[R] Re : left truncated data survival analysis package

Sir, This kind of analysis is new to me, s oI m sorry if I m asking "stupid" questions below... In my study, patients might have been sick for years before the diagnosis is made, then they can die few months later, once diagnosed, either from their disease or because they are elderly patien

Re: [R] Does The Randvar package contain a virus(Malware) ?

there were only minor changes in the latest version of RandVar (from 0.6.6 to 0.6.7). Might this be a mirror problem? Best Matthias Timthy Chang wrote: Today,I update the packages in R. but AntiVir Guard dectects the Randvar package as affected file. What happen ?? Thank you for your answer.

Re: [R] rounding problem

I think your subject line should read 'Excel bug'. From the R help for round() Note that for rounding off a 5, the IEC 60559 standard is expected to be used, '_go to the even digit_'. In case you did not recognize it, IEC 60559 is an international standard: Excel is not. R is Open

[R] nls does not accept start values

Hi to all OK as I did not get any response and I really need some insight I try again with different subject line I have troubles with correct evaluating/structure of nls input Here is an example # data x <-1:10 y <-1/(.5-x)+rnorm(10)/100 # formula list form <- structure(list(a = list(quote(y

Re: [R] Adjusting confidence intervals for paired t-tests of multiple endpoints

Hi Erich, Look at the SimComp package, which handles multiple endpoints, i.e. columns of response variables. Ratio-comparisons are also handled. Good ready-made range of comparisons; you can also set up your own. Regards, Mark. Erich Studerus wrote: > > Johannes Huesing wrote: >> Couldn't

Re: [R] probleme with savePlot (to eps)

I don't see an OS mentioned in this thread. There are two separate functions called savePlot(), one for Windows devices and one for cairo-based X11(); the latter being quite recent. We do ask for 'at a minimum information' in the posting guide, and providing this helps the readers to know whi

[R] question of correlation structure in gls

Dear R users, I want to fit a model with within-subject correlations but with no random effects. So I could use gls to set correlation=corSymm(~1 | group). Here the problem I encountered is that I have 90 groups, and for the first, second and third 30 groups I want them to have three different u

Re: [R] How to normalize to a set of internal references

you should better ask this question on the Bioconductor mailing list. For qPCR normalisation strategies take a look at http://www.gene-quantification.info/ Best, Matthias Waverley wrote: Thanks for the advice. My question is more on how to do this? Let me use a biology gene analysis example t

[R] How to normalize to a set of internal references

Thanks for the advice. My question is more on how to do this? Let me use a biology gene analysis example to illustrate: In biology, there are always some house keeping genes which differ little even at pathological conditions. We know that at different batches, there are external factors affect

Re: [R] Need help extracting info from XML file using XML package

A bit over a year ago I got useful advice from Gabor Grothendieck and Duncan Temple Lang in this thread: http://finzi.psych.upenn.edu/R/Rhelp02/archive/117140.html If the coordinates are nested deeply, then it probably safer to search for a specific tag or tags that are just above them . You

Re: [R] rounding problem

Yes, round(1.5)=2. but round(2.5)=2. I want round(2.5)=3 just like the what the excel do. Can we change the setting or do some trick so that the computer will work like what we usually do with respect to rounding. My system is R 2.8.1, winXP, Intel core 2 dual . Thanks. Daniel Nordlund-2 wrot

Re: [R] Partial sum of a vector

Per the help page rollapply needs to be given a zoo or ts object, so you just coerce the matrix to zoo: > data_m <- matrix(1:20, ncol=2) > data_q <-matrix(,nrow=7,ncol=2) # then you can vectorize the process > data_q[,] <-rollapply(as.zoo(data_m[,]),4,FUN=sum) > data_q [,1] [,2] [1,] 10

Re: [R] Partial sum of a vector

Thanks,   It worked. --- On Sun, 3/1/09, Jorge Ivan Velez wrote: From: Jorge Ivan Velez Subject: Re: [R] Partial sum of a vector To: "Mohammad Sabr" Cc: r-help@r-project.org Date: Sunday, March 1, 2009, 11:20 PM Hi Mohammad, You need to download and then install the zoo package. Here is

[R] Need help extracting info from XML file using XML package

I have an XML file that has within it the coordinates of some polygons that I would like to extract and use in R. The polygons are nested rather deeply. For example, I found by trial and error that I can extract the coordinates of one of them using functions from the XML package: doc <- xml

[R] Does The Randvar package contain a virus(Malware) ?

