(0:6, runif(7), xaxt=n) axis(1, at=0:6, labels=c(08:00, 12:00, 16:00, 20:00, 24:00, 04:00, 08:00), cex=0.8) You need the xaxt=n in the plot statement, and the

Re: [R] how to print km square in the form of km2

2012-02-20 Thread Rolf Turner
On 21/02/12 12:54, Elaine Kuo wrote: Hello, This is Elaine. I am drawing a plot with x-axis label with km square as the unit. Now I want to print km square in the form of km2 and output 2 as the uppercase. Please kindly help suggest command to show the uppercase. When you say as [the]

[R] bootstrap in time dependent Cox model‏

2012-02-20 Thread Ehsan Karim
Dear R-list, I am wondering how to perform a bootstrap in R for the weighted time dependent Cox model‏ (Andersen–Gill format, with multiple observations from each patients) to obtain the bootstrap standard error of the treatment effect. Below is an example dataset. Would 'censboot' be

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