Re: [R] Building packages in R - 'private' functions
On Wed, 2006-06-07 at 01:14 -0400, Dan Rabosky wrote:
Hello.
I am creating an R package that I'd like to submit to CRAN (OS Windows
XP). How do I distinguish among 'public' functions, e.g., those that are
intended to be called by users of the package and for which I am providing
documentation examples, and 'private' functions, which are used
internally by the 'public' functions, but for which I do not wish to
provide documentation? The private functions are all coded in R (nothing
in C or Fortran) and are essential to the operation of several public
functions.
Hi Dan,
The answer is in the Writing R Extensions manual.
You could do either:
1) Put the code for your private functions in a file names
internal.R. You then provide a simple file named
package-name-internal.Rd which lists in individual \alias{}
markup the names of the private functions, eg;
\name{mypackage-internal}
\alias{foo1}
\alias{foo2}
\alias{foo3}
\alias{foo4}
\title{Internal mypackage Functions}
\description{
Internal mypackage functions
}
\details{
These are not to be called by the user.
}
\keyword{ internal }
But even here, you aren't documenting the internal functions,
just working round the package checks.
2) Place your package in a namespace, which is documented fully
in Writing R Extensions.
Not sure what the best advice is - I'd guess that for all but the
simplest packages, namespaces are the preferred way, but the internal.R
way works just fine also.
By the way, in future, questions of this nature are best asked on the
R-Devel list, not here.
HTH,
Gavin
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Re: [R] knn - 10 fold cross validation
10-fold cross-validation is easily done at R level: there is generic code
in MASS, the book knn was written to support.
knn and lda have options for leave-one-out cross-validation just because
there are compuiationally efficient algorithms for those cases.
On Tue, 6 Jun 2006, Liaw, Andy wrote:
You might want to check out the function tune.knn() in the e1071 package.
Andy
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From: [EMAIL PROTECTED] on behalf of Tim Smith
Sent: Tue 6/6/2006 8:29 PM
To: r-help@stat.math.ethz.ch
Subject: [R] knn - 10 fold cross validation [Broadcast]
Hi,
I was trying to get the optimal 'k' for the knn. To do this I was using
the following function :
knn.cvk - function(datmat, cl, k = 2:9) {
datmatT - (datmat)
cv.err - cl.pred - c()
for (i in k) {
newpre - as.vector(knn.cv(datmatT, cl, k = i))
cl.pred - cbind(cl.pred, newpre)
cv.err - c(cv.err, sum(cl != newpre))
}
k0 - k[which.min(cv.err)]
print(k0)
return(k0)
}
However, the knn.cv function does a 'leave one out' cross validation. I
checked the documentation to see if I could change this, but it appears that
I cannot. Since I have large datasets, I would like to do 10 fold cross
validation, instead of the 'leave one out'.
Is there some other function that I can use that will give me a 10 fold
cross validation for KNN ?
many thanks.
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Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
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Re: [R] build R with Visual Studio
On Tue, 6 Jun 2006, Jennifer Lai wrote: Hi, Has anyone had success in building R source with Visual Studio? I followed the instructions in README.packages, but failed on the very first step, where it's looking for R.dll. I looked through R source and couldn't find the file. Can someone point me to where this file is located or generated? Thanks! R.dll is the main file generated, and the first step is to build Rpwd.exe. Do you really mean the R source? People have built R for Windows with Visual Studio (using their own projects/makefiles and other tools to generate .def files) but it did not work correctly. It seems that the IEC60559 (aka IEEE754) compliance of VC++ was not adequate -- as I recall it thought -Inf 3. This isn't the list for such programming questions: R-devel would be more appropriate. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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] vague errors on R CMD check for very minimal S4-style package
This is an S4-using package but missing a dependence on 'methods'. To run R CMD check the package has to load under minimal conditions, e.g. R_DEFAULT_PACKAGES=NULL R ... library(foo) should work. 'methods' is quite expensive to load, and so is only used in checking if explicitly requested. On Tue, 6 Jun 2006, Seth Falcon wrote: Roels, Steven [EMAIL PROTECTED] writes: Hello, I have a very minimal package simplepkg (DESCRIPTION, NAMESPACE, and R) with S4 classes/methods (defines a class foo and a show method for that class - both the class and show method are exported). I can seemingly install the package, then load and use it: Error: package/namespace load failed for 'simplepkg' Call sequence: 2: stop(gettextf(package/namespace load failed for '%s', libraryPkgName(package)), call. = FALSE, domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Execution halted Here are the file contents: --- sun890% cat DESCRIPTION Package: simplepkg Type: Package Title: Does stuff Version: 0.1-1 Date: 2006-06-06 Author: Me Maintainer: Also Me [EMAIL PROTECTED] Description: Does interesting stuff License: GPL Try adding LazyLoad: yes to DESCRIPTION (or SaveImage: yes). And Depends: methods Package stats4 is provided in part as an example of a small S4-using package for people to copy. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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] x y averaging