Today,I update the packages in R. but AntiVir Guard dectects the Randvar package as affected file. What happen ?? Thank you for your answer. http://www.nabble.com/file/p22281513/qq.gif -- View this message in context: http://www.nabble.com/Does-The-Randvar-package-contain-a-virus%28Malware%2

Re: [R] Partial sum of a vector

perhaps this? M <- dim(data_m)[2] for(j in 1:M){ for (i in 4:T) { data_q[i-3,j]=sum(data_m[(i-3):i,j]) } } of course, you can vectorize this and speed it up significantly, but there is something evil about premature optimization. On Mar 2, 1:29 pm, Mohammad Sabr wrote: > I am t

Re: [R] Partial sum of a vector

Hi Mohammad, You need to download and then install the zoo package. Here is an example: > install.packages('zoo') > require(zoo) > x<-1:20 > 4*rollmean(x,4) [1] 10 14 18 22 26 30 34 38 42 46 50 54 58 62 66 70 74 HTH, Jorge On Sun, Mar 1, 2009 at 10:16 PM, Mohammad Sabr wrote: > Thanks Jorge,

Re: [R] Partial sum of a vector

Thanks Jorge,   I tried to use the rollapply function as follows:   rollapply(data_m ,4 , sum, by =1 , by.column = TRUE)   but it is giving me the following error message:   Error in UseMethod("rollapply") : no applicable method for "rollapply"   Is there any file that I need to install or update.

Re: [R] Partial sum of a vector

?filter > x [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 > filter(x, rep(1,4)) Time Series: Start = 1 End = 20 Frequency = 1 [1] NA 10 14 18 22 26 30 34 38 42 46 50 54 58 62 66 70 74 NA NA On Sun, Mar 1, 2009 at 9:29 PM, Mohammad Sabr wrote: > I am trying to run a loop wher

Re: [R] Partial sum of a vector

Dear Mohammad, Take a look at the rollmean function in the zoo package. HTH, Jorge On Sun, Mar 1, 2009 at 9:29 PM, Mohammad Sabr wrote: > I am trying to run a loop where I can sum parts of a matrix. For example, I > want at each step in the loop to sum the the next 4-values of a vector. I > tri

Re: [R] Question about normalization to a set of internal standards

Waverley wrote: Hi, I have a question of the method as how to normalize the data sets according to a set of the internal measurements. For example, I have performed two batches of experiments contrasting two different conditions (positive versus negative conditions): one at a time. 1. each exp

[R] Question about normalization to a set of internal standards

Hi, I have a question of the method as how to normalize the data sets according to a set of the internal measurements. For example, I have performed two batches of experiments contrasting two different conditions (positive versus negative conditions): one at a time. 1. each experiment, I measure

[R] Partial sum of a vector

I am trying to run a loop where I can sum parts of a matrix. For example, I want at each step in the loop to sum the the next 4-values of a vector. I tried to do the following but the result were wrong:   for (i in 4:T) { data_q[i-3,]=sum(data_m[i-3,]:data_m[i,]) }   can anyone please direct me o

Re: [R] Formatted text output

Bye Chuckles, killfiled. - Greg From: Charles C. Berry Cc: R-help Sent: Sunday, March 1, 2009 2:47:51 PM Subject: Re: [R] Formatted text output On Sun, 1 Mar 2009, Gregory Propf wrote: > How does one write formatted, say "C style", output to a text file. I

Re: [R] Understanding Anova (car) output

Dear Ista, > -Original Message- > From: istaz...@gmail.com [mailto:istaz...@gmail.com] On Behalf Of Ista Zahn > Sent: March-01-09 6:22 PM > To: r-help@r-project.org > Cc: John Fox > Subject: Understanding Anova (car) output > > Dear professor Fox and R helpers, > I have a quick question a

Re: [R] Statistic community?

