Re: [R] gsubfn, strapply, REGEX Problem

. The NEWS file in the gsubfn distribution does mention the change. On Tue, Oct 28, 2008 at 8:32 AM, Johannes Graumann [EMAIL PROTECTED] wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Thanks for looking at this. The \ was an oversight for the example, but the backref bit solves my

[R] Best way of figuring out whether graphical elements overlap?

Hi all, I'm plotting impulses, where some of them should have labels hovering above them. I know of plotrix' spread.labels function, but would like to save that for instances where there truely is to little space for the label. Does anybody have any hints what' the most efficient way might be

[R] heatmap on pre-established hclust output?

Hi, Can someone please guide me towards how to produce heatmap output from the output of hclust run prior to the actual heatmap call? I have some rather lengthy clustering going on and tweeking the visual output with heatmap recalculating the clustering every time is not feasible. Thanks, Joh

Re: [R] vioplot kernel smooth via density kernel smooth

posted mailed Johannes Graumann wrote: Vioplots have great appeal to me, as they manage to squeeze so much information into so little space ... Now some evaluation has made me suspicious about the implementation in the package vioplot and I would like to hear what you say about the appended

Re: [R] Feed list of vectors to vioplot()?

not # vioplot expects names as a plain vector, not in the # form names=c(One,Two,Three) ... names - c(One,Two,Three) do.call(vioplot,c(mylist,col=white,names)) Any help on how to do this? Thanks, Joh Johannes Graumann wrote: Off-list it was pointed out to me that the trivial solution to this would

Re: [R] Feed list of vectors to vioplot()?

Dirty solution: switched off x-axis plotting via 'par' and added it the personalized way with 'axis'. Joh Johannes Graumann wrote: Hm, now I have trouble using additional vioplot parameters. mu-2 si-0.6 bimodal-c(rnorm(1000,-mu,si),rnorm(1000,mu,si)) uniform-runif(2000,-4,4) normal

Re: [R] Feed list of vectors to vioplot()?

Johannes Graumann wrote: Hi, I have a list of vectors and am trying to coerce them into something that vioplot will take as groups of data to be plotted independently. Can someone nudge me into the right direction? Thanks, Joh __ R-help@r

Re: [R] Feed list of vectors to vioplot()?

a solution if we do not understand the problem to be solved. Sample data would be helpful along with an understanding of what you would expect for output. On Wed, Apr 23, 2008 at 10:11 AM, Johannes Graumann [EMAIL PROTECTED] wrote: Johannes Graumann wrote: Hi, I have a list of vectors

Re: [R] Feed list of vectors to vioplot()?

Off-list it was pointed out to me that the trivial solution to this would look like this: myfunction2 - function(x, ...){ mylist - list(x, ...) # plenty of lapply stuff do.call(vioplot,mylist) } Thanks for everybodies patience, Joh Johannes Graumann wrote: posted mailed Thanks

Re: [R] R CMD check PACKAGE Error

Prof Brian Ripley wrote: One thing I should add for the archives -- R 2.7.0 and later have oNew function showNonASCII() in package tools to aid detection of non-ASCII characters in .R and .Rd files. Is there any chance of having the output of this show up in the test log when

[R] Feed list of vectors to vioplot()?

Hi, I have a list of vectors and am trying to coerce them into something that vioplot will take as groups of data to be plotted independently. Can someone nudge me into the right direction? Thanks, Joh __ R-help@r-project.org mailing list

[R] R CMD check PACKAGE Error

Hi, Can anyone give me a hint on what's wrong if R CMD check PACKAGE gives me this error: Rd files with unknown encoding: FILENAME.Rd I have checked that file over and over and can't find any weired characters or some such. How can I fix this? Thanks for your time, Joh

[R] read.table and column class

Hi, I read in some tabular data using this: read.table(file, quote = \, header = TRUE, sep = \t, stringsAsFactors = FALSE, comment.char = ) One slight problem I have now is that some columns in the data set contain either or +, which means FALSE or TRUE respectively. The command