It's confusing to have time values that are different but `match', so first you want to reduce your times to hh:mm (e.g. with substr). Then you can cbind() the data frames, and use tapply() to do the averaging. E.g. d1 - read.table(foo1) d2 - read.table(foo2) d - cbind(d1, d2) d$time - factor(substr(as.character(d$x), 1, 5)) tapply(d$y, d$time, mean) 14:56 14:62 14:68 15:59 16:05 16:11 16:17 16:23 16:33 16:39 0.3250 0.1110 0.2140 0.2575 0.2545 0.3040 0.2550 0.2630 0.2630 0.3000 There are other ways, e.g. aggregate(d[y], list(d$time), mean) or via ave(). On Tue, 6 Jun 2006, Randy Zelick wrote: Hello, I am trying to average a number of data sets where the x vector contains times and the Y data are instrument readings. The vectors all have different numbers of values, but many X time values match. For example: A fragment of the first data set: x vectvalue 14:56:10 0.325 14:62:11 0.111 14:68:11 0.214 . . . this can go on for 100's of values, spaced by 6 minutes, but there can be gaps too, like: 16:05:18 0.245 16:11:09 0.266 16:17:05 0.271 16:33:00 0.304 16:39:05 0.300 A fragment of the second data set: 15:59:08 0.255 16:05:44 0.281 16:11:25 0.249 16:17:39 0.238 16:23:51 0.288 ...and the result I am looking for is a new vector that looks like this: 14:56:10 0.325 14:62:11 0.111 14:68:11 0.214 . . . 15:59:08 0.255 16:05:18 0.2630 * matches, so average 16:11:09 0.2575 * matches, so average 16:17:05 0.2545 * matches, so average 16:33:00 0.304 16:39:05 0.300 The times values in the new X vector are properly interleaved taking data across the datasets, but when there is a match the Y values are averaged. Note that the seconds don't matter. I am using R Version 2.2.1 on a PC Thanks for thinking about it, =Randy= R. Zelick email: [EMAIL PROTECTED] Department of Biology voice: 503-725-3086 Portland State University fax: 503-725-3888 mailing: P.O. Box 751 Portland, OR 97207 shipping: 1719 SW 10th Ave, Room 246 Portland, OR 97201 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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] Building packages in R - 'private' functions
Dan Rabosky wrote: Hello. I am creating an R package that I'd like to submit to CRAN (OS Windows XP). How do I distinguish among 'public' functions, e.g., those that are intended to be called by users of the package and for which I am providing documentation examples, and 'private' functions, which are used internally by the 'public' functions, but for which I do not wish to provide documentation? The private functions are all coded in R (nothing in C or Fortran) and are essential to the operation of several public functions. I have been unable to find any documentation on this in the 'writing r extensions' manual', on previous posts to R-help, or through any other source. One possibility is to include the source code for the 'private' functions within the public functions. However, since multiple public functions utilize the same core set of 'private' functions, this seems unwieldy and redundant at best. If I simply include the source for the 'private' functions in the R directory (without corresponding *.Rd and *.html documentation in /man), then check the package with R CMD check', it does appear to process the private functions (and successfully builds with R CMD build). However, I do receive a warning for including undocumented code objects. Is this the recommended approach and/or is there a better way to do this? One potential problem with this approach is that - should an error occur within a private function, it may be very difficult for the user to decipher the nature of the problem. Any suggestions will be greatly appreciated. ~Dan Rabosky Dan Rabosky Department of Ecology and Evolutionary Biology 237 Corson Hall Cornell University Ithaca, NY14853-2701 USA [EMAIL PROTECTED] web: http://www.birds.cornell.edu/evb/Graduates_Dan.htm __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html it's in the 'extensions' manual, including an example I believe: 1. create a file `NAMESPACE' in the package top level dir (beside `R' and `man') containing the single line exportPattern(^[^\\.]) 2. name all private functions with a leading `.' (more precisely: all functions starting with a `.' are private in this setting). of course, you can modify the pattern to suit another naming convention. joerg __ R-help@stat.math.ethz.ch 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] Building packages in R - 'private' functions
1. If you have time to change internal functions naming, you can rename internal functions by putting a leading '.'. Even without namespace, I have noticed there is no check for corresponding docs for such functions. 2. If you don't want to rename all internal functions, the best way is writing an 'internals.Rd' file with an alias for each internal function (documented in 'writing R extensions'). 3.Finally, you can add a NAMESPACE (see writing R extensions). However, if you use S3/S4 classes, this can be much more tedious to do. I think the no. 2 to be the fastest/safer way. Antonio. 2006/6/7, Dan Rabosky [EMAIL PROTECTED]: Hello. I am creating an R package that I'd like to submit to CRAN (OS Windows XP). How do I distinguish among 'public' functions, e.g., those that are intended to be called by users of the package and for which I am providing documentation examples, and 'private' functions, which are used internally by the 'public' functions, but for which I do not wish to provide documentation? The private functions are all coded in R (nothing in C or Fortran) and are essential to the operation of several public functions. I have been unable to find any documentation on this in the 'writing r extensions' manual', on previous posts to R-help, or through any other source. One possibility is to include the source code for the 'private' functions within the public functions. However, since multiple public functions utilize the same core set of 'private' functions, this seems unwieldy and redundant at best. If I simply include the source for the 'private' functions in the R directory (without corresponding *.Rd and *.html documentation in /man), then check the package with R CMD check', it does appear to process the private functions (and successfully builds with R CMD build). However, I do receive a warning for including undocumented code objects. Is this the recommended approach and/or is there a better way to do this? One potential problem with this approach is that - should an error occur within a private function, it may be very difficult for the user to decipher the nature of the problem. Any suggestions will be greatly appreciated. ~Dan Rabosky Dan Rabosky Department of Ecology and Evolutionary Biology 237 Corson Hall Cornell University Ithaca, NY14853-2701 USA [EMAIL PROTECTED] web: http://www.birds.cornell.edu/evb/Graduates_Dan.htm __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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 create list of objects?