statisticians_gr...@yahoogroups.co.in On Sat, Feb 28, 2009 at 5:40 PM, John Kane wrote: > Usenet groups sci.stat.math, sci.stat.consult ? > > > --- On Wed, 2/25/09, Peters Gj (PSYCHOLOGY) < > gj.pet...@psychology.unimaas.nl> wrote: > > > From: Peters Gj (PSYCHOLOGY) > > Subject: Re: [R] Statist

Re: [R] a very basic question: calling c function from R

On 01/03/2009 7:23 PM, Wang Chun wrote: Dear R users, I want to call C function from R. I follow the following instruction using the example of foo.c http://www.stat.umn.edu/~charlie/rc/ I save the foo.c in my current directory. Is that right? After I enter the command R CMD SHLIB foo.c, I ge

[R] a very basic question: calling c function from R

Dear R users, I want to call C function from R. I follow the following instruction using the example of foo.c http://www.stat.umn.edu/~charlie/rc/ I save the foo.c in my current directory. Is that right? After I enter the command R CMD SHLIB foo.c, I get the following message Error: unexpect

[R] gamm (mgvc) and time-varying coefficient model

Dear R users, I have repeated measurements on individuals. I want to estimate the time-varying effect of a factor variable X (taking three levels), e.g. a model in the spirit of Hastie and Tibshirani (1993). I am considering using the package "mgvc" which implements generalized additive model

Re: [R] probleme with savePlot (to eps)

So I guess the question to be answered by the OP now is what code he was using and what machine specifics he is working with. The bottom of my savePlot help page says [Package grDevices version 2.8.1 Index]. Is the difference due to our respective platforms (here Mac 10.5.6, sessionInfo

Re: [R] rgl persp3d bounding box color problem.

Thanks Duncan. I haven't got a chance to try it in windows yet. But I won't be surprised if it's my driver's fault. I had OpenGL problems on this dell laptop before. > Date: Sun, 1 Mar 2009 18:29:20 -0500 > From: murd...@stats.uwo.ca > To: bozhou1...@hotmail.com > CC: remkoduur...@gmail.com

Re: [R] rgl persp3d bounding box color problem.

On 01/03/2009 5:54 PM, Bo Zhou wrote: site down.. here is the code library(rgl) plot1: persp3d(x=1:11,y=1:210,z=matrix(rep(1,11*210),11,210),col=matrix(rep("#FF",11*210),11,210)) plot2: persp3d(x=1:11,y=1:10,z=matrix(rep(1,11*10),11,10),col=matrix(rep("#FF",11*10),11,10)) Works

[R] gamm (mgvc) and time-varying coefficient model

Dear R users, I have repeated measurements on individuals. I want to estimate the time-varying effect of a factor variable X (taking three levels), e.g. a model in the spirit of Hastie and Tibshirani (1993). I am considering using the package "mgvc" which implements generalized additive models,

[R] Modifying a built-in R function

Hello, Something incredible (at least for me) has happen. Yesterday night I downloaded biplot.R to edit this function and add new features I wished. Namely I wanted to plot points belonging to different groups using different colors and symbols. I identified which part of the original code I had

Re: [R] rgl persp3d bounding box color problem.

On 01/03/2009 4:16 PM, Bo Zhou wrote: Thanks, Duncan. What's your platform? Could this be an issues related to my platform? I'm on Ubuntu 8.10 64bit using cran's R package. I built rgl package on my machine using install.packages(). I'm going to give it a try in windows. I tested on Windows

[R] Understanding Anova (car) output

Dear professor Fox and R helpers, I have a quick question about the Anova function in the car package. When using the default "type II" SS I get results that I don't understand (see below). library(car) Data <- data.frame(y=rnorm(10), x1=factor(c(rep("a",4), rep("b",6))), x2 = factor(c(rep("j", 2)

Re: [R] probleme with savePlot (to eps)

If you are able to switch to Windows it does seem to be supported there on savePlot. Usage savePlot(filename = "Rplot", type = c("wmf", "emf", "png", "jpg", "jpeg", "bmp", "tif", "tiff", "ps", "eps", "pdf"), device = dev.cur(), restoreConsole = TRUE) O

Re: [R] probleme with savePlot (to eps)

Unfortunately your burning desire to use savePlot for this purpose is not going to reconfigure the capabilities of that function. Just read the help page of savePlot: savePlot {grDevices} R Documentation Save Cairo X11 Plot to FileDescription Save the current page of a cairo X11() device to a