Re: [R] read.table and column class

, TRUE) y [1] FALSE FALSE TRUE FALSE TRUE Or define a custom class with an as() method and use that in colClasses. On Tue, Apr 15, 2008 at 5:10 AM, Johannes Graumann [EMAIL PROTECTED] wrote: Hi, I read in some tabular data using this: read.table(file, quote = \, header = TRUE, sep = \t

[R] Windows-GUI: Install Packages from local zip files and dependencies

Hi, When using the Packages -- Install packages from local zip files menu item in the windows-gui: 1) is that supposed to automatically pull in dependencies (in that case I have to fix something in my package). 2) If that's not the default: is there a way to make it so? Thanks, Joh

[R] layout: how to check whether a pending plot is going to happen within layout or not?

How can I test whether a plot I'm about to call will be within a layout or not? I need to fix some par options based on that ... Thanks, Joh __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

[R] Package Building and Name Space

Hello, I just don't get this and would appreciate if someone could write a line or two: I'm trying to build this package and it stops installing after I add the following to the NAMESPACES file: importFrom(gsubfn,strapply) The error during the package test is: Error in MyPackage::MyFunction :

Re: [R] Package Building and Name Space

need to rely on the old mechanism using require(). Apart from that, it also seems that 'strapply' package is not even in the R search path. Do you see it in the listing created by a call to library()? HTH, Michal Johannes Graumann-2 wrote: Hello, I just don't get this and would

Re: [R] non-plot plotting

Marc, you are kind of crazy ... I asked for a discussion of the path to take to get there, not to have it done ... but hey, what am I complaining about? ;0) Thank you very much! Joh Marc Schwartz wrote: Johannes Graumann wrote: I really do not know ho to else title this ... I want to draw

[R] Regex magic anyone?

Hi again, how to elegantly split s - ABCDEFGT(P)HIJK into A B C D E F G T(P) H I J K (independently of which letters 'T' or 'P' actually represent ...). Please jumstart my regexing, Joh __ R-help@r-project.org mailing list

Re: [R] Regex magic anyone?

at: http://gsubfn.googlecode.com and vignette: library(gsubfn); vignette(gsubfn) On Jan 18, 2008 9:09 AM, Johannes Graumann [EMAIL PROTECTED] wrote: Hi again, how to elegantly split s - ABCDEFGT(P)HIJK into A B C D E F G T(P) H I J K (independently of which letters 'T

[R] multiple text placements and expressions revisited

Hi all, I asked something like this earlier but decided that a proper minimal example might be helpfull ;0) Why does this work with regards to the expression (substitution): require(stats) plot(cars) text(5,120,labels=substitute(i^{z+phantom()}*(*a* AMU),list(i=yx,z=2,a=0)))

Re: [R] multiple text placements and expressions revisited

Thanks for your help! Works like a charm now - I can even append to an expression abject as if it was plain 'c()' ... Joh Prof Brian Ripley wrote: On Thu, 17 Jan 2008, Johannes Graumann wrote: Hi all, I asked something like this earlier but decided that a proper minimal example might

[R] non-plot plotting

I really do not know ho to else title this ... I want to draw something like the attached png with R and would like to poll you on how to start ... make an empty plot first and then start positioning the characterstring by 'text' and then drawing the lines ... Joh attachment:

Re: [R] plot labeling and expressions

Uwe Ligges wrote: Johannes Graumann wrote: Hi all, I'm trying to use an iteration that appends something to vector 'peaklabels' like so: peaklabelNames - append( peaklabelNames, substitute(i^{z+phantom()}* (*a*AMU),list(i=y2,z=2,a=0)) ) The vector is supposed

[R] plot labeling and expressions

Hi all, I'm trying to use an iteration that appends something to vector 'peaklabels' like so: peaklabelNames - append( peaklabelNames, substitute(i^{z+phantom()}* (*a*AMU),list(i=y2,z=2,a=0)) ) The vector is supposed to be used with 'text' to put labels on signals in an impulse

Re: [R] Plotting labeled impulses: label collision

Jim, I finally got back to this implementation of mine and dude, this function is amazing! Thank you so much! Joh On Saturday 05 January 2008 11:42:30 Jim Lemon wrote: Johannes Graumann wrote: Dear all, As you can see from the attachment I'm using R to automatically annotate peptide

[R] Efficient way to substract all entries in two vectors from each other

Hi all, I'm to inexperienced to come up with the matrix solution elusively appearing on the horizon for the following problem and would appreciate if you could give me a nudge ... I have two vectors a, and b and need to find the closest match for each value of a in b. How to do that efficiently?

Re: [R] Efficient way to substract all entries in two vectors from eachother

: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Johannes Graumann Sent: Monday, January 07, 2008 11:19 AM To: [EMAIL PROTECTED] Subject: [R] Efficient way to substract all entries in two vectors from eachother Hi all, I'm to inexperienced to come up with the matrix solution

Re: [R] Efficient way to substract all entries in two vectors from each other

Ido M. Tamir wrote: matchpt Thanks for this hint. It is exactly what I'm looking for. Cheers, Joh __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] Plotting labeled impulses: label collision

Dear all, As you can see from the attachment I'm using R to automatically annotate peptide fragmentation mass spectra, which are represented by impulse plots. I'd like to poll you on approaches of how to deal as generally as possible with the two biggest annotation issues I run into: 1) very

Re: [R] Finding overlaps in vector

. Split the output of cutree, instead. Continuing from the prior code: for(el in split(unname(vv), names(vv))) print(el) [1] 0.00 0.45 [1] 1 [1] 2 [1] 3.00 3.25 3.33 3.75 4.10 [1] 5 [1] 6.00 6.45 [1] 7.0 7.1 [1] 8 On Dec 21, 2007 3:24 PM, Johannes Graumann [EMAIL PROTECTED] wrote: Hm

Re: [R] Finding overlaps in vector

of cutree, instead. Continuing from the prior code: for(el in split(unname(vv), names(vv))) print(el) [1] 0.00 0.45 [1] 1 [1] 2 [1] 3.00 3.25 3.33 3.75 4.10 [1] 5 [1] 6.00 6.45 [1] 7.0 7.1 [1] 8 On Dec 21, 2007 3:24 PM, Johannes Graumann [EMAIL PROTECTED] wrote: Hm, hm, rect.hclust

Re: [R] Finding overlaps in vector

want to retain groups with 2+ elements then you can just Filter then out: twoplus - function(x) length(x) = 2 Filter(twoplus, split(seq_along(v), ct)) On Dec 22, 2007 5:12 AM, Johannes Graumann [EMAIL PROTECTED] wrote: But cutree does away with the indexes from the original input, which

[R] Finding overlaps in vector

posted mailed Dear all, I'm trying to solve the problem, of how to find clusters of values in a vector that are closer than a given value. Illustrated this might look as follows: vector - c(0,0.45,1,2,3,3.25,3.33,3.75,4.1,5,6,6.45,7,7.1,8) When using '0.5' as the proximity requirement, the

Re: [R] Finding overlaps in vector

6.45 7.00 7.10 8.00 On Dec 21, 2007 4:56 AM, Johannes Graumann [EMAIL PROTECTED] wrote: posted mailed Dear all, I'm trying to solve the problem, of how to find clusters of values in a vector that are closer than a given value. Illustrated this might look as follows: vector - c

Re: [R] Finding overlaps in vector

with more than 2 x.subsets - x.groups[sapply(x.groups, length) = 3] # print out the subsets invisible(lapply(x.subsets, function(a) print(vector[unique(a)]))) [1] 0.00 0.45 [1] 3.00 3.25 3.33 3.75 4.10 [1] 6.00 6.45 [1] 7.0 7.1 On Dec 21, 2007 4:56 AM, Johannes Graumann [EMAIL PROTECTED] wrote

Re: [R] Factor Madness

). This means that it will split matrix columns in data frame arguments, and convert character columns to factors unless stringsAsFactors = TRUE is passed. (I'm guessing 'spectrum' is a data.frame before the code fragment you've shown) hope this helps, Tony Plate Johannes Graumann wrote: Why

[R] All anchored series from a vector?

Hi all, What may be a smart, efficient way to get the following result: myvector - c(A,B,C,D,E) myseries - miracle(myvector) myseries [1] [[1]] A [2] [[1]] A B [3] [[1]] A B [4] [[1]] A B C [5] [[1]] A B C D [6] [[1]] A B C D E Thanks for any hints, Joh

Re: [R] All anchored series from a vector?

Debugged version: lapply(1:length(myvector), function(.length) { myvector[1:.length] }) Thanks for showing the direction! Joh [EMAIL PROTECTED] wrote: From: Johannes Graumann [EMAIL PROTECTED] Date: 2007/12/18 Tue PM 04:40:37 CST To: [EMAIL PROTECTED] Subject: [R] All anchored series from

Re: [R] All anchored series from a vector?

Nothing to be sorry about. You suggested a viable solution untested ... my job to figure it out ;0) Joh [EMAIL PROTECTED] wrote: From: [EMAIL PROTECTED] Date: 2007/12/18 Tue PM 02:50:52 CST To: Johannes Graumann [EMAIL PROTECTED] Cc: r-help@r-project.org Subject: Re: [R] All anchored series

Re: [R] Extracting clusters from Data Frame

Gustaf Rydevik wrote: On Dec 10, 2007 2:28 PM, Johannes Graumann [EMAIL PROTECTED] wrote: Hello, I have a large data frame (1006222 rows), which I subject to a crude clustering attempt that results in a vector stating whether the datapoint represented by a row belongs to a cluster

[R] R CMD Build feature searches or requests

Hello, I'm missing two features in R CMD build: 1) Easy building of Windows/zip packaged package version alongside the *nix-style *.tar.gz. Right now I'm doing a scripted version of R CMD build PACKAGE R CMD INSTALL PACKAGE mkdir tmp cp -r

[R] Building package - tab delimited example data issue

Hello, I'm trying to integrate example data in the shape of a tab delimited ASCII file into my package and therefore dropped it into the data subdirectory. The build works out just fine, but when I attempt to install I get: ** building package indices ... Error in scan(file, what, nmax, sep,

Re: [R] Building package - tab delimited example data issue

Johannes Graumann wrote: On Thursday 06 December 2007 11:52:46 Peter Dalgaard wrote: Johannes Graumann wrote: Hello, I'm trying to integrate example data in the shape of a tab delimited ASCII file into my package and therefore dropped it into the data subdirectory. The build works out

Re: [R] Building package - tab delimited example data issue

Peter Dalgaard wrote: Answering to myself and staying with the same example: system.file(data/stroke.csv,package=ISwR) allows direct access to the example file (name). Yes, but... This works right until you turn on LazyData for your package, then you end up with only

[R] Attempt at package documentation on debian: link to data.frame broken

Hello, I'm trying to document this little package I'm working on and have the following issue: one of the man files (*.Rd) contains this bit \value{ Returns a \code{\link[base]{data.frame}} representing the tabular data. } The resulting link is broken on my debian system. It points to

Re: [R] Attempt at package documentation on debian: link to data.frame broken

Prof Brian Ripley wrote: So you are talking about the HTML conversion of your help (.Rd) file? (Links appear in other versions too.) The HTML links are intended to be used via help.start(), not directly, and I think you find it actually points to ../../base/html/data.frame.html, which is

Re: [R] Attempt at package documentation on debian: link to data.frame broken

posted mailed Prof Brian Ripley wrote: Using non-linked HTML file: style sheet and hyperlinks may be incorrect - which is what happens ... how to switch to linked HTML file? It all works via help.start() (as I did say), at least in a reliable R front end. Running help.start() is how you

Re: [R] Attempt at package documentation on debian: link to data.frame broken

December 2007 14:08:47 Prof Brian Ripley wrote: On Mon, 3 Dec 2007, Johannes Graumann wrote: posted mailed Prof Brian Ripley wrote: Using non-linked HTML file: style sheet and hyperlinks may be incorrect - which is what happens ... how to switch to linked HTML file? It all works via

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