Thanks everybody - it's working Rainer Dimitris Rizopoulos wrote: try something like: lapply(f, summary) sapply(f, function(x) AIC(logLik(x))) Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Rainer M Krug [EMAIL PROTECTED] To: R help list r-help@stat.math.ethz.ch Sent: Tuesday, June 06, 2006 4:38 PM Subject: [R] How to create list of objects? Hi I am doing several mle and want to store them in a list (or whatever is the right construct) to be able to analyse them later. at the moment I am doing: f - list() f$IP - mle(...) f$NE - mle(...) but when I say: summary(f) I get: Length Class Mode IP 0 mle list NE 0 mle list I don't get the output I would have, i.e. the one from summary(f$IP) summary(f$IP) Maximum likelihood estimation Call: mle(minuslogl = IPNeglogPoisL, method = L-BFGS-B, fixed = list(), control = list(maxit = 1e+08, factr = 1e-20)) Coefficients: Estimate Std. Error a 1242.0185506 44.92341097 b0.8802538 0.01685811 -2 log L: 145.3509 What I want to do is something like: AICs - AIC(logLik(f)) and then have all the AICs in the vector AICs. It must be possible or is this again a namespace issue? Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] making matrix monotonous
Spencer Graves a écrit : I agree it would be great to sort the variables in a correlation matrix to make it easier to read and see patterns. I don't know any functions for doing that. If it were my problem, I might order the variables by their first principal component. There may also be some cluster analysis way to do that, but I don't know it well enough to say. Hope this helps. Spencer Graves Thanks for your answer Spencer. Here is a first result of a very simple and naive approach. http://7d4.com/r/ Of course, there is no assumption the sorting is optimal, but on this little example it helps the matrix being more readable. Vincent __ R-help@stat.math.ethz.ch 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] smoothing plot(x, type ='l')
Hi All, I am using plot(x, type = 'l') for some plotting, but I would like rounded edges rather than jagged edges in the plot (purely for aestetic reasons). How could I achieve that? Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@stat.math.ethz.ch 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] smoothing plot(x, type ='l')
probably you want to use the `lend' argument of ?par(); 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/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Federico Calboli [EMAIL PROTECTED] To: r-help r-help@stat.math.ethz.ch Sent: Wednesday, June 07, 2006 12:40 PM Subject: [R] smoothing plot(x, type ='l') Hi All, I am using plot(x, type = 'l') for some plotting, but I would like rounded edges rather than jagged edges in the plot (purely for aestetic reasons). How could I achieve that? Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@stat.math.ethz.ch 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] smoothing plot(x, type ='l')
Dimitris Rizopoulos wrote: probably you want to use the `lend' argument of ?par(); I hope it helps. Does not seem to work in my case. F -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@stat.math.ethz.ch 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] making matrix monotonous
Le 07.06.2006 11:20, [EMAIL PROTECTED] a écrit :
Spencer Graves a écrit :
I agree it would be great to sort the variables in a correlation
matrix to make it easier to read and see patterns. I don't know any
functions for doing that. If it were my problem, I might order the
variables by their first principal component. There may also be some
cluster analysis way to do that, but I don't know it well enough to say.
Hope this helps.
Spencer Graves
Thanks for your answer Spencer.
Here is a first result of a very simple and naive approach.
http://7d4.com/r/
Of course, there is no assumption the sorting is optimal,
but on this little example it helps the matrix being
more readable.
Vincent
Hello Vincent,
Ahhh, the double for loop, the semicolon, the return call. you still
believe in R code looking like C don't you.
Try this one :
matrix.sort2 - function(M, fun = function(m) colSums(abs(m)) ){
M[or - order(fun(M) , decreasing=T), or]
}
Romain
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Re: [R] smoothing plot(x, type ='l')
On Wed, 7 Jun 2006, Federico Calboli wrote: Hi All, I am using plot(x, type = 'l') for some plotting, but I would like rounded edges rather than jagged edges in the plot (purely for aestetic reasons). How could I achieve that? It I understand you aright, that is done by par(lend) but the default is round. So maybe your graphics device (unstated) on your OS (unstated) does not support this. We need more details, and preferably a simple reproducible example. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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] making matrix monotonous
On 6/7/06, Romain Francois [EMAIL PROTECTED] wrote:
Le 07.06.2006 11:20, [EMAIL PROTECTED] a écrit :
Spencer Graves a écrit :
I agree it would be great to sort the variables in a correlation
matrix to make it easier to read and see patterns. I don't know any
functions for doing that. If it were my problem, I might order the
variables by their first principal component. There may also be some
cluster analysis way to do that, but I don't know it well enough to say.
Hope this helps.
Spencer Graves
Thanks for your answer Spencer.
Here is a first result of a very simple and naive approach.
http://7d4.com/r/
Of course, there is no assumption the sorting is optimal,
but on this little example it helps the matrix being
more readable.
Vincent
Hello Vincent,
Ahhh, the double for loop, the semicolon, the return call. you still
believe in R code looking like C don't you.
Try this one :
matrix.sort2 - function(M, fun = function(m) colSums(abs(m)) ){
M[or - order(fun(M) , decreasing=T), or]
}
Even if this works I don't think its guaranteed since one cannot
be sure the first argument, or-..., is evaluated before the second, or.
Also use TRUE in case there is a T variable in workspace:
matrix.sort3 - function(M, fun = function(m) colSums(abs(m)) ) {
or - order(fun(M), decreasing = TRUE)
M[or, or]
}
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Re: [R] smoothing plot(x, type ='l')
Prof Brian Ripley wrote: It I understand you aright, that is done by par(lend) but the default is round. So maybe your graphics device (unstated) on your OS (unstated) does not support this. graphics device = X11 (xserver-xorg) OS = Debian GNU/Linux, Kernel 2.4.27-2-686-smp We need more details, and preferably a simple reproducible example. s.off.dist [1] 27 26 15 7 32 50 31 19 1 11 8 4 4 5 11 28 4 32 5 39 15 32 3 3 4 [26] 1 2 2 22 1 23 4 2 8 40 14 42 3 1 4 3 4 4 6 2 29 4 8 5 9 [51] 37 2 1 13 13 35 6 9 2 5 31 10 7 1 4 22 3 23 4 10 8 57 1 6 1 [76] 1 4 10 16 3 12 3 10 8 10 11 16 19 5 5 9 9 3 4 1 8 3 12 3 65 [101] 1 7 21 7 2 4 35 15 6 2 6 4 1 14 4 10 24 3 4 3 2 4 11 4 7 [126] 13 7 1 6 2 4 16 3 13 66 10 4 7 2 17 6 4 3 5 6 8 3 3 10 19 [151] 7 3 17 6 6 6 2 9 5 4 4 18 2 3 17 43 22 12 1 3 1 9 3 5 1 [176] 2 5 36 12 23 1 8 10 6 7 19 5 13 2 5 3 9 3 1 12 4 5 3 6 3 [201] 5 1 1 16 6 12 1 5 4 2 2 4 9 9 3 11 7 4 8 14 5 17 3 3 15 [226] 2 4 2 11 13 1 19 7 4 3 20 2 8 5 2 3 4 2 5 5 10 1 9 10 8 [251] 4 4 2 1 3 5 3 1 4 5 13 12 6 5 4 3 10 5 4 1 plot(hist(s.off.dist, breaks = 'fd')$counts ~ hist(s.off.dist, breaks = 'fd')$m, type = 'l') I want the edges to look round, if at all possible. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@stat.math.ethz.ch 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] smoothing plot(x, type ='l')
Federico Calboli wrote: Hi All, I am using plot(x, type = 'l') for some plotting, but I would like rounded edges rather than jagged edges in the plot (purely for aestetic reasons). How could I achieve that? Perhaps you want something like: x-rnorm(50) plot(spline(1:50,x),type=l) Jim __ R-help@stat.math.ethz.ch 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] Help with selecting data from irregular time series {its} objects
If I understood correctly in irregular time series (its) objects, values are indexed by time stamps in POSIX format. But if I try to select the value of my time series corresponding to specific time stamp in the following way: x - its object i - as.POSIXct(2006-05-19 15:30:00) x[i,] or x[i] or x[i,1] I get the error message: subscript out of bounds. If I use integers: x[1,1] it is ok I get the first element of time series. Is there a way to select elements by their corresponding dates? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Edit function
Dear all R users, I have a query on Edit function. Suppose I have a data frame named data. I can use EDIT function to see the materials contained in data, by using the command: edit(data) But when I close the window then again the materials contained in data is displayed in the command window. But I do not want to see these materials again. Can anyone give me any idea on how to do this? Thanks and regards, stat Send instant messages to your online friends http://in.messenger.yahoo.com Stay connected with your friends even when away from PC. Link: http://in.mobile.yahoo.com/new/messenger/ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] making matrix monotonous
[Presuming you mean monotone; many matrices are already monotonous.]
General solutions to this problem are discussed in
@ARTICLE{Friendly:02:corrgram,
author = {M. Friendly},
title = {Corrgrams: Exploratory displays for correlation matrices},
journal = {The American Statistician},
year = {2002},
volume = {56},
pages = {316--324},
number = {4},
url = {http://www.math.yorku.ca/SCS/Papers/corrgram.pdf},
}
and implemented (in SAS)
http://www.math.yorku.ca/SCS/sasmac/corrgram.html
Rather than just the first principal component, it is usually better
to order the variables by the angles between the first 2 PC,
corresponding to their order around a 2D biplot, using
sort(atan(V2/V1))
-Michael
[EMAIL PROTECTED] wrote:
Spencer Graves a écrit :
I agree it would be great to sort the variables in a correlation
matrix to make it easier to read and see patterns. I don't know any
functions for doing that. If it were my problem, I might order the
variables by their first principal component. There may also be some
cluster analysis way to do that, but I don't know it well enough to say.
Hope this helps.
Spencer Graves
Thanks for your answer Spencer.
Here is a first result of a very simple and naive approach.
http://7d4.com/r/
Of course, there is no assumption the sorting is optimal,
but on this little example it helps the matrix being
more readable.
Vincent
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--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT M3J 1P3 CANADA
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Re: [R] Help with selecting data from irregular time series {its} objects
See: ?itsSubset On 6/7/06, Ivan Kalafatic [EMAIL PROTECTED] wrote: If I understood correctly in irregular time series (its) objects, values are indexed by time stamps in POSIX format. But if I try to select the value of my time series corresponding to specific time stamp in the following way: x - its object i - as.POSIXct(2006-05-19 15:30:00) x[i,] or x[i] or x[i,1] I get the error message: subscript out of bounds. If I use integers: x[1,1] it is ok I get the first element of time series. Is there a way to select elements by their corresponding dates? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Edit function
On Wed, 7 Jun 2006, stat stat wrote: Dear all R users, I have a query on Edit function. Suppose I have a data frame named data. I can use EDIT function to see the materials contained in data, by using the command: edit(data) But when I close the window then again the materials contained in data is displayed in the command window. But I do not want to see these materials again. Can anyone give me any idea on how to do this? ?invisible Thanks and regards, stat -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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] Help needed using lattice for area plots lpolygon, xyplot.
I am trying to learn how to use the graphics from the lattice package (
and am very new to R).
I am trying to replicate the example plot referenced below, by using the
lattice xyplot lpolygon to create panels. I get what appears to be the
correct shape of the filled region, but cannot get the position to overlay
properly. I have attempted with various settings of position. ( i.e.
position = c(0,0,1,1) etc settings as well. I am not understanding
something about the positioning panels. I am missing some subtle
difference between polygon lpolygon, or am missing something about panel
overlays /or panel postions.
#http://addictedtor.free.fr/graphiques/graphcode.php?graph=7.
par(bg=white)
n - 100
set.seed(43214) #just so we have the same exact graph
x - c(0,cumsum(rnorm(n)))
y - c(0,cumsum(rnorm(n)))
xx - c(0:n, n:0)
yy - c(x, rev(y))
plot(xx, yy, type=n, xlab=Time, ylab=Distance)
polygon(xx, yy, col=gray)
title(Distance Between Brownian Motions)
# using lattice.
p1 - xyplot( yy~xx,type='l');
p2 - lpolygon(xx,yy,col='blue');
print(p1,position=c(0,0,1,1), more=TRUE);
print(p2,position=c(0,0,1,1));
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[R] how to read hdf files under R?
Hi! I am trying to install in my R environment the rhdf5 package and library but it seems to have vanished from either the CRAN or BioConductors sites. Can you tell me where it would be possible to find it or any R library (or function) able to read hdf files? Sincerely, Nicolas Degallier UMR 7159 / IRD UR182 Laboratoire d'Océanographie et du Climat, Expérimentation et Approches Numériques (LOCEAN) Tour 45-55, 4e ét., case 100, 4 place Jussieu 75252 Paris Cedex 5 France tél: (33) 01 44 27 51 57 fax: (33) 01 44 27 38 05 E-mail: [EMAIL PROTECTED] Publications (anonymous ftp): ftp://ftp.lodyc.jussieu.fr/LOCEAN/ndelod __ R-help@stat.math.ethz.ch 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] x y averaging thanks
I have three completely different(!) but workable solutions. Thanks much for your help. =Randy= R. Zelick email: [EMAIL PROTECTED] Department of Biology voice: 503-725-3086 Portland State University fax: 503-725-3888 mailing: P.O. Box 751 Portland, OR 97207 shipping: 1719 SW 10th Ave, Room 246 Portland, OR 97201 __ R-help@stat.math.ethz.ch 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 read hdf files under R?
On Wed, 7 Jun 2006, Nicolas Degallier wrote: I am trying to install in my R environment the rhdf5 package and library but it seems to have vanished from either the CRAN or BioConductors sites. Can you tell me where it would be possible to find it or any R library (or function) able to read hdf files? How about the hdf5 package on CRAN? Works for me. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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] Fw: Help needed using lattice for area plots lpolygon, xyplot.
I am trying to learn how to use the graphics from the lattice package (
and am very new to R).
I am trying to replicate the example plot referenced below, by using the
lattice xyplot lpolygon to create panels. I get what appears to be the
correct shape of the filled region, but cannot get the position to overlay
properly. I have attempted with various settings of position. ( i.e.
position = c(0,0,1,1) etc settings as well. I am not understanding
something about the positioning panels. I am missing some subtle
difference between polygon lpolygon, or am missing something about panel
overlays /or panel postions.
#http://addictedtor.free.fr/graphiques/graphcode.php?graph=7.
par(bg=white)
n - 100
set.seed(43214) #just so we have the same exact graph
x - c(0,cumsum(rnorm(n)))
y - c(0,cumsum(rnorm(n)))
xx - c(0:n, n:0)
yy - c(x, rev(y))
plot(xx, yy, type=n, xlab=Time, ylab=Distance)
polygon(xx, yy, col=gray)
title(Distance Between Brownian Motions)
# using lattice.
p1 - xyplot( yy~xx,type='l');
p2 - lpolygon(xx,yy,col='blue');
print(p1,position=c(0,0,1,1), more=TRUE);
print(p2,position=c(0,0,1,1));
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Re: [R] Edit function
fix(data) will invoke edit(data) and store changes you make in data without displaying anything. stat stat schrieb: Dear all R users, I have a query on Edit function. Suppose I have a data frame named data. I can use EDIT function to see the materials contained in data, by using the command: edit(data) But when I close the window then again the materials contained in data is displayed in the command window. But I do not want to see these materials again. Can anyone give me any idea on how to do this? Thanks and regards, stat Send instant messages to your online friends http://in.messenger.yahoo.com Stay connected with your friends even when away from PC. Link: http://in.mobile.yahoo.com/new/messenger/ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Building packages in R - 'private' functions
Antonio, Fabio Di Narzo [EMAIL PROTECTED] writes: 1. If you have time to change internal functions naming, you can rename internal functions by putting a leading '.'. Even without namespace, I have noticed there is no check for corresponding docs for such functions. 2. If you don't want to rename all internal functions, the best way is writing an 'internals.Rd' file with an alias for each internal function (documented in 'writing R extensions'). 3.Finally, you can add a NAMESPACE (see writing R extensions). However, if you use S3/S4 classes, this can be much more tedious to do. I think the no. 2 to be the fastest/safer way. I think adding a NAMESPACE file is the best solution and I don't think that the process needs to be particularly tedious. Having a naming convention for private functions is fine and you can still do that with a NAMESPACE. Non-exported functions do not get checked for documentation, so there is no need for an internals.Rd (of course, it doesn't hurt to give yourself some documentation for when you return to the project 3 months later :-) Besides hiding your private functions, a NAMESPACE protects you from users or other packages redefining functions that you rely on. As an extreme example, if a user redefined length(), many packages without namespaces would break. + seth __ R-help@stat.math.ethz.ch 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] Edit function
If you want to change the data,_fix_ will be a good option.But if you just want to browse the data ,then invisible(edit(data)) is better one. I remember this question showed up some time ago. 2006/6/7, Ulrich Keller [EMAIL PROTECTED]: fix(data) will invoke edit(data) and store changes you make in data without displaying anything. stat stat schrieb: Dear all R users, I have a query on Edit function. Suppose I have a data frame named data. I can use EDIT function to see the materials contained in data, by using the command: edit(data) But when I close the window then again the materials contained in data is displayed in the command window. But I do not want to see these materials again. Can anyone give me any idea on how to do this? Thanks and regards, stat Send instant messages to your online friends http://in.messenger.yahoo.com Stay connected with your friends even when away from PC. Link: http://in.mobile.yahoo.com/new/messenger/ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- ronggui huang Deparment of Sociology Fudan University __ R-help@stat.math.ethz.ch 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] Help with sample function
I have generated some some survival times and censoring indicators. Thus I have an ordered pair for each observation. How do I sample these ordered paris? I only know how to sample from a vector? I would appreciate any help I could get. Thanks Matt __ R-help@stat.math.ethz.ch 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] Help with sample function
try something like: surv.data - data.frame(times = rexp(100, 1/10), events = rbinom(100, 1, 0.7)) surv.data[sample(nrow(surv.data), replace = TRUE), ] 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/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Matthew Austin [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Sent: Wednesday, June 07, 2006 3:57 PM Subject: [R] Help with sample function I have generated some some survival times and censoring indicators. Thus I have an ordered pair for each observation. How do I sample these ordered paris? I only know how to sample from a vector? I would appreciate any help I could get. Thanks Matt __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@stat.math.ethz.ch 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] Help with sample function
I couldn't help but respond to this one, it's not often I see my own name.
