Re: [R] Removing constants from a data frame
On 17 Sep 2004 at 19:17, Kjetil Brinchmann Halvorsen wrote:
David Forrest wrote:
Suppose I have
x-data.frame(v1=1:4, v2=c(2,4,NA,7), v3=rep(1,4),
v4=LETTERS[1:4],v5=rep('Z',4))
or a much larger frame, and I wish to test for and remove the
constant numeric columns.
I made:
is.constant-function(x){identical(min(x),max(x))}
and
apply(x,2,is.constant) # Works for numerics
x[,-which(apply(x,2,is.constant))]
I'd really like to be able to delete the constant columns without
losing my non-numerics. Ignoring the character columns would be OK.
Any suggestions?
Dave
what about defing is.constant as
is.constant - function(x) {
if (is.numeric(x)) identical(min(x), max(x))
else
FALSE }
Kjetil halvorsen
Hi
Maybe this will do it
fff-function(a) if(is.numeric(a)) diff(range(a, na.rm=T))==0 else FALSE
x[,!mapply(fff,x)]
v1 v2 v4 v5
1 1 2 A Z
2 2 4 B Z
3 3 NA C Z
4 4 7 D Z
Cheers
Petr
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Kjetil Halvorsen.
Peace is the most effective weapon of mass construction.
-- Mahdi Elmandjra
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Re: [R] WARNING: terminal is not fully functional
Hello, A.J. Rossini schrieb: Thomas Schönhoff [EMAIL PROTECTED] writes: Peter Dalgaard schrieb: Thomas Schönhoff [EMAIL PROTECTED] writes: Hmm, by the way, is there any tutorial or something similar point to how to use Emacs, ESS and GNU R? There are a few, some at http://ESS.R-Project.org/ I'll put my versions up after I get settled in Basel (mid November). Thanks for advice! Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] compilation failed for package
Hello, I am new to R on Linux (and to LINUX), running a 1.9.1 on a Linux MDK10.0. When updating or installing different packages, I get messages like this (under), the package doesn't install. Can anyone help me? I know this is all to little information, but I don't know were to start. I think there is something wrong in how or were the C++ or fortran compilator is installed?? Thanks, Geir S. gcc -shared -L/usr/local/lib -o survival.so agexact.o agfit2.o agfit3.o agfit5.o agfit_null.o agmart2.o agmart.o agscore.o agsurv1.o agsurv2.o agsurv3.o char_date.o chinv2.o chinv3.o cholesky2.o cholesky3.o chsolve2.o chsolve3.o coxdetail.o coxfit2.o coxfit5.o coxmart.o coxph_wtest.o cox_Rcallback.o coxscho.o coxscore.o dmatrix.o doloop.o pyears1.o pyears2.o pyears3.o pystep.o surv_callback.o survdiff2.o survfit2.o survfit3.o survindex2.o survindex3.o survreg2.o survreg3.o survreg4.o survreg5.o /usr/bin/ld: unrecognized option '--as-needed' /usr/bin/ld: use the --help option for usage information collect2: ld returned 1 exit status make: *** [survival.so] Error 1 ERROR: compilation failed for package 'survival' ** Removing '/usr/lib/R/library/survival' ** Restoring previous '/usr/lib/R/library/survival' __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Removing constants from a data frame
From: Kjetil Brinchmann Halvorsen
David Forrest wrote:
Suppose I have
x-data.frame(v1=1:4, v2=c(2,4,NA,7), v3=rep(1,4),
v4=LETTERS[1:4],v5=rep('Z',4))
or a much larger frame, and I wish to test for and remove
the constant
numeric columns.
I made:
is.constant-function(x){identical(min(x),max(x))}
and
apply(x,2,is.constant) # Works for numerics
x[,-which(apply(x,2,is.constant))]
I'd really like to be able to delete the constant columns
without losing
my non-numerics. Ignoring the character columns would be OK.
Any suggestions?
Dave
what about defing is.constant as
is.constant - function(x) {
if (is.numeric(x)) identical(min(x),
max(x)) else
FALSE }
identical() is probably not the safest thing to use:
x - c(1, 2, NA)
is.constant(x)
[1] TRUE
For data such as c(1, 1, 1, NA), I should think the safest answer should be
NA, because one really doesn't know whether that last number is 1 or not.
Andy
--
Kjetil Halvorsen.
Peace is the most effective weapon of mass construction.
-- Mahdi Elmandjra
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[R] Memory Problem???
DeaR useRs: I am working with 1 files at the same time. These files are in some lists. When I begin to operate the memory size grows, but never exceeds the computers RAM. And suddenly R reports: Error: cannot allocate vector of size 23 Kb Somebody know what can I do? Thanks and excuse my English. --- [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Memory Problem???
Perez Martin, Agustin wrote: DeaR useRs: I am working with 1 files at the same time. These files are in some lists. When I begin to operate the memory size grows, but never exceeds the computers RAM. And suddenly R reports: Error: cannot allocate vector of size 23 Kb Read the FAQs and see ?Memory, in partilcuar if you are under Windows. Uwe Ligges Somebody know what can I do? Thanks and excuse my English. --- [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] persiting complex R objects
Is there a method to save a large and complex R object (either as a binary or text file) so that it can be loaded and reused at a later time? Specifically, I am creating large lists (several thousand elements), each element of which is either a vector or a matrix (with ~ 2000 rows). The dimensions of the matrices are not all the same. My ideal would be a set of functions of the form obj - create() # computes the object save(obj,filename) obj - load(filename) -- Richard Mott | Wellcome Trust Centre tel 01865 287588 | for Human Genetics fax 01865 287697 | Roosevelt Drive, Oxford OX3 7BN __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] findInterval in compiled code.
TobyP == [EMAIL PROTECTED]
on Mon, 20 Sep 2004 14:22:27 +1000 writes:
TobyP Hi all,
TobyP I am writing some C code where I want to use the findInterval function
TobyP documented in Writing R extensions/Utility functions. i.e. the
TobyP C-version not the R version.
(so, typically this should rather go to R-devel than R-help;
but never mind for this time.)
TobyP It all compiles but the shared library is causing seg-faults and I'm
TobyP obviously stuffing something up.
probably
TobyP Has anyone got any examples of calling this function
TobyP they'd be will to share? I've searched through the
TobyP source of quite a few libraries and can't find any.
indeed, there aren't any in the CRAN packages.
If you don't get other feedback, do try to isolate the problem
into a very minimalistic example, and if the problem persists,
use R-devel
and give the details {maybe a URL to download the package source}
of your (minimalistic!) package setup.
Then, we can help you further.
Regards,
Martin Maechler
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Re: [R] persiting complex R objects
Richard, Check out ?save and ?load. You were correct on those. Do you have questions about create? If so, you will probably have to be more specific. Sean - Original Message - From: Richard Mott [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Monday, September 20, 2004 7:00 AM Subject: [R] persiting complex R objects Is there a method to save a large and complex R object (either as a binary or text file) so that it can be loaded and reused at a later time? Specifically, I am creating large lists (several thousand elements), each element of which is either a vector or a matrix (with ~ 2000 rows). The dimensions of the matrices are not all the same. My ideal would be a set of functions of the form obj - create() # computes the object save(obj,filename) obj - load(filename) -- Richard Mott | Wellcome Trust Centre tel 01865 287588 | for Human Genetics fax 01865 287697 | Roosevelt Drive, Oxford OX3 7BN __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] persisting complex R objects
Richard == Richard Mott [EMAIL PROTECTED] on Mon, 20 Sep 2004 12:00:49 +0100 writes: Richard Is there a method to save a large and complex R Richard object (either as a binary or text file) so that it Richard can be loaded and reused at a later time? Richard Specifically, I am creating large lists (several Richard thousand elements), each element of which is either Richard a vector or a matrix (with ~ 2000 rows). The Richard dimensions of the matrices are not all the same. My Richard ideal would be a set of functions of the form Richard obj - create() # computes the object Richard save(obj,filename) Richard obj - load(filename) that sounds alright. I'd use save(*, filename, compress = TRUE) ^^^ if dealing with largish objects. Also note that attach(filename) is an alternative that may be a bit cleaner for your situation that's probably not used enough. Regards, Martin Maechler __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Removing constants from a data frame
AndyL == Liaw, Andy [EMAIL PROTECTED]
on Mon, 20 Sep 2004 06:22:33 -0400 writes:
From: Kjetil Brinchmann Halvorsen
David Forrest wrote:
Suppose I have
x-data.frame(v1=1:4, v2=c(2,4,NA,7), v3=rep(1,4),
v4=LETTERS[1:4],v5=rep('Z',4))
or a much larger frame, and I wish to test for and remove
the constant
numeric columns.
I made:
is.constant-function(x){identical(min(x),max(x))}
and
apply(x,2,is.constant) # Works for numerics
x[,-which(apply(x,2,is.constant))]
I'd really like to be able to delete the constant columns
without losing
my non-numerics. Ignoring the character columns would be OK.
Any suggestions?
Dave
what about defing is.constant as
is.constant - function(x) {
if (is.numeric(x)) identical(min(x), max(x)) else FALSE }
AndyL identical() is probably not the safest thing to use:
x - c(1, 2, NA)
is.constant(x)
AndyL [1] TRUE
AndyL For data such as c(1, 1, 1, NA), I should think the
AndyL safest answer should be NA, because one really
AndyL doesn't know whether that last number is 1 or not.
yes.
Also note that is.numeric() is not what you want for data.frame
columns since it isn't true for factors and you may want to
remove constant factor columns as well.
Martin Maechler
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Re: [R] persiting complex R objects
did you look at ?save ?load ??? ingmar On 9/20/04 1:00 PM, Richard Mott [EMAIL PROTECTED] wrote: Is there a method to save a large and complex R object (either as a binary or text file) so that it can be loaded and reused at a later time? Specifically, I am creating large lists (several thousand elements), each element of which is either a vector or a matrix (with ~ 2000 rows). The dimensions of the matrices are not all the same. My ideal would be a set of functions of the form obj - create() # computes the object save(obj,filename) obj - load(filename) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] persiting complex R objects
Richard Mott wrote: Is there a method to save a large and complex R object (either as a binary or text file) so that it can be loaded and reused at a later time? Specifically, I am creating large lists (several thousand elements), each element of which is either a vector or a matrix (with ~ 2000 rows). The dimensions of the matrices are not all the same. My ideal would be a set of functions of the form obj - create() # computes the object save(obj,filename) obj - load(filename) Have a look at ? dump ? source Peter Wolf __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] persiting complex R objects
Thanks for the help; I feel rather foolish as I had not realised that the functions save() and load() already existed. They are not mentioned in the R docs (unless you know they exist and so can query them by name - the general docs describing how to manipulate R objects don't mention them) - Richard -- Richard Mott | Wellcome Trust Centre tel 01865 287588 | for Human Genetics fax 01865 287697 | Roosevelt Drive, Oxford OX3 7BN __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] persiting complex R objects
Hi! ?save 'save' writes an external representation of R objects to the specified file. The objects can be read back from the file at a later date by using the function 'load' (or 'data' in some cases). ?load Reload the datasets written to a file with the function 'save'. /E *** REPLY SEPARATOR *** On 9/20/2004 at 12:00 PM Richard Mott wrote: Is there a method to save a large and complex R object (either as a binary or text file) so that it can be loaded and reused at a later time? Specifically, I am creating large lists (several thousand elements), each element of which is either a vector or a matrix (with ~ 2000 rows). The dimensions of the matrices are not all the same. My ideal would be a set of functions of the form obj - create() # computes the object save(obj,filename) obj - load(filename) -- Richard Mott | Wellcome Trust Centre tel 01865 287588 | for Human Genetics fax 01865 287697 | Roosevelt Drive, Oxford OX3 7BN __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin'v' tel: 0049-30-83875219/ \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] plot.Map with pattern instead of colors
Hi, I am plotting shapefiles with plot.Map (package maptools). So far I use different colors for the shapes depending on the a value that belongs to the shape. Now, I need to produce maps only in black, gray and white for publication. Is it possible to fill shapes with pattern (e.g. hatched) instead of colors? Details of a simplified example: I want to show the percentage change of a variable in a map: e.g. following levels a) +10 b) +5% to +10% c) -5% to +5% d) -10% to -5% e) -10% Now I have following colors a) red b) orange c) white d) greenyellow e) green3 Printing this on a monochrome printer is - of course - stupid, because levels a) and e) as well as b) and d) have approximately the same grayscale. I could fill a) = black and e) = white, and everything inbetween with an appropriate grayscale, but I prefer to have areas with no change to appear white rather than medium gray. Therefore, I thought of doing following: a) black b) gray c) white d) hatched with thin lines e) hatched with thick lines (or double-hatched) Any hints and ideas are welcome! (BTW: I use R 1.9.1 on SuSE Linux 9.0) Thanks, Arne -- Arne Henningsen Department of Agricultural Economics University of Kiel Olshausenstr. 40 D-24098 Kiel (Germany) Tel: +49-431-880 4445 Fax: +49-431-880 1397 [EMAIL PROTECTED] http://www.uni-kiel.de/agrarpol/ahenningsen/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] GARCH model query
Hello, I am trying to find an easy way to estimate the following: y = Function(x) + lag(x,1) + garch_error_component Any clues? Best regards, Costas --- __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] plot.Map with pattern instead of colors
On Mon, 20 Sep 2004, Arne Henningsen wrote: Hi, I am plotting shapefiles with plot.Map (package maptools). So far I use different colors for the shapes depending on the a value that belongs to the shape. Now, I need to produce maps only in black, gray and white for publication. Is it possible to fill shapes with pattern (e.g. hatched) instead of colors? Not in plot.Map(). This is supported if you convert the shapefile polygons to a polylist object (Map2poly()), then use plot.polylist() - but this may not be your choice. Within plot.Map, I would suggest using the RColorBrewer package and the sequential Greys palette, which differentiates five grey colours very well for most media. If you run this after example(plot.Map), it should illustrate a solution: library(RColorBrewer) pal - brewer.pal(5, Greys) fgs - pal[findInterval(x$att.data$BIR74, res$breaks, all.inside=TRUE)] plot(x, fg=fgs) for the default quantile breaks. Details of a simplified example: I want to show the percentage change of a variable in a map: e.g. following levels a) +10 b) +5% to +10% c) -5% to +5% d) -10% to -5% e) -10% Now I have following colors a) red b) orange c) white d) greenyellow e) green3 Printing this on a monochrome printer is - of course - stupid, because levels a) and e) as well as b) and d) have approximately the same grayscale. I could fill a) = black and e) = white, and everything inbetween with an appropriate grayscale, but I prefer to have areas with no change to appear white rather than medium gray. Therefore, I thought of doing following: a) black b) gray c) white d) hatched with thin lines e) hatched with thick lines (or double-hatched) Any hints and ideas are welcome! (BTW: I use R 1.9.1 on SuSE Linux 9.0) Thanks, Arne -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Breiviksveien 40, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 93 93 e-mail: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] montecarlo simulation
Hy! I would like to know how run a montecarlo simulation with R. Thank you Francesca Matalucci __ Accesso Internet Gratis per utenti Excite! Attivalo subito! http://www.excite.it/hitech/accesso Il Mio Excite. Personalizza la tua Home page Excite come vuoi tu! http://www.excite.it AAA/Relazioni. Sfoglia gli annunci e trova la tua anima gemella http://www.excite.it/relazioni __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] asypow.noncent: how does it work?
I am trying to do power calculations for the proportional odds model using the asypow library. The code noncenta90b10-asypow.noncent(theta.ha=a9010,info.mat=infomatrixa90b10,constraints=constrt) returns Error in max(..., na.rm = na.rm) : invalid mode of argument. the various arguments I've used are: a9010 [,1] [1,] -1.7357568 [2,] -0.1928619 specifying the theta.ha array as a row not a column makes no difference infomatrixa90b10 [,1] [,2] [1,] 0.967005807 -0.004699262 [2,] -0.004699262 0.903852346 constrt [,1] [,2] [,3] [1,] 1 a -1.92861865194525 [2,] 1 b 0 I'm probably missing something very simple, but I can't see what it is. Can anyone help? ___ Most doctors use http://www.Doctors.net.uk e-mail. Move to a free professional address with spam and virus protection. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] asypow.noncent: how does it work?
[EMAIL PROTECTED] wrote: I am trying to do power calculations for the proportional odds model using the asypow library. The code noncenta90b10-asypow.noncent(theta.ha=a9010,info.mat=infomatrixa90b10,constraints=constrt) returns Error in max(..., na.rm = na.rm) : invalid mode of argument. the various arguments I've used are: a9010 [,1] [1,] -1.7357568 [2,] -0.1928619 specifying the theta.ha array as a row not a column makes no difference infomatrixa90b10 [,1] [,2] [1,] 0.967005807 -0.004699262 [2,] -0.004699262 0.903852346 constrt [,1] [,2] [,3] [1,] 1 a -1.92861865194525 [2,] 1 b 0 I don't think you can specify a character matrix as constraints -- for sure the package maintainer knows better. Uwe Ligges I'm probably missing something very simple, but I can't see what it is. Can anyone help? ___ Most doctors use http://www.Doctors.net.uk e-mail. Move to a free professional address with spam and virus protection. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Re: What is nu-regression for svm?
Look up the reference given at the help-page, it tells you exactly what nu-regression does. best, -d Date: Fri, 17 Sep 2004 11:24:03 +0100 From: [EMAIL PROTECTED] Subject: [R] What is nu-regression for svm? To: [EMAIL PROTECTED] Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Does anyone knows what is the nu-regression option for the type parameter in svm (from package e1071)? I cannot find any explanation on that and I have a reasonable understanding on svm fundamentals. Thanks Joao Moreira - David Meyer Department of Information Systems Vienna University of Economics and Business Administration Augasse 2-6, A-1090 Wien, Austria, Europe Fax: +43-1-313 36x746 Tel: +43-1-313 36x4393 HP: http://wi.wu-wien.ac.at/Wer_sind_wir/meyer/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] R/web interface
I am trying to develop an interactive software and would like to know how I can hook up R to the web. Thanks Joe Warfield __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] montecarlo simulation
imho one easy example:
n - 50
reps - 1000
ms - single(reps)
set.seed(378216)
for(i in 1:reps) {
x - exp(rnorm(n))
ms[i] - median(x)
}
hist(ms)
regards, christian
Am Montag, 20. September 2004 14:30 schrieb [EMAIL PROTECTED]:
Hy!
I would like to know how run a montecarlo simulation with R.
Thank you
Francesca Matalucci
__
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Il Mio Excite. Personalizza la tua Home page Excite come vuoi tu!
http://www.excite.it
AAA/Relazioni. Sfoglia gli annunci e trova la tua anima gemella
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RE: [R] R/web interface
Some possibilities are RWeb, RPad and Rcgi. I only have experience with RWeb myself. A decent collection of relevant links for this subject is: http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/StatCompCourse [The 2nd block of the page, titled 'WWW Statistical Computing Applications using R'] Mark Fowler Marine Fish Division Bedford Inst of Oceanography Dept Fisheries Oceans Dartmouth NS Canada [EMAIL PROTECTED] -Original Message- From: Warfield Jr., Joseph D. [mailto:[EMAIL PROTECTED] Sent: September 20, 2004 10:00 AM To: '[EMAIL PROTECTED]' Subject: [R] R/web interface I am trying to develop an interactive software and would like to know how I can hook up R to the web. Thanks Joe Warfield __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] persisting complex R objects
Richard == Richard Mott [EMAIL PROTECTED] on Mon, 20 Sep 2004 12:29:30 +0100 writes: Richard Thanks for the help; I feel rather foolish as I had Richard not realised that the functions save() and load() Richard already existed. aha! Richard They are not mentioned in the R Richard docs (unless you know they exist and so can query Richard them by name - the general docs describing how to Richard manipulate R objects don't mention them) which ones (don't mention them) did you mean? In any case, help.search(save) would have helped you, too. That's another function that is still not used often enough it seems. Regards, Martin __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Getting the real names of variables within functions
Greetings.
These days I find myself writing a lot of functions to handle routine
things. One of these is a function to create a scatterplot of
variables and draw a lowessed line so I can get some idea if there's
any relationship between them.
lowessed.plot - function(x, y)
{ plot(x, y)
lines(lowess(x, y))
}
However, there's a slight problem: the plot axes come out labeled x
and y, which isn't what I want. I want the plot axes labeled with
the names of the variables I passed into lowessed.plot for x and y. Is
there any way to do that? Thanks in advance for any help anyone can
provide.
Aaron
-
Aaron Solomon (ben Saul Joseph) Adelman
E-mail: [EMAIL PROTECTED]
Web site: http://people.musc.edu/~adelmaas/
AOL Instant Messenger Yahoo! Messenger: Hiergargo (YM account
now sometimes with the Worlds first statistical Webcam, Morans Eye)
AIM chat-room (preferred): Adelmania
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Re: [R] Getting the real names of variables within functions
Hi Aaron,
try to use:
plot( x, y, xlab=deparse(substitute(x)),
ylab=deparse(substitute(y)) )
I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/396887
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm
- Original Message -
From: [EMAIL PROTECTED]
To: list [EMAIL PROTECTED]
Sent: Monday, September 20, 2004 4:00 PM
Subject: [R] Getting the real names of variables within functions
Greetings.
These days I find myself writing a lot of functions to handle
routine things. One of these is a function to create a scatterplot
of variables and draw a lowessed line so I can get some idea if
there's any relationship between them.
lowessed.plot - function(x, y)
{ plot(x, y)
lines(lowess(x, y))
}
However, there's a slight problem: the plot axes come out labeled
x and y, which isn't what I want. I want the plot axes labeled
with the names of the variables I passed into lowessed.plot for x
and y. Is there any way to do that? Thanks in advance for any help
anyone can provide.
Aaron
-
Aaron Solomon (ben Saul Joseph) Adelman
E-mail: [EMAIL PROTECTED]
Web site: http://people.musc.edu/~adelmaas/
AOL Instant Messenger Yahoo! Messenger: Hiergargo (YM
account now sometimes with the Worlds first statistical Webcam,
Morans Eye)
AIM chat-room (preferred): Adelmania
__
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PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
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Re: [R] Getting the real names of variables within functions
On Mon, 20 Sep 2004 10:00:19 -0400, [EMAIL PROTECTED] wrote :
Greetings.
These days I find myself writing a lot of functions to handle routine
things. One of these is a function to create a scatterplot of
variables and draw a lowessed line so I can get some idea if there's
any relationship between them.
lowessed.plot - function(x, y)
{ plot(x, y)
lines(lowess(x, y))
}
However, there's a slight problem: the plot axes come out labeled x
and y, which isn't what I want. I want the plot axes labeled with
the names of the variables I passed into lowessed.plot for x and y. Is
there any way to do that? Thanks in advance for any help anyone can
provide.
You could do this with
plot(x, y, xlab=deparse(substitute(x)), ylab=deparse(substitute(y)))
But it's better to add two arguments to the function with those as
default values, then pass them on to plot(); that way you can change
the labels if you want. And add dots for other customization.
For example,
lowessed.plot - function(x, y, xlab=deparse(substitute(x)),
ylab=deparse(substitute(y)), ...)
{ plot(x, y, xlab=xlab, ylab=ylab, ...)
lines(lowess(x, y))
}
Duncan Murdoch
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Re: [R] Getting the real names of variables within functions
It works great now. Thanks, guys!
Aaron
On 20 2004, at 10:10, Duncan Murdoch wrote:
On Mon, 20 Sep 2004 10:00:19 -0400, [EMAIL PROTECTED] wrote :
Greetings.
These days I find myself writing a lot of functions to handle routine
things. One of these is a function to create a scatterplot of
variables and draw a lowessed line so I can get some idea if there's
any relationship between them.
lowessed.plot - function(x, y)
{ plot(x, y)
lines(lowess(x, y))
}
However, there's a slight problem: the plot axes come out labeled x
and y, which isn't what I want. I want the plot axes labeled with
the names of the variables I passed into lowessed.plot for x and y.
Is
there any way to do that? Thanks in advance for any help anyone can
provide.
You could do this with
plot(x, y, xlab=deparse(substitute(x)), ylab=deparse(substitute(y)))
But it's better to add two arguments to the function with those as
default values, then pass them on to plot(); that way you can change
the labels if you want. And add dots for other customization.
For example,
lowessed.plot - function(x, y, xlab=deparse(substitute(x)),
ylab=deparse(substitute(y)), ...)
{ plot(x, y, xlab=xlab, ylab=ylab, ...)
lines(lowess(x, y))
}
Duncan Murdoch
-
Aaron Solomon (ben Saul Joseph) Adelman
E-mail: [EMAIL PROTECTED]
Web site: http://people.musc.edu/~adelmaas/
AOL Instant Messenger Yahoo! Messenger: Hiergargo
AIM chat-room (preferred): Adelmania
__
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Re: [R] montecarlo simulation
Francesca, Do help.search(monte carlo). That will be a good start. Sean - Original Message - From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Monday, September 20, 2004 8:30 AM Subject: [R] montecarlo simulation Hy! I would like to know how run a montecarlo simulation with R. Thank you Francesca Matalucci __ Accesso Internet Gratis per utenti Excite! Attivalo subito! http://www.excite.it/hitech/accesso Il Mio Excite. Personalizza la tua Home page Excite come vuoi tu! http://www.excite.it AAA/Relazioni. Sfoglia gli annunci e trova la tua anima gemella http://www.excite.it/relazioni __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R/web interface
Joe, You can use CGI scripts to do the coordination between R and HTML served to the browser. There is a new R package: http://www.rpad.org/Rpad/ that might be of use, also. Sean - Original Message - From: Warfield Jr., Joseph D. [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Monday, September 20, 2004 9:00 AM Subject: [R] R/web interface I am trying to develop an interactive software and would like to know how I can hook up R to the web. Thanks Joe Warfield __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] montecarlo simulation
Ciao Francesca,
here are some examples or R code using montecarlo
simulation concernig parameters estimates of sever
random variables:
Estimate of parameter theta of a uniform variable with
ML method
Stima del parametro theta di una v.a. unif(0,theta)
con metodo
dei momenti e confronto con la stima di massima
verosimiglianza (M.V.)
theta-5
n-50
x-runif(n,0,theta)
est.theta-2*mean(x) ## stima con metodo dei momenti
var.theta-(est.theta^3)/(3*n) ## stima della varianza
di theta
mlest.theta-max(x) ## stima di theta con il metodo
della M.V.
acc1-(theta-est.theta)/theta
acc2-(theta-mlest.theta)/theta
est.theta-mlest.theta
Simulazione di una v.a. uniforme (0,t), stima di theta
con metodo dei
momenti e della M.V. e stampa dei relativi grafici
t-2.5 ## valore parametro
n-20 ## dimensione campionaria
k-200 ## numero di campioni da simulare
X-matrix(runif(n*k,0,t),nrow=n)
est.tmom-2*apply(X,2,mean)
est.tml-apply(X,2,max)
hist(est.tmom,nclass=10)
hist(est.tml, nclass=10,add=T,col=red)
var.x-apply(X,2,var) ## varianza della v.a.
var.mom-var(est.tmom)## varianza della stima com
metodo dei momenti
var.ml-var(est.tml) ## varianza della stima com
metodo della M.V.
medie.stime-c(mean(est.tml),mean(est.tmom))
var.stime-c(var.ml,var.mom)
tabella-data.frame(medie.stime,var.stime,metodo-c(Stima
ML,Stima Momenti))
names(tabella)[3]-Metodo
tabella
Weibull simulation
n-50
k-500
X-matrix(rweibull(n*k,shape=10,scale=5),nrow=n)
mediana-apply(X,2,median)
avg.med-mean(mediana)
var.med-var(mediana)
hist(mediana,freq=T)
media-apply(X,2,mean)
avg.media-mean(media)
var.media-var(media)
hist(media,freq=T)
tabella-data.frame(c(avg.med,avg.media),c(var.med,var.media))
names(tabella)-c(statistica,varianza)
qqnorm(mediana)
qqnorm(media)
shapiro.test(mediana)
shapiro.test(media)
qqplot(mediana,media)
Beta pdf simulation
Simulazione di una variabile beta
N-1000 ##numero osservazioni totali
n-50 ##numero di elementi per campione
k-N/n ##numero dei campioni
for (i in 1:n)
{
X-matrix(rbeta(N,10,20),nrow=n)
}
n-20
k-200
X-matrix(rbeta(n*k,10,20),nrow=n)
Estimate of parameters of a beta pdf with ML method
using nlm()
Stima dei parametri di una v.a. Beta con metodo della
massima verosimiglianza
usando la funzione nlm() per un campione di ampiezza
n=100 e dei relativi errori standard
x-rbeta(100,10,20)
f-function(p)
100*log(beta(p[1],p[2]))+(1-p[1])*sum(log(x))+(1-p[2])*sum(log(1-x))
out-nlm(f,p=c(20,20),hessian=TRUE)
Estimate of parameters of a Gamma pdf with ML method
using nlm().
Stima di massima verosimiglianza dei parametri di una
v.a. Gamma da cui è stato estratto un campione di
ampiezza n=200 con l'uso della funzione nlm()
x-rgamma(200,10,5)
f-function(p)
(-200*p[1]*log(p[2])+200*log(gamma(p[1]))+(1-p[1])*sum(log(x))+p[2]*sum(x))
out-nlm(f,p=c(15,10),hessian=TRUE)
out
Best
Vito
Hy!
I would like to know how run a montecarlo simulation
with R.
Thank you
Francesca Matalucci
=
Diventare costruttori di soluzioni
Visitate il portale http://www.modugno.it/
e in particolare la sezione su Palese http://www.modugno.it/archivio/cat_palese.shtml
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[R] adding function to a Package
As a shortcut I have previously added my own functions to a Package (ipred)
under R-1.8.1, changing the NAMESPACE file to accomodate this then
reinstalling. This doesn't now seem possible in R-1.9.0 is this correct?-- I
am getting an error saying:
files NAMESPACE, R/ipred have the wrong MD5 checksums
after I try to reinstall (which I can understand). Is there a quick way
round this avoiding having to build my own Package?
Thanks
Stephen
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[R] Multiple operations on list
Hello, suppose I have a list with matrices: a=list(x1=matrix(rnorm(10),5,2),x2=matrix(rnorm(10),5,2),x3=matrix(rnorm(10),5,2)) I want to compute for all combination of xi and xj (x1,x2 x1,x3 and x2,x3) a value. This value is given for the pair x1,x2 by trace(x1%*%t(x1)%*%x2%*%t(x2)) / trace(x1%*%t(x1))*trace(x2%*%t(x2)) I know that product matrices t(xi)%*%xi can be obtained by: aa=lapply(a,crossprod) but I do not know how to mix the values in aa to obtain the desired values. Is there a way to do it without for loop ? Thanks in advances, sincerely Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : (514) 343-6111 poste 1233 Fax : (514) 343-2293 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Multiple operations on list
Hi! Not sure if I got your point. But if it is to compute apply a function to all pairs (x1,x2);(x1,x3);(x2,x3) where x1,x2,x3 are stored in a list you can take look at the sources of function listdist which computes an object of class dist from a list, in the package pairseqsim available from bioconducor, to get an idea how to do this. /E *** REPLY SEPARATOR *** On 20.09.2004 at 13:24 Stephane DRAY wrote: Hello, suppose I have a list with matrices: a=list(x1=matrix(rnorm(10),5,2),x2=matrix(rnorm(10),5,2),x3=matrix(rnorm(10),5,2)) I want to compute for all combination of xi and xj (x1,x2 x1,x3 and x2,x3) a value. This value is given for the pair x1,x2 by trace(x1%*%t(x1)%*%x2%*%t(x2)) / trace(x1%*%t(x1))*trace(x2%*%t(x2)) I know that product matrices t(xi)%*%xi can be obtained by: aa=lapply(a,crossprod) but I do not know how to mix the values in aa to obtain the desired values. Is there a way to do it without for loop ? Thanks in advances, sincerely Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : (514) 343-6111 poste 1233 Fax : (514) 343-2293 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Multiple operations on list
Stephane: 1. apply() functions ARE (implicit) loops. 2. ?outer might be useful, but I suspect would be even more inefficient ... so I think the answer is, no, you must loop either explicitly or implicitly. However, my guess is that whatever you're trying to do is either built into R or can be done much more efficiently. Explicit matrix multiplication is almost always avoidable in statistics. -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA The business of the statistician is to catalyze the scientific learning process. - George E. P. Box -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Stephane DRAY Sent: Monday, September 20, 2004 10:25 AM To: [EMAIL PROTECTED] Subject: [R] Multiple operations on list Hello, suppose I have a list with matrices: a=list(x1=matrix(rnorm(10),5,2),x2=matrix(rnorm(10),5,2),x3=ma trix(rnorm(10),5,2)) I want to compute for all combination of xi and xj (x1,x2 x1,x3 and x2,x3) a value. This value is given for the pair x1,x2 by trace(x1%*%t(x1)%*%x2%*%t(x2)) / trace(x1%*%t(x1))*trace(x2%*%t(x2)) I know that product matrices t(xi)%*%xi can be obtained by: aa=lapply(a,crossprod) but I do not know how to mix the values in aa to obtain the desired values. Is there a way to do it without for loop ? Thanks in advances, sincerely Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : (514) 343-6111 poste 1233 Fax : (514) 343-2293 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] ?glmm with correlation structure?
Hi folks, I am looking for the package that will allow me to do a generalized (poisson) linear mixed model with spatial correlation structure. If gls() in nlme does this, I don't understand how to implement different families. If glmmPQL() in MASS does this, I don't understand what correlation models it accepts. It does not appear to accept the same models as gls(), but I may be doing something wrong. Is there a mixed model package or function I am overlooking? Thanks, Hank Martin Henry H. Stevens 338 Pearson Hall Department of Botany Ecology Graduate Program Miami University Oxford, OH 45056 USA tel: 513-529-4206 fax: 513-529-4243 http://www.cas.muohio.edu/botany/bot/henry.html http://www.units.muohio.edu/ecology/ http://www.cas.muohio.edu/botany/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Multiple operations on list
You could do it with a double sapply like this: tr - function(x) sum(diag(x)) sapply(a, function(x1) sapply(a, function(x2) tr(x1%*%t(x1)%*%x2%*%t(x2)) / (tr(x1%*%t(x1))*tr(x2%*%t(x2) Date: Mon, 20 Sep 2004 13:24:49 -0400 From: Stephane DRAY [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject:[R] Multiple operations on list Hello, suppose I have a list with matrices: a=list(x1=matrix(rnorm(10),5,2),x2=matrix(rnorm(10),5,2),x3=matrix(rnorm(10),5,2)) I want to compute for all combination of xi and xj (x1,x2 x1,x3 and x2,x3) a value. This value is given for the pair x1,x2 by trace(x1%*%t(x1)%*%x2%*%t(x2)) / trace(x1%*%t(x1))*trace(x2%*%t(x2)) I know that product matrices t(xi)%*%xi can be obtained by: aa=lapply(a,crossprod) but I do not know how to mix the values in aa to obtain the desired values. Is there a way to do it without for loop ? Thanks in advances, sincerely Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : (514) 343-6111 poste 1233 Fax : (514) 343-2293 E-mail : [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Nnet: Returning the response
I don't think so. ?nnet does not mention any `y=' arugment for that purpose (and in fact `y' is used by the default method to specify the response for training, not as a flag for returning values). Andy From: Rui Dantas Hello list. Maybe this is a simple question but I can't find the answer anywhere. With lm I use the parameter y=TRUE to have the response returned in $y. Of course, namely because of NA's in the data frame, this might not include all the values in the original column. For example: data(airquality) length(airquality$Day) [1] 153 my.lm - lm(Day~.,data=airquality,y=TRUE) length(my.lm$y) [1] 111 When using nnet, is there a way to have the response returned in a similar way? Thanks in advance, Rui Dantas [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] ASA Stat. Computing and Stat. Graphics 2005 Student Paper competition
The Statistical Computing and Statistical Graphics Sections of the ASA are co-sponsoring a student paper competition on the topics of Statistical Computing and Statistical Graphics. Students are encouraged to submit a paper in one of these areas, which might be original methodological research, some novel computing or graphical application in statistics, or any other suitable contribution (for example, a software-related project). The selected winners will present their papers in a topic-contributed session at the 2005 Joint Statistical Meetings. The Sections will pay registration fees for the winners as well as a substantial allowance for transportation to the meetings and lodging. Enclosed below is the full text of the award announcement. More details can be found at the Stat. Computing Section website at http://www.statcomputing.org. Best Regards, --José Pinheiro Awards Chair ASA Statistical Computing Section Statistical Computing and Statistical Graphics Sections American Statistical Association Student Paper Competition 2005 The Statistical Computing and Statistical Graphics Sections of the ASA are co-sponsoring a student paper competition on the topics of Statistical Computing and Statistical Graphics. Students are encouraged to submit a paper in one of these areas, which might be original methodological research, some novel computing or graphical application in statistics, or any other suitable contribution (for example, a software-related project). The selected winners will present their papers in a topic-contributed session at the 2005 Joint Statistical Meetings. The Sections will pay registration fees for the winners as well as a substantial allowance for transportation to the meetings and lodging (which in most cases covers these expenses completely). Anyone who is a student (graduate or undergraduate) on or after September 1, 2004 is eligible to participate. An entry must include an abstract, a six page manuscript (including figures, tables and references), a C.V., and a letter from a faculty member familiar with the student's work. The applicant must be the first author of the paper. The faculty letter must include a verification of the applicant's student status and, in the case of joint authorship, should indicate what fraction of the contribution is attributable to the applicant. We prefer that electronic submissions of papers be in Postscript or PDF. All materials must be in English. All application materials MUST BE RECEIVED by 5:00 PM EST, Monday, December 20, 2004 at the address below. They will be reviewed by the Student Paper Competition Award committee of the Statistical Computing and Graphics Sections. The selection criteria used by the committee will include innovation and significance of the contribution. Award announcements will be made in late January, 2005. Additional important information on the competition can be accessed on the website of the Statistical Computing Section, www.statcomputing.org. A current pointer to the website is available from the ASA website at www.amstat.org. Inquiries and application materials should be emailed or mailed to: Student Paper Competition c/o Dr. José Pinheiro Biostatistics, Novartis Pharmaceuticals One Health Plaza, Room 419/2115 East Hanover, NJ 07936 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] installing on alpha
I am trying to install R-1.9.1 on an alpha (Tru64 unix) platform. I had no problem previously installing R-1.4.0, but cannot get the new installation to work. First I ran configure specifying an alternate installation directory: ./configure --prefix=/appl/R-1.9.1 then ran make (note that this is NOT gmake, which may make the difference). The error message I get is: Make: cannot open /share/make/vars.mk. Stop. The file share/make/vars.mk is there and readable, but share is a subdirectory of the main installation directory. Upon examining Makefile and associated files, I found a statement in Makeconf include $(top_srcdir)/share/make/vars.mk which I suspected was the problem -- perhaps the definition of top_srcdir not is carrying over from the Makefile that references Makeconf. (One reason I suspect this statement is that it is new since the version of R that I installed easily, as well as the early reference to this particular file.) I have tried a bunch of ways of modifying this statement, including an explicit path in this statement. I think that did work, but a similar problem then occurred at a later point that I haven't yet located. Has anyone gotten this installation to work on this platform? Alexa J. M. Sorant NIH/NHGRI 333 Cassell Drive Suite 2000 Baltimore, MD 21224 [EMAIL PROTECTED] (410) 550-7512 voice (410) 550-7513 fax __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] unable to load shared library /home/hpc1367/runs/taper/taper.so
I am trying to load a .so file and get the following error message: dyn.load(taper.so,local=F) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library /home/hpc1367/runs/taper/taper.so: ld.so.1: /usr/local/lib/R/bin/R.bin: fatal: relocation error: file /home/hpc1367/runs/taper/taper.so: symbol f90_init: referenced symbol not found also tried with default local=T and got same error. my makefile (used to produce the .so) is included below F90S = taper.f90 OBJS = taper.o LIBS = -lsocket -lnsl -lintl OPT = -fast MODS = -M/opt/NAG/fnsol04dbl/nag_mod_dir NAG = /opt/NAG/fnsol04dbl/libnagfl90.a STATNAG = /opt/NAG/flsol20dal/libnag.a taper.o : taper.f90 f95 -c -dalign $(OPT) $(MODS) taper.f90 taper.so: taper.f90 f95 -o taper.so -G -dalign $(OPT) $(MODS) taper.f90 taper.x : taper.o f95 -o taper.x -dalign $(OPT) $(MODS) $(LIBS) taper.o $(OBJS) $(NAG) please, help thank you very much stoyan __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Multiple operations on list
Hope this does what you want: library(gregmisc) cmb - combinations(length(aa), 2) apply(cmb, 1, function(i) sum(diag(aa[[i[1]]] %*% aa[[i[2]]])) / + (sum(diag(aa[[i[1]]])) * sum(diag(aa[[i[2]]] [1] 0.5363973 0.3336318 0.6593545 Andy From: Stephane DRAY Hello, suppose I have a list with matrices: a=list(x1=matrix(rnorm(10),5,2),x2=matrix(rnorm(10),5,2),x3=ma trix(rnorm(10),5,2)) I want to compute for all combination of xi and xj (x1,x2 x1,x3 and x2,x3) a value. This value is given for the pair x1,x2 by trace(x1%*%t(x1)%*%x2%*%t(x2)) / trace(x1%*%t(x1))*trace(x2%*%t(x2)) I know that product matrices t(xi)%*%xi can be obtained by: aa=lapply(a,crossprod) but I do not know how to mix the values in aa to obtain the desired values. Is there a way to do it without for loop ? Thanks in advances, sincerely Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : (514) 343-6111 poste 1233 Fax : (514) 343-2293 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] unable to download
Hi, I am currently trying to install packages from BioConductor to R. However, I received a error stating: unable to connect to 'www.bioconductor.org' on port 80 May I know what is wrong and how may I correct it?? If possible give a step by step procedures on how can I do it... Thanks alot, Amelia PS: Please reply ASAP as I am currently doing a Final Year Project on microarray analysis and already beyond scheduled. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] unable to download
I am currently trying to install packages from BioConductor to R. Then you probably want to post to the bioconductor mailing list instead of the R mailing list. However, I received a error stating: unable to connect to 'www.bioconductor.org' on port 80 May I know what is wrong and how There are lots of things that could be wrong, but since the site actually is currently active they are most likely to be related to your end. may I correct it?? If possible give a step by step procedures on how can I do it... Thanks alot, Amelia The first step is to see if install functionality (install.packages, download.packages, the pulldown if you're using Windows) work for non-bioconductor software. If not, then the second step is to see question 2.17 in the R for Windows FAQ. -J __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] unable to download
You may need to supply some additional information about your setup. What operating system and version are you using? How are you connecting to the internet? Can you download packages from other sources (such as CRAN)? Exactly what procedure are you using to download the packages? Have you tried to download individual packages and install locally? Asking for help ASAP because you are running late is not considerate to those willing to provide help, because most of us are already behind on our own projects. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of #AMELIA ANWAR# Sent: Monday, September 20, 2004 19:40 PM To: [EMAIL PROTECTED] Subject: [R] unable to download Hi, I am currently trying to install packages from BioConductor to R. However, I received a error stating: unable to connect to 'www.bioconductor.org' on port 80 May I know what is wrong and how may I correct it?? If possible give a step by step procedures on how can I do it... Thanks alot, Amelia PS: Please reply ASAP as I am currently doing a Final Year Project on microarray analysis and already beyond scheduled. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] how to take this experiment with R?
i want to generate 30 independent variables and 1 dependent variable,each has 50 draws from a unit normal distribution. then, searching for the independent variables that together would do the best job for fitting the denpendent variabe. my way to generate the data is. x-data.frame(matrix(rnorm(1550),c(50,31))) but is there more better way to do it? i want to use the followling is to search the model. model-step(lm(X1~X2+X3+X4.)) but i don't know the to express the formula with lm function.i think there is a way the express it efficently. i try ?lm .but on result be found. any help is welcome! __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] how to take this experiment with R?
You can express your model like this: lm(X1 ~., x) ?formula gives some help on formulas although the . notation above does not seem to be referred to there. Date: Tue, 21 Sep 2004 11:52:04 +0800 From: rongguiwong [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject:[R] how to take this experiment with R? i want to generate 30 independent variables and 1 dependent variable,each has 50 draws from a unit normal distribution. then, searching for the independent variables that together would do the best job for fitting the denpendent variabe. my way to generate the data is. x-data.frame(matrix(rnorm(1550),c(50,31))) but is there more better way to do it? i want to use the followling is to search the model. model-step(lm(X1~X2+X3+X4.)) but i don't know the to express the formula with lm function.i think there is a way the express it efficently. i try ?lm .but on result be found. any help is welcome! __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] can't understand R
hi. i really need help using this program. computer language is a foreign language to me, and thus, i cannot make heads nor tails of the user manuals from the website. i need to locate step-by-step examples of simple problems such as graph f(x)+g(x) and f(g(x)) for the domain 0x2 and graph 2H(x), H(x)+1, H(x+1) i do know how to define the functions, but that's it. is there any help you could provide me? i would appreciate some help asap. thank you very much erin leisz __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to take this experiment with R?
ÔÚ 2004Äê9ÔÂ21ÈÕ ÐÇÆÚ¶þ 12:10£¬Gabor Grothendieck дµÀ£º it works. but i come across anather problem. i just wnat to select 3 of the best indepent variables. but the reslut from step(lm(X1 ~., x)) is : Step: AIC= -37.64 X1 ~ X2 + X3 + X4 + X8 + X10 + X11 + X13 + X14 + X15 + X18 + X21 + X22 + X25 + X26 + X27 + X29 + X30 + X31 Df Sum of Sq RSS AIC none 11.014 -37.642 - X81 0.559 11.574 -37.165 - X27 1 0.867 11.881 -35.853 - X21 0.971 11.986 -35.416 - X18 1 0.978 11.992 -35.390 - X31 1 1.122 12.136 -34.793 - X10 1 1.400 12.414 -33.659 - X15 1 1.563 12.578 -33.005 - X29 1 1.608 12.622 -32.828 - X13 1 1.805 12.819 -32.055 - X30 1 1.880 12.894 -31.763 - X41 2.368 13.382 -29.906 - X14 1 2.495 13.509 -29.433 - X31 2.983 13.997 -27.659 - X22 1 2.999 14.013 -27.600 - X21 1 3.377 14.391 -26.271 - X25 1 4.323 15.338 -23.086 - X11 1 6.775 17.789 -15.672 - X26 1 7.232 18.246 -14.403 You can express your model like this: lm(X1 ~., x) ?formula gives some help on formulas although the . notation above does not seem to be referred to there. Date: Tue, 21 Sep 2004 11:52:04 +0800 From: rongguiwong [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: [R] how to take this experiment with R? i want to generate 30 independent variables and 1 dependent variable,each has 50 draws from a unit normal distribution. then, searching for the independent variables that together would do the best job for fitting the denpendent variabe. my way to generate the data is. x-data.frame(matrix(rnorm(1550),c(50,31))) but is there more better way to do it? i want to use the followling is to search the model. model-step(lm(X1~X2+X3+X4.)) but i don't know the to express the formula with lm function.i think there is a way the express it efficently. i try ?lm .but on result be found. any help is welcome! ___ No banners. No pop-ups. No kidding. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to take this experiment with R?
Suppose you just wanted variables 2,4 and 7 (which are in columns 3, 5 and 8, respectively). Then you could do this: lm(X1 ~ X2 + X4 + X7, x) or lm(X1 ~., x[,c(2,4,7)+1]) Date: Tue, 21 Sep 2004 12:27:38 +0800 From: rongguiwong [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject:Re: [R] how to take this experiment with R? ÔÚ 2004Äê9ÔÂ21ÈÕ ÐÇÆÚ¶þ 12:10£¬Gabor Grothendieck дµÀ£º it works. but i come across anather problem. i just wnat to select 3 of the best indepent variables. but the reslut from step(lm(X1 ~., x)) is : Step: AIC= -37.64 X1 ~ X2 + X3 + X4 + X8 + X10 + X11 + X13 + X14 + X15 + X18 + X21 + X22 + X25 + X26 + X27 + X29 + X30 + X31 Df Sum of Sq RSS AIC none 11.014 -37.642 - X8 1 0.559 11.574 -37.165 - X27 1 0.867 11.881 -35.853 - X2 1 0.971 11.986 -35.416 - X18 1 0.978 11.992 -35.390 - X31 1 1.122 12.136 -34.793 - X10 1 1.400 12.414 -33.659 - X15 1 1.563 12.578 -33.005 - X29 1 1.608 12.622 -32.828 - X13 1 1.805 12.819 -32.055 - X30 1 1.880 12.894 -31.763 - X4 1 2.368 13.382 -29.906 - X14 1 2.495 13.509 -29.433 - X3 1 2.983 13.997 -27.659 - X22 1 2.999 14.013 -27.600 - X21 1 3.377 14.391 -26.271 - X25 1 4.323 15.338 -23.086 - X11 1 6.775 17.789 -15.672 - X26 1 7.232 18.246 -14.403 You can express your model like this: lm(X1 ~., x) ?formula gives some help on formulas although the . notation above does not seem to be referred to there. Date: Tue, 21 Sep 2004 11:52:04 +0800 From: rongguiwong [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: [R] how to take this experiment with R? i want to generate 30 independent variables and 1 dependent variable,each has 50 draws from a unit normal distribution. then, searching for the independent variables that together would do the best job for fitting the denpendent variabe. my way to generate the data is. x-data.frame(matrix(rnorm(1550),c(50,31))) but is there more better way to do it? i want to use the followling is to search the model. model-step(lm(X1~X2+X3+X4.)) but i don't know the to express the formula with lm function.i think there is a way the express it efficently. i try ?lm .but on result be found. any help is welcome! __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] how to take this experiment with R?
My mistake, you can't use the structure I proposed with lm() in combination with step(). If what was suggested earlier by Gabor was not what you wanted, and instead you want the 'best' three variable model, then it may be easier to use the leaps package. library(leaps) x - data.frame(matrix(rnorm(1550),c(50,31))) model - regsubsets(y=x[,1], x=x[,2:31]) m1-summary(model, matrix=TRUE, matrix.logical=TRUE) apply(m1$outmat, 1, which)[3] $3 ( 1 ) X10 X14 X15 9 13 14 lm.fit(x=as.matrix(x[,as.vector(unlist(apply(m1$outmat, 1, which)[3])+1)]), y=x[,1]) $coefficients X10X14X15 -0.2694923 -0.4055546 -0.2692063 --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Gabor Grothendieck Sent: Monday, September 20, 2004 21:57 PM To: [EMAIL PROTECTED]; [EMAIL PROTECTED] Subject: Re: [R] how to take this experiment with R? Suppose you just wanted variables 2,4 and 7 (which are in columns 3, 5 and 8, respectively). Then you could do this: lm(X1 ~ X2 + X4 + X7, x) or lm(X1 ~., x[,c(2,4,7)+1]) Date: Tue, 21 Sep 2004 12:27:38 +0800 From: rongguiwong [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject:Re: [R] how to take this experiment with R? ÔÚ 2004Äê9ÔÂ21ÈÕ ÐÇÆÚ¶þ 12:10£¬Gabor Grothendieck дµÀ£º it works. but i come across anather problem. i just wnat to select 3 of the best indepent variables. but the reslut from step(lm(X1 ~., x)) is : Step: AIC= -37.64 X1 ~ X2 + X3 + X4 + X8 + X10 + X11 + X13 + X14 + X15 + X18 + X21 + X22 + X25 + X26 + X27 + X29 + X30 + X31 Df Sum of Sq RSS AIC none 11.014 -37.642 - X8 1 0.559 11.574 -37.165 - X27 1 0.867 11.881 -35.853 - X2 1 0.971 11.986 -35.416 - X18 1 0.978 11.992 -35.390 - X31 1 1.122 12.136 -34.793 - X10 1 1.400 12.414 -33.659 - X15 1 1.563 12.578 -33.005 - X29 1 1.608 12.622 -32.828 - X13 1 1.805 12.819 -32.055 - X30 1 1.880 12.894 -31.763 - X4 1 2.368 13.382 -29.906 - X14 1 2.495 13.509 -29.433 - X3 1 2.983 13.997 -27.659 - X22 1 2.999 14.013 -27.600 - X21 1 3.377 14.391 -26.271 - X25 1 4.323 15.338 -23.086 - X11 1 6.775 17.789 -15.672 - X26 1 7.232 18.246 -14.403 You can express your model like this: lm(X1 ~., x) ?formula gives some help on formulas although the . notation above does not seem to be referred to there. Date: Tue, 21 Sep 2004 11:52:04 +0800 From: rongguiwong [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: [R] how to take this experiment with R? i want to generate 30 independent variables and 1 dependent variable,each has 50 draws from a unit normal distribution. then, searching for the independent variables that together would do the best job for fitting the denpendent variabe. my way to generate the data is. x-data.frame(matrix(rnorm(1550),c(50,31))) but is there more better way to do it? i want to use the followling is to search the model. model-step(lm(X1~X2+X3+X4.)) but i don't know the to express the formula with lm function.i think there is a way the express it efficently. i try ?lm .but on result be found. any help is welcome! __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
