Re: [R] Saving/exporting graphs
> HI:
>
> I have tried to find a way in which to export/save graphs via the command
> line. I know i can right click on it and save it as wmf etc.
> But I was wandering if there is a function such as Splus'
> export.graph
?win.metafile
as in
win.metafile("c:/foo.wmf")
plot(blah,blah,blah)
dev.off()
Cheers
Jason
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Re: [R] SCO & R
On Thu, May 27, 2004 at 12:53:46PM -0700, Greg Tarpinian wrote: ... > recently > I read an article in Forbes which discussed how SCO > was going after companies that have been using Linux. It couldn't have been that recent; SCO dropped the most Linux- relevant portions of its lawsuit back in January. http://www.groklaw.net/article.php?story=20040206175445975 Further, SCO is under investigation for racketeering in Australia. The "pay us money, because we own Unix" letters may be a form of illegal shakedown in Oz. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] problems with quantreg installation
> make: g77: Command not found > make: *** [akj.o] Error 127 You need a fortran compiler. Search the RPM lists for g77 (or just "fortran"). Cheers Jason __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ffnet problem
> Anyway, what steps should I take now? "should" isn't quite what I'm telling you; just free advice. :) I use nnet from the nnet package (VR bundle), and find it very good. And it doesn't require any additional libraries. If you've got a binary installation, you've probably got it already... library(nnet) ?nnet I found nnet isn't as "quick and dirty" out of the box as ffnet, but gives you much more control over the fit and diagnostics (less "black-box"-ish). Cheers Jason __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] zipping a new package
On Sun, May 30, 2004 at 03:19:24PM -0500, Laura Holt wrote: > Dear R People: > > I have finally created a little R package. > > Do I need to do anything special to create a zip file for that package, or > just use Winzip, please? > > thanks so much > > R Windows Version 1.9.0 > Re-read "Writing R Extensions" for a full description, particularly "Checking and building packages". In your case, from the directory just above the top-level directory of your package. Rcmd BUILD --binary yourpackagename This takes care of a lot of things related to the build; zipping is only part of it. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Little question
On Tue, 2004-06-08 at 21:44, zze-PELAY Nicolas FTRD/DMR/BEL wrote:
> Here I got a function :
>
> f<-function(x){
> res<-list()
> res$bool=(x>=0)
> res$tot=x
> return(res)
> }
>
> I want that a=res$bool and b=res$tot
> I know that a possible solution is :
>
Like
foo <- function(x,...){
list(a=(x>=0),b=x)
}
Cheers
Jason
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Re: [R] off topic publication question
On Wed, 2004-06-09 at 05:11, Erin Hodgess wrote:
> If a single author is writing a journal article,
> should she use "We performed a test"
> or "I performed a test",
> please?
Does the particular journal specify a style manual or style sheet? The
Chicago Manual of Style \cite{Chicago2003}, p160, says "'We' is
sometimes used by an individual who is speaking for a group... called
the editorial 'we'. Some writers also use 'we' to make their prose
appear less personal and to draw in the reader or listener."
Although journals may vary in their requirements, you are presumably
speaking for a group (the University of Houston Downtown), and "we" is
probably safer than "I". Probably.
It's important to note that the Chicago Manual does *not* claim to be
authoritative, merely helpful.
Cheers
Jason
@Book{Chicago2003,
editor = {University of Chicago Press Staff},
title ={The Chicago Manual of Style},
publisher ={University of Chicago Press},
year = 2003,
address = {Chicago},
edition = {Fifteenth}
}
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Re: [R] more obvious contribution mechanism?
On Wed, 2004-06-09 at 13:22, ivo welch wrote: > can we put a "how to donate money to R" on the R webpage? perhaps with > a paypal button? > Does the R Foundation link meet this need? http://www.r-project.org/foundation/main.html Cheers Jason __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] moving data and output?
> Hello,
>
> I have a few questions now:
Yes. Since the mail is archived to help other people, in future please
send a small mail for each question, with a descriptive subject line for
each. This makes it easier for everyone.
> 1. How can I move data the following way:
>
> I have 2 variables:
>
> one two
> 1 5 ^
> 3 4 |
> 1 3 |
> 4 4 |
>
> Now I want to move the two one arround (sorry I don't know how to say
> that in english). That means: I want to move the first item at the
> end of my column and move the second at the first place, the third at
> the second, and so on. You can see it at the arrow next to the 'two'
> column. The colum named 'one' should be as it is.
By using indexing. If this is a matrix called mymatrix:
mymatrix[,2] <- mymatrix[c(4,1:3),2]
If it's a data frame called mydf:
mydf$two <- mydf$two[c(4,1:3)]
> 2. How can I make outputs of the grafics (plot, hist, ...) into a file?
See the help pages and examples...
?postscript
?Devices
?pdf
> 3. Can I make latex output of the grafics (any tool, like texdraw or
> pictex ...)?
I use either eps or pdf for inclusion into LaTeX. You also have the fig
file format, so you can use xfig to edit before inclusion.
> 4. I know about sink(). But can I format the output for LaTeX, like a
> \begin{tabular} ... \end{tabular} for a dist() matrix or similar?
Two ways:
1) Install the Hmisc package, and see ?latex
2) Install the xtable package, and see ?xtable.
> 5. Acording to the other questions, where can I find answers for this
> questions, if I'm not the first one who is asking?
1) help.search("some keyword")
2) go to http://cran.r-project.org, and follow the "Search" link to search
the mail archives.
Cheers
Jason
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Re: [R] rownames of single row matrices
On Fri, 2004-06-11 at 20:09, Robin Hankin wrote:
> Hi
>
> I want to extract rows of a matrix, and preserve rownames even if only
> one row is selected.
The infamous drop=TRUE default. help("[") goes into this.
Your toy example, two ways:
> a <- matrix(1:9,3,3)
> rownames(a) <- letters[1:3]
> colnames(a) <- letters[1:3]
> a[1,,drop=FALSE]
a b c
a 1 4 7
> a[1,,drop=TRUE]
a b c
1 4 7
Does that help?
Cheers
Jason
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Re: [R] R can't find some functions in assist package
> Oh yes. The "load package" under the "packages menu" in the Windows > version > does that. To check I typed "library(assist)" after starting R. Same > behavior, ssr is found, but others like predict.ssr, and plot.ssr, give a > "not found" message. Short answer: Try using "predict" instead of "predict.ssr". I think you're meant to quietly use the predict and plot methods provided, and not mention their inner names. Long answer: Namespaces. This means that a method for an object isn't visible to R as a whole. This avoids conflics should another package pick the same names. Does this work? getAnywhere(predict.ssr) Cheers Jason __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] recommended citation
> Dear Sirs,
>
> I used the nlme package for the statistical analysis of my data for
> prepared MS. Please, can you write me what is your recommended form of
> citation of this program?
> Thanks in advance for your reply.
>
I "cheat" and cite the book that supports it:
@Book{Pinheiro:2000:MMS,
author = "Jose C. Pinheiro and Douglas M. Bates",
title ="Mixed-effects models in {S} and {S-PLUS}",
publisher =Springer Verlag,
address = New York,
year = "2000",
}
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Re: [R] System memory
> Dear All,
>
> I have been experiencing the following problem when I use a lot of system
> memory when using R heavily.
...
What version of R, Xemacs, ESS, and Debian? What are the "crash" symptoms
(error message?). Have you tried upgrading everything you can (ESS has
recently released a new stable (5.2.x) version).
As a possible item to check, run
ps ajx | grep R
from a terminal after you exit R from within ESS. On my Win XP box, I've
found that R sometimes fails to exit cleanly after a q("no"), and remains
running after ESS has tried to disengage. The ESS "*R*" buffer remains
hung, and Rterm's user CPU usage goes to about 98%. Killing R from the
task manager stopped this. The same might (might!) be an issue under
Debian, and killing it from the command line might help.
Cheers
Jason
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Re: [R] Slight problem in sort
Frank E Harrell Jr wrote: sort(c(3,1,NA)) [1] 1 3 Shouldn't NAs be retained by default? help(sort) sort(c(3,1,NA),na.last=TRUE) Cheers Jason -- Indigo Industrial Controls Ltd. 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Question about 'NA'
Christian Mora wrote: Hi all, Ive got a database with 10 columns (different variables) for 100 subjects, each column with different # of NA's. I'd like to know if it is possible to use a function to exclude the NA's using only a specific column, lets say: Data2 <- omit.exclude(Data1$column1) ??, then Data3 <- omit.exclude(Data1$column2) and so on I use indexing for that. Data2 <- Data1[!is.na(Data1$column1),] nb - don't use this: # WRONG WRONG WRONG! Data2 <- Data1[! (Data1$column1 == NA),] NA means you don't know. Therefore, it doesn't equal anything, including NA. For example, I don't know your birthday, and I don't know Napoleon's birthday. That doesn't mean you two have the same birthday, even though they'd both be represented as NA. Cheers Jason -- Indigo Industrial Controls Ltd. 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] evaluating and walking in names
Cezar Augusto de Freitas Anselmo wrote:
Hi, all.
Suppose I have an object with names (like a data.frame) and I want to walk
in a loop with your names. How can I do this? The idea is like this:
my.data<-data.frame(matrix(runif(6),ncol=2))
names(my.data)
[1] "X1" "X2"
for(i in names(my.data)){
my.variable <- cat(paste("my.data$", i, "\n", sep=""))
print(mean(my.variable))
}
#it doesn't work.
Thnaks for all,
C.
Cezar Freitas (ICQ 109128967)
IMECC - UNICAMP
Campinas, SP - Brasil
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You want assign().
df <- data.frame(matrix(runif(20),ncol=2))
# using ii instead of i makes searches *much* easier with
# a text editor.
for(ii in names(df)) {
assign(ii,df[[ii]])
}
ls()
[1] "X1" "X2" "df" "ii"
# might not be exactly the same on your machine due
# to floating point rounding.
all.equal(X1,df$X1)
[1] TRUE
all.equal(X2,df$X2)
[1] TRUE
Cheers
Jason
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Re: [R] Books for R
[EMAIL PROTECTED] wrote: Then the best book is Venables & Ripley (2002) for R. A.S. Agreed. V&R (2002) also cites Bates & Pinheiro's "Mixed Effects Models in S and S-PLUS" (2000) is particularly good for linear and non-linear mixed-effects models. Highly recommended. Cheers Jason -- Indigo Industrial Controls Ltd. 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] "subscript out of range" message
[EMAIL PROTECTED] wrote: Hi All: I was recently working with a dataset on arsenic poisoning. Among the variables in the dataset, I used the following three variables to produce crosstabulations (variable names: FOLSTAT, GENDER, ASBIN; all three were categorical variables, FOLSTAT denoted follow up status for the subjects and had seven levels, GENDER denoted sex (two levels: male,female), and ASBIN denoted binarized arsenic concentrations (two levels: "<0.05", ">0.05" denoting less than 0.05 mg/L and more than 0.05 mg/L respectively). To illustrate, I used the following code for crosstabulation: x <- table(FOLSTAT,GENDER,ASBIN) # from the results, I then wanted to subset a table for the ASBIN value ">0.05" I used the following code to subset the table: y <- x[,,ASBIN=">0.05"] Two errors. 1) Your logical index won't work. For the second level of ASBIN, use x[,,2]. Since the third dimension of the table x has only 2 elements (one for each level of ASBIN), sending it a logical vector that is as long as your number of subjects (N) is only going to confuse it. It's going to run out of levels of table. And it did - "subscript out of ..." 1) Is this a cut-and-paste error? > y <- x[,,ASBIN=">0.05"] It won't work anyway, but for future reference, logical "equals" is ==, not =. In other words, "==" is a question, "=" is an assignment. Cheers Jason -- Indigo Industrial Controls Ltd. 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] problem compiling R in suse8.2
Ernesto Jardim wrote: Hi I'm trying to compile R in SuSE 8.2 (updated with the gcc 3.3.1) but I'm getting the following error: Works fine on my SuSE 8.2 box. [EMAIL PROTECTED]:~/> gcc -vgcc -v ... gcc version 3.3 20030226 (prerelease) (SuSE Linux) [EMAIL PROTECTED]:~> uname -a Linux kryten 2.4.20-4GB-athlon #1 Fri Jul 11 20:16:51 UTC 2003 i686 unknown unknown GNU/Linux /usr/X11R6/include/X11/keysymdef.h:1181:2: invalid preprocessing directive #d make[4]: *** [dataentry.lo] Error 1 make[4]: Leaving directory `/usr/local/src/compile/R-1.7.1/src/modules/X11' make[3]: *** [R] Error 2 make[3]: Leaving directory `/usr/local/src/compile/R-1.7.1/src/modules/X11' make[2]: *** [R] Error 1 make[2]: Leaving directory `/usr/local/src/compile/R-1.7.1/src/modules' make[1]: *** [R] Error 1 make[1]: Leaving directory `/usr/local/src/compile/R-1.7.1/src' make: *** [R] Error 1 Maybe an XFree86-devel library? [EMAIL PROTECTED]:~> rpm -q -a | grep X XFree86-fonts-75dpi-4.3.0-15 XFree86-fonts-scalable-4.3.0-15 XFree86-man-4.3.0-15 XFree86-server-4.3.0-15 XFree86-devel-4.3.0-15 XFree86-GLX-4.3.0-15 XFree86-4.3.0-15 XFree86-libs-4.3.0-42 ... Hope it helps Cheers Jason -- Indigo Industrial Controls Ltd. 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] advise for modeling a linear mixed model
Frank Mattes wrote: Dear R help-list reader, I'm trying to investigate my data with linear mixed model and are seeking advise how to write the model in R. I was trying to get hold of the recommended book from Bates et al, but neither the major bookshop nor our university library had the book. ... Is gated a continuous variable? You could compare it as... (gated as fixed effect) lme(freq ~ day*group + gated, random = ~day | ID data=frame, method = "ML") vs (gated as random effect) lme(freq ~ day*group, random = ~day + gated | ID data=frame, method = "ML") and use anova() to compare. Note that you'll need the "ML" as opposed to REML to compare using anova. Or have I missed something? check out ?corClasses, too, to help with correlated error terms. As for the book, Bates & Pinheiro, I'm working my way slowly through it, and it's well worth it. Well written, and very informative. The "slowly" working through it is because my spare time is very short these days. I strongly urge you to purchase it from your favorite on-line book retailer (or pop by Foyles to grab one - just a couple blocks up from Charring Cross station, if memory serves). In the mean time, if you can't immediately grab a copy, go over here: http://www.insightful.com/support/documentation.asp?DID=3 and select "S-PLUS 6 Guide to Statistics (Part I)", and read the chapter on Linear and Non-Linear Mixed-effects models (Chapter 14 in my copy). I've got this, and a copy of Bates & Pinheiro. The free guide isn't bad, B&P is excellent. Cheers Jason -- Indigo Industrial Controls Ltd. 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] package xtable
Ernesto Jardim wrote: Hi, How can I avoid xtable of printing rownumbers when exporting a data.frame ? Are there more packages that deal with LaTeX besides xtable and Sweave ? Check out Frank Harrell Jr's "Hmisc" and "Design" packages (on CRAN). He also published a great booklet, available at the URL below, that includes the full LaTeX/S code used to produce it. Nice. http://hesweb1.med.virginia.edu/biostat/s/doc/summary.pdf Cheers Jason -- Indigo Industrial Controls Ltd. 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Calling functions of R from Perl?
Bernhard Bals wrote: Hi, I've already asked this question, but unfortunately I've combined it with another question. So it was ignored in almost all cases. Thanks to those who have already given some hints. Here again: I don't want to use R interactively (issue commands after the prompt > ..), but use some functionality of R from inside a Perl script. Can I use methods of R from a Perl script: Is there an interface from Perl (or at least from C/C++) to R (f.e. invoke R functions from Perl, C, C++ or some other language)? If so, can you please point me to the documentation on the Web or in literature where this is decribed? Do you have some trivial demo Perl script (or C/C++ program) that uses this technique, f.e. calls an R method like "mean" or "standard deviation"? Haven't used it myself, so I don't know how well it works, but this one might do what you want... http://www.omegahat.org/RSPerl/index.html Cheers Jason -- Indigo Industrial Controls Ltd. 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] help.start( )
Ming wrote: Dear R experts, I installed R-1.7.1 on Linux (Red Hat 9.0) starting from R-1.7.1.tgz without a problem. Then I fired up R and tried things and found that help.start( ) does not work. I downloaded Sun Java j2re1.4.2, installed that and re-installed R-1.7.1 from scratch. I tried help.start( ) again and the browser (Mozilla 1.2.1) crashed. I read about copying libjavaplugin_oji.so into mozilla/plugins and installed R-1.7.1 (again from scratch). Mozilla still crashed. Can you tell me how to make help.start( ) work in R-1.7.1? It doesn't help much, but it works fine on my SuSE 8.2 box, using R-1.7.1 (patched) and Mozlla 1.2.1. I've also used Konqueror (the KDE browser/file manager) using help.start(browser="konqueror"). Have you tried that (or Galleon, or Opera, or ...)? Cheers Jason -- Indigo Industrial Controls Ltd. 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Newbie question about plotting density objects
cmprobst wrote:
Dear List,
I have an array of 6400 x 56 elements. I want to calculate the density function for each column and plot all 56 density functions in one plot.
I have tried several procedures, but they all failed.
What can I do?
56 lines could even confuse a spider, so you might want to re-think your
plotting approach. However
## untested code!
## get a density object for each column.
den.list <- apply(zz,2,density)
## set up your plot window
all.x <- sapply(den.list,function(d,...) {d$x})
all.y <- sapply(den.list,function(d,...) {d$y})
plot(all.x,all.y,type="n")
## now plot each one on that graph
## this will make each line the same colour; for
## different line types or colours, you'll probably
## have to use a for() loop.
lapply(den.list,function(d,...) {lines(d$x,d$y)})
There's probably a much, much cleaner way to do that, though. I think
the sm library has the sm.density function that takes an "add" argument
to its plots... too busy to check that out on this box, however.
Cheers
Jason
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Re: [R] R book
On Fri, 2003-09-12 at 03:09, [EMAIL PROTECTED] wrote: > Hi All, > > I'd be interested in your opinions of the book > > "Introductory Statistics with R" by Peter Dalgaard > > Does it well describe the R object concept, the language itself and > statistical aspects (I am not a statistician)? The title of the book is accurate. It's concerned mostly with introducing statistics gently, and is very kind to non-statisticians. It teaches enough R to perform the statistics it teaches (table of contents should be available online from your favorite online bookstore), but doesn't get deeply into the language itself. I find it a good book for a gentle introduction; once you're past the stage of needing it, it's a good "loaner" to coleagues who don't yet use R. "Here, borrow this for a week, and if you find it helps, buy a copy". After graduating from this book, the next sensible purchase is "Modern Applied Statistics with S" (Venables and Ripley). Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz +64-(0)21-343-545 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] how to print a plot
On Tue, 2003-09-16 at 08:56, Weiming Zhang wrote: > Hi, > > I am using R-1.7.1 on Linux. I integrated XEMACS with R. Could anybody > tell me how to print a plot? I used plot function to make some graphs > and then I wanted to print them or to save them to files. But I could > not find out how to do it. Have you tried: help(Devices) help(pdf) What I do: pdf(file="myplots.pdf") plot(...) dev.off() Use Acrobat or gv to view the pdf files. Postscript is also good, but not as universally understood; I have many coleagues who work in very standard Windows environments, where ghostscript is unknown. PDF is a very sensible choice for e-mailing graphs. -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz +64-(0)21-343-545 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Quit asking me if I want to save the workspace!
On Wed, 2003-09-17 at 14:26, Murray Jorgensen wrote:
> Rafael A. Irizarry wrote:
> > you can type this:
> >
> > q("no")
> >
> > see the help file for q
>
> Still more work than two mouse clicks.
Two clicks! How awful! ;)
Actually, it bugs me too, so my desktop shortcut (under Win XP) has this
for "Target".
###
"C:\Program Files\R\rw1071\bin\Rgui.exe" --no-save
###
(my mail client might've line-wrapped that by the time you see it.
Everything between the ### marks is one line. *Include* the quotes.
There is a space between Rgui.exe" and --no-save)
See Appendix B of "An Introduction to R" if you need more info.
Hope that helps.
Jason
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Re: [R] Date on x-axis of xyplot
On Wed, 2003-09-17 at 16:31, Deepayan Sarkar wrote: ... > Is the date class standard enough to warrant including a check for it in > lattice ? > I've never used it myself, but the lack of POSIXct support in the lattice graphics axes has often caused me to think up new ways around the plot. Unless I'm missing an obvious way to apply that... Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz +64-(0)21-343-545 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Date on x-axis of xyplot
On Wed, 2003-09-17 at 17:29, Deepayan Sarkar wrote: > On Tuesday 16 September 2003 23:51, Jason Turner wrote: > > ... the lack of POSIXct support in the > > lattice graphics axes has often caused me to think up new ways around > > the plot. Unless I'm missing an obvious way to apply that... > > Actually, lattice does support POSIXct for some time now, My bad. Will check this further. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz +64-(0)21-343-545 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] using matrix data for function
On Thu, 2003-09-18 at 06:02, Bing Zhang wrote: > Hi All, > > I have a function, f(x,y) > I have a matrix of data, m, with the 1st column is x and the 2nd column is y > What's the best way to get f(x,y) for each row of the matrix? > I tried > result<-f(m[,1],m[,2]) but it doesn't work. That is the best way, provided your function handles vectors nicely. Apparently, yours doesn't. Next best is something like apply(m,2,f) Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz +64-(0)21-343-545 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] using matrix data for function
On Thu, 2003-09-18 at 06:41, Bing Zhang wrote: > Thanks. How about I have a third parameter for the function, which is a fixed > object? i.e. the function is f(o,x,y) 1) My earlier reply had a typo. Should've been apply(m,1,f). 2) Luckily, the answer to this question, and any more you're likely to have about apply(), are documented quite nicly. help(apply) Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz +64-(0)21-343-545 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Using POSIX?t rather than "chron" or "date"
On Wed, 2003-09-17 at 19:03, Gabor Grothendieck wrote: > The problem with POSIXt is that you must consider timezones > and daylight vs. standard time issues even if you don't want > to. ... > I had previously suggested that we either put chron into the base > or create a new timezone-less version of POSIXt to complement what > is already in the base. See: When I don't want to be bothered with time zones, DST, etc, I set all time zones to UTC. Works fine for me. I'd love to say I thought of it myself, but it's an old trick frequently used in industrial real-time control systems that have daylight savings features when they're not welcome. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz +64-(0)21-343-545 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] aov and data behind plots
On Mon, 2003-09-22 at 00:57, Monica Palaseanu-Lovejoy wrote: > Now i have a question relating "aov". When i use aov i end up with > 4 plots. How do i "see" the data behind those plots? I know about > summary - but this gives me only some statistical info. There's more than one (very different) answer to that question; it depends what you mean by "the data behind those points". The functions fitted(), resid(), cooks.distance(), and qqnorm() are all handy functions, used by those plots. coef() is also quite useful, as is dummy.coef(). Failing that, have you tried str(your.aov.object)? This gives a detailed summary of each object element. str(summary(your.aov.object)) might also be helpful. Be careful about picking out object components directly, however; if a nice, pre-packaged generic function exists to do the job you want, it's much better to use that, rather than depend on the internal object structure never changing. > Also, if i > want to identify which of my set of values gives a certain segment > of the plot - how do i identify these values? See the help pages for locator() and identify(). The tricky bit for you is making the four plots appear separately. plot.lm() is the function that makes those four plots; pick through it to find what you want. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz +64-(0)21-343-545 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Updating a linear model
On Tue, 2003-09-23 at 07:02, Paul Meagher wrote:
> My google search for Plackett's Algorithm didn't return too much except that
> Plackett's algorithm appears to be useful in Control Theory - it is
> elaborated as "Plackett's algorithm for on-line recursive least squares
> estimation". Sounds something like what I want.
Recursive least squares is touched upon in Ogata, pp 861-863.
@Book{Ogata1987,
author = {Katsuhiko Ogata},
title ={Discrete-Time Control Systems},
publisher ={Prentice-Hall},
year = 1987,
address = {Englewood Cliffs, New Jersey}
}
These algorithms are built for speed, not robustness. They are written
for online real-time systems that might have to solve many of these
identification problems in under a second. As such, you won't get the
nice features of things like a trimmed least squares (though weighting
is covered in Ogata).
Cheers
Jason
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Re: [R] loops in Sweave
On Wed, 2003-09-24 at 03:06, Millo Giovanni wrote:
> Dear all,
>
> I was wondering whether there is a way to make loops in Sweave, i.e. for example to:
> 1) calculate a parameter, say, a=length(b)
> 2) according to that, add #a# chapters to the document, each including some
> repetitive analysis, each time done on a particular subset of the data indexed by
> the elements of 1:a.
> This would be of great help for repeating exploratory data analyses on, say,
> questionaries when the number of questions changes without having to change the
> Sweave .snw file.
Two possible ways, off the top of my head:
1) Within LaTeX, use \Sexpr{a} to get the length, then loop within
LaTeX. I believe Lamport includes an example of looping within LaTeX,
but I haven't got the book handy.
2) Within the R chunk, generate the table using xtable() (package
"xtable") or Latex (package "Hmisc") and print directly within R. I
haven't tried it, but something like
<>=
## build your table in R
tt <- xtable(foo)
print(tt)
@
might do the trick. I'd been meaning to look at this anyway; you
question prompted me ;)
Check the Sweave manual at Herr Dr Leisch's site.
http://www.ci.tuwein.ac.at/~leisch/Sweave
This has the R chunk options required to produce the above, if my
untested example is not correct.
Cheers
Jason
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Re: [R] least squares regression line
On Wed, 2003-09-24 at 11:04, Carmen Fridell wrote: > I can't seem to find the command to find the least squares regression line > for my bivariate data set. Can you please help? ~Carmen Any time you're lost in R, you can type "help.start()". This will start a web browser, which loads the starting help page. Click on "Keyword Search". Once the new page loads, type in some of the words you're looking for. "regression" is a good place to start. That will lead to a list of potential matches by subject. Hint - you're looking for a function to estimate a *linear* model. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz +64-(0)21-343-545 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] storing objects (lm results) in an array
On Thu, 2003-09-25 at 05:34, Christoph Lehmann wrote: > Hi > > I have calculated lots (>1000) of linear models and would like to store > each single result as an element of a 3D matrix or a similar storage: > something like > > glm[i][j][k] = lm(...) > > Since I read that results are lists: Is it possible to define a matrix > of type list? > > Or what do you recommend? 1) glm is already a function name in R. I'd suggest a different name. 2) I don't recommend a matrix. Matricies require contiguous memory chunks - it's possible to not have a long enough "block" of memory available, even when the total free memory is sufficient, when storing large matricies. What's wrong with nested lists? Something like my.lms[[i]][[j]][[k]] <- lm(...) This can "scatter" its storage across discontinuous chunks of memory. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz +64-(0)21-343-545 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] models with I(1) errors
On Wed, 2003-09-24 at 19:31, Vito Muggeo wrote:
> Dear all,
> I'm interested in fitting time-series linear models with I(1) errors. Namely
> given
> y_t=a+b*t+u_t
> the random term u_t are such that
> u_t-u_{t-1}=e_t~iid N(0,\sigma)
>
library(nlme)
help(lme) #note the optional correlation argument
help(corClasses)
You can specify AR(1) (among other) correlation structures in the error
term with lme().
The cannonical reference for the nlme library is
@Book{
PinheiroBates2000,
author = {Jos\'e C. Pinheiro and Douglas M. Bates},
title ={Mixed-Effects Models in S and S-PLUS},
publisher ={Springer-Verlag},
year = {2000},
address = {New York}
}
Cheers
Jason
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Re: [R] Sweave \Sexpr() issue
On Thu, 2003-09-25 at 11:20, Fernando Henrique Ferraz wrote:
>Hi, I'm having a little issue with \Sexpr{bla} relating to the number of digits
> it is using to print its output.
Try \Sexpr{format(bla,digits=3)}
Cheers
Jason
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Re: [R] geodata conversion
On Sun, 2003-09-28 at 13:10, Yaqing Gu wrote:
> Hey,
> I have a data set of 1.20MB. I used read.table( ) to read in the data and then
> tried to convert it to geodata type. But it failed and I got
> "Error in vector("double", length) : cannot allocate vector of length 1351974000"
> message.
> All the commands I used were:
>
> rawdata<-read.table(file=" ")
>datag<-as.geodata(rawdata)
>
> BTW, what is the biggest origin data size as.geodata( ) can convert?
Depends how much memory R can give it.
Check
help(Memory)
and read the FAQs. You'll find them under "Miscelaneous Items", in the
browser, after you use the command "help.start()"
Cheers
Jason
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Re: [R] Help needed: plotting with no device
Ross Boylan wrote: On Mon, Sep 29, 2003 at 05:09:49PM -0400, Ben Bolker wrote: Can you use save.image() to rescue your results? I would try save.image(file="salvage.RData") and see if the file appears. Otherwise I would say you're probably out of luck. The problem is I can't get back to the command prompt, so I can't do save.image() or anything else. It may be possible to reconstruct the state from a core dump. I say "may" with not much confidence it'll be worth the effort, but it might be possible. Only problem is, there's no way I know under Linux to dump core and continue; you only get one shot at it. man 7 signal on my SuSE box gives a list of which signals cause a process to dump core. After that, you'll have to find a Local Guru to pick it apart - and R's memory structures aren't trivial. It might be easier to start again. Hope it helps Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] subsetting a matrix
(Ted Harding) wrote: On 30-Sep-03 Rajarshi Guha wrote: Hi, I'm trying to take a set of rows and columns out of a matrix. I hve been using the index aray approach. My overll matrix is X and is 179 x 65. I want to take out 4 columns and 161 rows. ... This is documented in "An Introduction to R", under the section "Arrays and Matricies". There's lots of good stuff in there. From R: help.start() And click on "An Introduction to R". The short answer to this particular question: a) negative indicies remove rows or columns. Since you only want to remove 4 columns, I'd use that. b) Since you only want to keep 18 rows, I'd use the numbers of the rows you want to keep. As a toy example, say you wanted to remove columns 51 to 54, and keep the last 18 rows: newX <- X[162:179,-(51:54)] There's even more handy stuff in the document mentioned above. cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] variables
forkusam wrote:
Hi,
can someone please help me.
I will give a simple example of my problem.
p <- function()
{
i <- 1
sr <- function(){
i<-i+3
i<- sqrt(i)
}
cat(i)
}
This is just an example. My main problem is defining
i like a global variable which I can use in the sub-
and main functions without any complicated switches.
Thanks in advance.
cilver
Within the function p(), it should "just work". Try this slight
variation of your example:
p <- function()
{
i <- 1
sr <- function(){
i<-i+3
i<- sqrt(i)
i #explicitly return the newly calculated value
}
cat("sr() returned ",sr(),"\n")
#now check if i was actually modified outside sr()
cat("i = ",i,"\n")
}
When I load this into R...
> p()
sr() returned 2
i = 1
note that i is not visible outside the function p(). It disappears when
p() exits.
> i
Error: Object "i" not found
The internal function variables being available to sub-fuctions is an
example of "lexical scoping", and it's one of the things that makes R so
nice to work with. Try demo(scoping) for a very interesting use of
lexical scoping.
Cheers
Jason
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Re: [R] truncating axis
Diego Riano wrote: Hello Does anyone know how to truncate and axis in R? Not sure what you mean, but do to plot arguments xlim and ylim do what you want? See help(par) for these and other plot controls. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Text cutoff in legends
Marcel Sutter wrote:
Dear r-help
If I display plots on the X11 device, the legends looks fine. But if
make an EPS, the longer entry in the legend is cutoff (and also in the
.pdf I do from the .eps)
Can you give me a hint and tell me what I do wrong, please ?
Probably nothing. The X11 and postscript devices have different
boundaries. The plot is made to fit them, and the legend added to that.
I don't usually use dev.copy(); I just repeat the plot commands after
the postscript() device is opened. Try that; if that doesn't work,
adjust your legend placement.
postscript("plot.eps",paper="special",horizontal=F,onefile=F,width=8.0,height=7.0)
dev.set (2)
dev.copy (which=3)
dev.off (3)
R Version 1.6.1 (2002-11-01) on SuSE Linux 8.0
Might as well upgrade R while you're at it. 1.8 will be out Real Soon Now.
Cheers
Jason
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Re: [R] Re: Mandelbrot set and C code
[EMAIL PROTECTED] wrote: I decided to take on the 'proper' solution to calculate the Mandelbrot set in R, i.e. to do the raw calculations in C and then link that code with R. This is very cool. I did a slight tweak to your mandelbrot.R code, so that x can be a list with components x and y. This allows you to keep zooming in using your mouse to click on the plot (one of the incredibly nifty features of such sets). Using the "tweaked" version below, call the function as you suggested: image(mandelbrot(), col = c(heat.colors(49), "black")) Then use locator(2) to define your next view: image(mandelbrot(locator(2)), col = c(heat.colors(49), "black")) Click the mouse in the corners of the zoom window, and away you go. Lather. Rinse. Repeat. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] lda source code
Wei Geng wrote:
I am new to R. Trying to find out how lda() {in MASS R1.8.0 Windows} was
implemented in R. Does anyone know where to find out lda source code ?
Thanks.
Here:
http://cran.r-project.org
Hint: MASS is a *package*. You want to view its *source*.
Same with most other R packages. Or just about anything else you want
to know about R.
Cheers
Jason
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Re: [R] lda source code
Wei Geng wrote: Hi Jason, Spencer, Thanks for the prompt response. The strange thing about MASS is that it's not in "Package Sources" as most of other R packages are. It seems to come with the binary R installation. I checked out the Rxx/library/MASS on my laptop, there are source code (script) for Venables & Ripley's book but no source code for lda(). Ah. On CRAN, the MASS library is part of a bundle called VR. Download the source for that. There are a few bundles on the CRAN source pages - if you encounter this problem again, just follow the Package Sources link, and search the page for "MASS" (or whatever the package name is). Use "Edit->Find", or Ctrl-F, or whatever. In the case of MASS, you find this one: VR: Functions and datasets to support Venables and Ripley, `Modern Applied Statistics with S' (4th edition). Bundle of: MASS class nnet spatial It's the "Bundle of" part you're looking for. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Re: Mandelbrot set and C code
Jason Turner wrote:
...I did a slight tweak to your mandelbrot.R code, so
that x can be a list with components x and y. This allows you to keep
zooming in using your mouse to click on the plot (one of the incredibly
nifty features of such sets).
Using the "tweaked" version below, call the function as you suggested:
image(mandelbrot(), col = c(heat.colors(49), "black"))
Then use locator(2) to define your next view:
image(mandelbrot(locator(2)), col = c(heat.colors(49), "black"))
Of course, I would've been nice if I'd included the tweaked version. D'ho!
###
# Function to calculate the Mandelbrot set. This function calls a #
# C routine in order to perform the calculations faster. #
# #
# Written by Mario dos Reis. September 2003 #
# Modified: added if(is.list(x)){...} at start to check if co-ords#
# are from locator() or similar - jason turner oct 2 2003 #
###
mandelbrot <- function(x = c(-3, 1),# x limits
y = c(-1.8, 1.8),# y limits
nx = 600,# x resolution
ny = 600,# y resolution
iter = 20) # maximun number of iterations
{
if(is.list(x)) {
y <- range(x$y)
x <- range(x$x)
}
xcoo <- seq(x[1], x[2], len = nx) # x coordinates
ycoo <- seq(y[1], y[2], len = ny) # y coordinates
set = numeric(nx*ny) # this will store the output of
# the C routine
# This is the call to the C function itself
the.set = .C("mandelbrot",
xcoo = as.double(xcoo),
ycoo = as.double(ycoo),
nx = as.integer(nx),
ny = as.integer(ny),
set = as.integer(set),
iter = as.integer(iter))$set
# Create a list with elements x, y and z,
# suitable for image(), persp(), etc. and return it.
return(list(x = xcoo, y = ycoo, z = matrix(the.set, ncol = ny, byrow
= T)));
}
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Re: [R] indexing a vector
morozov wrote: Dear All: I'd like to know how to sort and then index a vector of floats by several levels in R. For example x<-rnorm(100) MyLevels<-quantile(x,probs=c(0,.5,1)) MyLevels 0% 50%100% -2.11978442 -0.03770613 2.00186397 next i want to replace each x[i] in x by 1,2,3 or 4 depending on which quantile that x[i] falls. How do I do that in a "vector" fashion? I think rank() is the function you're looking for. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] foo.RData or foo.r?
Federico Calboli wrote: On Fri, 2003-10-03 at 13:16, Adaikalavan RAMASAMY wrote: *.R is for the script file and is ASCII type. *.Rdata (or sometimes *.rda) is the usual extension for R data and contains binary information. If you try to cat a *.Rdata file, you will end up with gibberish as it is binary. Try opening *.Rdata with emacs if you can. Emacs will recognise it as a fundamental type and not as an ESS type. There might be ways to associate Rdata files with ESS. But other people might not consider reading your "*.Rdata" files. I dunno about this, but if I open R under emacs first and then I load my foo.RData, it loads fine. By "fine", you mean it looks like normal R code? On Un*x systems(including Linux), the extension is a matter of convenience, not necessity. It's possible to save your R code, transcripts, etc with any extension you want (.R, .S, or even silly things, like .exe if you want). And Emacs will still cheerfully read them just fine. However, just because you *can*, doesn't mean you *should* ;) There is a *convention* in R that workspace images or saved objects (using save.image() or save() ) should have filenames that end in .RData . R code should have filenames that end in .R . This isn't necessary, but it helps keep things tidy and easy to organise. ESS also has some built-ins to recognise .R as R code, so it can do nice things like highlight syntax, indent well, and send code to an R session to be evaluated. Short answer: anything that's R code *should* be named with .R at the end. Anthing R created after you told it save() or save.image() or answered "y" to the "Save workspace image" question *should* have a name ending with .RData . None of this is strictly necessary, but there are a bunch of nice things that happen if you do. Clear as mud? ;) Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: R: [R] r editors
Nick Drew wrote: On a similar note, what are some alternative data editors that one might use instead of the default R data editor? I'm not interested in Excel but something that's freeware, easy to install and use. Any recommendations? If you don't like Excel for financial or license reasons, Open office works quite well these days (www.openoffice.org). If you don't like Excel because you find spreadsheets clunky, the next step for me perl or some such thing. Something in between? I'm all ears. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Placing legends
Doug Bourne wrote: I'm trying to automate making a bunch of figures and I need a way to automate legend position. As I understand it the legend is placed based on coordinates. I don't know before hand what the coordinates are going to be. On one graph my y axis might go from -50 to -10. On another it might go from 0 to 180. Easiest way is to: 1) make your plot. 2) change to co-ordinate system. 3) add the legend. plot(...some stuff...) par(usr=c(0,1,0,1)) # say you want you legend at 60% across, 80% up. legend(x=0.6,y=0.8,...legend stuff...) ?par has this. Check out "usr" Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Point and click
Cliff Lunneborg wrote: The following query raises the question: What is it that students learn from point and click dialogs?" [long boring ramble - I'm sure you know how to find the delete key when it gets tedious ;) ] I think it's fair to say that they don't learn the software, or its internal structures/methods/etc at all (Mac users have always told me that this is the point; I'm not getting into that holy war). I will state one thing - the point and click interface *can* teach about the underlying software mechanisms, but it has to be a well thought-out interface. Example - I never used a computer that had a heirarchical filesystem until I went to university. I then had to learn two: IBM PC clones were used to teach us AutoCAD (ever seen AutoCAD run on an 8086 with 640K of RAM? It's not pretty ;). I also worked on the student newspaper, which was a Mac-only shop. The Macs came later; I was working in layout initially, back when layout really involved printouts, big cardboard sheets, and wax to stick the articles to the cardboard. I did not understand directory structure on the PCs at all. It never clicked. I simply "parroted" the commands I was taught to use, and managed to stay out of trouble. "Polly wanna .dwg file." Then I worked on the Macs. The display of folders made it clear to me, in about five seconds. I realised right away what I'd been missing, and flew back into the PC world with a bit more insight. As a result, I know that nice point-and-drool GUIs can educate about the underlying design and approach, but the design really must be considered very carefully. It's also important to take away the "crutch" from time to time, too (going back to PCs, in the above example). I've yet to see a GUI for a statistical software system that meets this criteria, and I can't imagine what one would look like (I'm an engineer, not a designer ;). I don't even know if it can be done. I'm sure anybody who understood heirarchical filesystems prior to GUIs would've thought similar things - that if one can't understand something so basic, there's really no simplifying or alternate explanation that'll work. Had that thinking prevailed, I might've been another engineer who doesn't know a thing about how computers actually work (there's no shortage, believe me). Just my $0.05 NZ (exchange rates, and all) Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] please help me on this problem
Yong Wang wrote: Dear all: I am totally new to R, actually, statistics software.I get two very simple, even stupid question: 1) where I should put the data file in order to use it , I tried to build a work dir in library( package:base) and save the text file (data) there, I'm not sure where such a work directory might be, but it sounds like you need to show a TA what you did. It sounds like you need to carefully read the FAQ. help.start() the follow the "Frequently Asked Questions" link, and (if you're using R on windows) the "FAQ for Windows Port" then, I use read.table(filename), not work; I tried the full path, still not work. I must have done something wrong. Quite likely. But without more details, there's no way to say more. There isn't only one way to make a mistake, so there isn't one answer to "it didn't work". Read the FAQ. It really does help. Read it carefully, and not in a frame of mind where you're saying to yourself "I'll never understand this, this can't possibly help." You will, it can. 2) is it possible to create a data file in R instead of put data in a txt file and then save the file under R? Yes, after you've got a grip on the above. *After* the above is clear, read the help pages for "save" and "load". Read the FAQ. I tried to find answer from the introduction, failed. But not the FAQ, presumably. I really appreciate your help, thank you very much. No problem. By the way, read the FAQ. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Generating automatic plots
Xavier Fernández i MarÃn wrote:
...
varlist <- c("var1", "var2", "var3", "var4", ...)
Instead of a character vector with the names, it'd make life easier if
you had a list of the vectors...
# make sure you use the naming - makes life easier later.
mylist <- list(var1=var1, var2=var2, var3=var3, var4=var4)
Then...
for(i in seq(along=mylist)) { # seq(along=...) is safest.
jpeg(names(mylist)[i], width=...)
boxplot(mylist[[i]] ~ missing, xlab=...)
dev.off() # you didn't have this. it's required.
}
# but I don't see how "missing" gets correctly passed in your example,
# so I'm not sure what it's supposed to do.
I suppose that is because I forget something related to the extraction of
values in vectors, but I can't find it on the R manual neither in other books
about R that I have checked.
Nope. It's about passing a strings of text to plot, instead of actual
data. You'd have to actually parse the string to produce the value.
And that's getting tricky (at least, it's tricky to my brain). The
above is pretty simple by comparison.
Cheers
Jason
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Re: [R] using split.screen() in Sweave
Christoph Lehmann wrote: Dear R and sweave users A further problem, which I couldn't resolve, using the manual: In R I use the split.screen command to put e.g. two timecourses one above the other into one plot: split.screen(c(2,1)) screen(1) plot(stick,type='h', col="red",lwd=2) screen(2) plot(deconvolution.amplitude,type='h',col="blue",lwd=2) Is there a similar way, doing this in Sweave? I've never used split.screen. Check out ?par, and read the entries for mfcol and mfrow. Also check out ?layout. HTH Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Why does a[which(b == c[d])] not work?
Achim Zeileis wrote: On Wednesday 08 October 2003 11:27, Thomas Bock wrote: ... I can not understand why the expression in the subject does not work correct: > dcrn[which(fn == inve[2])] numeric(0) > inve[2] [1] 406.7 ... 1.) `==' comparisons have a certain tolerance 2.) the print output is not necessarily "precisely" your number Instead of using `==' you should use a comparison with a certain tolerance you can specify... I usually specify... tol <- sqrt(.Machine$double.eps) dcrn[(fn - inve[2]) < tol] See ?.Machine for details. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Why does a[which(b == c[d])] not work?
Whoops. Hit "send" too quickly. Jason Turner wrote: tol <- sqrt(.Machine$double.eps) dcrn[(fn - inve[2]) < tol] that should be dcrn[abs(fn - inve[2]) < tol] -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] run R under unix
Zhen Pang wrote: ... I now want to run the code under unix. However, I do not know how to run this code in txt file under unix. I just log in to the unix and enter the R, what should I do next? One more question is: if I log off my computer when R is running under unix (i.e., disconnect my computer from server), will I get the result when I log in my computer next time? ... You'll lose it if you run R in the normal, interactive way. Running it in the background will allow you to log out and still have it running, but! 1) If you're not the only person using this machine, you learn the command "nice" before you begin. 2) I'm not certain you'll be able to produce jpeg or png graphics when backgrounded; your backgrounded task needs access to the windowing system for graphics rendering, and local security policy might prohibit this. 3) Save early, save often. You probably already know that, but it bears repeating. Here are some suggested steps to run your simulation in background mode. Unfortunately, the exact commands will depend on which version of Unix you're using, and what command shells are available. Consult your local expert. 1) transfer the text file of commands to the unix machine. FTP, using ASCII mode is safest. 2) log onto the Unix machine. 3) run sh, ksh, or bash. (the syntax for what follows is different for the C shell, and I don't know it). 4) using a stripped-down version of your script which will complete in a short time (say, a minute or two), just to check that things work, type nohup nice 15 R < my.small.script >my.output 2>&1 & (again, learn what "nice" means before you use it. This may not be suitable, and it's impossible for me to tell from here if it is). I know that's not the full answer, but only someone who knows the local setup can give you that answer. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Previous Commands
Rau, Roland wrote: Dear All, yesterday I took the R-1.8.0-source file and compiled it on my own. As I am using Linux just for a couple of weeks, it was my first compiling session with ./configure, make, Everything went fine, except for one thing: if I want to look at the commands history by using the cursor keys, it does not work. Instead of displaying the previous commands, it returns something like "[[A". Is this a common problem? Does anyone have a solution? I had R-1.7.1 installed previously via an RPM-package for my Mandrake 9.1 distribution and everything went fine. You need the readline-devel libraries installed. Depending on what Linux distro you're currently on (still Mandrake?), they may be available as an RPM or Debian package. Install them, then if you still have the source directory, do a "make distclean ; configure ; make", then make install and try again. If you've deleted the source directory, just untar the source and rebuild. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Fitting AR(p) models
Laura Quinn wrote: I am wanting to fit AR(p) models to column data for a series of matrices I have. Rather than trying to compute the AR models "per column" I was hoping to be able to do this per matrix (i.e. one AR model for each column in said matrix). However, when i attempt this, if there is just one "NA" value in any of the columns, the program refuses to compute AR models for any of the columns.(I am using na.action=na.omit) Is there a way I can force the calculation to provide AR models for complete columns, or alternatively, a better way to deal with NA's to provide an AR model, (eg via interpolation?) despite some missing values? Interpolation might not make sense for your data. Can't tell from here. Certainly it's quick, but it can also be pretty dirty - it over-weights those data regions. You can get around this by interpolating, then selecting a lower resolution (window with a larger deltat), and build your model from that. If the NAs are few and far between, some additional code to pick where the NAs are in each column, and build AR models from the longest continuous segment might be preferable. Apart from that, there's not much else I can add. Other takers? Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] command line limit under unix?
Zhen Pang wrote: I have made my testing program to run successfully under unix in the background. However, my simulation work does not work. I read the foo.results file, I found it only have part of my code and not any output I want. Is there any line limit? My code is nearly 400 line. I can cut some of them, but I want to know whether there is any limit or exactly the number of limit is. Thanks. 400 lines of input isn't large. Were there any error messages? Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] don't display rulers in image() command and script file input
Ernie Adorio wrote: Dear R experts, 1. How can I turn off the display of rulers in image() command? Are rulers the same as axes? If so, try image(...,axes = FALSE) See example(image) for detials. 2. Rather than typing my commands at the command line, how can I input a file contents aside from doing a copy and paste operation? ?source Also, see the FAQ, 7.18. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Matrix of Index Variables
[EMAIL PROTECTED] wrote: What is a good way to create a matrix of index variables based on all possible combinations of a list of factors in a data-frame, say list(age, sex)? "age" and "sex" are numeric and factor variables in a dataframe, with 99 and 2 values, respectively. I would like to use these for subsetting the data-frame, apply functions to subset and collecting the results. Rather than creating a new index, I think you want the function "by()". Something like foo <- by(mydata,list(age=mydata$age, sex=mydata$sex), your.summary.function) Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] selecting subsets of data from matrix
Laura Quinn wrote: Thanks for your help everyone, My data is a matrix. However if i use the command: x[(x[,20] > 315 | x[,20] < 45), ] and then request a summary, I get a warning message saying that a large number of the row names have been duplicated - I don't understand this? If x is the original matrix, and subx is the subseted matrix (x[(x[,20] > 315 | x[,20] < 45), ]) ... Do you get this warning message when you type summary(x)? If you're not explicitly using the rownames for anything other than labeling, it can be safely ignored. Duplicate rownames are a bit strange to R, but they're not illegal in matricies. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] run R under linux
Zhen Pang wrote:
I want to do 200 simulations. I found during the fisrt 128 simulations,
some parameters may be NAs, since I use if (abs(aold-anew)<1e-5) {print
(anew) break} to break the one estimation.
...
> I want to know how to resume my program with the seeds saved, and do
like continueing the 130th one without break. If possible, the results
of the first 128 simulations can be saved and combine with the remaining
simulation.
help(try)
Cheers
Jason
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Re: [R] BEGINNER: please help me to write my VERY simple function
Michele Grassi wrote: Hi. 1)I have two variables: call a<-c(e.g.0,3,6,7...) b<-c(e.g.6,8,3,4...) I want to create a third vector z wich contain the pairs values z<-c(0,6,3,8,6,3,7,4and so on for each pairs (a,b)). There is a specific function? How can i write my own function? For that, you don't need to. help(expand.grid) 2)When i try to write a function and then i save it like "function.R" file, i try to retrieve it with source comand. As result i obtain an error message "error in parse: sintax error on line...". I apply deparse() and i see an incorrect parsing: how avoid unwanted parsing? I'm really not sure what you're trying to do with deparse here, but I don't think it's supposed to do what you meant. The error message is what should be attended to - fix that with your favorite text editor. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] run R under linux
Zhen Pang wrote:
We are not allowed to submit job directly, so I never type R to use R,
just make a batch. How can I use try() to correct my codes? In the
interactive mode, I know how to continue, but now I never enter the R
window, where to find my results and save seed to continue?
Like you'd program any exception handling. A toy example to get you
started might look like this:
(somewhere inside your script file)
...
results <- vector(length=200,mode="numeric") #or whatever you use
set.seed(123)
...
errors <- list()
for(ii in 1:200) {
foo <- try(some.simulation.thingy(your.params))
if(inherits(foo,"try-error")) { #something bombed
results[ii] <- NA
errors[[as.character(ii)]] <- foo
} else { #it worked
results[ii] <- foo
}
}
...
save(results,errors,file="results+errors.RData")
...
The end.
Play with that, and see if you get some useful ideas.
Cheers
Jason
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Re: [R] select text using only the keyboard
Simon Fear wrote: I have a different wish: I want to be able to mouseclick in the middle of a line to get the cursor there (as in SPlus). While I appreciate that to get my wish I should just write a little patch, I estimate it would take me about 2 years to reach the point where I was capable of it, assuming I did nothing else, and I would certainly have to understand Windows, which in previous brushes I have found to be very bad for the brain. Or you could get a copy of (X)Emacs, and use ESS. Total install and learning warm-up time should be in the order of a week at most. It does all these nice things, and much more. In my short experience with it, XEmacs plays nicer with ESS under Windows than GNU Emacs - YMMV. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] multivariate ARMA analysis with R
Vincent Spiesser wrote: Hi, I try to make a multivariate ARMA analysis. Function arima (from ts packages only accept univariate argument. Does an R function exist for multivariate analysis ? Thanks Vincent Spiesser The dse bundle on CRAN has functions for VARX multivariate time series models. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Searching a Table
Nicole Baggette wrote:
Is there any way to search a column of a table?
I read in a table and I want to create a subset based on the criteria that a
certain column (filled with words) has a word which starts with a certain
letter. The only method I have seen that searches this way is apropos(), but
that doesn't seem to search the location I want. If anyone can make a
recommendation I would appreciate it.
help(grep)
To search for words that start with "W" or "w" (minus the quotes) in a
data frame called "mydata", column 3,
grep("\\bw", mydata[,3], ignore.case=TRUE, perl=TRUE)
Which means - "\\b" - word boundary.
The "w" and ignore.case should be self-explanatory.
perl - use perl style regular expressions.
example:
foo <- c("now is The Time","for all good llamas","to come to the party")
foo
#find lines that contain words starting with "t" or "T"
grep("\\bt",foo,ignore.case=TRUE,perl=TRUE)
foo[grep("\\bt",foo,ignore.case=TRUE,perl=TRUE)]
Cheers
Jason
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Re: [R] Scan() question
Janice Warner wrote:
I am just beginning to use R 1.7.1 on Windows XP and can not do a simple
> scan of a .txt file with integer data separated by tabs.
First I figured out that I need to open a connection to the file
>(which isn't mentioned in scan()).
It isn't mentioned because it isn't needed.
I'd try
read.csv(filename,sep="\t") # for tab-separated files
> But now when I scan, I get "Read 0 items". What can I do?
Shouldn't happen quite like that.
I have a file on my XP box, in my "My Documents" folder, called
"foo.txt". It's a two-column text file, tab-separated. First column is
the numbers 1 to 12. Second column is some random numbers.
> scan("c:/documents and settings/jason turner/my documents/foo.csv")
Read 24 items
[1] 1. 0.05905332 2. 0.21829890 3.
0.07104709
[7] 4. 0.67140721 5. 0.44471572 6.
0.75093844
[13] 7. 0.40647603 8. 0.85937071 9. 0.31583605
[19] 10. 0.77993103 11. 0.55067598 12. 0.25861385
Notice the "/" rather than the "\" as the directory delimiter.
Cheers
Jason
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Re: [R] how to remove NaN columns ?
[EMAIL PROTECTED] wrote:
How can I remove columns with NaN entries ?
Here is my simple example:
data <- read.csv("test.csv")
xdata <- data[3:length(data)]
xs <- lapply(xdata, function(x){(x - mean(x))/sqrt(var(x))})
x <- data.frame(xs)
x
C D EF
1 -0.7071068 NaN -0.7071068 -0.7071068
2 0.7071068 NaN 0.7071068 0.7071068
I am sure it is possible to remove column D (with NaN's) in some simple
fashion, using is.nan function
without explicitly looping through, and I am sure I was able to do it in
the past, but I cannot recall how.
In addition to Andy's helpful suggestion, if your data is a matrix
rather than a data.frame, you can use which() with arr.ind=TRUE. For
this example, Andy's suggestion is cleaner, however.
> foo <- as.matrix(foo)
> foo
C D E F
1 -0.7071068 NaN -0.7071068 -0.7071068
2 0.7071068 NaN 0.7071068 0.7071068
> which(is.nan(foo))
[1] 3 4
> which(is.nan(foo),arr.ind=TRUE)
row col
1 1 2
2 2 2
> unique(which(is.nan(foo),arr.ind=TRUE)[,2])
[1] 2
>
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Re: [R] questions please
Simone Panigada wrote: ... * I am running a glm to model animal abundance relating it to research effort and other variables. I have 10 years of data and I am treating year as a factor, R is comparing each year with the first year my data sheet, while I would like to compare each year with each other. Is there any function in R to do this? ... Short answer: If your model was glm(critters ~ year, ...), change this to your.model <- glm(critters ~ year - 1,...) In other words, drop the intercept if you don't want to compare to a particular year. A model that defines coefficients for each year *and* an overall intercept is over-defined; there's no additional information given by the extra term. You might also benefit from the package multcomp (which requires mvtnorm) which has the function simint(). Long answer: Get your hands on a copy of "Modern Applied Statistics with S" by Venables and Ripley, and read chapters 6 and 7 rather thoroughly. This goes into the reasons behind the choice of comparing one year to others. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Scan() question
Oops. The file name is obviously "foo.csv", not "foo.txt". Sorry if
that caused confusion.
Jason Turner wrote:
I have a file on my XP box, in my "My Documents" folder, called
"foo.txt". It's a two-column text file, tab-separated. First column is
the numbers 1 to 12. Second column is some random numbers.
> scan("c:/documents and settings/jason turner/my documents/foo.csv")
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Re: [R] R performance on Unix
morozov wrote: Hi I'm observing a huge difference in the performance speed of R on Windows and Unix, even though I know that my Unix machine is much more powerful than my Win machine. In particular, any character processing task is very time consuming on Unix. strptime(x,"%H:%M:%S") is about 10 times slower on Unix for vector x of the length of ~ 500. read.table() also is very slow. is there any way to speed up these ? As was pointed out, the strptime issue sounds like a C-library problem on your machine. The text processing might be the same. Is this a development version of a Un*x OS? What's the output of uname -a? Is it a source or binary build of R? If binary, try building and installing from source (provided you've got the disk space, you can do this, even if you're not root). Is the problem apparent on other boxen with similar OSs (ie is it hardware)? If you absolutely must continue to use that box and OS and R build, read.table() can be sped up using the colClasses argument (R doesn't have to guess what class each column should be), but it sounds like a problematic installation. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] ts vs. POSIX
Erin Hodgess wrote:
What if I have a time series which is collected every Monday, please?
What is the proper way to use the start option within the ts command
in order to indicate that this is Monday data, please?
ts objects don't directly support dates. There is some provision for
monthly data, but this isn't the same as uniform, across-the-board date
support. What they do have is a start time, a deltat, and frequency
(observations per period). The main reason to use ts objects *isn't*
the date/time handling, but for the nice functions (acf, spectrum, etc)
you can use for regularly spaces time samples.
For weekly data, I'd use one of the following approaches (assuming the
series starts in the first Monday of 2003):
1)
# dates in a year,week format
> foo <- ts(1:100,start=c(2003,1),frequency=52)
or
2)
# dates as numeric representation of POSIXct objects
foo <- ts(1:100,start=as.numeric(as.POSIXct("2003-1-6")),deltat=60*60*24*7)
> start(foo)
[1] 1041764400
> end(foo)
[1] 1101639600
> last <- end(foo)
> class(last) <- "POSIXct"
> last
[1] "2004-11-29 New Zealand Daylight Time"
(2) depends on as.numeric(POSIXct.object) giving a sensible,
single-digit answer. This is not guaranteed. It works today, but
nobody promised this approach would work tomorrow.
Hope that helps.
Cheers
Jason
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Re: [R] Question about the high dimensional density estimation
[EMAIL PROTECTED] wrote: > Hi, > I found that the R package "KernSmooth" can deal with > only 1D and 2D data. But now I have a collection of > 4-dimensional data (x1,x2,x3,x4) and would like to estimate > the "mode" of the underlying density. What can I do > about it ? The gss package might do what you want here. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R]A matrix is full rank is equal to having independent columns?
Feng Zhang wrote: Dear R listers, Just a simple question. If we say an nxm matrix (n>m) is full rank of m, does this mean that this matrix has linearly independent columns? Yes. Now be careful how you define rank. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R for various ports of linux
Nathan Leon Pace, MD, MStat wrote: To all: I currently download the R binaries for Redhat 7.x Linux. There is considerable turmoil in the vendors of Linux. Redhat apparently is changing it's business model to paid versions. This might motivate my department to use a different vendor of Linux. Is there anything predictable about which vendors/versions of Linux will have R binaries in the future? Short answer: build from source. You won't regret it. Long answer: The "build from source" approach is remarkably painless under any Linux distribution I've tried (RH, SuSE, Slackware, et. al.). It's also painless under Solaris. The days of having to be a programmer to build R from source have been over for years. If you're computer literate enough to use R, you're probably over-qualified to build from sources. Kudos to R-core for their attention to detail in making what's complicated "under the hood" quite simple for the end user. Alternate answer: If you absolutely must have binaries, there will be binaries as long as there are users of your OS with time they wish to commit to building them. This may be where your sysadmin steps in :) Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] building r-patch
Vadim Ogranovich wrote: ... I am building r-patch from the sources (rsync-ed today). make check produced the following message: running tests of Internet and socket functions expect some differences ... assorted error messages, then ... OK I noticed that I had to expect some differences so my question is how to tell whether it's harmless or not? The "OK". If made exited without an error, the regression tests were passed. In this case, the differences between the maintainers' results and yours were due to local login and network setup differences. Hope that helps Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R input file scanning
Mathieu Drapeau wrote: Hi, I would like to know how can I solve my problem... I want to load some data (surrounded by a tag) that are stored in a file that contains also some scrap (header and descriptions) that I want to skip. How can I do that? By writing some code to use readLines() or scan(). I'll be more specific if you will. :) Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] precision in operations
javier garcia - CEBAS wrote: Hi all; could you remind me what is the function to change the precision of the operations done in R? I can't remember nor find it. There isn't one. R does all its calculations with system defined double-precision or integers (on most platforms where R is used, these are both 32 bits). See help(is.single) Are you thinking of format(...,digits=n) ? This only affects display (i.e. printing). Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] precision in operations
Douglas Bates wrote: Jason Turner <[EMAIL PROTECTED]> writes: ... There isn't one. R does all its calculations with system defined double-precision or integers (on most platforms where R is used, these are both 32 bits). See help(is.single) Usually the double-precision representation is 64 bits in memory and, for the IA-32 processors (Intel and AMD x86 family), 80 bits in the floating point registers. Blush. Of course. I hate it when I hit "send" without checking if I was thinking when I wrote. Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] kmeans error (bug?)
Murad Nayal wrote:
I am running kmeans in a loop for a range of possible cluster numbers.
The error terminates the loop. is there a mechanism by which I can
'trap' the error so that I can rerun kmeans with another set of initial
centers and hence allow the loop to run to completion. something like
try {} catch() mechanism of C++ for example.
For R version < 1.8.0, ?try
For R version >= 1.8.0, see also ?tryCatch
Jason
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Re: [R] (no subject)
Stefan Wagner wrote: Hi all, I am looking for a clever way to create the following graph using R: I got information on the shares of some subgroups over time (summing > up to 1 in each year). The graph I want to create should display the > evelopment of the individual shares over time by shading rectangulars > for each share in a different color. ?polygon to start. Also have a look at the code for barplot. But given that about eight percent of adult males are colour-blind to some degree, be careful how you pick your colours, or you'll just confuse some of your audience. http://www.visibone.com/colorblind/ shows how "web-safe" colours look to people with colour deficient vision. Don't bet on everyone who has these issues knowing they have it; I know people who discovered they were partially colour blind when they were in their fourties. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Running R-program as queue jobs
Philipp Pagel wrote: Hi! On Thu, Nov 13, 2003 at 09:59:48AM +, Arne Gjuvsland wrote: I have a problem with running my R programs as queue jobs. When I try to submit a batch file to the queue with qsub I get the following error message: /home/gjuvslan/kluster/R-1.7.1/bin/R.bin: error while loading shared libraries: libpcre.so.0: cannot load shared object file: No such file or directory When executed from the command prompt the batch file does its job. Did you run the script on the same machine in both cases? I got burnt a couple of times with different machines running different versions of the OS, non-identical versions of shared libraries etc... In addition to Philipp's good sugestion, I've been burnt on the same machine, but with the batch job running as a different user. When environment variables are needed, or private libraries need to be loaded, things go bad very quickly. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] ISOdate() and strptime()
Thomas Lumley wrote: On Fri, 14 Nov 2003, Simon Fear wrote: Is the behaviour of ISOtime() and strptime() determined by ISO or POSIX standard? Seems not to fit R's "no nannying" policy at all. It's determined by your operating system, so you're complaining to the wrong people. And since R is written to be portable across multiple OSs, you might get an idea how tricky this becomes. Hence the "iron fist" approach to date handling. Believe me, I've programmed date handling - it's always a terrible, nasty, messy business when international locales and different operating systems clash. I'm stunned it's as good as it is, subtle traps and all. Cheers Jason __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] remove 0 rows from a data frame
Tord Snall wrote:
Dear all,
As part of a larger function, I am randomly removing rows from a data
frame. The number of removed rows is determmined by a Poisson distribution
with a low mean. Sometimes, the random number is 0, and that's when the
problem starts:
...
However, sometimes rpois(1, 2) lead to nft=0, and in that case I do not want
temp2<- temp[-sample(nrow(temp), 0), ]
temp2
[1] occ x y dbh age
<0 rows> (or 0-length row.names)
This is a language feature, not a bug. The easiest way around it is to
catch the case where it's an issue. Something like
if(nft==0) {
rows <- 1:nrow(temp)
} else {
rows <- -1 * sample(1:nrow(temp),nft)
}
temp2 <- temp[rows,]
Cheers
Jason
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[R] Stangle - dropping re-used code chunks
My question is: is there a way for Rtangle() to *not* print re-used
code chunks? It'd be easy enough to brew up a perl script to do just
this, but if methods exist already, I'd rather use them. My reading of
the help pages and FAQs has missed something, if it's there.
Background:
I have course notes on R, written using Sweave. I want to provide the R
code separately so the course attendees don't have to re-type everthing
in the manual.
In this manual, I typically show a command, then re-use the chunk to
produce a plot. Something like this:
%% first, show how the plot is done...
<>=
par(mfrow=c(2,2))
mottle.acf <- acf(mottle.t[,1], lag.max=45)
mottle.pacf <- pacf(mottle.t[,1], lag.max=45)
mottle.acf <- acf(mottle.t[,1], lag.max=45, ci.type="ma")
mottle.pacf <- pacf(mottle.t[,1], lag.max=45, ci.type="ma")
@
%% then plot it.
\begin{figure}[tbh]
\centering
<>=
<>
@
\caption{Autocorrelation plot of the \Data{mottle} dataset.}
\label{fig:ex.ts.acf.mottle}
\end{figure}
%% example ends
Stangle will (correctly) print the <> chunk twice,
since it is called twice; once to create it, and once to re-use it.
Cheers
Jason
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Re: [R] Time series indexing/subsetting
[EMAIL PROTECTED] wrote: R-listers: I may be asking too much from R, but is there a way to use time indexing on a time series object. For instance: tsobject <- ts(1:12, start =1999, freq = 4) tsobject Qtr1 Qtr2 Qtr3 Qtr4 19991234 20005678 20019 10 11 12 tsobject[1999,Qtr4] Qtr4 isn't a part of the tsobject. It's produced by the print method for ts objects in general. I believe you want "window" Something like... > window(tsobject, start=c(1999,4), deltat =1) Time Series: Start = 1999.8 End = 2001.8 Frequency = 1 [1] 4 8 12 Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] hist plot and custom "band" width
Mathieu Drapeau wrote: Hi, I have some difficulties to figure how to set a range to my histogram bands. I have values that are [0,50] and they appear once in my list. How can I do a histogram that include all the values between a range of 1 together? [0,1],[10001,2],[21,3], ... ?hist see the "breaks" argument. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] weighted mean
[EMAIL PROTECTED] wrote: How do I go about generating a WEIGHTED mean (and standard error) of a variable (e.g., expenditures) for each level of a categorical variable (e.g., geographic region)? I'm looking for something comparable to PROC MEANS in SAS with both a class and weight statement. That's two questions. 1) to apply a weighted mean to a vector, see ?weighted.mean 2) to apply a function to data grouped by categorical variable, you probably need "by" or "tapply". See the help pages and examples for both. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] strptime Usage
Ko-Kang Kevin Wang wrote: Hi, I have a column in a dataframe in the form of: as.vector(SLDATX[1:20]) [1] "1/6/1986" "1/17/1986" "2/2/1986" "2/4/1986" "2/4/1986" [6] "2/21/1986" "3/6/1986" "3/25/1986" "4/6/1986" "4/10/1986" [11] "4/23/1986" "4/30/1986" "5/8/1986" "5/29/1986" "6/15/1986" [16] "6/18/1986" "6/23/1986" "6/29/1986" "7/16/1986" "7/25/1986" ... First, you have to make this character vector into a time object. You want something like: times <- strptime(as.vector(SLDATX[1:20]),"%d/%m/%Y") so R knows what format you're using for dates. From there, format(times,"%Y/%m") will work. Subtle trap - strptime produces a list of 9 vectors; "times" will always have length 9. If you want to include this into a data frame, you'll need to convert to a POSIX time type: as.POSIXct(times) to get the right length. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] creating graphs in BATCH mode
Reinhard Sy wrote:
Hi
a short question is there a way to generate jpeg's etc. in BATCH mode ? The
following example does not work in BATCH:
...
Error in jpeg("/tmp/my.jpg") : R_X11 module cannot be loaded
In addition: Warning message:
X11 module is not available under this GUI
Execution halted
[EMAIL PROTECTED]:09][~][57]>
Under Unix and Unix-like systems, R needs a running X server to produce
JPEGs. You needn't start the X-server; check out XVFB - X Virtual Frame
Buffer - which sets up a virtual X server, but with no display. You may
already have this installed: "man Xvfb" will tell you.
http://www.visualmining.com/support/server/XvfbonUnix.html
Cheers
Jason
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Re: [R] check WARNING...
Jeff D. Hamann wrote: I've been developing a package and have been getting the following warning when running the check command: * checking S3 generic/method consistency ... WARNING plot: function(x, ...) plot.summaries: function(trees, sp) I'm unclear; is "summaries" a class? If not, try naming the function plotSummaries, or some such thing (no dot ".") Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Two questions about the creating new package
Song Baiyi wrote:
Hello everyone,
I am just trying to colloct all my function into a new packages. I met
two questions which hurt me so much:
1. when I use the "prompt" to help to write Rd file for a variable x
which is character vector, say x <- c("a","b"), it always give the error
informaion:
Error in get(x, envir, mode, inherits) : variable "a" was not found.
Obvious it regards the "a" as the variable name instead of the item of a
vector. So how can I put a character vector into the pacakge, or it must
be a data.frame to put into a package?
Use the "name" argument to prompt.
prompt(name="x")
should work.
2. Also about the constant character vector. I have a constant vector
which record the column names. I hope when the package is loaded, this
vector will be loaded without explict writing "data(***)". Therefore the
users and other functions can use it. How can I do it? A more generate
question is where should I put those R codes which will be excuted after
the package is loaded?
See help(.First.lib) . In this case, you'd want something like
.First.lib <- function(lib,pkg){
data(foo)
}
When writing a package, these functions are traditionally (but not
manditorily) stored in a file called zzz.R .
Cheers
Jason
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Re: [R] add a point to regression line and cook's distance
[EMAIL PROTECTED] wrote: Hi, MY question is like the following: I would like to have a robust regression line. The data I have are > mostly clustered around a small range. So the regression line tend to be influenced strongly by outlier points > (with large cook's distance). From the application's > background, I know that the line should pass (0,0), which is far > away from the data cloud. I would like to add this point to have a more robust line. The question is: > does it make sense to do this? what are the negative impacts if any? Have you tried a more robust fit (ltsreg() in the package lqs springs to mind)? Using this, without forcing the intercept to zero, might give you some idea if your idea makes sense. Venables and Ripley (Modern Applied Statistics with S, Springer-Verlag, 2002) give a good introduction to robust linear models, and how to estimate their error distribution. Julian Faraway also gives an overview of the same, in his "Practical Regression and ANOVA using R". http://cran.r-project.org/doc/contrib/Faraway-PRA.pdf Hope that helps Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] bug in as.POSIXct ?
[EMAIL PROTECTED] wrote: I think that there is a bug in the as.POSIXct function on Windows. Here is what I get on Win2000, Pentium III machine in R 1.8.1. dd1 <- ISOdatetime(2003, 10, 26, 0, 59, 59) dd2 <- ISOdatetime(2003, 10, 26, 1, 0, 0) dd2 - dd1 Time difference of 1.000278 hours Now, the 26th of October was the day that change to the standard time occurred, so I suspect that this has something to do with that. In fact dd1 [1] "2003-10-26 00:59:59 Central Daylight Time" dd2 [1] "2003-10-26 01:00:00 Central Standard Time" so it looks like the switch from CDT to CST happens at 1:00 (instead of 2:00 ?). Or, it did happen at 2:00 CDT, when the time fell back one hour to 1:00 CST. 1:00 am occured twice on that day, once as CDT and once as CST. R picked the last one. A bit pathological at first glance, but date-handling often is. As for the dd2 - dd1 value, the "correct" value depends which 1:00 am was chosen. On Windows, this should be 1 hour, 1 second, no? I'm thinking 1:00 am CST == 2:00 am CDT, so in CDT entirely, your expression is basicly 02:00:00 CDT - 00:59:59 CDT. This makes me suspect that Linux picked the former 1:00 am, from your report. Since R gets its date intricacies from the OS, there really isn't much that can be done about this, until someone builds a full POSIX time implementation that takes all the world's locales and time zones into account, and welds it into R. Volunteers? It's things like this that make me convert everything to UCT (GMT, or Zulu, if you prefer). Not R's fault; stupid calendar tricks are to blame here. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