Re: [R] probleme with savePlot (to eps)

Thanks for your answer. Use the postscript device to save .ps or .eps files. Unfortunatly, I can't. I am using savePlot in a package. Several graphs (up to 100) are exported at the same time and I would like the user to chose the extension. It is why I need savePlot. Beside, I did not find an

Re: [R] rgl persp3d bounding box color problem.

site down.. here is the code library(rgl) plot1: persp3d(x=1:11,y=1:210,z=matrix(rep(1,11*210),11,210),col=matrix(rep("#FF",11*210),11,210)) plot2: persp3d(x=1:11,y=1:10,z=matrix(rep(1,11*10),11,10),col=matrix(rep("#FF",11*10),11,10)) Thanks! Bo > Date: Mon, 2 Mar 2009 09:28:31 +

Re: [R] Formatted text output

On Sun, 1 Mar 2009, Gregory Propf wrote: How does one write formatted, say "C style", output to a text file. I want something like "y=mx+b" for my linear regressions but with m and b derived from the fit objects. Also, how does one go about extracting just the slope or intercept from such an

Re: [R] probleme with savePlot (to eps)

Use the postscript device to save .ps or .eps files. The help page for savePlot does not suggest that it would be of any value in saving plots as postscript files. ?postscript ?Devices -- David Winsemius On Mar 1, 2009, at 5:28 PM, Christophe Genolini wrote: Hi the list, I used savePlot

[R] probleme with savePlot (to eps)

Hi the list, I used savePlot to export some eps graph but it seems that the graph file hold a bug. I include the graph.eps in a LaTeX file. Running latex is ok. But the dvi file contain some mistake, the graph overprint on some text and hide it. Then, when I try to convert it to another format

Re: [R] smoothing a matrix (interpolate in plane)

Žroutík gmail.com> writes: > I'd like to smooth a matrix to dismiss spikes and to interpolate in plane > interp.loess in package tgp works nicely for me. Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE

Re: [R] projecting GIS coordinates for analysis with spatstat package

https://answers.google.com/answers/threadview?id=577262 On Mar 1, 2009, at 3:22 PM, Markus Weisner wrote: I am working on creating an R package for doing fire department analysis and am trying to create a function that can display emergency incident densities. The following code sort of doe

Re: [R] rgl persp3d bounding box color problem.

Thanks, Duncan. What's your platform? Could this be an issues related to my platform? I'm on Ubuntu 8.10 64bit using cran's R package. I built rgl package on my machine using install.packages(). I'm going to give it a try in windows. I would be very grateful if anyone using similar setup coul

[R] projecting GIS coordinates for analysis with spatstat package

I am working on creating an R package for doing fire department analysis and am trying to create a function that can display emergency incident densities. The following code sort of does the trick, but I need a display that shows the number of incidents per square mile. I believe the code below s

Re: [R] Legend outside plot box?

On Mar 1, 2009, at 2:45 PM, Gregory Propf wrote: I'm trying to put the legend in my matplot plot outside the plot box and it just doesn't seem to want me to. If I use a negative value for "inset" I just see only the part of the legend that is inside the plot box. Any ideas? - Greg H

Re: [R] Formatted text output

The innards of an object can be revealed with the str function and the coef function should have been a link off the lm page (assuming that was the sort of "fit" you were creating.) For output to files see ?cat On Mar 1, 2009, at 3:15 PM, Gregory Propf wrote: How does one write formatted,

[R] Formatted text output

How does one write formatted, say "C style", output to a text file. I want something like "y=mx+b" for my linear regressions but with m and b derived from the fit objects. Also, how does one go about extracting just the slope or intercept from such an object. - Greg [[alterna

Re: [R] Combining 2 arrays into a third array via a function

Better to not use c as a variable name. It's such a useful function name. This is what I would have tried: col3 <- expand.grid(item=params.data$item, examinee=examinees.data $examinee) col3$p_val <- p( c( params.data[ col3["item"], c("a1", "a2", "b1", "b2", "c") ], exami

[R] Legend outside plot box?