Using data from the survival library:
library(survival)
lung[1:10, c('time', 'status')]
Surv(lung$time, lung$status)[1:10]
--Matt
Matt Austin
Statistician
Amgen, Inc
800 9AMGEN9 x77431
805-447-7431
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Matthew Austin
Sent: Wednesday, June 07, 2006 6:57 AM
To: r-help@stat.math.ethz.ch
Subject: [R] Help with sample function
I have generated some some survival times and censoring indicators.
Thus I have an ordered pair for each observation. How do I sample these
ordered paris? I only know how to sample from a vector? I would
appreciate any help I could get.
Thanks
Matt
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Re: [R] error bars in lattice xyplot *with groups*
Hi Mike,
If you're not committed to using a panel function, another option is to
use the function lineplot.CI, available in the package sciplot at
http://mutualism.williams.edu/sciplot
E.g.
# Define and generate variables in long format
range - vector()
voice - vector()
string - strsplit(as.character(singer$voice.part), )
for(i in 1:dim(singer)[1]) {
range[i] - string[[i]][1]
voice[i] - string[[i]][2]
}
# Define function for CI
conf.int - function(x) {
st - boxplot.stats(x)
c((st$conf[2]-st$conf[1])/2)
}
# Plot
library(sciplot)
lineplot.CI(response=height, x.factor=voice, trace.factor=range,
data=singer, fun=median, ci.fun=conf.int)
lineplot.CI(response=height, x.factor=voice.part, data=singer,
fun=median, ci.fun=conf.int)
Manuel
On Tue, 2006-06-06 at 00:20 -0300, Mike Lawrence wrote:
Hi all,
I'm trying to plot error bars in a lattice plot generated with xyplot.
Deepayan
Sarkar has provided a very useful solution for simple circumstances
(https://stat.ethz.ch/pipermail/r-help/2005-October/081571.html), yet I am
having trouble getting it to work when the groups setting is enabled in
xyplot (i.e. multiple lines). To illustrate this, consider the singer data
generated by the above linked solution previously submitted:
#
library(lattice)
singer.split -
with(singer,
split(height, voice.part))
singer.ucl -
sapply(singer.split,
function(x) {
st - boxplot.stats(x)
c(st$stats[3], st$conf)
})
singer.ucl - as.data.frame(t(singer.ucl))
names(singer.ucl) - c(median, lower, upper)
singer.ucl$voice.part -
factor(rownames(singer.ucl),
levels = rownames(singer.ucl))
#now let's split up the voice.part factor into two factors,
singer.ucl$voice=factor(rep(c(1,2),4))
singer.ucl$range=factor(rep(c(Bass,Tenor,Alto,Soprano),each=2))
#here's Deepayan's previous solution, slightly modified to depict
# the dependent variable (median) and the error bars on the y-axis
# and the independent variable (voice.part) on the x-axis
prepanel.ci - function(x, y, ly, uy, subscripts, ...)
{
x - as.numeric(x)
ly - as.numeric(ly[subscripts])
uy - as.numeric(uy[subscripts])
list(ylim = range(y, uy, ly, finite = TRUE))
}
panel.ci - function(x, y, ly, uy, subscripts, pch = 16, ...)
{
x - as.numeric(x)
y - as.numeric(y)
ly - as.numeric(ly[subscripts])
uy - as.numeric(uy[subscripts])
panel.arrows(x, ly, x, uy, col = black,
length = 0.25, unit = native,
angle = 90, code = 3)
panel.xyplot(x, y, pch = pch, ...)
}
#this graph works
xyplot(median ~ voice.part,
data=singer.ucl,
ly = singer.ucl$lower,
uy = singer.ucl$upper,
prepanel = prepanel.ci,
panel = panel.ci,
type=b
)
#this one does not (it will plot, but will not seperate the groups)
xyplot(median ~ voice,
groups=range,
data=singer.ucl,
ly = singer.ucl$lower,
uy = singer.ucl$upper,
prepanel = prepanel.ci,
panel = panel.ci,
type=b
)
Any suggestions?
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[R] multiple data sets on one plot
Hello, I am learning how to use R, and I cannot figure out how to plot more than one data set on a single plot. Can you help me out? Cheers, Mark -- Mark Sessing CIMMS Research Fellow Meteorologist NWS Warning Decision Training Branch 3200 Marshall Ave Ste. 202 Norman, OK 73072 Phone: 405-573-3332 Fax: 405-573-3462 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] use of R in big companies (references) R-support esp in Germany
The best rebuttal I've heard recently to arguments like that is Linux (www.linux.org): It's distributed under the same general public license (GNU) license as R. A perspective that I don't recall having seen on this list is that the cost of producing and distributing software has become too cheap to meter, unless you want to charge for it. Open source projects like Linux and R (and Mozilla, Subversion, and others) were much more difficult and less common before the Internet, just because the costs of coordinating development plus producing and distributing the product made such efforts much more difficult. For a discussion of these phenomena by two Economics professors at UC-Berkeley, see Shapiro and Varian (1998) Information Rules (Harvard Business School Pr.). A newer, similar title by these same authors is The Economics of Information Technology; I haven't read this newer book, but it looks like it could be relevant also. I mention this, because I suspect some of the opposition to open source, free software is ideology: Rabid capitalists refuse to believe that anything free can be any good. (We could talk about air and water, but that might be a digression.) Books like this backed by solid research might help counter such opposition. Hope this helps. Spencer Graves Armin Roehrl wrote: Dear R users, sorry for this general email and I am sure it has been asked way too many times. IT departements in big companies only want to support the big standards. Whatever big standards means apart from being expensive. We are in the process of trying to get a risk management project for a big conservative company in Germany. As part of the project we would use R to run simulations, but the company is afraid of R. 1) If anybody has any reference projects using R I can quote, please drop me an email. Best would be companies like Siemens, Allianz, Munich Re, Daimler Chrysler, Credit Suisse etc. 2) Are there any software companies around with R know-how and are interested in paid R-projects? The bigger the company, the better as this client seems to be scared of software companies with less than 200 developers. Thanks, -Armin __ R-help@stat.math.ethz.ch 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 data sets on one plot
Without more inormation about what you are specifically trying to do, see ?line ?points Sarah On 6/7/06, Mark L Sessing [EMAIL PROTECTED] wrote: Hello, I am learning how to use R, and I cannot figure out how to plot more than one data set on a single plot. Can you help me out? Cheers, Mark -- Sarah Goslee [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Edit function
I use a simple-minded, dirty wrapper on edit:
view - function(x) {
warnopt - options()$warn
options(warn=-1)
on.exit({sink(); options(warn=warnopt)})
edit(x)
invisible()
}
I say dirty, because sometimes the output is re-directed from stdout
somewhere else as an unintended side effect, which is why I have the first
sink() statement in there. (Note the help file on sink() advises in numerous
places on using sink()-related calls with care.) I have not been ambitious
enough to make the above version robust and well-understood, as it works
well for me nearly every time, and when it does not, the side effect and
cleanup is neither damaging nor annoying enough.
Also, I have only really used this under Windows R GUI.
Hope that helps,
Bill
---
Bill Pikounis, PhD
Nonclinical Statistics
Centocor, Inc.
edit(data)
But when I close the window then again the materials
contained in data is displayed in the command window. But I
do not want to see these materials again. Can anyone give me
any idea on how to do this?
Hope that helps,
Bill
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of stat stat
Sent: Wednesday, June 07, 2006 8:36 AM
To: r-help@stat.math.ethz.ch
Subject: [R] Edit function
Dear all R users,
I have a query on Edit function. Suppose I have a data
frame named data. I can use EDIT function to see the
materials contained in data, by using the command:
edit(data)
But when I close the window then again the materials
contained in data is displayed in the command window. But I
do not want to see these materials again. Can anyone give me
any idea on how to do this?
Thanks and regards,
stat
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Re: [R] multiple data sets on one plot
On Wed, 2006-06-07 at 10:30 -0500, Mark L Sessing wrote: Hello, I am learning how to use R, and I cannot figure out how to plot more than one data set on a single plot. Can you help me out? Cheers, Mark It depends upon the type of plot (scatter, lines, bar, etc.) and whether or not you are using R's base graphics or lattice graphics. With more information, we can offer specific guidance. For example, with base graphics, you can add additional plot components with: ?lines ?points ?segments ?matpoints (Note also matplot() on the same page) ?curve ?arrows A good starting place would be Chapter 12 Graphical Procedures in An Introduction to R, which is available within your R installation (on Windows from the GUI menus) or from the Documentation links on the R home page. An additional resource is the R Graph Gallery: http://addictedtor.free.fr/graphiques/index.php and Chapter 3 From Data to Graphics by Vincent Zoonekynd here: http://zoonek2.free.fr/UNIX/48_R/all.html HTH, Marc Schwartz __ R-help@stat.math.ethz.ch 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 do multiple comparison in the nonparametric statistical analysis?
Dear Rusers, As we all know , there are many methods to do multiple comparison in the parametric statistical analysis, But i can't find some in nonparametric statistical analysis. Could anybody give some suggestions? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Fw: Help needed using lattice for area plots lpolygon, xyplot.
On 6/7/06, [EMAIL PROTECTED]
[EMAIL PROTECTED] wrote:
I am trying to learn how to use the graphics from the lattice package (
and am very new to R).
I am trying to replicate the example plot referenced below, by using the
lattice xyplot lpolygon to create panels. I get what appears to be the
correct shape of the filled region, but cannot get the position to overlay
properly. I have attempted with various settings of position. ( i.e.
position = c(0,0,1,1) etc settings as well. I am not understanding
something about the positioning panels. I am missing some subtle
difference between polygon lpolygon, or am missing something about panel
overlays /or panel postions.
#http://addictedtor.free.fr/graphiques/graphcode.php?graph=7.
par(bg=white)
n - 100
set.seed(43214) #just so we have the same exact graph
x - c(0,cumsum(rnorm(n)))
y - c(0,cumsum(rnorm(n)))
xx - c(0:n, n:0)
yy - c(x, rev(y))
plot(xx, yy, type=n, xlab=Time, ylab=Distance)
polygon(xx, yy, col=gray)
title(Distance Between Brownian Motions)
# using lattice.
p1 - xyplot( yy~xx,type='l');
p2 - lpolygon(xx,yy,col='blue');
print(p1,position=c(0,0,1,1), more=TRUE);
print(p2,position=c(0,0,1,1));
You are missing a fundamental concept in lattice, namely that of panel
functions. A literal translation of that example would be
xyplot(yy ~ xx, panel = lpolygon, col = gray)
which is more or less equivalent to
xyplot(yy ~ xx,
panel = function(x, y, ...) {
# panel.xyplot(x, y, ...) # unnecessary
lpolygon(x, y, col = gray)
})
The line commented out is the equivalent of plot(...type='n'), but is
unnecessary here.
Deepayan
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Re: [R] Fw: Help needed using lattice for area plots lpolygon, xyplot.
Perfect. Thank-you!
Deepayan Sarkar [EMAIL PROTECTED]
06/07/2006 11:19 AM
To
[EMAIL PROTECTED] [EMAIL PROTECTED]
cc
r-help@stat.math.ethz.ch
Subject
Re: [R] Fw: Help needed using lattice for area plots lpolygon, xyplot.
On 6/7/06, [EMAIL PROTECTED]
[EMAIL PROTECTED] wrote:
I am trying to learn how to use the graphics from the lattice package (
and am very new to R).
I am trying to replicate the example plot referenced below, by using the
lattice xyplot lpolygon to create panels. I get what appears to be
the
correct shape of the filled region, but cannot get the position to
overlay
properly. I have attempted with various settings of position. ( i.e.
position = c(0,0,1,1) etc settings as well. I am not understanding
something about the positioning panels. I am missing some subtle
difference between polygon lpolygon, or am missing something about
panel
overlays /or panel postions.
#http://addictedtor.free.fr/graphiques/graphcode.php?graph=7.
par(bg=white)
n - 100
set.seed(43214) #just so we have the same exact graph
x - c(0,cumsum(rnorm(n)))
y - c(0,cumsum(rnorm(n)))
xx - c(0:n, n:0)
yy - c(x, rev(y))
plot(xx, yy, type=n, xlab=Time, ylab=Distance)
polygon(xx, yy, col=gray)
title(Distance Between Brownian Motions)
# using lattice.
p1 - xyplot( yy~xx,type='l');
p2 - lpolygon(xx,yy,col='blue');
print(p1,position=c(0,0,1,1), more=TRUE);
print(p2,position=c(0,0,1,1));
You are missing a fundamental concept in lattice, namely that of panel
functions. A literal translation of that example would be
xyplot(yy ~ xx, panel = lpolygon, col = gray)
which is more or less equivalent to
xyplot(yy ~ xx,
panel = function(x, y, ...) {
# panel.xyplot(x, y, ...) # unnecessary
lpolygon(x, y, col = gray)
})
The line commented out is the equivalent of plot(...type='n'), but is
unnecessary here.
Deepayan
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Re: [R] how to do multiple comparison in the nonparametric statistical analysis?
On Thu, 2006-06-08 at 00:10 +0800, zhijie zhang wrote: Dear Rusers, As we all know , there are many methods to do multiple comparison in the parametric statistical analysis, But i can't find some in nonparametric statistical analysis. Could anybody give some suggestions? Have you looked at the npmc package on CRAN? As a text reference, there is also: Multiple Comparisons: Theory and methods by Jason C. Hsu Chapman Hall 1996 More information here: http://www.stat.ohio-state.edu/~jch/mc.html Amazon.com link: http://www.amazon.com/gp/product/0412982811 HTH, Marc Schwartz __ R-help@stat.math.ethz.ch 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 do multiple comparison in the nonparametric statis tical analysis?
Also Consider Bonferroni Hochberg Holm type procedures or . Dunn OJ. Multiple contrasts using rank sum tests. Technometrics 1964;6:241#/52. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Density Estimation
Dear R-list, I have made a simple kernel density estimation by x - c(2,1,3,2,3,0,4,5,10,11,12,11,10) kde - density(x,n=100) Now I would like to know the estimated probability that a new observation falls into the interval 0x3. How can I integrate over the corresponding interval? In several R-packages for kernel density estimation I did not found a corresponding function. I could apply Simpson's Rule for integrating, but perhaps somebody knows a better solution. Thanks a lot for help! Pedro _ __ R-help@stat.math.ethz.ch 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] Density Estimation
Not a direct answer to your question, but if you use a logspline density estimate rather than a kernal density estimate then the logspline package will help you and it has built in functions for dlogspline, qlogspline, and plogspline that do the integrals for you. If you want to stick with the KDE, then you could find the area under each of the kernals for the range you are interested in (need to work out the standard deviation used from the bandwidth, then use pnorm for the default gaussian kernal), then just sum the individual areas. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Pedro Ramirez Sent: Wednesday, June 07, 2006 11:00 AM To: r-help@stat.math.ethz.ch Subject: [R] Density Estimation Dear R-list, I have made a simple kernel density estimation by x - c(2,1,3,2,3,0,4,5,10,11,12,11,10) kde - density(x,n=100) Now I would like to know the estimated probability that a new observation falls into the interval 0x3. How can I integrate over the corresponding interval? In several R-packages for kernel density estimation I did not found a corresponding function. I could apply Simpson's Rule for integrating, but perhaps somebody knows a better solution. Thanks a lot for help! Pedro _ __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] use of R in big companies (references) R-support esp in Germany
Spencer, I agree that there exist biases within large organizations toward commercial software packages, but I humbly disagree that this can be reduced to geopolitical differences. I work for a US Government Agency and while there is some truth to the feeling [they] refuse to believe that anything free can be any good, it has little-to-nothing to do with Capitalism vs whatever… I think the feeling has to do more with the *perceived* issues related to support and what is tried true — it's a very conservative approach, one that I face on nearly a daily basis. Apart from my use of R, I am also a heavy user of the open source Geographic Information System (GIS) called GRASS, in which the *dominant* GIS company internationally is ESRI and their very expensive software called ArcGIS. There is very little that ArcGIS can do that GRASS can not do. What is especially troublesome is that ArcGIS is restricted to the MS-Windows platform, whereas GRASS runs on Linux, MacOS X, UNIX, and MS-Windows with Cygwin. Thank you for your references as I hope to use them. Regards, Tom Spencer Graves wrote: The best rebuttal I've heard recently to arguments like that is Linux (www.linux.org): It's distributed under the same general public license (GNU) license as R. A perspective that I don't recall having seen on this list is that the cost of producing and distributing software has become too cheap to meter, unless you want to charge for it. Open source projects like Linux and R (and Mozilla, Subversion, and others) were much more difficult and less common before the Internet, just because the costs of coordinating development plus producing and distributing the product made such efforts much more difficult. For a discussion of these phenomena by two Economics professors at UC-Berkeley, see Shapiro and Varian (1998) Information Rules (Harvard Business School Pr.). A newer, similar title by these same authors is The Economics of Information Technology; I haven't read this newer book, but it looks like it could be relevant also. I mention this, because I suspect some of the opposition to open source, free software is ideology: Rabid capitalists refuse to believe that anything free can be any good. (We could talk about air and water, but that might be a digression.) