Re: [R] Problem reading binaries created with fortran
On 17/12/2009 3:48 PM, kapo coulibaly wrote: Is it possible to read fortran binaries with R? I tried unsucessfully and my understanding is that fortran write binaries with leading and trailing bytes. I get numbers but not the right ones. Thanks ps: the binary I'm interested in reading is a MODFLOW output with a mix of character, double and integers. R can read most binary files, as long as you tell it the right format to read. You need to consult the documentation of the program that produced the file to find out the format. If it adds leading or trailing bytes, just tell R to skip over those --- but you need to know how much to skip. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem reading binaries created with fortran
On 17/12/2009 3:48 PM, kapo coulibaly wrote: Is it possible to read fortran binaries with R? I tried unsucessfully and my understanding is that fortran write binaries with leading and trailing bytes. I get numbers but not the right ones. Thanks ps: the binary I'm interested in reading is a MODFLOW output with a mix of character, double and integers. One other thing: the hexView package does a very nice job of displaying the file, so you can work out what the structure is if the documentation is unclear (or nonexistent). Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave Makefile issue
On 17/12/2009 3:19 PM, Luc Villandré wrote:
Dear R-specialists,
I am trying to create a Makefile that will first convert all my .Rnw
files into .tex files and then, that will run the LaTeX compiler to
produce a pdf document. This issue has been discussed before. Hence,
I've basically adapted a Makefile I found at
http://n4.nabble.com/R-Sweave-R-and-complex-latex-projects-td810020.html#a810023
to make it compatible with a Windows XP environment. You will find my
version of it at the end of this message.
It doesn't exactly address your question, but you might also want to
look at the patchDVI package on R-forge. It takes a Rnw file as input,
runs Sweave and some version of latex, then patches the result so that
reverse search (from the .dvi or a .pdf with synctex) goes back to the
Rnw file instead of going to the .tex file.
It doesn't address the problem of an output file depending on multiple
.Rnw files, but it does at least handle the case of one .Rnw being
included by a master .tex file. For example, I use something close to
this in a batch file to process one .Rnw and display the whole thing:
echo library(patchDVI);SweaveMiktex('%2', '%3.tex') | Rterm --slave
yap -1 -s%1%2 %3.dvi
The arguments are
%1=line number,
%2=filename of .Rnw file,
%3=basename of master file (or of the filename)
Duncan Murdoch
However, it's not doing what I expect it to do. Instead of only using
pdfTeX on total_article.tex (which is the file with the necessary
headers and \include's), it tries to convert all my tex files into pdf,
which of course cannot be done since only total_article.tex has the
necessary structure to be understood by the compiler.
What's wrong then with this Makefile (I am using GNU Make 3.81)?
I will be grateful for any help you can provide.
_
MASTER = total_article.pdf
# the master document depends on all of the tex files
Rfile = prepareScript.R
RNWFILES = $(wildcard *.Rnw)
TEXFILES = $(wildcard *.tex)
DEPENDS = $(patsubst %.Rnw,%.tex,$(RNWFILES)) $(TEXFILES)
RERUN = (There were undefined references|Rerun to get
(citations|cross-references|the bars) (correct|right)|Table widths have
changed. Rerun LaTeX.|Linenumber reference failed)
RERUNBIB = No file.*\.bbl|Citation.*undefined
all : $(MASTER)
$(MASTER) : $(DEPENDS)
%.tex : %.Rnw
SWEAVE '$'
%.pdf : %.tex
@pdflatex $
@egrep -c $(RERUNBIB) $*.log (bibtex $*;pdflatex $); true
@egrep $(RERUN) $*.log (pdflatex $) ; true
@egrep $(RERUN) $*.log (pdflatex $) ; true
clean:
@del *.aux *.log *.bbl *.blg *.brf *.cb *.ind *.idx *.ilg \
*.inx *.ps *.dvi *.toc *.out *.lot *~ *.lof *.ttt *.fff \
*.eps *.pdf
@del -f $(patsubst %.Rnw,%.tex,$(RNWFILES))
script :
Rcmd BATCH $(Rfile)
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem reading binaries created with fortran (More infos)
On 17/12/2009 4:30 PM, kapo coulibaly wrote: The structure of the file is clear (see below) the first line is made of integers and doubles with the fifth being a text string followed by arrays of double precision number.: int1 int2 double1 double2 text int3 int4 int5 (array of double) here is an example of file: 1 1 1.0 1.0 HEAD 160 224 3 23.4 34.5 .. That's not the file that readBin is reading, that's the output from something that knows how to read it. If you show us the hex dump from hexView, it's likely we can suggest what to do to read it, especially knowing the above output. Duncan Murdoch I tried to read the first line with readBin (results are copied below): zz - file(heads.hds, rb) readBin(zz,what=integer,n=2) [1] 1 1 readBin(zz,what=double,n=2) [1] 7.812502e-03 6.013470e-154 readBin(zz,what=character,n=1) [1] HEAD readBin(zz,what=integer,n=3) [1] 14680064655360 Thanks On Thu, Dec 17, 2009 at 3:52 PM, Phil Spector spec...@stat.berkeley.eduwrote: Kapo - You'll get a better response if you tell us what you've already tried, and an even better response if you can provide a reproducible example. - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley spec...@stat.berkeley.edu On Thu, 17 Dec 2009, kapo coulibaly wrote: Is it possible to read fortran binaries with R? I tried unsucessfully and my understanding is that fortran write binaries with leading and trailing bytes. I get numbers but not the right ones. Thanks ps: the binary I'm interested in reading is a MODFLOW output with a mix of character, double and integers. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Getting Rd pages right for redefined S3 generic
On 17/12/2009 11:08 PM, S Ellison wrote: I'm writing a package, and would appreciate advice on controlling the help documentation cross-references for a redefined generic. I wanted to define a cbind equivalent for an object that mostly behaves like a data frame. base::cbind dispatches to a data frame method if _any_ parameter is a data frame, so I defined a new S3 cbind and cbind.default to handle dispatch on first object only. Though I confess that redefining cbind leaves me a tad nervous, that all works OK so far. However, R cmd tells me (rightly) that I haven't documented the generic and new default. But I don't want to; I want ?cbind to point to the base package help pages, not to mine. But then the documentation will be incorrect, since it mentions the non-standard handling of dataframes, which you've done away with. Assuming that's not unwise (?), what do I have to do to tell R cmd that it should not look for Rd docs for cbind and cbind.default in my package whilst still having my generic handle dispatch correctly? It looks like one answer _might_ be not to export my redefined cbind - but will a local generic still work properly if it's not exported? I would say that what you've done is unwise. I would rename the function to avoid future confusion, especially if you decide to export it. Even if it's for internal use only, won't you want a reminder in 2 years time that cbind(a,b) doesn't mean what the documentation says it means? Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to define new operators
On 18/12/2009 10:22 AM, berga...@gmail.com wrote:
Dear R community
I try to create a new operator to build a special sum of two CashFlows. (my
S4 Class)
I tried the following but this is actually not what I want.
setGeneric(++,function(e1,e2)standardGeneric(++))
setMethod(+,signature=list(CashFlow,CashFlow),function(e1,e2){
print(+)
})
setMethod(++,signature=list(CashFlow,CashFlow),function(e1,e2){
print(++)
})
The problem here is that this work but it treats ++ as a general
function.. the call is ++(e1,e2).
I'm looking for somthing like e3 - e1 ++ e2
The R parser limits the operators it recognizes to the predefined ones,
plus user-defined ones of the form %op% (where op could be ++ if you
liked). You can't define ++ as an operator because the parser will see
it as two plus signs, not as a single infix operator.
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Inserting .png plots in MS Word.
On 19/12/2009 1:28 PM, Wenjie Lee wrote: Hi R Users, I'm using following sample code to save png plots. png(file=sample.png, width=8, height=6) Then I copy or use insert pictures function to get the image into MS Word. After copying, if I try to stretch or re-size the image it starts getting distorted. Is there a way to standardized graph pixels so that the sharpness of the graph is maintained (at least for minor stretching/re-sizing). Is it possible to achieve this? I know I can change width and height, but I have to submit this .doc file to my adviser and he may need to re-size it. Any suggestion would be highly appreciated, If you want to resize the graphic, you shouldn't use a bitmap format. Use .pdf, .eps, .wmf, etc. It's still best to generate the graph at the final size (to get fonts and line widths right), but you'll get better results than with resizing a bitmap. I don't know which vector formats your advisor's version of MS Word supports, but presumably their docs will tell you. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Inserting .png plots in MS Word.
On 19/12/2009 3:06 PM, Wenjie Lee wrote: Thanks David and Duncan, pdf()/eps() are good options. Can you please tell which function produces .wmf images. win.metafile() (on Windows only, I think) produces .wmf images. I finally want to copy/insert these images into word file (.doc) and submit it to my adviser, and keep a possibility to re-size pictures. Is it possible to add these .pdf / .eps images into word (instead of latex). I don't know, I rarely use it. Duncan Murdoch Thanks, Wenjie On Sat, Dec 19, 2009 at 1:49 PM, Duncan Murdoch murd...@stats.uwo.ca mailto:murd...@stats.uwo.ca wrote: On 19/12/2009 1:28 PM, Wenjie Lee wrote: Hi R Users, I'm using following sample code to save png plots. png(file=sample.png, width=8, height=6) Then I copy or use insert pictures function to get the image into MS Word. After copying, if I try to stretch or re-size the image it starts getting distorted. Is there a way to standardized graph pixels so that the sharpness of the graph is maintained (at least for minor stretching/re-sizing). Is it possible to achieve this? I know I can change width and height, but I have to submit this .doc file to my adviser and he may need to re-size it. Any suggestion would be highly appreciated, If you want to resize the graphic, you shouldn't use a bitmap format. Use .pdf, .eps, .wmf, etc. It's still best to generate the graph at the final size (to get fonts and line widths right), but you'll get better results than with resizing a bitmap. I don't know which vector formats your advisor's version of MS Word supports, but presumably their docs will tell you. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Limit on number of times Realloc can be called?
Adam Waldemar Kowalewski wrote:
Hello,
I've been writing a program in C that will be called by R. I seem to have
stumbled upon an odd error that seems to suggest there is a limit on the
number of times Realloc (the R version as defined in the manual
R-extenstions not the C version realloc) when I try to use the
following program:
#include R.h
#include Rinternals.h
SEXP test_mem_alloc(SEXP z) {
double *t = Calloc(sizeof(double), double);
*t = 2;
SEXP end_product;
int i = 0;
for(i=1; i 20; i++) {
t = Realloc(t, sizeof(t) + sizeof(double), double);
The second argument to Realloc is supposed to be the number of elements
to allocate. sizeof(t) is 4 or 8 (32 bit or 64 bit), sizeof double is
8, so you always allocate 12 or 16 elements. Then in the next line you
write out of bounds.
Duncan Murdoch
t[i] = i;
}
PROTECT(end_product = allocVector(REALSXP,6));
for(i = 0; i 20; i++) {
REAL(end_product)[i] = t[i];
}
UNPROTECT(1);
Free(t);
return end_product;
}
I call it from R using the following script:
z - 1
test_mem_alloc - function(z) {
if(!(is.loaded(test_mem_alloc_v6))) dyn.load(test_mem_alloc_v6.dll)
out - .Call(test_mem_alloc,
as.double(z))
return(out)
dyn.unload(test_mem_alloc_v6.dll)
}
Basically I get the following error messages:
First:
Runtime Error!
Program: C:\Program Files\R\R-2.10.0\bin\Rgui.exe
This application has requested the Runtime to terminate it in an unusual
way. Please contact the application's support team for more information.
The second error message is:
The instruction at 0x002c. The memory could not be read.
Now, if change the number of times the program goes through the for loop
from 20 to say 6, and hence calls Realloc fewer times, then the program
runs without any problems. It does not seem to have anything to do with
the size of the memory being allocated as I changed the size of the total
memory being allocated with a for loop with only 6 iterations to
something that is substantially larger than the memory being allocated in
the for loop when calling Realloc twenty times and the program ran
successfully. Has anyone else come across this problem or knows about some
sort of limitation on using Realloc that is not specified in the R
documentation?
Any help would be greatly appreciated.
Yours sincerely
Adam Kowalewski
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Playing with rgl: a Youtube video
I've just posted a demo made with the rgl package to Youtube, visible here: http://www.youtube.com/watch?v=prdZWQD7L5c For future reference, here are the steps I used: 1. Design a shape to be displayed, and then play with the animation functions to make it change over time. Use play3d to do it live in R, movie3d to write the individual frames of the movie to .png files. 2. Use the ffmpeg package (not an R package, a separate project at http://ffmpeg.org) to convert the .png files to an .mp4 file. The individual frames totalled about 1 GB; the compressed movie is about 45 MB. 3. Upload to Youtube. I'm not a musician, so I had to use one of their licensed background tracks, I couldn't write my own. I spent a lot of time picking one and then adjusting the timing of the video to compensate. Each render/upload cycle at full resolution took about an hour and a half. It's a lot faster to render in a smaller window with fewer frames per second, but it's still tedious. It's easier to synchronize if you actually have a copy of the music locally, but Youtube doesn't let you download their music. So the timing isn't perfect, but it's good enough for me! Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with expand.grid
On 22/12/2009 11:19 AM, Keith Jewell wrote: Just confirming it isn't the bug fixed in 2.11.0dev, and giving an even simpler example: The docs for expand.grid say it works on lists, but they don't mention dataframes. Although a dataframe is in many ways a list with extra structure, apparently something in the subsetting done in expand.grid assumes it has a regular list, not a dataframe. So you might get what you want with expand.grid(as.list(dDF)), though this doesn't really make sense: do you really want 10^7 rows, with lots of repetition? I suspect you want to expand the grid of unique values in each column, which you could do using expand.grid(lapply(dDF, unique)) Duncan Murdoch R version 2.11.0 Under development (unstable) (2009-12-20 r50794) expand.grid(data.frame(y=1:10, t=1:10)) Error in `[[-.data.frame`(`*tmp*`, i, value = c(1L, 2L, 3L, 4L, 5L, 6L, : replacement has 100 rows, data has 10 Keith Jewell k.jew...@campden.co.uk wrote in message news:hgqqja$rk...@ger.gmane.org... Hi All, This example code dDF - structure(list(y = c(4.75587, 4.8451, 5.04139, 4.85733, 5.20412, 5.92428, 5.69897, 4.78958, 4, 4), t = c(0, 48, 144, 192, 240, 312, 360, 0, 48, 144), Batch = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ), T = c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2), pH = c(4.6, 4.6, 4.6, 4.6, 4.6, 4.6, 4.6, 4.6, 4.6, 4.6), S = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), N = c(0, 0, 0, 0, 0, 0, 0, 80, 80, 80)), .Names = c(y, t, Batch, T, pH, S, N), row.names = c(NA, 10L), class = data.frame) str(dDF) expand.grid(dDF) 'hangs' for a while and then gives an error Error in `[[-.data.frame`(`*tmp*`, i, value = c(4.75587, 4.8451, 5.04139, : replacement has 1000 rows, data has 10 In NEWS.R-2.11.0dev I read: o The new (in 2.9.0) 'stringsAsFactors' argument to expand.grid() was not working: it now does work but has default TRUE for backwards compatibility. but I don't think that's relevant, I have no factors. I'm probably being silly. Can anyone point out where? Best... Keith Jewell --please do not edit the information below-- Version: platform = i386-pc-mingw32 arch = i386 os = mingw32 system = i386, mingw32 status = Patched major = 2 minor = 10.1 year = 2009 month = 12 day = 21 svn rev = 50796 language = R version.string = R version 2.10.1 Patched (2009-12-21 r50796) Windows Server 2003 x64 (build 3790) Service Pack 2 Locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 Search Path: .GlobalEnv, package:stats, package:graphics, package:grDevices, package:utils, package:datasets, package:methods, Autoloads, package:base __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Playing with rgl: a Youtube video
On 22/12/2009 12:49 PM, Mark Knecht wrote: On Mon, Dec 21, 2009 at 4:42 AM, Duncan Murdoch murd...@stats.uwo.ca wrote: I've just posted a demo made with the rgl package to Youtube, visible here: http://www.youtube.com/watch?v=prdZWQD7L5c For future reference, here are the steps I used: 1. Design a shape to be displayed, and then play with the animation functions to make it change over time. Use play3d to do it live in R, movie3d to write the individual frames of the movie to .png files. 2. Use the ffmpeg package (not an R package, a separate project at http://ffmpeg.org) to convert the .png files to an .mp4 file. The individual frames totalled about 1 GB; the compressed movie is about 45 MB. 3. Upload to Youtube. I'm not a musician, so I had to use one of their licensed background tracks, I couldn't write my own. I spent a lot of time picking one and then adjusting the timing of the video to compensate. Each render/upload cycle at full resolution took about an hour and a half. It's a lot faster to render in a smaller window with fewer frames per second, but it's still tedious. It's easier to synchronize if you actually have a copy of the music locally, but Youtube doesn't let you download their music. So the timing isn't perfect, but it's good enough for me! Duncan Murdoch Cool enough video. Thanks for sharing. I'm curious - did you do the equations for the knot in R? If so what did they look like, assuming there's no reason you cannot share it. The knot has equation cbind(sin(theta)+2*sin(2*theta), 2*sin(3*theta), cos(theta)-2*cos(2*theta)) The threads in the braid have equation cbind(sin(theta) + sin(2*theta)/2, sin(theta-pi) + sin(2*theta)/2, theta) in the local coordinates of the knot. Overall it's about 100 lines of R code, too ugly to post. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Playing with rgl: a Youtube video
On 23/12/2009 7:13 AM, Rainer M Krug wrote: On Tue, Dec 22, 2009 at 8:10 PM, Duncan Murdoch murd...@stats.uwo.ca mailto:murd...@stats.uwo.ca wrote: On 22/12/2009 12:49 PM, Mark Knecht wrote: On Mon, Dec 21, 2009 at 4:42 AM, Duncan Murdoch murd...@stats.uwo.ca mailto:murd...@stats.uwo.ca wrote: I've just posted a demo made with the rgl package to Youtube, visible here: http://www.youtube.com/watch?v=prdZWQD7L5c For future reference, here are the steps I used: 1. Design a shape to be displayed, and then play with the animation functions to make it change over time. Use play3d to do it live in R, movie3d to write the individual frames of the movie to .png files. 2. Use the ffmpeg package (not an R package, a separate project at http://ffmpeg.org) to convert the .png files to an .mp4 file. The individual frames totalled about 1 GB; the compressed movie is about 45 MB. Could you please post the command line options you used for ffmpeg? I remember I wanted to do an animation, also from .png, and I struggled a lot. Sure. The png files were 1024 by 768, designed to be displayed at 24fps. The command line was ffmpeg -b 240 -r 24 -i movie%03d.png -s xga movie.mp4 The -b option controls the target bit rate. The -r option says how many frames per second, -i includes all the files (named things like movie001.png, etc.), -s sets the output size, with xga being a quick way to say 1024x768, and movie.mp4 is the output file. There are tons of options to change codec, etc., but I found the -b option was the only one I needed to play with. Duncan Murdoch Rainer 3. Upload to Youtube. I'm not a musician, so I had to use one of their licensed background tracks, I couldn't write my own. I spent a lot of time picking one and then adjusting the timing of the video to compensate. Each render/upload cycle at full resolution took about an hour and a half. It's a lot faster to render in a smaller window with fewer frames per second, but it's still tedious. It's easier to synchronize if you actually have a copy of the music locally, but Youtube doesn't let you download their music. So the timing isn't perfect, but it's good enough for me! Duncan Murdoch Cool enough video. Thanks for sharing. I'm curious - did you do the equations for the knot in R? If so what did they look like, assuming there's no reason you cannot share it. The knot has equation cbind(sin(theta)+2*sin(2*theta), 2*sin(3*theta), cos(theta)-2*cos(2*theta)) The threads in the braid have equation cbind(sin(theta) + sin(2*theta)/2, sin(theta-pi) + sin(2*theta)/2, theta) in the local coordinates of the knot. Overall it's about 100 lines of R code, too ugly to post. Duncan Murdoch __ R-help@r-project.org mailto:R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- NEW GERMAN FAX NUMBER!!! Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)321 2125 2244 email: rai...@krugs.de mailto:rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com mailto:r.m.k...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Unwanted association between a function and a namespace
On 23/12/2009 3:36 PM, p_conno...@slingshot.co.nz wrote: I can't understand how the plyr package is turning up here: sessionInfo() R version 2.10.1 (2009-12-14) i686-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grDevices utils stats graphics methods base other attached packages: [1] lattice_0.17-26 loaded via a namespace (and not attached): [1] grid_2.10.1 plyr_0.1.9 I can understand that lattice would be using grid without having that package loaded, but I can't understand how plyr got there. One way for this to happen is if you have a copy of a function from plyr in your global environment. The functions in plyr reference its namespace, so you'd get it loaded that way. It wouldn't matter if that namespace hadn't become associated somehow with a function I have somewhere else on the search path (thereby rendering the function unfindable). This doesn't make sense. If the function is on the search path, it doesn't matter what namespace is associated with it: you'll find it. If you have a function with the same name in globalenv() then you'll have problems. The simple solution is to remove it (e.g. rm(f)); a better long term solution is to *never* store anything in your workspace between sessions. Start with a clean global environment each time. Duncan Murdoch My guess is that if I knew how that happened, I'd then know why plyr is loaded by namespace. However, I'm lost for ideas on how that could have happened. Suggestions as to where I should be looking greatly appreciated. Or, even if that's unknowable, how to remove the association between the namespace and the function. TIA -- Patrick Connolly Plant Food Research Mt Albert Auckland New Zealand ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ I have the world`s largest collection of seashells. I keep it on all the beaches of the world ... Perhaps you`ve seen it. ---Steven Wright ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Unwanted association between a function and a namespace
On 23/12/2009 6:08 PM, p_conno...@slingshot.co.nz wrote:
Quoting Duncan Murdoch murd...@stats.uwo.ca:
On 23/12/2009 3:36 PM, p_conno...@slingshot.co.nz wrote:
I can't understand how the plyr package is turning up here:
[...]
I can understand that lattice would be using grid without having that
package loaded, but I can't understand how plyr got there.
One way for this to happen is if you have a copy of a function from plyr
in your global environment. The functions in plyr reference its
namespace, so you'd get it loaded that way.
I've never loaded the plyr package, except for when I used the reshape
package. It's possible at that time, I had occasion to use a function
I have of the same name as one in the plyr package, but I would not
have saved a copy of either function in the global environment.
It wouldn't matter if that namespace hadn't become associated somehow
with a function I have somewhere else on the search path (thereby
rendering the function unfindable).
This doesn't make sense. If the function is on the search path, it
doesn't matter what namespace is associated with it: you'll find it.
Perhaps I need to be more explicit. The find() function does indeed
find it, and I can edit it in ESS using the normal C-c C-d sequence.
HOWEVER, when I do args() of it, I get the args of the plyr function
-- even when I've not loaded that package. Trying to use the function
in code ends up calling the plyr function.
If you have a function with the same name in globalenv() then you'll
have problems. The simple solution is to remove it (e.g. rm(f)); a
better long term solution is to *never* store anything in your workspace
between sessions. Start with a clean global environment each time.
I thought I'd found a fix when I specifically loaded plyr and then
detached it with the unload = TRUE argument. sessionInfo() seems to
show that I had gotten rid of the plyr by namespace, but I still get this:
summarize
function(.data, ...) {
eval(substitute(data.frame(...)), .data, parent.frame())
}
environment: namespace:plyr
Curiouser and curiouser as Alice would say.
And where is that function? find(summarize) should tell you. The
fact that it has the plyr namespace as its environment doesn't mean it
is stored there.
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Remove double quotation marks
On 29/12/2009 1:16 PM, Lisa wrote: Dear All, I am not sure how to remove double quotation marks in a string, e.g., paste(variable, 1). Can anybody please help me solve it? Thank you in advance. I think you need to tell us what is wrong with what you get from that. When I look at the result: cat(paste(variable, 1), \n) variable 1 I see no quotation marks. (If you use print() you'll see some, but they aren't part of the string, they are just used in the default display by print().) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] pass functions and arguments to function
On 29/12/2009 3:08 PM, Hao Cen wrote:
Hi,
I wonder how to pass several functions and their arguments as arguments to
a function. For example, the main function is
f = function(X ) {
process1(X)
...
process2(X)
}
I have a few functions that operate on X, e.g. g1(X, par1), g2(X, par2),
g3(X, par3). par1, par2 and par3 are parameters and of different types. I
would like to pass g1, g2, g3 and their arguments to f and g1, g2, g3 may
appear to be in different orders. So that final effect of the passing is
Just pass them. If you know there are three functions, set up f as
f - function(X, f1, f2, f3, par1, par2, par3) {
process1(X)
f1(X, par1)
f2(X, par2)
f3(X, par3)
process2(X)
}
and call it as
f(X, g1, g2, g3, par1, par2, par3)
If you don't know how many functions there will be, put them in a list:
f - function(X, fs, pars) {
process1(X)
for (i in 1:length(fs)) fs[[i]](pars[[i]])
process2(X)
}
and call it as
f(X, list(g1, g2, g3), list(par1, par2, par3))
Duncan Murdoch
f = function(X ) {
process1(X)
g1(X, par1)
g2(X, par2)
g3(X, par3)
process2(X)
}
If I pass g2(X, par2),g3(X, par3), g1(X, par1) to f, I would expect to get
the effect of
f = function(X ) {
process1(X)
g2(X, par2)
g3(X, par3)
g1(X, par1)
process2(X)
}
Appreciate any suggestions.
thanks
Jeff
ps please ignore my previous blank subject email. It was accidentally sent
before the letter was completed.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] pass functions and arguments to function
On 29/12/2009 5:24 PM, Hao Cen wrote:
Thanks. I don't know how many functions there will be.
What if g1, g2, g3 have variable number of parameters? say g1 has parg1a,
parg1b, and g3 has parg3a, parg3b, parg3c, parg4d.
pars could be a list of lists of parameters instead of a list of
parameters, then the calls could be
do.call(fs[[i]], pars[[i]])
But it's very unlikely that you are doing something that's a good idea.
Duncan Murdoch
f - function(X, fs, pars) {
process1(X)
for (i in 1:length(fs))
fs[[i]](pars[[i]]) # doesn't work here
process2(X)
}
On Tue, December 29, 2009 4:57 pm, Duncan Murdoch wrote:
On 29/12/2009 3:08 PM, Hao Cen wrote:
Hi,
I wonder how to pass several functions and their arguments as arguments
to a function. For example, the main function is
f = function(X ) { process1(X) ...
process2(X) }
I have a few functions that operate on X, e.g. g1(X, par1), g2(X,
par2), g3(X, par3). par1, par2 and par3 are parameters and of different
types. I would like to pass g1, g2, g3 and their arguments to f and g1,
g2, g3 may appear to be in different orders. So that final effect of the
passing is
Just pass them. If you know there are three functions, set up f as
f - function(X, f1, f2, f3, par1, par2, par3) { process1(X) f1(X, par1)
f2(X, par2) f3(X, par3) process2(X) }
and call it as
f(X, g1, g2, g3, par1, par2, par3)
If you don't know how many functions there will be, put them in a list:
f - function(X, fs, pars) { process1(X) for (i in 1:length(fs))
fs[[i]](pars[[i]]) process2(X) }
and call it as
f(X, list(g1, g2, g3), list(par1, par2, par3))
Duncan Murdoch
f = function(X ) { process1(X) g1(X, par1) g2(X, par2) g3(X, par3)
process2(X) }
If I pass g2(X, par2),g3(X, par3), g1(X, par1) to f, I would expect to
get the effect of f = function(X ) { process1(X) g2(X, par2) g3(X, par3)
g1(X, par1) process2(X) }
Appreciate any suggestions.
thanks
Jeff
ps please ignore my previous blank subject email. It was accidentally
sent before the letter was completed.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] seg-fault... but on what
On 30/12/2009 9:20 AM, Nick Torenvliet wrote:
I got the following after running succesfully through this loop 28 million
times... the loop opens text files in a directory and inserts line by line
into a database...
This looks like a bug in RMySql or possibly R. What versions are you
using? Can you make it happen reproducibly with the same script? Can
you simplify the script so it happens quickly, rather than requiring 28
million iterations? Without a simple recipe to reproduce it, I doubt if
anyone would be able to track down the problem.
Duncan Murdoch
*** caught segfault ***
address 0xc010, cause 'memory not mapped'
Traceback:
1: .getGeneric(f, where, package)
2: getGeneric(coerce, where = where)
3: as(obj, integer)
4: mysqlConnectionInfo(dbObj, ...)
5: dbGetInfo(conn, rsId)
6: dbGetInfo(conn, rsId)
7: dbListResults(con)
8: dbListResults(con)
9: mysqlQuickSQL(conn, statement, ...)
10: dbGetQuery(con, sql)
11: dbGetQuery(con, sql)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(expr, error = function(e) {call - conditionCall(e)if
(!is.null(call)) {if (identical(call[[1L]],
quote(doTryCatch))) call - sys.call(-4L)dcall -
deparse(call)[1L]prefix - paste(Error in, dcall, : )
LONG - 75Lmsg - conditionMessage(e)sm - strsplit(msg,
\n)[[1L]]if (14L + nchar(dcall, type = w) + nchar(sm[1L], type =
w) LONG) prefix - paste(prefix, \n , sep =
)}else prefix - Error : msg - paste(prefix,
conditionMessage(e), \n, sep = ).Internal(seterrmessage(msg[1L]))
if (!silent identical(getOption(show.error.messages), TRUE))
{cat(msg, file = stderr())
.Internal(printDeferredWarnings())}invisible(structure(msg, class =
try-error))})
16: try(dbGetQuery(con, sql))
17: eval.with.vis(expr, envir, enclos)
18: eval.with.vis(ei, envir)
19: source(~/SoothSayer/EODData/DBScripts/loadEODQuotes.r)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
The code is pretty simple...
library(RMySQL)
drv - dbDriver(MySQL)
con - dbConnect(drv, host=localhost, dbname=markets, user=root,
pass=embryoni3)
fileList - list.files(pattern = [[:upper:]]{2,}, all.files = FALSE,
full.names = FALSE, recursive = FALSE, ignore.case = FALSE)
for (x in 1:length(fileList)){
string - strsplit(fileList[x], _, fixed = TRUE)
string - string[[1]][1]
fileLines - read.csv(fileList[x],header = FALSE,row.names = NULL )
for ( j in 1:length(fileLines[,1])){
sql - paste(insert into endOfDayData
(date,market,symbol,open,high,low,close,volume) values (',
fileLines[j,2],',',string,',',as.character(fileLines[j,1]),',',fileLines[j,3],',',fileLines[j,4],',',fileLines[j
,5],',',fileLines[j,6],',',fileLines[j,7],'),sep=)
#print(sql)
atmpt - try(dbGetQuery(con,sql))
options(show.error.messages = TRUE)
if(inherits(atmpt, try-error)){
}
}
}
dbDisconnect(con)
My understanding was that in general R liked to put a placekeeper like NA or
NULL in for non-existent elements of defined structures... so I was
surprised to see a seg fault... I'm having trouble interpretting the
error... any clues would be appreciated.
Nick
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Obtaining partial output from a function that does not run to completion.
On 31/12/2009 9:29 AM, John Sorkin wrote:
I have written a function that contains runs
lm()
vif() and
glm()
When the glm() blows up with an error message, I don't get the output from
either the lm() or vf() even thought neither lm() nor vif() have any problems .
How can I force the function to print sequential results rather than wait for
the entire function to complete before listing the functhion's output?
Call print, e.g.
print(x - lm(...))
print(y - vif(...))
etc.
Duncan Murdoch
Thanks,
John
minBMI-function(SS,SimData)
{
SampleData-sample(1:SS,size=SS,replace=TRUE)
fitBMIEpiRevlm-lm(AAMTCARE~BMIEpiRevAdjc+BMIEpiRevAdjcSq+SEX+jPHI+jMEDICAID+H_AGE+jMARSTAT+factor(jEDUCATION)+factor(jsmokercat)+factor(jrace)+log(INCOME_C+1),data=SimData[SampleData,],x=TRUE)
print(summary(fitBMIEpiRevlm))
print(vif(fitBMIEpiRevlm))
fitBMIEpiRev-
glm(AAMTCARE~BMIEpiRevAdjc+BMIEpiRevAdjcSq+SEX+jPHI+jMEDICAID+H_AGE+jMARSTAT+factor(jEDUCATION)+factor(jsmokercat)+factor(jrace)+log(INCOME_C+1),data=SimData[SampleData,],family=Gamma(link=log))
print(summary(fitBMIEpiRev))
}
minBMI(SS,SimData)
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for th...{{dropped:6}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Obtaining partial output from a function that does not run to completion.
John Sorkin wrote:
Duncan,
Thank you, however, if you will look at my function (bottom of this Email
message), you will see that I have used print(). It appears that the print
function is not run until the entire function completes running.
No, statements are run in the order you give them. The output of the
prints might not appear immediately, but they will be executed.
You haven't posted any code that I can run, so I can't tell you what is
going wrong in your case, but here's what I see with my own example:
f - function(x) {
+ print(1)
+ print(2)
+ stop('error')
+ }
f(2)
[1] 1
[1] 2
Error in f(2) : error
Duncan Murdoch
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing) Duncan Murdoch
murd...@stats.uwo.ca 12/31/2009 10:19 AM
On 31/12/2009 9:29 AM, John Sorkin wrote:
I have written a function that contains runs
lm()
vif() and
glm()
When the glm() blows up with an error message, I don't get the output from
either the lm() or vf() even thought neither lm() nor vif() have any problems .
How can I force the function to print sequential results rather than wait for
the entire function to complete before listing the functhion's output?
Call print, e.g.
print(x - lm(...))
print(y - vif(...))
etc.
Duncan Murdoch
Thanks,
John
minBMI-function(SS,SimData)
{
SampleData-sample(1:SS,size=SS,replace=TRUE)
fitBMIEpiRevlm-lm(AAMTCARE~BMIEpiRevAdjc+BMIEpiRevAdjcSq+SEX+jPHI+jMEDICAID+H_AGE+jMARSTAT+factor(jEDUCATION)+factor(jsmokercat)+factor(jrace)+log(INCOME_C+1),data=SimData[SampleData,],x=TRUE)
print(summary(fitBMIEpiRevlm))
print(vif(fitBMIEpiRevlm))
fitBMIEpiRev-
glm(AAMTCARE~BMIEpiRevAdjc+BMIEpiRevAdjcSq+SEX+jPHI+jMEDICAID+H_AGE+jMARSTAT+factor(jEDUCATION)+factor(jsmokercat)+factor(jrace)+log(INCOME_C+1),data=SimData[SampleData,],family=Gamma(link=log))
print(summary(fitBMIEpiRev))
}
minBMI(SS,SimData)
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for th...{{dropped:6}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Confidentiality Statement:
This email message, including any attachments, is for ...{{dropped:3}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] using optim
On 01/01/2010 11:45 PM, Erin Hodgess wrote: Dear R People: I know that you can use optim for a function with several parameters. Is there an equivalent for 2 functions, please? Or should I put together a finite difference type of matrix, etc., please? What is the goal? optim optimizes a scalar value. If you have a length 2 vector to optimize, what does that mean? Duncan Murdoch Thanks, Happy New Year, Erin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] package license questions
On 02/01/2010 11:19 PM, Markus Weisner wrote: I am looking for some advice on licenses. Here is my situation: Over the last couple years, I have developed a rather large number of fire department analysis functions. I am in the process of trying to publish some packages to make these functions available to the public. I am trying to release two packages that essentially define S4 classes for common types of fire department data. Then, I would like to publish a package that essentially reads in these fire department data types and returns analysis results. My concern is that I may eventually want to build and sell some proprietary functions and I am trying not to box myself out of this future option. It is my understanding that if I use the GPL license, all work based on my packages would have to take on the GPL license (effectively making it impossible to sell software). That only applies to other people unless you choose to incorporate other people's GPL'd code into your package. The GPL imposes no conditions on the copyright holder, it's a license given by the copyright holder to other people to allow them to do things (basically copying, modifying, and redistributing) that otherwise would be copyright violations. The obligation the other people need to follow is that *they* must offer the GPL license if they include your code. So they'll have some trouble commercializing it (but it's not impossible to commercialize GPL'd code, it's just supposed to be impossible to do it in a closed source way). The trap with GPL is that other people may make improvements to your code that you'd like to use. If you do, they become copyright holders as well, and then the combined work has to be licensed using GPL unless all of you can agree otherwise. But at that point you've accepted a free contribution from someone else, it's only fair to share the ownership of the product with them. It looks like the Lesser General Public License (LGPL) may suit my needs by allowing me to make public my current work without eliminating the possibility of future proprietary work. I have a couple questions I am hoping somebody can answer. - It says that libraries licensed under a LGPL can be used by proprietary software. What is meant by libraries? Are class definitions and functions considered libraries? - If I use the LGPL for all my packages, do I maintain the right to build and sell software that is based on these LGPL packages? For instance, could I use the class definitions from a LGPL package as inputs for analysis in a piece of proprietary software? - Other than potentially allowing competitors to also use my LGPL packages in their proprietary software, are there any big disadvantages to using a LGPL? - If somebody improves on my LGPL S4 class definitions, can I still then use them in a proprietary package despite their being modified? The LGPL puts weaker constraints on users of your code. You still maintain all the rights you ever did, but it doesn't stop them from commercializing closed-source products using your code as a library, whatever that means. Duncan Murdoch I am a big supporter of the open source community and have personally benefitted greately from open source software. My intentions are to release my work as open source, but just don't want to be boxed out of future proprietary developments. These licenses can be pretty confusing, so I appreciate any information that can help me figure this out. Thanks, Markus [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] F77_CALL, F77_NAME definition
On 03/01/2010 9:11 AM, rkevinbur...@charter.net wrote: I give up. Maybe it is my search (Windows) but I cannot seem to find the definition of the F77_CALL or F77_NAME macros. Either there are too many matches or the search just doesn't find it. For example where is the source for: F77_CALL(dpotri) ? It's your search. The definition is in src/include/R_ext/RS.h. BTW, this sort of question is much more of an R-devel question than an R-help one. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] F77_CALL, F77_NAME definition
On 03/01/2010 9:43 AM, Barry Rowlingson wrote: On Sun, Jan 3, 2010 at 2:11 PM, rkevinbur...@charter.net wrote: I give up. Maybe it is my search (Windows) but I cannot seem to find the definition of the F77_CALL or F77_NAME macros. Either there are too many matches or the search just doesn't find it. For example where is the source for: F77_CALL(dpotri) ? I'm not sure what the Windows equivalent of 'grep -r F77_CALL .' is, but the developer who wrote lbfgsb.c left a blatant clue which popped up as the third match: ./appl/lbfgsb.c:#include R_ext/RS.h /* for F77_CALL */ About three screenfulls later the actual definition itself appeared. If you are going to do a lot of this on a windows box, get cygwin and learn to use the unix utilities in a cygwin bash shell! I think it's better to use a reasonable text editor here; I used Textpad. I don't think there's anything too special about it, but it does have Search | Find in files, and I can list the file pattern (obviously *.h for a macro definition), and the folder (R-devel/src on my system), and then I only get six hits: two definitions and 4 uses. That's a lot better than 3 screenfuls. You can also use the Windows search facility to find the file, but I find it clunky, and rarely use it. It does also make it easy to limit the searches in the same way as the above, but it won't show the results as nicely. I'm sure you can do the same thing with grep, but I can never remember the syntax to say to search only in *.h files, whereas with the GUI searches it's easy. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] F77_CALL, F77_NAME definition
On 03/01/2010 10:32 AM, Barry Rowlingson wrote: On Sun, Jan 3, 2010 at 3:20 PM, Duncan Murdoch murd...@stats.uwo.ca wrote: I think it's better to use a reasonable text editor here; I used Textpad. I don't think there's anything too special about it, but it does have Search | Find in files, and I can list the file pattern (obviously *.h for a macro definition), and the folder (R-devel/src on my system), and then I only get six hits: two definitions and 4 uses. That's a lot better than 3 screenfuls. Of course. Emacs + Etags. Then it's about four keystrokes :) But of course to reduce Search for F77_CALL to 4 keystrokes you need to be able to do Lempel-Ziv encoding in your head; that's what I hate about Emacs. Duncan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] locator and print
On 04/01/2010 10:18 AM, Thomas Roth wrote:
Hi,
Using the following R-Code the printing via print takes place after locator
although print is placed before locator
###
test = function()
{
plot(1:10)
print(test)
locator(1)
}
test
###
Is there some way to force the printing before locator is being evaluated. I
assume that there is some buffer that needs to be turned off? Where do I
have to look. Locator and print help page don't cover this problem.
flush.console() will flush output to the console in systems that support
it. In the Windows GUI, there's a menu item Misc | Buffered output
that can control buffering.
Duncan Murdoch
Thanks in advance,
Thomas
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to dynamically display title for a graph
On 04/01/2010 11:30 AM, noclue_ wrote:
I have written a function (see below) which encloses a boxplot. My function
xbox takes in a variable name (such as age), and do a boxplot. Now I
would like to add a title for the graph dynamically displaying the variable
name as part of title.
But, in reality, the title displays VALUES of my variable.
Obviously, sprintf does not work.
Can somebody shed light on how to solve my problem in properly displaying a
title ?
Thanks.
-
xbox- function(X)
{
boxplot(_expenses ~ X, data=my_tab,main=sprintf(title is %s,X))
}
xbox(age)
Use deparse(substitute(X)) in the sprintf. This says: get the
expression passed as X, and convert it to text.
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] polygamma or Hurwitz zeta function
On 04/01/2010 5:27 PM, HAKAN DEMIRTAS wrote: Hi, Is there any R library that is capable of handling polygamma function (Hurwitz zeta function also works)? I am aware of digamma(0 and trigamma(), but could not find more advanced versions. RSiteSearch(polygamma) points to the psigamma function, on the same man page as digamma and trigamma. Duncan Murdoch I'd appreciate any help. Hakan Demirtas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Dynamic arguments in rbind function
On 04/01/2010 7:31 PM, Steven Kang wrote:
Hi, all
Basically, I have unknown number of data that need to be imported and
collapsed row-wisely.
The code below works fine, however the rbind function may require 50
arguments if there are 50 data files...
Thus, I would like to explore whether there are any methods in using dynamic
objects (i.e from the resulting objects in the for loop) as an argument in
the *rbind* function.
setwd(.)
import.files - c(a.txt, b.txt, c.txt, d.txt, e.txt)
for (i in 1:length(import.files)) {
assign(paste(imp, i, sep = .), read.delim(eval(paste(.\\,
import.files[i], sep = )), header = TRUE))
Computing names like this is almost always a bad idea. It's better to
just put the items in a list:
imp - list()
for (i in 1:length(import.files)) {
imp[[i]] - read.delim(eval(paste(.\\,
import.files[i], sep = )), header = TRUE)
}
Then to bind them all, simply use do.call(rbind, imp).
Duncan Murdoch
}
combined - rbind(*imp.1, imp.2, imp.3, imp.4, imp.5, imp.6*)
Your expertise in resolving this issue would be greatly appreciated.
Steve
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] mean for subset
On 05/01/2010 1:29 PM, Geoffrey Smith wrote: Hello, does anyone know how to take the mean for a subset of observations? For example, suppose my data looks like this: OBS NAME SCORE 1 Tom 92 2 Tom 88 3 Tom 56 4 James85 5 James75 6 James32 7 Dawn 56 8 Dawn 91 9 Clara 95 10Clara 84 Is there a way to get the mean of the SCORE variable by NAME but only when the number of observations is equal to 3? In other words, is there a way to get the mean of the SCORE variable for Tom and James, but not for Dawn and Clara? Thank you. You probably want to do it in two steps: first, find which names have 3 observations, and take that subset of the dataset; then do the mean on all groups. This is one way: counts - table(dataset$NAME) keep - names(counts)[counts == 3] subset - dataset[ dataset$NAME %in% keep,] tapply(subset$SCORE, subset$NAME, mean) Clara DawnJames Tom NA NA 64.0 78.7 Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] adding 3D arrows to 3D plots
Eben J. Gering wrote: Greetings, I would like to add 3D arrows (i.e. arrow-headed vectors linking X1Y1Z1 to X2,Y2,Z2) to a 3D plot; ideally the sort of plot that can be rotated interactively. Is this possible using plot3d, or another 3d plotter in R? While it is easy to draw segments in plot3d (e.g. below), I haven't figured out how to add arrow heads, or to create 3d arrows from scratch. ##two headless segments: library(rgl) matrix(1:2,2,3)-segment1 matrix(1:3,2,3)-segment2 plot3d(segment2,type=l,col=red,xlim=c(0,3),ylim=c(0,3),zlim=c(0,3)) plot3d(segment1,type=l,add=TRUE,col=blue) There isn't any current code to do that in rgl, but if you have a particular shape of arrow in mind, you could probably draw it with some combination of functions. The main problem is that I've never seen any very appealing rotatable 3d arrows. There's a Matlab function to draw some here: http://www.mathworks.com/matlabcentral/fileexchange/8396-draw-3d-arrows; it could probably be translated into rgl if you wanted that. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building static HTML help pages in R 2.10.x on Windows
Michal Kulich wrote: On 7.1.2010 9:49, Dieter Menne wrote: Thanks for that code. I fully agree that the current help system is a step back. For stable bookmarking, my workaround is to put options(help.ports=6800) into the profile, so I can created links like http://127.0.0.1:6800/library/gmodels/html/estimable.html but this still required that I start RGui and the help system once. Dieter Thanks for this, too. Btw, is there a way to start the dynamic Rhelp server in the background without manually launching RGui? That, combined with Dieter's suggestion, would bring the help system sort of back to its original state. You don't need Rgui, you could run Rterm, which would have a smaller footprint. It's not very hard to start it and minimize it, but if you want it running invisibly, you'll need to figure out how to hide the icon. A disadvantage of doing this is that you won't see help relevant to your current session, you'll see help relevant to the background task. In 2.10.x there aren't many differences, but you'll find it more limiting in 2.11.x and later. Duncan Murdoch I am sorry to say that the new dynamic help is a HUGE nuisance to me. Had to revert back to R 2.9 because of that :-(. Michal __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Strange behaviour of as.integer()
On 07/01/2010 7:31 AM, Ulrich Keller wrote: I have encountered a strange behaviour of as.integer() which does not seem correct to me. Sorry if this is just an indication of me not understanding floating point arithmetic. .57 * 100 [1] 57 .29 * 100 [1] 29 So far, so good. But: as.integer(.57 * 100) [1] 56 as.integer(.29 * 100) [1] 28 Then again: all.equal(.57 * 100, as.integer(57)) [1] TRUE all.equal(.29 * 100, as.integer(29)) [1] TRUE This behaviour is the same in R 2.10.1 (Ubuntu and Windows) and 2.9.2 (Windows), all 32 bit versions. Is this really intended? Yes, as the man page states, non-integer values are truncated towards zero. Normal printing rounds them. So .57*100, which is slightly less than 57, is rounded to 57 for printing, but is truncated to 56 by as.integer. .57*100 57 [1] TRUE Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to report or correct translations typos?
On 07/01/2010 9:04 AM, Kenneth Roy Cabrera Torres wrote: Hi R users and developers: Thanks to Mr Pablo Emilio Verde for his constribution to the spanish translation for R messages he makes a very good job. I find a tiny typo on the translation, in particular on the es.po file line 7312 it says: pueto it should be: puerto How can anybody might correct a typo or which is the best way to correct it on a future patch? You can see the translation teams listed on http://developer.r-project.org/TranslationTeams.html. You send your corrections to them (as you have already done; this message is just to confirm you've done what you should do). Duncan Murdoch Thank you for your help. Kenneth __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building static HTML help pages in R 2.10.x on Windows
On 07/01/2010 9:05 AM, Michael Friendly wrote: Michal Kulich wrote: On 7.1.2010 9:49, Dieter Menne wrote: I am sorry to say that the new dynamic help is a HUGE nuisance to me. Had to revert back to R 2.9 because of that :-(. Michal I too have reverted to 2.9.2 on Win XP because I find html help to be far less convenient than the compiled CHM help I had before. CHM help is so much easier because the Contents, Index and Search panels make it easy to *see* all the items defined for a package, and I get a separate help window for each package. I very much appreciate the efforts of the R-core team to move R forward, but I think the change in help is a step back. You can see the items for the package on the index page for the package, which is linked from every page. You can put together a package that displays the help in your favourite format, if you don't like the default format. There's nothing that we used in CHM help that couldn't be duplicated in Javascript, without the security holes. I see it as more important that R core enables others to do what they want, rather than to maintain ancient designs. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] diag, diag- and [ , [-
On 07/01/2010 9:31 AM, berga...@gmail.com wrote: Dear all I have the following problem. M - matrix(0,3,3) # dimension of M is dinamic and this can lead to the next subscript diag(M[1,1]) - rep(100,1) #Error in `diag-`(`*tmp*`, value = 100) : # only matrix diagonals can be replaced diag(M[1,1,drop=F]) - rep(100,1) #Error in diag(M[1, 1, drop = F]) - rep(100, 1) : # incorrect number of subscripts diag(M[2:3,1:2]) - rep(100,2) # works fine Is there a way to usw diag as replacement function when the input matrix is subscript to a one by one matrix. I don't want extra if(dim==1)... etc. The problem isn't with diag, it's with [-. When you include drop=F, it doesn't appear to handle properly the matrix indexing that diag() uses. So a simpler example is just M[1,1, drop=FALSE] - 1 which generates the same error you saw. I'd call this a bug; I'll look into it. ([- is done internally in some fairly ugly code, so this might take a while.) As a workaround, I think this does what you want: n - 1 submatrix - M[1:n,1:n,drop=FALSE] diag(submatrix) - rep(100, n) M[1:n,1:n] - submatrix Duncan Murdoch Thanks a lot in advance. Best regards, Roger [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building static HTML help pages in R 2.10.x on Windows
On 07/01/2010 9:47 AM, Michal Kulich wrote: On 7.1.2010 12:18, Duncan Murdoch wrote: You don't need Rgui, you could run Rterm, which would have a smaller footprint. It's not very hard to start it and minimize it, but if you want it running invisibly, you'll need to figure out how to hide the icon. This works. Not entirely invisible but not a big deal about that. The R code run within Rterm is options(help_type=html,help.ports=6800) help.start() library(audio) wait(-1) [couldn't find another way to hang R indefinitely in batch mode] A disadvantage of doing this is that you won't see help relevant to your current session, you'll see help relevant to the background task. In 2.10.x there aren't many differences, but you'll find it more limiting in 2.11.x and later. Not a problem if one is not switching between different versions of R. The current version is on the path and the path will get updated (manually) after a new version is installed. Thus, the relevant help will be always displayed. Not necessarily. The current help system can display information about the current session, e.g. the result of ls(), as a simple example. But if you use a single background session you won't get relevant information. Duncan Murdoch Thanks, this is a kind of solution. Now I can use bookmarks to HTML help for the favorite libraries when working in ESS - the impossibility to set those and the need to start Rgui was the big nuisance. I am sure the new help system will get gradually improved in the future. Best, Michal __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building static HTML help pages in R 2.10.x on Windows
On 07/01/2010 9:51 AM, Gabor Grothendieck wrote: On Thu, Jan 7, 2010 at 9:20 AM, Duncan Murdoch murd...@stats.uwo.ca wrote: On 07/01/2010 9:05 AM, Michael Friendly wrote: Michal Kulich wrote: On 7.1.2010 9:49, Dieter Menne wrote: I am sorry to say that the new dynamic help is a HUGE nuisance to me. Had to revert back to R 2.9 because of that :-(. Michal I too have reverted to 2.9.2 on Win XP because I find html help to be far less convenient than the compiled CHM help I had before. CHM help is so much easier because the Contents, Index and Search panels make it easy to *see* all the items defined for a package, and I get a separate help window for each package. I very much appreciate the efforts of the R-core team to move R forward, but I think the change in help is a step back. You can see the items for the package on the index page for the package, which is linked from every page. You can put together a package that displays the help in your favourite format, if you don't like the default format. There's nothing that we used in CHM help that couldn't be duplicated in Javascript, without the security holes. I see it as more important that R core enables others to do what they want, rather than to maintain ancient designs. Perhaps the link to the Index could be placed at both the top and bottom rather than just at the bottom since its a nuisance to have to scroll down and its less noticeable at the bottom as its typically off the screen. Yes, I may do that at some point, to make the layout of the help pages more consistent. Most higher level pages have a consistent header (more so in R-devel), but the individual topic pages don't. What I'd really like is for someone who has good taste to redesign the look of the whole system. I think one or two people are working on packages to do this, and I'd much rather spend time providing whatever low level support they need, rather than doing it myself. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building static HTML help pages in R 2.10.x on Windows
On 07/01/2010 10:00 AM, Michal Kulich wrote: On 7.1.2010 15:52, Duncan Murdoch wrote: Not necessarily. The current help system can display information about the current session, e.g. the result of ls(), as a simple example. But if you use a single background session you won't get relevant information. Duncan Murdoch Sorry, I must admit I don't get it. A more useful example than ls() would be methods(). I think it would be nice to have a list of methods included in the man page for a generic function, and links to their pages if they have their own man pages. You might want to list all installed methods, with some sort of highlighting to indicate which ones are already attached, or perhaps be able to toggle between installed and attached, or whatever. None of that is possible with static help, not even a list of installed methods, because someone might install a new package that offers some others after the static help has already been built. You just need to use some imagination. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building static HTML help pages in R 2.10.x on Windows
On 07/01/2010 11:36 AM, Jonathan Baron wrote: For what it is worth, I would gladly sacrifice this capability in order to be able to consult all my R help pages through a Firefox bookmark to the packages listing (which is what I used to do, and will do again, when I get time to either rebuild from source or get the forthcoming Fedora RPM, which will have static pages as the default), without starting an R session. What's so hard about leaving an R session running, and using bookmarks as Dieter described? Duncan Murdoch Jon On 01/07/10 10:32, Duncan Murdoch wrote: A more useful example than ls() would be methods(). I think it would be nice to have a list of methods included in the man page for a generic function, and links to their pages if they have their own man pages. You might want to list all installed methods, with some sort of highlighting to indicate which ones are already attached, or perhaps be able to toggle between installed and attached, or whatever. None of that is possible with static help, not even a list of installed methods, because someone might install a new package that offers some others after the static help has already been built. You just need to use some imagination. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with writeBin and importing into gfortran compiled programs
On 07/01/2010 2:05 PM, jgar...@ija.csic.es wrote: Hi all, I'm having problems trying to export binary arrays from R and importing them into fortran (linux openSUSE 10.3 (x86_64), gfortran compiler, fortran 90/95 program). Let's say the problem can be expressed as: R part whini - runif(1000) writeBin(whini,fwhini.dat) f90 part PROGRAM foo INTEGER, PARAMETER :: DP = KIND(1.0D0) INTEGER :: status REAL(DP), DIMENSION(10,100) :: whini OPEN(UNIT=5, FILE='fwhini.dat', STATUS='OLD', ACTION='READ', FORM='UNFORMATTED', IOSTAT=status) READ(5) whini CLOSE(5) WRITE(*,*) whini END PROGRAM Now, if within the R session I check typeof(whini) [1] double and try whini.copy - readBin(fwhini.dat,what=double(),n=1000) the copy of whini is right. However, execution of the fortran program gives the message: Fortran runtime error: Unformatted file structure has been corrupted. I've tried also to declare whini in the fortran part as SINGLE precision, and to force writeBin using the size argument. size=4 and size=8 give the same error (whini as double in the fortran part), while size=16 gives the alternative error Fortran runtime error: I/O past end of record on unformatted file Please, could you help me with this problem? I've never used Fortran 90, so I can't tell if your type declaration is really declaring double precision values. So what I'd do is to create an array (say the values 1 to 1000) within your Fortran program, and write it out. Then do the same in R, and do a binary compare of the files to see what the differences are. The things to look for are: Size of values (4 or 8 bytes or something else). Byte order within values (big or little endian). R is very flexible in what it writes, and probably Fortran is flexible in what it can read, but you need to figure out what the differences are before you can match them up. The viewRaw() function in the hexView package is a simple way to look at the bytes in the files. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building static HTML help pages in R 2.10.x on Windows
On 07/01/2010 2:16 PM, Kevin Wright wrote: Well, among other things, if my global environment becomes cluttered/corrupt/etc and I quit R, then restart R, the links in my browser are now dead. You weren't following Dieter's instructions, then. I have to close all the tabs and call help to open them again. Also, the R-supplied java tool for searching help is ancient and underwhelming. Then contribute a new one. A desktop search tool (X1/Copernic/GoogleDesktop/etc) can be very handy, but only if it has pre-built help files to index. Imperfect, stale, non-dynamic help is better than no help at all! Then fix the search tool so it can search dynamic web pages. They can be spidered too, just like static ones. Duncan Murdoch As others have done, I have switched back to 2.9.2 until I can build all help files (on Windows). Thanks to those people who are figuring out how to do this. Kevin On Thu, Jan 7, 2010 at 11:50 AM, Duncan Murdoch murd...@stats.uwo.cawrote: On 07/01/2010 11:36 AM, Jonathan Baron wrote: For what it is worth, I would gladly sacrifice this capability in order to be able to consult all my R help pages through a Firefox bookmark to the packages listing (which is what I used to do, and will do again, when I get time to either rebuild from source or get the forthcoming Fedora RPM, which will have static pages as the default), without starting an R session. What's so hard about leaving an R session running, and using bookmarks as Dieter described? Duncan Murdoch Jon On 01/07/10 10:32, Duncan Murdoch wrote: A more useful example than ls() would be methods(). I think it would be nice to have a list of methods included in the man page for a generic function, and links to their pages if they have their own man pages. You might want to list all installed methods, with some sort of highlighting to indicate which ones are already attached, or perhaps be able to toggle between installed and attached, or whatever. None of that is possible with static help, not even a list of installed methods, because someone might install a new package that offers some others after the static help has already been built. You just need to use some imagination. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Debugging issues encountered during the R CMD check process
On 07/01/2010 2:48 PM, Jason Rupert wrote: I read through the Writing R Extensions and the Debugging in R website (http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/), looking for some hints about how to solve the issue of debugging problems encountered during the R CMD check process, but nothing seems to be mentioned about addressing issues encountered. Specifically, I am working with the R signal package which is hosted at the following location: http://code.google.com/p/r-signal/ I would like to debug the problem that is shown below, and is encountered when I run R CMD check signal. Thank you for any insights that are provided as the R signal package is nice and it would be good to have it working again with R 2.9.x and beyond. Thank you again for the help. From the 00check.log * using log directory '/Users/jasonkrupert/Documents/RStuff/Rsignal/r-signal/signal.Rcheck' * using R version 2.9.2 (2009-08-24) * using session charset: UTF-8 * checking for file 'signal/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'signal' version '0.6' * checking package dependencies ... OK * checking if this is a source package ... WARNING ### Name: interp ### Title: Interpolate / Increase the sample rate ### Aliases: interp ### Keywords: math ### ** Examples # The graph shows interpolated signal following through the # sample points of the original signal. t = seq(0, 2, by = 0.01) x = chirp(t,2,.5,10,'quadratic') + sin(2*pi*t*0.4) y = interp(x[seq(1, length(x), by = 4)],4,4,1) # interpolate a sub-sample Warning in rbind(x, array(val, dim = c(n - nx, NCOL(x : number of columns of result is not a multiple of vector length (arg 1) Warning in Fft(postpad(x, N)) * B : longer object length is not a multiple of shorter object length Error in ifft(Fft(postpad(x, N)) * B) : dims [product 36] do not match the length of object [256] Calls: interp - fftfilt - fftfiltx - ifft Execution halted You'll often get more informative error messages in recent R releases if you set the environment variable R_KEEP_PKG_SOURCE=yes I don't know if it will help in this case. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] startup file
On 07/01/2010 4:10 PM, mkna005 mkna005 wrote: Hi! I was wondering if it is possible to have a startup script similar to matlab as such when R starts up the script is automatically executed? Thanks Yes, see ?Startup. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] %d/%m/%Y can not be displayed in a .rd file
On 07/01/2010 2:09 PM, rusers.sh wrote:
Hi all,
I found the date format (e.g.%d/%m/%Y) in the .rd file cannot be
displayed after building the package. See below,
###.rd file
\examples{
a-10/20/1999
DateConversion(a,DateIn=%m/%d/%Y,DateOut=%d/%m/%Y)
}
The result is
Examples:
a-10-20-1999
DateConversion(a,DateIn=
??%m/%d/%Y seems cannot be recognized.
Is there some method to solve this and make it visible?
Thanks a lot.
The % character is a comment character in Rd files. You need to escape it:
DateConversion(a,DateIn=\%m/\%d/\%Y,DateOut=\%d/\%m/\%Y)
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building static HTML help pages in R 2.10.x on Windows
On 07/01/2010 2:58 PM, Kevin Wright wrote: On Thu, Jan 7, 2010 at 9:32 AM, Duncan Murdoch murd...@stats.uwo.ca wrote: On 07/01/2010 10:00 AM, Michal Kulich wrote: On 7.1.2010 15:52, Duncan Murdoch wrote: Not necessarily. The current help system can display information about the current session, e.g. the result of ls(), as a simple example. But if you use a single background session you won't get relevant information. Duncan Murdoch Sorry, I must admit I don't get it. A more useful example than ls() would be methods(). I think it would be nice to have a list of methods included in the man page for a generic function, and links to their pages if they have their own man pages. You might want to list all installed methods, with some sort of highlighting to indicate which ones are already attached, or perhaps be able to toggle between installed and attached, or whatever. None of that is possible with static help, not even a list of installed methods, because someone might install a new package that offers some others after the static help has already been built. You just need to use some imagination. OK, I'll try imagining this approach: - Static help pages are installed with R. - install.packages() launches a subroutine to fix the \link references that need updating. Uninstalling needs to do the same. (Busywork, but that's why we have computers.) - I have an R object foo. I type ShowMeAllMethodsFor(foo, installed=TRUE, attached=TRUE) which checks all installed packages and attached packages for appropriate methods, then serves up a dynamic help page with links to the relevant static help pages, color-coded by installed/attached. I don't like the fragmentation of the R help system. This just produces yet another set of pages which are not reachable from anywhere but one place. The help system should be a network of pages which are all interconnected. I should be able to click on something in the ?plot page and get to the ?plot.formula page (which I can do now, based on a static link) or the ?plot.foo page (which hasn't been written yet, but will be by the time I look at ?plot). Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [Fwd: snowfall on Win7]
On 07/01/2010 4:39 PM, Murph wrote: Jochen Knaus wrote: . Anybody having experiences with Win7 yet? R 2.10.1 installed today on win7 works fine for this new user. Although the demos fail with a complaint about unable to setwdI suspect it's a privaleges problem. Win7 is awkward about install privaleges. I suspect my working directory is in Admin land; and I'm trying to execute from /user/tom If I could figure out a function to have R list my environmental variables; I could probably figure it out. Sys.getenv() will list them (possibly on very long lines; you'll need to scroll to the right to see anything). Duncan Murdoch I have two processor on my Toshiba... Murph __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building static HTML help pages in R 2.10.x on Windows
Michal Kulich wrote: On 7.1.2010 20:22, Duncan Murdoch wrote: A more useful example than ls() would be methods(). I think it would be nice to have a list of methods included in the man page for a generic function, and links to their pages if they have their own man pages. You might want to list all installed methods, with some sort of highlighting to indicate which ones are already attached, or perhaps be able to toggle between installed and attached, or whatever. None of that is possible with static help, not even a list of installed methods, because someone might install a new package that offers some others after the static help has already been built. I see. Well, I never lacked any of these capabilities... Please understand that people who use R to do their work may have different objectives than the developers - and they form the majority of R users. Then they should contribute to the development. I don't owe you anything. You owe us a lot. Duncan Murdoch On 07/01/2010 2:16 PM, Kevin Wright wrote: Well, among other things, if my global environment becomes cluttered/corrupt/etc and I quit R, then restart R, the links in my browser are now dead. You weren't following Dieter's instructions, then. Indeed, but that option is not documented, as far as I know - at least not in 2.10.0. And even if it was, most users would not be able to find it or use it because they have no clue what a port is. I have to close all the tabs and call help to open them again. Also, the R-supplied java tool for searching help is ancient and underwhelming. Then contribute a new one. Duncan, if even the quite advanced and computer-proficient users have trouble using the dynamic R help and have to resort to some quite complex and cumbersome home-made solutions to get back the basic functionality then something is not right. It's true that the help system was never a particular strength of R and that it needed an overhaul. What worked well in the late 90's with a few dozen packages does not work well with 1000 packages. However, 2.10.x does not seem to make things better. The work of the R developers should be widely appreciated and we really do appreciate it. The question is whether their effort is extended in the best direction... (Imho, that's an issue with most open-source projects and it's been much worse with Mozilla than with R). Just my 2c. Michal __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building static HTML help pages in R 2.10.x on Windows
Dieter Menne wrote: Duncan Murdoch wrote: What's so hard about leaving an R session running, and using bookmarks as Dieter described? It pollutes my space, and I am a Window-closing maniac, so it won't survive the next attack. http://www.microsoft.com/downloads/en/confirmation.aspx?familyId=9d467a69-57ff-4ae7-96ee-b18c4790cffddisplayLang=en It might be worth a try to use instsrv and srvany to install the batch as a server. The resource kit cries out loud when installed on Window 7 for being a stupid old dinosaur, but in similar case I could still use it. If that works, writing up instructions would be a useful contribution. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is there any function in R like ezplot in matlab?
On 09/01/2010 5:22 AM, 军 吕 wrote: Hi, Is there any function in R like ezplot in matlab? How to draw the relationship between x y like this x^y+y^(sinx)=log(x+y) It's not pre-packaged, but drawing a contour plot of the function f - function(x,y) x^y+y^sin(x) - log(x+y) should do it: xvals - yvals - seq(0, 30, len=1000) zvals - outer(xvals, yvals, f) contour(xvals, yvals, zvals, levels=0) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Online R documentation
On 09/01/2010 12:48 PM, Dieter Menne wrote: Karl Ove Hufthammer wrote: In case anybody is looking for ideas in how to improve the above site, inclusion of rendered example graphs, similar to the ones at http://www.metaresearch.de/exlib/;, would be nice. If the format you use on your site were accepted as the standard in R, this would be a great step forward in improving the dinosaur. I prefer to have help locally, though, because I would like to have the first search restricted to the packages I have installed, to avoid being drowned by 2000 packages I never need. Including graphical output in the man pages is one of the eventual goals of the new help system. I doubt it will make it into 2.11.x, but it will probably be there in 2.12.x. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Calling FING.EXE under RGui.EXE for windows.
On 07/01/2010 1:25 PM, Uwe Ligges wrote: Argh. I see it as well. Will dig a lit tomorrow. I don't know exactly what's going on, but it looks as though it is something specific to the find.exe utility, e.g. maybe it is assuming that it's being run inside a console and reading CONIN$ or writing to CONOUT$ without checking whether they can be opened. When you run it from Rterm, Rterm is in a console, which appears to be good enough. So it may be anyone who wants to use it will have to contact Microsoft to find out how... Duncan Murdoch Uwe On 07.01.2010 12:25, Gabor Grothendieck wrote: I get a problem with shell too: Under Rgui: R.version.string [1] R version 2.10.1 Patched (2010-01-01 r50884) system(C:\\windows\\system32\\find /?, intern = TRUE) character(0) system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE) character(0) shell(C:\\windows\\system32\\find /?) Warning message: In shell(C:\\windows\\system32\\find /?) : 'C:\windows\system32\find /?' execution failed with error code 1 They all work, i.e. they give the required help message, under Rterm and when I issue this from the Windows console it works: C:\windows\system32\find /? 2010/1/7 Uwe Liggeslig...@statistik.tu-dortmund.de: On 07.01.2010 02:04, Gabor Grothendieck wrote: If you have C:\Rtools\bin on your PATH note that it contains a UNIX-like find utility that conflicts with the find utility in Windows. If that is the problem then remove that from your PATH and then run the batch file. The batchfiles distribution at http://batchfiles.googlecode.com has utilities (Rgui.bat, R.bat, Rtools.bat, etc.) that will automatically add C:\Rtools\bin to your path temporarily or only while R is running so that you can leave it off your PATH. I guess it's the use of system() rather than shell() that causes the problem. Under Windows, you have to use shell in order to start a command interpreter. Uwe Ligges On Wed, Jan 6, 2010 at 6:51 PM, John Schexnayderjsc...@us.ibm.com wrote: This is sort of a strange bug. Not show stopping, but annoying. I was wondering if anyone else has noticed this and reported it before I submit a bug report. I noticed while running the RGui and attempting to debug one of my scripts that I encountered a Windows error informing me that Find String [grep] Utility has encountered a problem and needs to close. It is being generated by a call to a DOS batch file which contains a call to Find.exe. It can be reproduced by simply typing System(find) in RGui. What I found strange is that I have been running this script daily without this problem for months. I now realize I never ran that portion of the script while in RGui.exe. It has always run in batch mode which is done by Rterm.exe. I have tried this on three separate machines now all running Windows XP SP3, with versions of R 2.8.1 and R 2.10.1 If executing System(find) under RGui, an error window for the Find String Utility is generated and the command is not exectuted. If the same command is issued in Rterm the expected FIND: Parameter format not correct message is properly returned. It doesn't seem an important bug, but it could be the canary in the mine for a larger problem somewhere down the road. Re, John Schexnayder IBM Tape Manufacturing - Information Technology San Jose, CA 95138 jsc...@us.ibm.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Calling FING.EXE under RGui.EXE for windows.
On 09/01/2010 6:31 PM, Gabor Grothendieck wrote:
That doesn't explain why this returns character(o) even though we have
launched a console for it:
system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE)
I don't see any console launched. R redirects stdin and stdout (and
stderr, I think), and it appears that Windows doesn't open a console. I
do see a console flash by if I do
system('cmd /c c:/WINDOWS/system32/find.exe /?', wait=FALSE,
invisible=FALSE)
but of course then we don't capture the output, so it's not very useful.
Looking at the source, the only case where we ask to create a console
is the combination wait=FALSE, invisible=FALSE, but there might be
combinations of other options that make this a default. The MS
documentation says that a console will be created automatically for any
console application, but that doesn't appear to be happening.
So I guess you could get find.exe to work by calling it from a batch
file with a pause at the end and using the wait=FALSE,invisible=FALSE
options.
The above observations are in Win XP SP3, not anything newer.
Duncan Murdoch
On Sat, Jan 9, 2010 at 5:24 PM, Duncan Murdoch murd...@stats.uwo.ca wrote:
On 07/01/2010 1:25 PM, Uwe Ligges wrote:
Argh. I see it as well. Will dig a lit tomorrow.
I don't know exactly what's going on, but it looks as though it is something
specific to the find.exe utility, e.g. maybe it is assuming that it's being
run inside a console and reading CONIN$ or writing to CONOUT$ without
checking whether they can be opened. When you run it from Rterm, Rterm is
in a console, which appears to be good enough.
So it may be anyone who wants to use it will have to contact Microsoft to
find out how...
Duncan Murdoch
Uwe
On 07.01.2010 12:25, Gabor Grothendieck wrote:
I get a problem with shell too:
Under Rgui:
R.version.string
[1] R version 2.10.1 Patched (2010-01-01 r50884)
system(C:\\windows\\system32\\find /?, intern = TRUE)
character(0)
system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE)
character(0)
shell(C:\\windows\\system32\\find /?)
Warning message:
In shell(C:\\windows\\system32\\find /?) :
'C:\windows\system32\find /?' execution failed with error code 1
They all work, i.e. they give the required help message, under Rterm
and when I issue this from the Windows console it works:
C:\windows\system32\find /?
2010/1/7 Uwe Liggeslig...@statistik.tu-dortmund.de:
On 07.01.2010 02:04, Gabor Grothendieck wrote:
If you have C:\Rtools\bin on your PATH note that it contains a
UNIX-like find utility that conflicts with the find utility in
Windows. If that is the problem then remove that from your PATH and
then run the batch file.
The batchfiles distribution at http://batchfiles.googlecode.com has
utilities (Rgui.bat, R.bat, Rtools.bat, etc.) that will automatically
add C:\Rtools\bin to your path temporarily or only while R is running
so that you can leave it off your PATH.
I guess it's the use of system() rather than shell() that causes the
problem. Under Windows, you have to use shell in order to start a
command
interpreter.
Uwe Ligges
On Wed, Jan 6, 2010 at 6:51 PM, John Schexnayderjsc...@us.ibm.com
wrote:
This is sort of a strange bug. Not show stopping, but annoying. I
was
wondering if anyone else has noticed this and reported it before I
submit
a bug report.
I noticed while running the RGui and attempting to debug one of my
scripts
that I encountered a Windows error informing me that Find String
[grep]
Utility has encountered a problem and needs to close. It is being
generated by a call to a DOS batch file which contains a call to
Find.exe.
It can be reproduced by simply typing System(find) in RGui.
What I
found strange is that I have been running this script daily without
this
problem for months. I now realize I never ran that portion of the
script
while in RGui.exe. It has always run in batch mode which is done by
Rterm.exe.
I have tried this on three separate machines now all running Windows
XP
SP3, with versions of R 2.8.1 and R 2.10.1 If executing
System(find)
under RGui, an error window for the Find String Utility is generated
and
the command is not exectuted. If the same command is issued in Rterm
the
expected FIND: Parameter format not correct message is properly
returned.
It doesn't seem an important bug, but it could be the canary in the
mine
for a larger problem somewhere down the road.
Re,
John Schexnayder
IBM Tape Manufacturing - Information Technology
San Jose, CA 95138
jsc...@us.ibm.com
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do
Re: [R] Calling FING.EXE under RGui.EXE for windows.
Gabor Grothendieck wrote:
I noticed this does work, i.e. it displays the requested help info, in
Rgui on my Vista system:
library(tcltk)
.Tcl(exec find /?)
Yes, here too. It stores the output in a tclObj, so it's doing what we
want to do. Anyone familiar with the Tcl source, and can spot the
difference between their exec and our system()?
Duncan Murdoch
On Sat, Jan 9, 2010 at 7:27 PM, Duncan Murdoch murd...@stats.uwo.ca wrote:
On 09/01/2010 6:31 PM, Gabor Grothendieck wrote:
That doesn't explain why this returns character(o) even though we have
launched a console for it:
system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE)
I don't see any console launched. R redirects stdin and stdout (and stderr,
I think), and it appears that Windows doesn't open a console. I do see a
console flash by if I do
system('cmd /c c:/WINDOWS/system32/find.exe /?', wait=FALSE,
invisible=FALSE)
but of course then we don't capture the output, so it's not very useful.
Looking at the source, the only case where we ask to create a console is
the combination wait=FALSE, invisible=FALSE, but there might be
combinations of other options that make this a default. The MS
documentation says that a console will be created automatically for any
console application, but that doesn't appear to be happening.
So I guess you could get find.exe to work by calling it from a batch file
with a pause at the end and using the wait=FALSE,invisible=FALSE options.
The above observations are in Win XP SP3, not anything newer.
Duncan Murdoch
On Sat, Jan 9, 2010 at 5:24 PM, Duncan Murdoch murd...@stats.uwo.ca
wrote:
On 07/01/2010 1:25 PM, Uwe Ligges wrote:
Argh. I see it as well. Will dig a lit tomorrow.
I don't know exactly what's going on, but it looks as though it is
something
specific to the find.exe utility, e.g. maybe it is assuming that it's
being
run inside a console and reading CONIN$ or writing to CONOUT$ without
checking whether they can be opened. When you run it from Rterm, Rterm
is
in a console, which appears to be good enough.
So it may be anyone who wants to use it will have to contact Microsoft to
find out how...
Duncan Murdoch
Uwe
On 07.01.2010 12:25, Gabor Grothendieck wrote:
I get a problem with shell too:
Under Rgui:
R.version.string
[1] R version 2.10.1 Patched (2010-01-01 r50884)
system(C:\\windows\\system32\\find /?, intern = TRUE)
character(0)
system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE)
character(0)
shell(C:\\windows\\system32\\find /?)
Warning message:
In shell(C:\\windows\\system32\\find /?) :
'C:\windows\system32\find /?' execution failed with error code 1
They all work, i.e. they give the required help message, under Rterm
and when I issue this from the Windows console it works:
C:\windows\system32\find /?
2010/1/7 Uwe Liggeslig...@statistik.tu-dortmund.de:
On 07.01.2010 02:04, Gabor Grothendieck wrote:
If you have C:\Rtools\bin on your PATH note that it contains a
UNIX-like find utility that conflicts with the find utility in
Windows. If that is the problem then remove that from your PATH and
then run the batch file.
The batchfiles distribution at http://batchfiles.googlecode.com has
utilities (Rgui.bat, R.bat, Rtools.bat, etc.) that will automatically
add C:\Rtools\bin to your path temporarily or only while R is running
so that you can leave it off your PATH.
I guess it's the use of system() rather than shell() that causes the
problem. Under Windows, you have to use shell in order to start a
command
interpreter.
Uwe Ligges
On Wed, Jan 6, 2010 at 6:51 PM, John Schexnayderjsc...@us.ibm.com
wrote:
This is sort of a strange bug. Not show stopping, but annoying. I
was
wondering if anyone else has noticed this and reported it before I
submit
a bug report.
I noticed while running the RGui and attempting to debug one of my
scripts
that I encountered a Windows error informing me that Find String
[grep]
Utility has encountered a problem and needs to close. It is being
generated by a call to a DOS batch file which contains a call to
Find.exe.
It can be reproduced by simply typing System(find) in RGui.
What I
found strange is that I have been running this script daily without
this
problem for months. I now realize I never ran that portion of the
script
while in RGui.exe. It has always run in batch mode which is done by
Rterm.exe.
I have tried this on three separate machines now all running Windows
XP
SP3, with versions of R 2.8.1 and R 2.10.1 If executing
System(find)
under RGui, an error window for the Find String Utility is generated
and
the command is not exectuted. If the same command is issued in
Rterm
the
expected FIND: Parameter format not correct message is properly
Re: [R] Calling FING.EXE under RGui.EXE for windows.
I'm quitting on this one. For the record, I took a look at a fairly old
version of the Tcl code (from 8.4.13) that I had around from an old
attempt to get it to work properly with MDI windows. There are a number
of differences between their exec code and our system() code, but I
couldn't find the right combination to get system() to be able to run
find. It always crashes with a seg fault in ulib.dll when run with
input coming from the pipe we send it.
If you use input redirection on the command line, it's fine, for example
system(cmd /c c:/WINDOWS/system32/find /? nul)
or
shell(c:/WINDOWS/system32/find \Hello\ c:/temp/foo.txt nul)
So perhaps we're not setting up the pipe correctly, but it works with
most other programs, so I'm going to assume find is using it
incorrectly, unless someone points out what we're doing wrong.
Duncan Murdoch
On 10/01/2010 8:18 AM, Gabor Grothendieck wrote:
I noticed this does work, i.e. it displays the requested help info, in
Rgui on my Vista system:
library(tcltk)
.Tcl(exec find /?)
On Sat, Jan 9, 2010 at 7:27 PM, Duncan Murdoch murd...@stats.uwo.ca wrote:
On 09/01/2010 6:31 PM, Gabor Grothendieck wrote:
That doesn't explain why this returns character(o) even though we have
launched a console for it:
system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE)
I don't see any console launched. R redirects stdin and stdout (and stderr,
I think), and it appears that Windows doesn't open a console. I do see a
console flash by if I do
system('cmd /c c:/WINDOWS/system32/find.exe /?', wait=FALSE,
invisible=FALSE)
but of course then we don't capture the output, so it's not very useful.
Looking at the source, the only case where we ask to create a console is
the combination wait=FALSE, invisible=FALSE, but there might be
combinations of other options that make this a default. The MS
documentation says that a console will be created automatically for any
console application, but that doesn't appear to be happening.
So I guess you could get find.exe to work by calling it from a batch file
with a pause at the end and using the wait=FALSE,invisible=FALSE options.
The above observations are in Win XP SP3, not anything newer.
Duncan Murdoch
On Sat, Jan 9, 2010 at 5:24 PM, Duncan Murdoch murd...@stats.uwo.ca
wrote:
On 07/01/2010 1:25 PM, Uwe Ligges wrote:
Argh. I see it as well. Will dig a lit tomorrow.
I don't know exactly what's going on, but it looks as though it is
something
specific to the find.exe utility, e.g. maybe it is assuming that it's
being
run inside a console and reading CONIN$ or writing to CONOUT$ without
checking whether they can be opened. When you run it from Rterm, Rterm
is
in a console, which appears to be good enough.
So it may be anyone who wants to use it will have to contact Microsoft to
find out how...
Duncan Murdoch
Uwe
On 07.01.2010 12:25, Gabor Grothendieck wrote:
I get a problem with shell too:
Under Rgui:
R.version.string
[1] R version 2.10.1 Patched (2010-01-01 r50884)
system(C:\\windows\\system32\\find /?, intern = TRUE)
character(0)
system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE)
character(0)
shell(C:\\windows\\system32\\find /?)
Warning message:
In shell(C:\\windows\\system32\\find /?) :
'C:\windows\system32\find /?' execution failed with error code 1
They all work, i.e. they give the required help message, under Rterm
and when I issue this from the Windows console it works:
C:\windows\system32\find /?
2010/1/7 Uwe Liggeslig...@statistik.tu-dortmund.de:
On 07.01.2010 02:04, Gabor Grothendieck wrote:
If you have C:\Rtools\bin on your PATH note that it contains a
UNIX-like find utility that conflicts with the find utility in
Windows. If that is the problem then remove that from your PATH and
then run the batch file.
The batchfiles distribution at http://batchfiles.googlecode.com has
utilities (Rgui.bat, R.bat, Rtools.bat, etc.) that will automatically
add C:\Rtools\bin to your path temporarily or only while R is running
so that you can leave it off your PATH.
I guess it's the use of system() rather than shell() that causes the
problem. Under Windows, you have to use shell in order to start a
command
interpreter.
Uwe Ligges
On Wed, Jan 6, 2010 at 6:51 PM, John Schexnayderjsc...@us.ibm.com
wrote:
This is sort of a strange bug. Not show stopping, but annoying. I
was
wondering if anyone else has noticed this and reported it before I
submit
a bug report.
I noticed while running the RGui and attempting to debug one of my
scripts
that I encountered a Windows error informing me that Find String
[grep]
Utility has encountered a problem and needs to close. It is being
generated by a call to a DOS batch file which contains a call to
Find.exe.
It can be reproduced by simply typing System(find) in RGui.
What I
found strange is that I have been running this script daily without
this
problem for months. I now realize I never ran that portion of the
script
while
Re: [R] Calling FING.EXE under RGui.EXE for windows.
On 10/01/2010 1:42 PM, Gabor Grothendieck wrote:
Perhaps you can add it to the bug list before you leave it including
what you tried in case its a symptom of some larger underlying
problem.
This list is archived, so there's a record. But I think this is a find
bug, not an R bug, so it doesn't make sense to add it to the R bug list.
Duncan Murdoch
On Sun, Jan 10, 2010 at 1:24 PM, Duncan Murdoch murd...@stats.uwo.ca wrote:
I'm quitting on this one. For the record, I took a look at a fairly old
version of the Tcl code (from 8.4.13) that I had around from an old attempt
to get it to work properly with MDI windows. There are a number of
differences between their exec code and our system() code, but I couldn't
find the right combination to get system() to be able to run find. It
always crashes with a seg fault in ulib.dll when run with input coming from
the pipe we send it.
If you use input redirection on the command line, it's fine, for example
system(cmd /c c:/WINDOWS/system32/find /? nul)
or
shell(c:/WINDOWS/system32/find \Hello\ c:/temp/foo.txt nul)
So perhaps we're not setting up the pipe correctly, but it works with most
other programs, so I'm going to assume find is using it incorrectly, unless
someone points out what we're doing wrong.
Duncan Murdoch
On 10/01/2010 8:18 AM, Gabor Grothendieck wrote:
I noticed this does work, i.e. it displays the requested help info, in
Rgui on my Vista system:
library(tcltk)
.Tcl(exec find /?)
On Sat, Jan 9, 2010 at 7:27 PM, Duncan Murdoch murd...@stats.uwo.ca
wrote:
On 09/01/2010 6:31 PM, Gabor Grothendieck wrote:
That doesn't explain why this returns character(o) even though we have
launched a console for it:
system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE)
I don't see any console launched. R redirects stdin and stdout (and
stderr,
I think), and it appears that Windows doesn't open a console. I do see a
console flash by if I do
system('cmd /c c:/WINDOWS/system32/find.exe /?', wait=FALSE,
invisible=FALSE)
but of course then we don't capture the output, so it's not very useful.
Looking at the source, the only case where we ask to create a console is
the combination wait=FALSE, invisible=FALSE, but there might be
combinations of other options that make this a default. The MS
documentation says that a console will be created automatically for any
console application, but that doesn't appear to be happening.
So I guess you could get find.exe to work by calling it from a batch file
with a pause at the end and using the wait=FALSE,invisible=FALSE
options.
The above observations are in Win XP SP3, not anything newer.
Duncan Murdoch
On Sat, Jan 9, 2010 at 5:24 PM, Duncan Murdoch murd...@stats.uwo.ca
wrote:
On 07/01/2010 1:25 PM, Uwe Ligges wrote:
Argh. I see it as well. Will dig a lit tomorrow.
I don't know exactly what's going on, but it looks as though it is
something
specific to the find.exe utility, e.g. maybe it is assuming that it's
being
run inside a console and reading CONIN$ or writing to CONOUT$ without
checking whether they can be opened. When you run it from Rterm, Rterm
is
in a console, which appears to be good enough.
So it may be anyone who wants to use it will have to contact Microsoft
to
find out how...
Duncan Murdoch
Uwe
On 07.01.2010 12:25, Gabor Grothendieck wrote:
I get a problem with shell too:
Under Rgui:
R.version.string
[1] R version 2.10.1 Patched (2010-01-01 r50884)
system(C:\\windows\\system32\\find /?, intern = TRUE)
character(0)
system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE)
character(0)
shell(C:\\windows\\system32\\find /?)
Warning message:
In shell(C:\\windows\\system32\\find /?) :
'C:\windows\system32\find /?' execution failed with error code 1
They all work, i.e. they give the required help message, under Rterm
and when I issue this from the Windows console it works:
C:\windows\system32\find /?
2010/1/7 Uwe Liggeslig...@statistik.tu-dortmund.de:
On 07.01.2010 02:04, Gabor Grothendieck wrote:
If you have C:\Rtools\bin on your PATH note that it contains a
UNIX-like find utility that conflicts with the find utility in
Windows. If that is the problem then remove that from your PATH
and
then run the batch file.
The batchfiles distribution at http://batchfiles.googlecode.com
has
utilities (Rgui.bat, R.bat, Rtools.bat, etc.) that will
automatically
add C:\Rtools\bin to your path temporarily or only while R is
running
so that you can leave it off your PATH.
I guess it's the use of system() rather than shell() that causes the
problem. Under Windows, you have to use shell in order to start a
command
interpreter.
Uwe Ligges
On Wed, Jan 6, 2010 at 6:51 PM, John Schexnayderjsc...@us.ibm.com
wrote:
This is sort of a strange bug. Not show stopping, but annoying.
I
was
wondering if anyone else has noticed this and reported it before I
submit
a bug report.
I noticed while running the RGui and attempting to debug one of my
scripts
that I encountered
Re: [R] Help with Order
On 11/01/2010 7:37 AM, Steve Sidney wrote:
Dear List
As a fairly new R programmer I seem to have run into a strange problem -
probably my inexperience with R
After reading and merging successive files into a single data frame, I find
that order does not sort the data as expected.
I have multiple references in each file but each file refers to measurement
data obtained at a different time.
Here's the code
library(reshape)
# Enter file name to Read Save data
FileName=readline(Enter File name:\n)
# Find first occurance of file
for ( round1 in 1 : 6) {
ReadFile=paste(round1,C_,FileName,_Stats.csv, sep=)
if (file.exists(ReadFile))
break
}
x = data.frame(read.csv(ReadFile, header=TRUE),rnd=round1)
for ( round2 in (round1+1) : 6) {
#
ReadFile=paste(round2,C_,FileName,_Stats.csv, sep=)
if (file.exists(ReadFile)) {
y = data.frame(read.csv(ReadFile, header=TRUE),rnd = round2)
if (round2 == (round1 +1))
z=data.frame(merge(x,y,all=TRUE))
z=data.frame(merge(y,z,all=TRUE))
}
}
ordered = order(z$lab_id)
results = z[ordered,]
res = data.frame(
lab=results[,lab_id],bw=results[,ZBW],wi=results[,ZWI],pf_zbw=0,pf_zwi=0,r
= results[,rnd])
#
# Establish no of samples recorded
nsmpls = length(res[,c(lab)])
# Evaluate Z_scores for Between Lab Results
for ( i in 1 : nsmpls) {
if (res[i,bw] 3 | res[i,bw] -3)
res[i,pf_zbw]=1
}
# Evaluate Z_scores for Within Lab Results
for ( i in 1 : nsmpls) {
if (res[i,wi] 3 | res[i,wi] -3)
res[i,pf_zwi]=1
}
dd = melt(res, id=c(lab,r), pf_zbw)
b = cast(dd, lab ~ r)
If anyone could see why the ordering only works for about 55 of 70 records
and could steer me in the right direction I would be obliged
I can't try out your code, but I'd guess it's due to conversion of
strings to factors. Sorting factors will sort them by their numerical
value, not by the strings.
So the solution is to set stringsAsFactors=FALSE, either in each
read.csv call, or globally with options(stringsAsFactors=FALSE).
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] example() leaves console prompting to press Enter for new graphs
On 11/01/2010 9:28 AM, Michael Friendly wrote:
Env: Win XP, R 2.9.2]
It's a minor annoyance, but I find that after I run example(), the
console state of prompting to press Enter for
each new graph remains as it is under example. It's more annoying that
it seems difficult to turn this behavior
off!
In a fresh session:
getOption(example.ask)
[1] default
Run an example:
example(plot)
plot require(stats)
plot plot(cars)
Waiting to confirm page change...
...
getOption(example.ask)
[1] default
# do another plot:
plot(sin, -pi, 2*pi)
Waiting to confirm page change...
# reset option to FALSE
options(example.ask=FALSE)
plot(sin, -pi, 2*pi)
Waiting to confirm page change...
# try resetting devAskNewPage
devAskNewPage(ask = NULL)
[1] TRUE
plot(sin, -pi, 2*pi)
Waiting to confirm page change...
There does seem to be code in example to reset this state on exit, and
I'm baffled why it doesn't actually
do it
...
if (ask == default)
ask - echo grDevices::dev.interactive(orNone = TRUE)
if (ask) {
if (.Device != null device) {
oldask - grDevices::devAskNewPage(ask = TRUE)
if (!oldask)
on.exit(grDevices::devAskNewPage(oldask), add = TRUE)
}
op - options(device.ask.default = TRUE)
on.exit(options(op), add = TRUE)
}
...
So, how can I restore the previous state of plotting w/out prompting?
It's not the console state that is left that way, it's the graphics
window. If you close it, the next window you open will have the state
you wanted. If you had had a window open before you called example, it
would have been restored.
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R for windows 64 bit
On 11/01/2010 11:29 AM, alessia matano wrote: Dear all, do you know if there is any particular version of R to implement with windows 64 bit, in such a way to increase the amount of memory it can use? There are two that I know of. Revolution Computing sells one, built with a commercial compiler. Brian Ripley made a posting last week on the R-devel list about an experimental build using gcc. Duncan Murdoch How should I increase the memory, and more importantly to set a higher max vector size? It still stops me saying Could not allocate vector of size 145 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Calling FING.EXE under RGui.EXE for windows.
On 11/01/2010 2:56 PM, John Schexnayder wrote:
I just wanted to add that it is not only caused by the FIND.EXE, but I
also noticed the same problem with DOSKEY.EXE. It too causes the same
fault, but the redirection (nul) prevents the fault just like Duncan
pointed out with FIND. I imagine there are number of other executables
that would produce the same results. Oddly enough FINDSTR.EXE does not
produce the fault. (You would think it would share code with FIND.EXE.)
I also noticed other strange differences now that I poke around with other
executables. For instance
shell(copy /?)
produces the desired help information in RGui.exe however
shell(xcopy /?)
does not. I know they are different in that copy is not an executable,
but a system call where Xcopy is an executable, but they should behave the
same way.
Especially considering they do behave properly in Rterm. Again this is an
RGui only phenomena.
I don't find it very surprising. cmd.exe doesn't have the bug, so copy
/? works fine. find.exe and apparently xcopy.exe do, so they fail.
It's not a bug in doskey that it doesn't work; it's supposed to talk to
the console, so if there is no console, it won't work. But find and
xcopy have no business talking to the console. They should simply work
with stdin/stdout.
Duncan Murdoch
Re,
John Schexnayder
IBM Tape Manufacturing - Information Technology
San Jose, CA 95138
jsc...@us.ibm.com
From:
Gabor Grothendieck ggrothendi...@gmail.com
To:
Duncan Murdoch murd...@stats.uwo.ca
Cc:
Uwe Ligges lig...@statistik.tu-dortmund.de, John Schexnayder/San
Jose/i...@ibmus, r-h...@stat.math.ethz.ch
Date:
01/10/2010 10:42 AM
Subject:
Re: [R] Calling FING.EXE under RGui.EXE for windows.
Perhaps you can add it to the bug list before you leave it including
what you tried in case its a symptom of some larger underlying
problem.
On Sun, Jan 10, 2010 at 1:24 PM, Duncan Murdoch murd...@stats.uwo.ca
wrote:
I'm quitting on this one. For the record, I took a look at a fairly old
version of the Tcl code (from 8.4.13) that I had around from an old
attempt
to get it to work properly with MDI windows. There are a number of
differences between their exec code and our system() code, but I
couldn't
find the right combination to get system() to be able to run find. It
always crashes with a seg fault in ulib.dll when run with input coming
from
the pipe we send it.
If you use input redirection on the command line, it's fine, for example
system(cmd /c c:/WINDOWS/system32/find /? nul)
or
shell(c:/WINDOWS/system32/find \Hello\ c:/temp/foo.txt nul)
So perhaps we're not setting up the pipe correctly, but it works with
most
other programs, so I'm going to assume find is using it incorrectly,
unless
someone points out what we're doing wrong.
Duncan Murdoch
On 10/01/2010 8:18 AM, Gabor Grothendieck wrote:
I noticed this does work, i.e. it displays the requested help info, in
Rgui on my Vista system:
library(tcltk)
.Tcl(exec find /?)
On Sat, Jan 9, 2010 at 7:27 PM, Duncan Murdoch murd...@stats.uwo.ca
wrote:
On 09/01/2010 6:31 PM, Gabor Grothendieck wrote:
That doesn't explain why this returns character(o) even though we
have
launched a console for it:
system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE)
I don't see any console launched. R redirects stdin and stdout (and
stderr,
I think), and it appears that Windows doesn't open a console. I do
see a
console flash by if I do
system('cmd /c c:/WINDOWS/system32/find.exe /?', wait=FALSE,
invisible=FALSE)
but of course then we don't capture the output, so it's not very
useful.
Looking at the source, the only case where we ask to create a console
is
the combination wait=FALSE, invisible=FALSE, but there might be
combinations of other options that make this a default. The MS
documentation says that a console will be created automatically for
any
console application, but that doesn't appear to be happening.
So I guess you could get find.exe to work by calling it from a batch
file
with a pause at the end and using the wait=FALSE,invisible=FALSE
options.
The above observations are in Win XP SP3, not anything newer.
Duncan Murdoch
On Sat, Jan 9, 2010 at 5:24 PM, Duncan Murdoch murd...@stats.uwo.ca
wrote:
On 07/01/2010 1:25 PM, Uwe Ligges wrote:
Argh. I see it as well. Will dig a lit tomorrow.
I don't know exactly what's going on, but it looks as though it is
something
specific to the find.exe utility, e.g. maybe it is assuming that
it's
being
run inside a console and reading CONIN$ or writing to CONOUT$
without
checking whether they can be opened. When you run it from Rterm,
Rterm
is
in a console, which appears to be good enough.
So it may be anyone who wants to use it will have to contact
Microsoft
to
find out how...
Duncan Murdoch
Uwe
On 07.01.2010 12:25, Gabor Grothendieck wrote:
I get a problem with shell
Re: [R] error variable names are limited to 256 bytes when sourcing code
Brian Frizzelle wrote: I've written a function that takes some input data output from a simulation model and creates some graphs. It's not very complicated code, and it works perfectly fine if I just run the code as is. But I have converted it into a function so we call it externally, and when I try to source the code to test the function, I get the error message variable names are limited to 256 bytes. I've tried searching online for a solution to this, but everything I have come across deals with this error in relation to input data, not a function. The code is 389 lines long, so I'd rather not paste it here and clog up inboxes. If you have an idea as to why this is happening and would like to see the code, please email me and I will send it to you. Current versions of R will tell you which line contained the error. Can't you find and post just that one line? If you aren't seeing an error report, you could divide and conquer: edit blocks out of your file until you can figure out which lines matter. My guess would be something involving backticks (i.e. things like `x`); R will see the first one, and collect characters until the next one as a single identifier. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to install an archived version of a package in windows
Nevil Amos wrote: How do I install an archived version of a package - in this case Geneland 3.1.5 in windows? The archived versions are available on CRAN and tar.gz. I can downland this, but then the only option to install a local copy is utils:::menuInstallLocal() or install from local zip file in the console packages menu, this does not work wither with the downlaoded tar.gz, or if I unzip it and save all its contents as Genland_3.1.5.zip in the R/bin direcotry. What do I need to do? The archived versions are source packages. So you need to install the tools to build from source (see the R Admin manual, or http://www.murdoch-sutherland.com/Rtools/), then simply do install.packages(foo.tar.gz, type=source, repos=NULL) from within R, or Rcmd INSTALL foo.tar.gz from outside. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rprofile: distinguish between Rgui, Rterm, JGR?
Michael Friendly wrote: [Environment: Win XP, R 2.10.1] In my Rprofile I have startup code to do various things, intended for when I use the Rgui console. Some of these are causing problems in JGR now that I've installed it. How can I test for R running with Rgui to do some of these things only there? Look at .Platform$GUI. It shows Rgui or RTerm for those two. I don't have JGR installed, but I'd guess it shows something differently there. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] difference in sort order linux/Windows (R.2.11.0)
carslaw wrote: Dear R users, I'm a bit perplexed with the effect sort has here, as it is different on Windows vs. linux. It makes my factor levels and subsequent plots different on the two systems. You are using different collation orders. On Linux, your sessionInfo shows en_GB.utf8 while Windows shows English_United Kingdom.1252 so you should be prepared for differences. That said, it certainly looks as though the string comparison is wrong on Linux. Using Ted Harding's examples, I get these results: AB CD ABCD [1] FALSE AB CD ABCD [1] FALSE on Windows in the English_Canada.1252 locale and on Linux in the C locale. However, when I use the locale that's default on our system, en_US.UTF-8, I get AB CD ABCD [1] TRUE AB CD ABCD [1] FALSE as Ted did, and that certainly looks wrong. Duncan Murdoch Given: types - c(PC-D-Euro-0, PC-D-Euro-1, PC-D-Euro-2, PC-D-Euro-3, PC-D-Euro-4, PC-D-Euro-5, PC-D-Euro-6, LCV-D-Euro-0, LCV-D-Euro-1, LCV-D-Euro-2, LCV-D-Euro-3, LCV-D-Euro-4, LCV-D-Euro-5, LCV-D-Euro-6, HGV-D-Euro-0, HGV-D-Euro-I, HGV-D-Euro-II, HGV-D-Euro-III, HGV-D-Euro-IV EGR, HGV-D-Euro-IV SCR, HGV-D-Euro-IV SCRb, HGV-D-Euro-V EGR, HGV-D-Euro-V SCR, HGV-D-Euro-V SCRb, HGV-D-Euro-VI, HGV-D-Euro-VIb) On linux, sort does: sort(types) [1] HGV-D-Euro-0 HGV-D-Euro-I HGV-D-Euro-II [4] HGV-D-Euro-III HGV-D-Euro-IV EGR HGV-D-Euro-IV SCR [7] HGV-D-Euro-IV SCRb HGV-D-Euro-V EGR HGV-D-Euro-VI [10] HGV-D-Euro-VIb HGV-D-Euro-V SCR HGV-D-Euro-V SCRb [13] LCV-D-Euro-0 LCV-D-Euro-1 LCV-D-Euro-2 [16] LCV-D-Euro-3 LCV-D-Euro-4 LCV-D-Euro-5 [19] LCV-D-Euro-6 PC-D-Euro-0PC-D-Euro-1 [22] PC-D-Euro-2PC-D-Euro-3PC-D-Euro-4 [25] PC-D-Euro-5PC-D-Euro-6 And on Windows: sort(types) [1] HGV-D-Euro-0 HGV-D-Euro-I HGV-D-Euro-II [4] HGV-D-Euro-III HGV-D-Euro-IV EGR HGV-D-Euro-IV SCR [7] HGV-D-Euro-IV SCRb HGV-D-Euro-V EGR HGV-D-Euro-V SCR [10] HGV-D-Euro-V SCRb HGV-D-Euro-VI HGV-D-Euro-VIb [13] LCV-D-Euro-0 LCV-D-Euro-1 LCV-D-Euro-2 [16] LCV-D-Euro-3 LCV-D-Euro-4 LCV-D-Euro-5 [19] LCV-D-Euro-6 PC-D-Euro-0PC-D-Euro-1 [22] PC-D-Euro-2PC-D-Euro-3PC-D-Euro-4 [25] PC-D-Euro-5PC-D-Euro-6 Session info for both systems is below. The order I actually want is the Windows one, but looking at it, the linux order is perhaps more intuitive. However, the problem is the order is inconsistent between the two systems. Any suggestions? sessionInfo() R version 2.11.0 (2010-04-22) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=en_GB.utf8 LC_NAME=en_GB.utf8 [9] LC_ADDRESS=en_GB.utf8LC_TELEPHONE=en_GB.utf8 [11] LC_MEASUREMENT=en_GB.utf8LC_IDENTIFICATION=en_GB.utf8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rkward_0.5.3 loaded via a namespace (and not attached): [1] tools_2.11.0 sessionInfo() R version 2.11.0 (2010-04-22) x86_64-pc-mingw32 locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base Dr David Carslaw King's College London Environmental Research Group Franklin Wilkins Building 150 Stamford Street London SE1 9NH __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] difference in sort order linux/Windows (R.2.11.0)
On 28/05/2010 9:24 AM, (Ted Harding) wrote: An experiment: sort(c(AACD,A CD)) # [1] AACD A CD sort(c(ABCD,A CD)) # [1] ABCD A CD sort(c(ACCD,A CD)) # [1] ACCD A CD sort(c(ADCD,A CD)) # [1] A CD ADCD sort(c(AECD,A CD)) # [1] A CD AECD ## (with results for AFCD, ... AZCD similar to the last two). LC_COLLATE=en_GB.UTF-8 (R version 2.11.0 (2010-04-22) on Linux). So this behaves, in en_GB.UTF-8, as though (SPACE) is between C and D. This is nuts!!! Curable if I set (e.g.) LC_LOCALE=C on startup. But what else might break if I do so? You have to realize that to a large extent this is not under our control. Your system will have linked to some library (outside of R) to do string collation, and the problem lies in that library. You should determine which system library is handling your collations. I'd like to tell you how to do that, but I don't know for your build. You can find out if you're using the recommended ICU library by running example(icuSetCollate); that gives a number of warnings like In icuSetCollate(locale = da_DK, case_first = default) : ICU is not supported on this build in Windows. If you don't see those, then you want to talk to the ICU people. If you do, then you'll need to look deeper to find out what you're actually using. Duncan Murdoch Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 28-May-10 Time: 14:24:08 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Gelman 2006 half-Cauchy distribution
On 28/05/2010 9:29 AM, Christopher David Desjardins wrote: Hi, I am trying to recreate the right graph on page 524 of Gelman's 2006 paper Prior distributions for variance parameters in hierarchical models in Bayesian Analysis, 3, 515-533. I am only interested, however, in recreating the portion of the graph for the overlain prior density for the half-Cauchy with scale 25 and not the posterior distribution. However, when I try: curve(dcauchy, from=0, to=200, location=0, scale=25) the probabilities for the half-Cauchy values seem to approach zero almost immediately after 0 whereas in Gelman 2006 the tail appears much fatter giving non-zero probabilities out to 100. Don't ignore the warnings!!! The scale argument is not being passed to dcauchy. (Nothing in the help page suggests it would be, but some other similar functions would have passed it, so I can see how you made the wrong assumption. But why did you ignore all those warnings?) You'll get what you want with curve( dcauchy(x, location=0, scale=25), from=0, to=200) or with den - function(x) dcauchy(x, location=0, scale=25) curve(den, from=0, to=200) if you don't like using the magic name x in the first one. Duncan Murdoch I am interested in replicating this because I want to use half-Cauchy priors and want to play around with the scale values but I want to know what my prior looks like before using it in models. Please cc me as I am digest subscriber. Thanks! Chris __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Gelman 2006 half-Cauchy distribution
On 28/05/2010 10:14 AM, Christopher David Desjardins wrote: Perfect. Thanks. Also using R 2.11.0 on Fedora I didn't get any warnings with my command. That's a serious problem. Can you give more details (i.e. just plain R, R under ESS, etc.)? Duncan Murdoch Chris On 05/28/2010 09:09 AM, Berwin A Turlach wrote: curve(2*dcauchy(x, location=0, scale=25), from=0, to=200) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Does Sweave run in the global environment ?
On 28/05/2010 1:58 PM, Paul wrote:
Hello
It seems that sweave always runs in the global environment.
By default it uses the RweaveEvalWithOpt function to evaluate
expressions, and they are evaluated in the global environment. It's
possible to change that. You need to make your own driver. I'd start
with the default one via
mydriver - RweaveLatex()
then replace the code running part with your own, e.g.
myenvironment - environment() # This will make the current environment
is the default, rather than globalenv()
myEvalWithOpt - function (expr, options){
if(options$eval){
res - try(withVisible(eval(expr, myenvironment)),
silent=TRUE)
if(inherits(res, try-error)) return(res)
if(options$print | (options$term res$visible))
print(res$value)
}
return(res)
}
mydriver$runcode - makeRweaveLatexCodeRunner(evalFunc = myEvalWithOpt)
and then run Sweave with your driver:
Sweave(file, driver=mydriver)
I haven't tried any of this, and it's possible some of the functions I
used above are not exported from the utils package. But this should get
you started if you (sensibly) want to avoid setting your variable as a
global.
Another approach (which I use) is to never run Sweave() from within R;
always use R CMD Sweave (or some equivalent), and define all the local
variables in the Sweave file. But this doesn't work if you want to
generate lots of Sweave output files.
Duncan Murdoch
I want to
run sweave from within a function, and pass a variable into sweave,
however when I do this, sweave doesn't see the variable.
Here's my example test_sweave.Rnw file
|%
\documentclass[a4paper]{article}
\usepackage[OT1]{fontenc}
\usepackage{Sweave}
\begin{document}
\title{Test Sweave Document}
\author{Paul Hurley}
\maketitle
=
if(exists(foo)){print(foo)}
ls()
Sys.time()
@
\end{document}
|
If I run this code;
|testFoo-function(){
foo-My Test String
Sweave(test_sweave.Rnw)
require(tools)
texi2dvi(file = test_sweave.tex, pdf = TRUE)
}
rm(foo) testFoo()
|
my resulting file does NOT contain the contents of the string foo.
| if (exists(foo)) {
+ print(foo)
+ }
ls()
[1] testFoo
|
If I run this code (i.e, the same thing, just run directly)
|rm(foo)
foo-My Test String
Sweave(test_sweave.Rnw)
require(tools)
texi2dvi(file = test_sweave.tex, pdf = TRUE)
|
my resulting file does contain the foo string
| if (exists(foo)) {
+ print(foo)
+ }
[1] My Test String
ls()
[1] foo testFoo
|
and if I run this code
|testBar-function(){
foo-My Test String
Sweave(test_sweave.Rnw)
require(tools)
texi2dvi(file = test_sweave.tex, pdf = TRUE)
}
rm(foo)
testBar()
|
My resulting file also contains the foo string
| if (exists(foo)) {
+ print(foo)
+ }
[1] My Test String
ls()
[1] foo testBar testFoo
|
So, it seems that sweave runs in the global environment, not in the
environment it was called from. This means the only way to pass
variables to sweave when sweave is run from a function is to use the -
operator to put the variable in the global environment. (I think).
Anyone else want to comment who knows more about environments ?
Thanks
Paul.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] ICD9 codes
I have received the Matched a Filter Rule message a number of times. I have some control over what the headers of my messages look like, so if I was told what the filter rule is, I could perhaps modify the messages to avoid it. You probably don't want to post that information to the list, but it might be worthwhile to send it privately to authors of false positive messages. Duncan Murdoch On 29/05/2010 6:43 AM, (Ted Harding) wrote: It is perhaps time to bring to people's general attention that there is an issue with postings from gmail.com addresses being held for moderation because The headers matched a filter rule. It is not only gmail.com, but there is a marked excess of these. Vishwanath (@gmail.com) is one of many victims. There is a group of about a dozen people who act as moderators, approving or discarding messages which have been held. Reasons for holding are almost always either Posting from Non-Member or Matched a Filter Rule. We do this somewhat non-systematically, looking at the list of held messages on a convenience basis. However, it would be unlikely that any valid message would be held for more than an hour or so; usually it would be less. The situation has been discussed recently amongst the moderators, including the list manager Martin Maechler. We are undecided about the best action (if any) -- while the excessive false trapping of gmail.com postings is at least an inconvenience for the trapped, and sometimes leads to visible distress or embarrassment, the presence of the filter rules does prevent spam from reaching the list. Vishwanath's reaction in repeatedly re-posting is perhaps understandable on the part of someone who is not familiar with how the moderation system operates. In fact he posted the same message 4 times (morning evening on 27 May, and again on 28 May) as can be seen from the archives. He is subscribed to the list, so would normally receive copies of his own postings via the list (and therefore know that it had got through) unless he has opted to not receive his own postings. In that case, having received the held for moderation message, not receiving his posting via the list, and not thinking of looking in the archives, he could form the impression that it/they had vanished into a black hole, and try again. Since we began to discuss this about a fortnight ago, I have been keeping a count of those held messages which I have seen myself. Not counting true spam, only genuine messages, the results are as follows. NM denote a posting from a non-member, FR denotes a posting that matched a filter rule, GM denotes a posting from a gmail.com address, NGM one not from gmail.com. FR NM +-+- GM | 45 | 4 +-+- NGM | 19 | 24 Fisher test: P=7.3e-07, OR=13.7, CI=(4.0, 62.0) About 30% of R-help subscribers have gmail.com addresses, so they are clearly over-represented in the FR group (70%)! It is suspected that the gmail.com filter rule may perhaps be triggered by HTML, though the reason is not yet clear. Meanwhile, a reminder to people who receive notification that their posting has been held for moderation: Please check the archives to see whether your message has reached the list within a reasonable time (say 2 hours -- there can be a delay before a message is placed in the archives) beforetrying to do anything about it: https://stat.ethz.ch/pipermail/r-help Hoping this helps to clarify an issue which can lead to unwanted consequences. Ted. On 29-May-10 05:42:27, Vishwanath Sindagi wrote: Dear Prof Frank Harrel: I am extremely sorry for having reposted the same question numerous times. Earlier when I had posted I got replies stating that my post had matched a filter rule and hence was being held by the moderator. So I assumed that the question was never posted and I reposted with different subject lines just to make sure that it gets posted. I sincerely apologise for the inconvenience caused. Regards, Vishwanath On Sat, May 29, 2010 at 4:10 AM, Frank E Harrell Jr f.harr...@vanderbilt.edu wrote: Your notes are bordering on harassment. _Do you expect that everyone who reads this list will reply I do not have anything that will help you if they don't? _By my count this is your 4th note asking for this help. That being said I hope that you do find help somewhere or implement it yourself and share the result, as your question is an important one. Also, please be sure to state your affiliation on your notes. Frank On 05/28/2010 02:19 PM, Vishwanath Sindagi wrote: Hello: I am working on getting some statistics related to clinical trials and stuff. I have to work with ICD9 codes. Is anyone aware of any R method that deals with ICD9 codes verification and manipulation. Thanks Vishwanath -- Frank E Harrell Jr _ Professor and Chairman _ _ _ _School of Medicine _ _ _ _ _ _ _ _ _ _ Department of Biostatistics _ Vanderbilt University __ R
Re: [R] warning In fun(...) : no DISPLAY variable so Tk is not available
Nevil Amos wrote: I am getting the above warning following loading of Geneland 3.1.5 on unix , while a simple plot sends output to the pdf file ( see attached code) no output results from Geneland functions, resulting in empty pdf files That message is saying it can't find an X11 server for Tcltk to use. If you do have X11 available, then just set the DISPLAY environment variable in the normal way; if you don't, then you're not going to be able to use that package on Unix. (The Windows implementation is self-contained, so it should work there.) Duncan Murdoch library (Geneland) Loading required package: RandomFields Loading required package: fields Loading required package: spam Package 'spam' is loaded. Spam version 0.21-0 (2010-03-13). Type demo( spam) for some demos, help( Spam) for an overview of this package. Help for individual functions is optained by adding the suffix '.spam' to the function name, e.g. 'help(chol.spam)'. Attaching package: 'spam' The following object(s) are masked from 'package:base': backsolve, forwardsolve, norm Try help(fields) for an overview of this library fields web: http://www.image.ucar.edu/Software/Fields Loading required package: mapproj Loading required package: maps Loading required package: snow Loading required package: tcltk Loading Tcl/Tk interface ... done ooo oGeneland is loaded o o o o* Please * o o o oRegister on o ohttp://folk.uio.no/gillesg/Geneland/register.php o o o oSee manual ono ohttp://folk.uio.no/gillesg/Geneland/Geneland.htmlo o o oThis is Geneland-3.1.5 o o o ooo Warning message: In fun(...) : no DISPLAY variable so Tk is not available pdf(test.pdf) plot(1:10,1:10) dev.off() null device __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Vector docs
i...@whywouldwe.com wrote:
Hi
The docs for R are very practical, which is quite refreshing compared to
other languages, however I can't find any details about all the things I
can do with a vector. I'm expecting methods like vector.contains('foo')
and vector.remove('foo'), maybe those methods don't exist but I'd love
to find a page that details the ones that do.
I'd also like to find some docs about foreach loops (unless there's a
better way to iterate through a vector), I've only found mailing list posts.
There may be such a page somewhere, but it is probably incomplete. The
object model in R has methods owned by generics, not by classes. So
even if someone wrote a list of all methods that worked on vectors,
someone else could add a new one without modifying the vector class.
You can ask R what methods are currently visible, e.g.
library(methods)
showMethods(classes=vector)
but it won't show methods in unattached packages.
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] error on Windows OS
M.Ribeiro wrote: I received by email an R package (file.tar.gz) that was created in Linux. The package was already installed in another computer in linux using install.packages and it worked I am not familiar with installing packages but I would like to install it on Windows I downloaded the Rtools29.exe and tryed to install using install.packages(foo.tar.gz, repos=NULL, type=source) but the message was Warning in install.packages(GR_1.0.tar.gz, repos = NULL, type = source) : argument 'lib' is missing: using 'C:\Documents and Settings\mr\My Documents/R/win-library/2.9' That's a funny name to use for the library for R 2.10.x, but it's not a serious error. 'sh' is not recognized as an internal or external command, operable program or batch file. That's the one that stopped the install. Apparently the Rtools bin directory is not being found by Windows in your PATH. The Rtools installer can put it there; maybe you should just reinstall Rtools and choose that option. Warning message: In install.packages(GR_1.0.tar.gz, repos = NULL, type = source) : installation of package 'GR_1.0.tar.gz' had non-zero exit status my questios are: Where shall I save the .tar.gz file?? That doesn't matter, as long as it's a readable directory. Do I need to do anything else with the Rtools besides installing (C:/Rtools)?? Set the Windows PATH variable. Is the problem with the way I did or with the package?? So far it looks like the Rtools install. Duncan Murdoch Thanks a lot Cheers __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building a what list for scan to use
On 31/05/2010 7:07 AM, Alex van der Spek wrote: Using read.table now on large files. Scan should be faster reading and parsing the files if a 'what' list is provided. How would I generate a what list that repeats the the last 4 elements n (n=14 or 10 or 8) times? whatlist=list(Tstamp=,Condition=0,A1=0,B1=0,C1=0,D1=0) All are numeric, either decimal or hexadecimal. Do it like this: n - 14 indices - c(1,2, rep(3:6, n)) biglist - whatlist[indices] This repeats the names too; if you want new names for the repeated columns, you can reassign the names afterwards, e.g. names(biglist) - paste(name, 1:(2+4*n)) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Y-axis range in histograms
On 31/05/2010 10:49 AM, Aarne Hovi wrote: Hi, I'm trying to create a histogram with R. The problem is that the frequency is high for a couple of x-axis categories (e.g. 1500) and low for most of the x-axis categories (e.g. 50) http://r.789695.n4.nabble.com/file/n2237476/LK3_hist.jpg . When I create the histogram, it is not very informative, because only the high frequencies can be seen clearly. Is there any way I could cut the y-axis from the middle so that the y-axis values ranged for example from 0 to 300, and then again from 900 to 1500? Using a bar chart like that takes away most of the value of using a bar chart: you lose both area and length as visual clues to the value. Why not do something different? For example, x - runif(1700) + rep(1:5, c(1500,50,55,45,50)) hist(x, breaks=5) # The one you don't like h - hist(x, breaks=5, plot=FALSE) # Get the data plot(h$mids, h$counts, log=y) # Plot on a log scale abline(v=h$breaks,col=lightgray) # Indicate the bins Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] error on Windows OS
On 31/05/2010 9:13 AM, M.Ribeiro wrote: Ok, I re-installed the Rtools (now Rtools211 because I was in another computer with R version 2.10) , and the message now when I tried to install the package was Warning: invalid package 'GWSR_1.0.tar.gz' Erro: ERROR: no packages specified Warning message: In install.packages(GWSR_1.0.tar.gz, repos = NULL, type = source) : installation of package 'GWSR_1.0.tar.gz' had non-zero exit status Any Clue? I would guess that the package didn't exist in the current directory. I'd recommend working in the CMD window rather than in R (using Rcmd INSTALL GWSR_1.0.tar.gz); it is sometimes tricky to see what the state of the system is from R. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Question about the license of an R package
Mauricio Zambrano wrote: Dear R-users, I'm developing a package that heavily depends on another package released under the GPL-2 license. Are you including code from that package in yours, or just making use of it? The former requires that you follow all the GPL rules about your own. If you just use their package, then license your package any way you like. In addition, some few functions depends on other packages released under the following licences (as described in the corresponding pages of http://cran.r-project.org/web/packages/): GPL GPL =2. I want to release my package under a GPL = 2 license, and after reading the section 1.1.1 of the R-exts manual and looking at the compatibility matrix found on http://gplv3.fsf.org/dd3-faq, I'm still in doubt if I can do that. I would appreciate if you could tell me if can I release my package under a GPL = 2 license considering the aforementioned licenses ? Finally, a general question: When a package is released under GPL =2, does it mean that the terms of the GPL-3 license apply or not ? I believe that's an offer to license under whatever version of the GPL (from 2 up) that the person using your code chooses. If GPL-3 offers something that GPL-2 doesn't (e.g. compatibility with other GPL-3 code), they can use that. If GPL-3 places restrictions they don't like (e.g. incompatibility with GPL-2 code), they can use GPL-2. Duncan Murdoch Thanks in advance for any help. Mauricio __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Seeking help on Vectorize()
Megh Dal wrote:
Dear falks, here I have written following function :
fn - Vectorize(function(x = 1:3, y = 3:6) {
x - matrix(x, nrow=1)
y - matrix(y, ncol=1)
dat - apply(x, 2, function(xx) {
apply(y, 1, function(yy) {
return(xx + yy) } ) })
return(dat)}, SIMPLIFY = TRUE)
If I run this function, I got some warning message, even format of the returned
object is not correct, for example :
fn(x = 1:3, y = 3:7)
[1] 4 6 8 7 9
Warning message:
In mapply(FUN = function (x = 1:3, y = 3:6) :
longer argument not a multiple of length of shorter
However if I run individual line of codes like :
x - 1:3; y = 3:7
x - matrix(x, nrow=1)
y - matrix(y, ncol=1)
dat - apply(x, 2, function(xx) {
+ apply(y, 1, function(yy) {
+ return(xx + yy) } ) })
dat
[,1] [,2] [,3]
[1,]456
[2,]567
[3,]678
[4,]789
[5,]89 10
I get exactly what I want. Where I am making fault?
I think you don't understand what Vectorize is trying to do. It is
basically a way to run a loop, calling your function with each matching
pair of x and y values, i.e. x=1, y=3 in the first call, then x=2 y=4 in
the second, etc. The warning comes because you have three x values and
five y values, so it will repeat the 1st two x values -- but it warns
you that's likely not what you intended.
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Your message to R-help awaits moderator approval
Gabor Grothendieck wrote: This has happened to me too. The last time it occurred I was replying to another post and on my second attempt I deleted the replied-to portion and reposted just my portion and it worked. On Fri, Jun 4, 2010 at 4:35 PM, yjmha69 yjmh...@yahoo.com wrote: What filter rule is violated? So frustrated, why can't I post question! The problem is that you are posting from gmail.com, and yjmha69 was posting from yahoo.com. The messages will eventually make it through if you are patient. Duncan Murdoch - Original Message From: r-help-boun...@r-project.org r-help-boun...@r-project.org To: yjmh...@yahoo.com Sent: Fri, June 4, 2010 12:28:37 PM Subject: Your message to R-help awaits moderator approval Your mail to 'R-help' with the subject subsetting a dataframe Is being held until the list moderator can review it for approval. The reason it is being held: The message headers matched a filter rule Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: https://stat.ethz.ch/mailman/confirm/r-help/151139c40b029d260fb9bde07e60a96a68dc572d __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Write.fwf works from Mac, throws different number of row error in Windows
You need to give us something reproducible or we won't likely be able to help you. Put together a small example that illustrates the problem, and it will likely be fixed pretty quickly, or your error will be pointed out. (You need to give us a way to construct outframe, we don't have it.) Duncan Murdoch mazibuko wrote: Hello, I am having a problem with write.fwf in Windows. I wrote a code to ingest a number of text files with weather data in them, process them, and then output a text file with two parts: 1) a set of column names, 2) the processed data table. I wrote and tested the program on my Mac, and it worked fine. However, on the windows machine, where I intend the work to be done, when I run the following line (last line of the script): write.fwf(outframe,file=outfile1,sep=,quote=FALSE,rownames=FALSE,colnames=FALSE, + width=c(4,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8),append=TRUE,justify='right') I get the following error: Error in data.frame(colname = colnamesMy, nlevels = 0, position = 0, width = 0, : arguments imply differing number of rows: 0, 1 In addition: Warning message: In write.fwf(outframe, file = outfile1, sep = , quote = FALSE, : recycling 'width' I can't see the reason for this. The data in outframe are all numeric, and it worked on the Mac, and outframe has 7 rows on Windows and on the Mac, so I am not sure what is going on here. Here is my traceback() and sessionInfo() in case it helps: traceback() 3: stop(arguments imply differing number of rows: , paste(unique(nrows), collapse = , )) 2: data.frame(colname = colnamesMy, nlevels = 0, position = 0, width = 0, digits = 0, exp = 0, stringsAsFactors = FALSE) 1: write.fwf(outframe, file = outfile1, sep = , quote = FALSE, rownames = FALSE, colnames = FALSE, width = c(4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8), append = TRUE, justify = right) sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] doBy_4.0.5 survival_2.35-7 gdata_2.7.1 chron_2.3-34 loaded via a namespace (and not attached): [1] cluster_1.12.1 grid_2.10.1gtools_2.6.1 Hmisc_3.7-0 [5] lattice_0.17-26Matrix_0.999375-33 Any advice on this will be much appreciated. Thanks. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD in 2.11.1 error
Andy Zhu wrote:
Hi,
I have a set of user defined package which I have installed in 2.8.1 for quite
some time. I installed 2.11.0 and 2.11.1 a couple of days ago while still
having 2.8.1 version in my system. For the package, package.skeleton works fine
in R 2.11. However, it comes problem when I run Rcmd check/intall. The
intall.out shows below.
I further tested that I reran R-2.8.1/bin/R CMD check in 2.8.1. it still
works. Then I ran and test the doomed function, gzWrite, in R-2.11.1/binRgui,
it also works fine. So, is this the problem in R-2.11.1/bin/Rcmd itself? How
do I fix it? I have MinGW, Perl, etc. installed in my system.
The problem is in the help file, not in the R code. You need to look
somewhere near line 92 of quantplus/man/gzWrite.Rd.
Duncan Murdoch
I also attached my function gzWrite below.
Thank you very much.
00check.out:
* install options are ' --no-html'
* installing *source* package 'quantplus' ...
** R
** preparing package for lazy loading
** help
Warning: newline within quoted string at gzWrite.Rd:92
Warning: ./man/gzWrite.Rd:99: unknown macro '\n'
Warning: newline within quoted string at gzWrite.Rd:92
Error in parse_Rd(./man/gzWrite.Rd, encoding = unknown, ...) :
Unexpected end of input (in quoted string opened at gzWrite.Rd:99:46)
ERROR: installing Rd objects failed for package 'quantplus'
* removing
'd:/developer/projects/quant+/package_builder/quantplus.Rcheck/quantplus'
the problem function:
**
gzWrite =
# write out a data frame into a gzip file in the format of write.table
function(ds, outdir, outpfx, datepfx, sep='\t', quote=TRUE, row.names=FALSE,
col.names=TRUE, na='NA', append=FALSE) {
if (F) {
ds = ds.price;
outdir = pathPrice;
outpfx = paste(pfx.price,'_',sep='');
datepfx = fdate;
sep = '\t';
quote = TRUE;
row.names = FALSE;
col.names = TRUE;
na = 'NULL';
append = FALSE;
}
file.out = paste(outdir, '\\', outpfx, datepfx, '.gz', sep='');
file.tmp = paste(outdir, '\\', outpfx, datepfx, '.txt',sep='');
write.table(ds, file=file.tmp, sep=sep, quote=quote, row.names=row.names,
col.names=col.names, na=na, append=append);
zz = gzfile(file.out, 'w');
raw = file(file.tmp, 'r');
cat(readLines(raw), file=zz, append=F, sep='\n');
close(zz);
close(raw);
unlink(file.tmp);
invisible(NA);
}
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Package not on CRAN mirrow - what now?
markw...@afrihost.co.za wrote: Package arulesSequences isn't on CRAN for automatic package install. I downloaded a *.tar.qz version because no *.zip for Windows offered. Why is this? I expanded *.tar.qz in ~R/R-2.11.0/library/arulesSequences I then assumed that R would list it in the packages list but it doesn't. What am I doing wrong ? You need to install it, it's not generally enough to just unpack it. But that will not work, because the package is marked as Unix-only. You could try to figure out what needs fixing to get it working on Windows, but it's probably not easy. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Capturing buffered output from Rterm
Keith Jewell wrote: In MS Windows I a) invoke Rterm from a batch file (test.bat) b) to execute commands from a script (m:\test.rsc) c) capturing output in a log file (m:\test.log) BUT if the script results in an error the error message is NOT written to the log file, leaving me problems when the error is from a complicated function. Simplified example:. test.bat REM ensure 'R' is in path path \\Server02\stats\R\R-Current\bin\;%PATH% Rterm --no-init-file --no-restore-data --no-save --silent m:\test.rsc m:\test.log - m:\test.rsc - print(this is a test) #generate an error nls() -- The error message: Error in .Internal(inherits(x, what, which)) : 'x' is missing is is NOT written to the log file, which just ends m:\test.log -- snip print(this is a test) [1] this is a test #generate an error nls() - I surmise this is due to output buffering (?). In an S-Plus version I turned off buffering with guiSetOption(option.name=BufferOutputWindows, value.string=F) but I don't think this is available in R (?). Has anyone any suggestions? It's not output buffering, it's because error messages go to a different file handle than regular ones. You need to redirect both stdout and stderr. I'm not sure of the syntax to do that in Windows CMD, but R CMD BATCH test.rsc instead of Rterm would do it. (The output should go to test.Rout.) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R in Linux: problem with special characters
daniel fernandes wrote: Hi, I’m working with the 64 bit version of R 2.11.0 for Linux. My session info is: R version 2.11.0 (2010-04-22) x86_64-redhat-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base When I try to print words with special characters the result is that the expression printed has some kind of code substituting the special character. For example, if I run print(“dúvida”) the result is: print(dúvida) [1] d\372vida This as problem has something to do with the locale settings? If I run the locale command in the Linux server, I get: Yes, it's your locale settings. The C locale doesn't support the ú character in your string, and displays it in octal. Duncan Murdoch [daniel.fernan...@pt-lnx13 ~]$ locale LANG=pt_PT.UTF-8 LC_CTYPE=C LC_NUMERIC=C LC_TIME=C LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C LC_ALL=C Thanks in advance for your help, Daniel TRANSFORME SUAS FOTOS EM EMOTICONS PARA O MESSENGER. CLIQUE AQUI E VEJA COMO. _ VEJA SEUS EMAILS ONDE QUER QUE VOCÊ ESTEJA, ACESSE O HOTMAIL PELO SEU CELULAR AGORA. =Live_Hotmailutm_medium=Taglineutm_content=VEJASEUSEM84utm_campaign=MobileServices [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rgui crashed on Windows XP Home
Jinsong Zhao wrote: Hi there, I just installed R 2.11.1 on my PC, which runs a Windows XP Home. The installation is successful, however, when I double click on the R icon, I get the following error message: R for Windows GUI front-end has encountered a problem and needs to close. We are sorry for the inconvenience. The error occurs in msvcrt.dll, a Microsoft dll. It happened after a call from one of the R dlls, setting up the GUI. I don't really know what to suggest to fix this, other than the usual things: try running R with the --vanilla command line argument, try shutting down everything else on your system, etc. Duncan Murdoch Error signature is: AppName: rgui.exeAppVer: 2.111.52157.0 ModName: msvcrt.dll ModVer: 7.0.2600.2180Offset: d2b5 I get a gdb, and then gdb the Rgui.exe, I get the following message: (gdb) run Starting program: D:\Program Files\R\R-2.11.1\bin/Rgui.exe [New Thread 2460.0xb7c] Program received signal SIGSEGV, Segmentation fault. 0x77c1d2b5 in msvcrt!mblen () from C:\WINDOWS\system32\msvcrt.dll (gdb) bt #0 0x77c1d2b5 in msvcrt!mblen () from C:\WINDOWS\system32\msvcrt.dll #1 0x77c1d3a9 in msvcrt!mbstowcs () from C:\WINDOWS\system32\msvcrt.dll #2 0x635597f9 in GA_newwindow () from D:\Program Files\R\R-2.11.1\bin\Rgraphapp.dll #3 0x63543a25 in GA_newcontrol () from D:\Program Files\R\R-2.11.1\bin\Rgraphapp.dll #4 0x63543c3f in GA_newimagebutton () from D:\Program Files\R\R-2.11.1\bin\Rgraphapp.dll #5 0x6c723d7e in setupui () from D:\Program Files\R\R-2.11.1\bin\R.dll #6 0x004014e2 in ?? () #7 0x00401425 in ?? () #8 0x00401708 in ?? () #9 0x0040124b in ?? () #10 0x004012b8 in ?? () #11 0x7c816fe7 in RegisterWaitForInputIdle () from C:\WINDOWS\system32\kernel32.dll #12 0x in ?? () (gdb) The Rterm.exe can run normally. I don't know it's a bug of Rgui or a bug of my system. Thanks for any help. Regards, Jinsong __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Html help
Murray Jorgensen wrote: I have just installed R 2.11.1 on my XP laptop. I like html help for browsing but text help for on-the-fly look-ups. I was a bit surprised when I was asked to choose between them during the installation. I chose text, thinking I could fix the html help later, which is what I am trying to do now. Now when I ask for html help my browser goes to 'http://-ip-number-/doc/html/index.html' instead of where I want on my computer: C:\apps\R\R-2.11.1\doc\html\index.html Now I can go where I want manually but then the package list on C:\apps\R\R-2.11.1\doc\html\packages.html does not include all the packages that I have installed and linked. I don't want to read my html help from the web because sometimes I am off-line or on a slow connection. How do I go about getting a local set of html help files? Since 2.10.0, HTML help is generated on demand. It doesn't go off your local computer, it works locally. This saves a bit of space (the HTML is generated from the same source as the text is generated from), but the main point is that it allows help pages to contain dynamic content. For example, Romain Francois posted some demo code a while ago to allow the display of graphics generated by R within help pages. (Unfortunately it depended on a particular browser feature not supported by Internet Explorer, so I'm going to need to put together something less elegant, but that's life.) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simple 3D Plot Question
Nick Torenvliet wrote:
Hi all,
I've got a simple 3D plot as follows...
xx - seq(-20,20,.5)
yy - seq(-20,20,.5)
zFunc - function(x,y){3*x^2*y}
z - outer(xx,yy,zFunc)
persp(xx,yy,z,theta=30,phi=30,ticktype=detailed)
Just beautiful!
My question is how do I constrain the plot to only display x^2 = y = 1?
If you set z values to NA, the surface mesh won't be plotted. Those
restrictions you give are a pretty small part of the range of xx and yy
though, so you'll want to restrict them, e.g.
xx - seq(-1,1,len=20)
yy - seq(0,1,len=20)
zFunc - function(x,y){ifelse(x^2 y y 1, 3*x^2*y, NA)}
z - outer(xx,yy,zFunc)
persp(xx,yy,z,theta=30,phi=30,ticktype=detailed)
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Package testing
Gábor Csárdi wrote: Dear all, I would like to write some tests for my R package, and the usual 'tests' directory seemed like a good solution, but there is something I cannot understand. It is possible to supply .Rout.save files with the expected output for the tests, which is great. But since the tests are not run with R --slave, the expected output needs to contain all the extra output from R, e.g. the startup message. The commands are echoed to the output, too. This makes it difficult to write proper tests, as they will necessarily fail on all but one R versions (the version number is always part of the output), and one would need to write the test programs twice, once in the normal .R file, and once in the .Rout.save file. Is there a way to work around these things? Or am I trying to use the 'tests' directory for something that was not intended? The normal workflow is to write the tests as R files, and run them. Then manually check every line of the Rout, and when you're satisfied it's fine, save it as an Rout.save file. After that R will only report changes to that file that occur after the header, so version numbering changes will be ignored, but changes that affect your output will not. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] trigonometric regression
William Simpson wrote: Suppose I do a trigonometric regression fit-lm(y~ cf + sf) where cf and sf are the cos and sine components. b-coef(fit) I have the fitted sine component b[2] and the cos component b[3]. Doing summary(fit) gives me the p-values and SEs for b[2] and b[3]. But I want the amplitude of the fitted waveform amp-sqrt(b[2]^2+b[3]^2) Can someone please tell me how to get the p-value for amp? the p-value for amp is ambiguous; p-values refer to tests, not functions. But let's assume you want to test whether amp = 0. Then this is achieved by an F test comparing the model with cf and sf versus one without it. You'll see it in summary(fit) at the bottom of the display. If you want to include other covariates in the model, you can use anova, e.g. anova(lm(y ~ other), lm(y ~ cf + sf + other)) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R licensing query
On 17/06/2010 10:26 AM, Jeff Newmiller wrote:
I think there is something else going on here, since no security organization
would accept an email from a nonexistent organization as justification for adding
software that they are suspicious of to their system.
The R Foundation is not nonexistent, but our answer to the questions
about compatibility and harmlessness are in the banner you get when you
start it:
R is free software and comes with ABSOLUTELY NO WARRANTY.
This is a shorter version of the longer non-warranty in paragraph 11 of
the GPL v2, which you can see by running
RShowDoc(COPYING)
from within R.
Duncan Murdoch
On the other hand, if you can't figure out what is really going on, and you can
loosen up some funds, you can probably get Revolutions R to provider you with
commercial support.
McAllister, Gina gina.mcallis...@luht.scot.nhs.uk wrote:
I have recently started a new job at an NHS hospital in Scotland. Since
I took up this post 6 months ago I have had an ongoing dispute with the
IT secutiry dept. who refuse to install R on my computer. I previously
worked in another branch of the NHS where R was widely used and yet
there is nothing I can say which will persuade the IT dept here to even
visit the website! With some help from our head of department, they
have now agreed to install R but only if they receive an email from 'R'
ensuring that it is licensed for commercial use, is compaitable with
Windows XP and will not affect the networked computer system here. My
only other option for data anlaysis is Excel, we have no money for
S-plus or any other stats programme. Can anyone suggest anything or
send me a suitable email?
Many thanks,
Georgina
*
The information contained in this message may be confide...{{dropped:12}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
---
Jeff NewmillerThe . . Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/BatteriesO.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
---
Sent from my phone. Please excuse my brevity.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] tempfile problem
On 17/06/2010 12:43 PM, Ben Madin wrote: G'day all, The documentation for tempfile states : The names are very likely to be unique among calls to tempfile in an R session and across simultaneous R sessions. The filenames are guaranteed not to be currently in use. My problem I think relates to the second part of the sentence, which is the guarantee... and it is being met ... but I need to save the files as .png files, in the same directory, so I am adding the suffix and I suppose therefore the next offering can be unique (as it doesn't have the prefix) I am using a command like : fname - basename(tempfile(nahis, /Library/WebServer/Documents/nahis/tmp)) on a mac, or fname - basename(tempfile(nahis, /htdocs/nahis/tmp)) on a FreeBSD system, as I need to be able to find the file from the web browser up to 24 hours later. and then this_filename - paste(fname, .png, sep = ) and saving the file as this_filename, hence the next call doesn't find it's own suggestion, and starts again. It sounds as though you are doing something strange with the random number seed, because those names are chosen at random, and then checked for uniqueness. If the seed is being reset you could get the same name twice in a row, but otherwise it's very unlikely. (And it's the C library function rand(), not R's RNG that is used.) Is there any alternative filenameing approach I can use to get around this? Do I need to manually scan and reject the name if it matches the names I already have? Should I just digest the current time ? (It's working so far!) If you use the current time, watch out for timer accuracy and fast computers. You may be able to get more than one file created before the next timer tick. I'd suggest that you should generate more than enough filenames once at the start, confirm they're all unique, and then just take them one by one as needed. Alternatively, create the tempfile() as well as the tempfile().png, but this is likely to be really slow if the seed is the same each time, because checking for the existence of the first n tries is going to be slow. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] 12th Root of a Square (Transition) Matrix
On 18/06/2010 2:01 AM, Corey Gallon wrote: Dear R-tisans, I am trying to calculate the 12th root of a transition (square) matrix, but can't seem to obtain an accurate result. I realize that this post is laced with intimations of quantitative finance, but the question is both R-related and broadly mathematical. That said, I'm happy to post this to R-SIG-Finance if I've erred in posting this to the general list. I've pulled down an annual transition matrix from the latest Moody's Corporate Default Study, and I'm using this (with the default row added manually) as the basis for this calculation. (I've pasted the dput of the resulting matrix below.) According to Hull, Appendix E [1], an arbitrary root of a square matrix (A) can be calculated by multiplying the inverse matrix of eigenvectors (X-inv) by the nth-root of diagonalized matrix of eigenvalues (Lambda-star) by the matrix of eigenvectors (X) -- all of these eigenvectors(values) being calculated from the matrix for which one wishes to calculate the nth root. The equation is as follows: A = X-inv %*% Lambda-star %*% X This is wrong: you've swapped X and X-inv. So your final line below should be nth_root - X %*% L_star %*% X_inv Duncan Murdoch I've written the code below to implement this, but the result doesn't seem to be correct. (I can't raise the resulting matrix to the 12th power to calculate the original matrix.) I believe that the reason for this is the order in which R returns the eigenvalues (i.e. a vector in descending order) and the order in which I've created the matrix of eigenvectors, but I may be wrong in this suspicion. I defer to the collective wisdom of the community, and hope that minds greater than mine may provide insight. Cheers, Corey dput(trans_matrix) structure(c(0.9426, 0.0047, 0, 4e-04, 0, 5e-04, 0, 0, 0, 0, 0, 0, 9e-04, 0, 0, 0, 0, 0, 0.0308, 0.8205, 0.0254, 4e-04, 9e-04, 0, 0, 0, 0, 4e-04, 0.0016, 0, 0, 0, 0, 0, 0, 0, 0.021, 0.1291, 0.7978, 0.034, 0.0043, 0.0025, 0.0011, 3e-04, 9e-04, 4e-04, 0, 0, 0, 0, 0, 0, 0, 0, 0.0056, 0.0394, 0.1174, 0.8366, 0.0509, 0.0094, 0.0023, 0.0022, 0.0014, 0.0017, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.0016, 0.0448, 0.0944, 0.8253, 0.0569, 0.011, 0.0051, 6e-04, 0.0021, 0.0016, 0, 0, 0, 0, 0, 0, 0, 0, 0.0016, 0.0067, 0.024, 0.0873, 0.8108, 0.0677, 0.0105, 0.004, 0.0017, 0, 9e-04, 0, 0, 0.0039, 0.0045, 0, 0, 0, 0.0016, 0.0024, 0.0064, 0.0179, 0.0833, 0.7838, 0.0758, 0.012, 0.0021, 0.0024, 0, 9e-04, 0, 0.0013, 0.0015, 0, 0, 0, 0, 0.0024, 0.0014, 0.0068, 0.0202, 0.0908, 0.7694, 0.0744, 0.0136, 0.0079, 0.0045, 9e-04, 0.0024, 0, 0, 0.0024, 0, 0, 0.0016, 0, 0.0014, 0.004, 0.0089, 0.0175, 0.0983, 0.8066, 0.1032, 0.0267, 0.0063, 0.0054, 0.0024, 0, 0.003, 0, 0, 0, 0, 0.0024, 0, 0.0022, 0.002, 0.0079, 0.0178, 0.0632, 0.7605, 0.1422, 0.0308, 0.0099, 0.006, 0.0013, 0.003, 0, 0, 0, 0, 0, 0, 0, 0.0017, 0.0014, 0.0086, 0.0117, 0.0574, 0.6787, 0.1014, 0.0425, 0.006, 0.0039, 0.003, 0.0047, 0, 0, 0, 0, 0, 3e-04, 0.0012, 0.0014, 0.0022, 0.0109, 0.0227, 0.0589, 0.6814, 0.1058, 0.041, 0.0078, 0.0045, 0.0024, 0, 0, 0, 6e-04, 0, 0, 2e-04, 0.0096, 0.0038, 0.0034, 0.012, 0.0212, 0.0661, 0.6609, 0.159, 0.0362, 0.012, 0.0024, 0, 0, 0, 0, 0, 0, 2e-04, 3e-04, 0.0016, 0.0029, 0.0058, 0.0118, 0.029, 0.0597, 0.6205, 0.1332, 0.0331, 0.0047, 0, 0, 0, 0, 0, 0, 0.001, 0.0011, 3e-04, 0.002, 0.0074, 0.0157, 0.0244, 0.0515, 0.0916, 0.6546, 0.1203, 0.0353, 0, 0, 0, 0, 4e-04, 0, 0, 3e-04, 0, 6e-04, 8e-04, 0.0047, 0.0199, 0.0172, 0.0325, 0.0699, 0.7098, 0.1318, 0, 0, 0, 0, 0, 0, 5e-04, 0.0017, 0.0022, 0.004, 0.0021, 0.0102, 0.0217, 0.0244, 0.0241, 0.044, 0.0737, 0.5271, 0, 0, 0, 0, 7e-04, 0, 7e-04, 0.0023, 0.0019, 0.0014, 0.0062, 0.0165, 0.0136, 0.0199, 0.0145, 0.044, 0.0316, 0.2894, 1), .Dim = c(18L, 18L), .Dimnames = list(c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18), c(AAA, AAp, AA, AAm, Ap, A, Am, BBBp, BBB, BBBm, BBp, BB, BBm, Bp, B, Bm, CCC.to.C, D))) -- BEGIN PASTE -- # create a matrix of eigenvectors of the transition matrix X - eigen(trans_matrix)$vectors # create a diagonalized matrix of the eigenvalues of the transition matrix L - diag(eigen(trans_matrix)$values) # calculate inverse of matrix of eigenvectors of the transition matrix X_inv - solve(X) # calculate the 12th root of the eigenvalues in the diagonal matrix L_star - L ^ (1/12) # calculate the 12th root of the transition matrix nth_root - X_inv %*% L_star %*% X -- END PASTE -- References: [1] Hull, John. Risk Management and Financial Institutions. Prentice Hall, 2007. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE
Re: [R] Use of .Fortran
On 18/06/2010 9:59 AM, David Scott wrote:
I have no experience with incorporating Fortran code and am probably
doing something pretty stupid.
I want to use the following Fortran subroutine (not written by me) in
the file SSFcoef.f
subroutine SSFcoef(nmax,nu,A,nrowA,ncolA)
implicit double precision(a-h,o-z)
implicit integer (i-n)
integer l,i,nmax
double precision nu,A(0:nmax,0:nmax)
A(0,0) = 1D0
do l=1,nmax
do i=1,l-1
A(l,i) = (-nu+i+l-1D0)*A(l-1,i)+A(l-1,i-1)
end do
A(l,0) = (-nu+l-1D0)*A(l-1,0)
A(l,l) = 1D0
end do
return
end
I created a dll (this is windows) using R CMD SHLIB SSFcoef.f
Then my R code is:
### Load the compiled shared library in.
dyn.load(SSFcoef.dll)
### Write a function that calls the Fortran subroutine
SSFcoef - function(nmax, nu){
.Fortran(SSFcoef,
as.integer(nmax),
as.integer(nu)
)$A
}
SSFcoef(10,2)
which when run gives
SSFcoef(10,2)
NULL
I am pretty sure the problem is that I am not dealing with the matrix A
properly. I also tried this on linux and got a segfault.
Can anyone supply the appropriate modification to my call (and possibly
to the subroutine) to make this work?
Two problems:
Your subroutine takes 5 arguments, you're only passing two.
You didn't name your arguments, but are trying to retrieve A by name.
So this will get you closer (it's untested, so there might still be
problems...):
SSFcoef - function(nmax, nu){
.Fortran(SSFcoef,
as.integer(nmax),
as.integer(nu),
A = numeric((nmax+1)^2),
nrowA = as.integer(nmax+1), # These are unused...
ncolA = as.integer(nmax+1)
)$A
}
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Call by reference or suggest workaround
On 19/06/2010 10:32 AM, Chidambaram Annamalai wrote:
I have written code to compute multi-indices in R [1] and due to the
recursive nature of the computation I need to pass around the *same*
matrix object (where each row corresponds to one multi-index). As pass
by reference wasn't the default behavior I declared a global matrix
(mat) and used the - operator to write to the global matrix. So the
usage would be to call genMultiIndices(3,2) for side effects to
generate all multi-indices of length 3 and sum 2. And then access the
global matrix.
However, after coding this I can't seem to export the global matrix
object (in the NAMESPACE file) and still retain mutability since its
binding is locked (R throws an error). Can I somehow unlock this?
Ideally I would want to pass around the same matrix to the recursive
function. Is that possible? If not, could someone please suggest a
workaround to use the code in an R package?
If you pass the object to multiple functions it will only create a new
copy when necessary due to modifying it, so the cost of passing it down
to every recursive call is not so large as you seem to think. But it's
not zero cost, passing arguments to functions costs a little bit.
You can avoid this using nested functions and - as you had before.
That is, instead of making your recursive function a top level function
so that - assigns into the namespace environment (which is what's
causing the error), make it a nested function within another, and do
your assignments to the outer frame. For example,
outer - function(args) {
mat - matrix(NA, 3,3)
recursive - function() {
mat - newvalue # does the assignment into outer's frame
if (!stop) recursive()
}
}
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Popularity of R, SAS, SPSS, Stata...
On 20/06/2010 6:36 PM, Muenchen, Robert A (Bob) wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Ivan Calandra Sent: Sunday, June 20, 2010 3:47 PM To: r-help@r-project.org Subject: Re: [R] Popularity of R, SAS, SPSS, Stata... Bob, I have no idea whether it is realistic, but if you look for the papers that used R or SAS (or anything), you might get better results by searching for the way R and SAS are cited. Hi Ivan, that was what I tried when more generic keywords failed. However, almost no one seems to use that citation. For example, in 2009, only 28 papers contain R Foundation and 61 contain Bioconductor, which uses R. One single paper contains both. I appreciate the idea though! If you use Web of Science, then the abbreviation for the author in the standard citation for R is R DEV COR TEAM. Doing a search for citations to that author in 2009 or 2010 finds 249 papers. Variations on the spelling that I see include R DEV C3R TEAM R DEV CAR GROUP R DEV CAR TEAM R DEV CIR TEAM R DEV COD TEAM R DEV COR R DEV COR T R DEV COR TEA R DEV COR TEAM R DEV COR TEAM C R DEV COR TEAM CO R DEV COR TEAM FD R DEV COR TEAM OR R DEV COR TEAM R R DEV COR TEAM RD R DEV COR TEAM VI R DEV COR TEAMR R DEV COR TEMA R DEV COR TRAM R DEV CORE TEAM R DEV CORETEAM R DEV CORR TEAM R DEV CORT TEAM R DEV CPR TEAM R DEV CT R DEV TEAM R DEVCOR TEAM R DEVELOPMENTCORE Not all of those might really be R. For example, there's probably a north Atlantic codfishing team named R DEV COD TEAM. But most of them are, and they lead to 289 cited papers in 2009/10. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Popularity of R, SAS, SPSS, Stata...
On 21/06/2010 2:49 AM, Peter Dalgaard wrote: Duncan Murdoch wrote: On 20/06/2010 6:36 PM, Muenchen, Robert A (Bob) wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Ivan Calandra Sent: Sunday, June 20, 2010 3:47 PM To: r-help@r-project.org Subject: Re: [R] Popularity of R, SAS, SPSS, Stata... Bob, I have no idea whether it is realistic, but if you look for the papers that used R or SAS (or anything), you might get better results by searching for the way R and SAS are cited. Hi Ivan, that was what I tried when more generic keywords failed. However, almost no one seems to use that citation. For example, in 2009, only 28 papers contain R Foundation and 61 contain Bioconductor, which uses R. One single paper contains both. I appreciate the idea though! If you use Web of Science, then the abbreviation for the author in the standard citation for R is R DEV COR TEAM. Doing a search for citations to that author in 2009 or 2010 finds 249 papers. Variations on the spelling that I see include R DEV C3R TEAM R DEV CAR GROUP R DEV CAR TEAM R DEV CIR TEAM R DEV COD TEAM R DEV COR R DEV COR T R DEV COR TEA R DEV COR TEAM R DEV COR TEAM C R DEV COR TEAM CO R DEV COR TEAM FD R DEV COR TEAM OR R DEV COR TEAM R R DEV COR TEAM RD R DEV COR TEAM VI R DEV COR TEAMR R DEV COR TEMA R DEV COR TRAM R DEV CORE TEAM R DEV CORETEAM R DEV CORR TEAM R DEV CORT TEAM R DEV CPR TEAM R DEV CT R DEV TEAM R DEVCOR TEAM R DEVELOPMENTCORE Not all of those might really be R. For example, there's probably a north Atlantic codfishing team named R DEV COD TEAM. But most of them are, and they lead to 289 cited papers in 2009/10. Duncan Murdoch That sound a bit low. Last I checked R DEV COR TEAM, for ALL publication years, it came up with about 13000 references within 511 different misspellings of the R manual reference ( a few more). Papers currently being registered tend to reference the version of R that was used when the research was done, and with review delays etc. that can be a few years back. Yes, you're right. The 289 count was the number of cited works (variations on R.) The number of papers citing a similar list was 6864. Duncan Murdoch Another matter is that software citation varies widely by field. Of the above 13000 references, I think about 3000 were from ecology (or was it environmental science?). In economics, or indeed in mathematical statistics, the tradition is to cite methods, but not software. (And one sinner is the R Journal, in which is would be absurd to have every paper cite R...) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] S3 generics need identical signature?
On 21/06/2010 9:31 AM, Gábor Csárdi wrote: Dear all, Writing R Extensions explicitly says that A method must have all the arguments of the generic, including ... if the generic does. A method must have arguments in exactly the same order as the generic. If the generic specifies defaults, all methods should use the same defaults. This is clear. R CMD check even checks for this. But then how is it possible that for plot(), which is an S3 generic, plot.default(), plot.formula() and plot.table(), etc. all have different arguments? The question is not simply theoretical, I have two S3 generics in my package, and one is reported by R CMD check, but the other not, and I fail to see why the difference. Moreover, R CMD check reports: * checking S3 generic/method consistency ... WARNING plot: function(x, ...) plot.communities: function(communities, graph, colbar, col, mark.groups, layout, edge.color, ...) But actually, the signature of plot() seems to be plot function (x, y, ...) [...] I am confused. What am I missing? The requirement is that the methods need to have signatures that contain all the arguments of the generic. If the generic includes ..., then the methods can add other arguments, too. So with the generic for plot() as you show above, any plot method is required to have x and y as the first two arguments, and ... as an argument, but they can have other args too. Looking at them: head(plot.default) 1 function (x, y = NULL, type = p, xlim = NULL, ylim = NULL, 2 log = , main = NULL, sub = NULL, xlab = NULL, ylab = NULL, 3 ann = par(ann), axes = TRUE, frame.plot = axes, panel.first = NULL, 4 panel.last = NULL, asp = NA, ...) This is okay. head(graphics:::plot.formula) 1 function (formula, data = parent.frame(), ..., subset, ylab = varnames[response], 2 ask = dev.interactive()) This violates the rule, so if someone does this: y - rnorm(10) x - 1:10 formula - y ~ x plot(formula) they'll get what they want, but plot(x = formula) they'll get an obscure error message: plot(x=formula) Error in terms.formula(formula, data = data) : argument is not a valid model head(graphics:::plot.table) 1 function (x, type = h, ylim = c(0, max(x)), lwd = 2, xlab = NULL, 2 ylab = NULL, frame.plot = is.num, ...) This also violates the rule, but it's hard to think of an example where it might cause trouble. HOWEVER, plot() is a very old function, and methods were written for it long before the current rule was established. So it is handled specially by the check code. The y argument is not required (see the checkArgs code in src/library/tools/R/QC.R), and apparently the first arg doesn't need to be named x in plot.formula, due to some other exception which I can't spot right now. So I would not use the base code for plot() as an example of what you should do. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to efficiently compute set unique?
On 21/06/2010 9:06 PM, G FANG wrote: Hi, I want to get the unique set from a large numeric k by 1 vector, k is in tens of millions when I used the matlab function unique, it takes less than 10 secs but when I tried to use the unique in R with similar CPU and memory, it is not done in minutes I am wondering, am I using the function in the right way? dim(cntxtn) [1] 135847631 uniqueCntxt = unique(cntxtn);# this is taking really long What type is cntxtn? If I do that sort of thing on a numeric vector, it's quite fast: x - sample(10, size=13584763, replace=T) system.time(unique(x)) user system elapsed 3.610.143.75 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with writing a CSV file in UTF-8 formate
On 22/06/2010 9:00 AM, venkata kirankumar wrote: Hi all, I have a problem with writing a *.CSV file in UTF-8 formate I tried to write a dataframe named dfPREINDX to the new file named preindx.csv in below formate write.table(dfPREINDX,PreIndex,fileEncoding=UTF-8,sep=|,row.names=FALSE) but its throed an error like Error in write.table(dfPREINDX, preindx.csv, fileEncoding = UTF-8, sep = |, : unused argument(s) (fileEncoding = UTF-8) can any one please help me how to create a file in UTF-8 formate. The write.table has no fileEncoding argument. To write to a non-native encoding, you need to open a connection with that encoding, and write to that. For example: con - file(preindx.csv, open=w, encoding=UTF-8) write.table(dfPREINDX, con, sep=|,row.names=FALSE) close(con) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Displaying Iteration Count
On 22/06/2010 9:14 AM, jim holtman wrote: Just put the code in yourself; use 'cat' with a test to print every 'n' iterations. You can also check out the 'winProgressBar' in the plyr package. In Windows (and other GUIs?) console output is buffered, so by default the results won't appear until the end. However, you can change this; in Windows you use the Misc | Buffered output menu item (or Ctrl-W), or make a call to flush.console() as Henrique showed. Duncan Murdoch On Tue, Jun 22, 2010 at 9:07 AM, Downey, Patrick pdow...@urban.org wrote: Hello, I'm running a very long for loop that usually takes hours. For my own piece of mind, it would be nice if I could check periodically and see which iteration the loop is on. A line of code that told R to print the iteration number every 100 or 200 iterations would be perfect. Does anyone know something like this? I've never known how to print anything within a for loop before the loop ends. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