I'm trying to put the legend in my matplot plot outside the plot box and it just doesn't seem to want me to. If I use a negative value for "inset" I just see only the part of the legend that is inside the plot box. Any ideas? - Greg [[alternative HTML version deleted]] __

Re: [R] Balanced design, differences in results using anova and lmer/anova

Not sure --- never sure with this stuff! :-) --- but I think that your problem might be (at least in part) that the coding for block is repeated within each location. Block 1 in location 1 is *not* the same as block 1 in location 2; this is what nesting in effect means. The structure of lm

Re: [R] R tools help

Hi , I have put screenshot of my path here http://docs.google.com/Doc?id=dcvss358_419cs3g8vht skeleton ran but had some errors ..R skeleton > package.skeleton("ohri") Creating directories ... Creating DESCRIPTION ... Creating Read-and-delete-me ... Saving functions and data ... Making help file

Re: [R] R tools help

On 01/03/2009 12:24 PM, Ajay ohri wrote: Dear List, I am trying to create a R package and having some issues with setting the path on a Windows XP . Could you point me to a tutorial that helps in creating R packages . I gave a tutorial on this at last year's useR meeting: the slides a

Re: [R] R tools help

On Sun, Mar 1, 2009 at 1:05 PM, Ajay ohri wrote: > Hi, > I ran it . I placed it in C:\Rtools > it ran for a sec and vanished Do you mean you placed Rcmd.bat in C:\Rtools? What you want to do is issue the command PATH from the Windows console and put it somewhere on the path shown. I keep a C:\b

Re: [R] creating log-log survival plots that are not inverted

Thanks Marc; That provides the answer that I had missed (and glaringly obvious now). The plot on p 128 of Therneau and Grambsch is correctly labeled with -Log(-Log(Survival). I was expecting Log(-Log(S)) based on my other references. -- David Winsemius On Mar 1, 2009, at 12:42 PM, Marc

[R] R package.skeleton

Hi I am getting the following error > package.skeleton("ohri") Creating directories ... Creating DESCRIPTION ... Creating Read-and-delete-me ... Saving functions and data ... Making help files ... Done. Further steps are described in './ohri/Read-and-delete-me'. Warning messages: 1: In dump(in

Re: [R] R tools help

Hi, I ran it . I placed it in C:\Rtools it ran for a sec and vanished Previously I have compiled R source code from command prompt and changed the path files already - do I need to change the path files back my path is this c:\rtools\bin I used this text for reference already and have be

Re: [R] R tools help

the exact problem is the gazillion tutorials when all i need is one standardized document which in bullet points lists do this, do this , bingo!. W. C. Fields - "I never drink water because of the disgusting things that fish do in it." On Sun, Mar 1, 2009 at 11:09 PM, Dirk Eddelbuettel wrote:

[R] Combining 2 arrays into a third array via a function

I'm completely stumped and seem to be going around for 2 days in the wrong circles. Here's what I have in 2 dataframes: > dim(params.data); head(params.data, n=2) [1] 284 6 itema1a2 b1 b2 c 11 0.6671587 0.9588642 -3.5 -3.437961 0.2 22 1.1296298 1.4899307 -3.5 -

Re: [R] creating log-log survival plots that are not inverted

Using Frank's survplot() which allows for user definable functions as the 'fun' argument, one could also do something like this: library(Design) neg.ll <- function(x) -log(-log(x)) survplot(fit, fun = neg.ll, conf = "none") and the subsequent examples seem to work as well, so if the output is

Re: [R] R tools help

On 1 March 2009 at 22:54, Ajay ohri wrote: | Dear List, | I am trying to create a R package and having some issues with setting the | path on a Windows XP . | | Could you point me to a tutorial that helps in creating R packages . http://lmgtfy.com/?q=create+a+R+package Seriously, there

Re: [R] R tools help

If you use Rcmd.bat from batchfiles (its a self-contained batch file that you place anywhere on your path which will find out where R is by looking in the registry and then run it and will also add MiKTeX and Rtools to your path temporarily as well): http://batchfiles.googlecode.com then you won'

Re: [R] creating log-log survival plots that are not inverted

Here is a modification of some simplistic code that I had sent Bob offlist for the gastric data specifically. I created a function and made it a bit more generic, for multiple 'strata', though there is no real error checking, etc. which would be needed to make it more robust for production along

[R] R tools help

Dear List, I am trying to create a R package and having some issues with setting the path on a Windows XP . Could you point me to a tutorial that helps in creating R packages . Also I tried installing Linux using the Windows installer wubi but it failed repeatedly and everytime it resets

Re: [R] SPSS repeated interaction contrast in R

Fast question:is the design well balanced ? Cause if not, it might be because R's aov goes with SS type 1, while SPSS goes with SS type 3. For more info on this search for discussions with: "car", Anova, SS type III, and repeated measures Tal On Sun, Mar 1, 2009 at 11:13 AM, René Mayer wrot

[R] Mersenne-Twister RNG

Hello, I have a question regarding the default RNG in R. The helps indicate that : The default is "Mersenne-Twister". From Matsumoto and Nishimura (1998). A twisted GFSR with period 2^19937 - 1 and equidistribution in 623 consecutive dimensions (over the whole period). The ‘seed’ is a

Re: [R] Adjusting confidence intervals for paired t-tests of multiple endpoints

Johannes Huesing wrote: Couldn't you re-phrase your model by including timepoint as a continuous regressor and scale as a factor? Well, the measuring time points are 70 170, 300 and 1440 minutes after drug intake. Since the influence of time is cerainly not linear, I think it's better to tr

[R] Would you please check my program

Dear All I have written a program in R for the calculation of Structure Function(SF). I have attached my data here which is the data of 3rd attachment here. ( they have calculated SF and p0lotted it. ) I want to check my results I have tried it on already published results. I thi

Re: [R] rgl persp3d bounding box color problem.

On 28/02/2009 4:20 PM, Bo Zhou wrote: Hi guys, I hit on a problem when I use rgl. Could you try to run the code here in this link and see why the first persp3d gives a red bounding box and the second shows black? They both show as black on my system. Duncan Murdoch http://rafb.net/p/g1i7

[R] smoothing a matrix (interpolate in plane)

Hi R-users, I'd like to smooth a matrix to dismiss spikes and to interpolate in plane example of a matrix: Map[1:3,1:3] [,1] [,2] [,3]... [1,] 34.4 34.2 35.1 [2,] 33.4 34.2 35.4 [3,] 34.1 33.2 32.1 dim(Map)[1] =/= dim(Map)[2] What functions can I use? Thanks a lot for any response,

Re: [R] rounding problem

> -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of tedzzx > Sent: Saturday, February 28, 2009 4:58 AM > To: r-help@r-project.org > Subject: [R] rounding problem > > > Hi all, > > According to the help page on round(), round(1.5

[R] SPSS repeated interaction contrast in R

dear all, i'm trying to reproduce an spss-anova in R. It is an 2x3x3 repeated measures desingn with repeated contrasts. In R i've coded a contrast matrix for all factors and made a split in the aov summary - but I can't get the repeated interaction contrasts. The output from SPSS looks like this

Re: [R] rounding problem

it the on-line help file of ?round, you can also find the functions: ceiling() floor() trunc() I hope it helps. Best, Dimitris tedzzx wrote: Hi all, According to the help page on round(), round(1.5) could be either 1 or 2. But I want to the answere to be 2 for sure just what we usually do.

[R] rounding problem

Hi all, According to the help page on round(), round(1.5) could be either 1 or 2. But I want to the answere to be 2 for sure just what we usually do. How can I do that? Thanks advance. Cheers Ted -- View this message in context: http://www.nabble.com/rounding-problem-tp22261852p22261852.html

[R] call lm function in R

Hello everybody, i have to make a c++ programm, which calls the function lm() in R. Therefore i installed the rcpp-package. There were some examples too. I tried something, but i have the problem with the SEXP structure: I want to call lm() without coming from R: class MyVectorFunc : public

Re: [R] Using JRI and Java 1.6 on MAC OS X

Thank you Prof. Ripley, Since I needed to build a prototype very quickly, I ended up using Rserve. I found it actually easier to use & setup with a couple of caveats (make sure to use the latest jave-new client from the Rserve sources from the rforge website – the version on rosuda.org seem

[R] arules: rules are built on item ordering in the dataframe, rather than

Hi, I'm trying out the package arules and I'm having a bit of trouble getting my data to work properly. I have a set of transactions with the purchased products but each product could appear in a different column in the data frame. This causes the rules to be built based on the ordering, which is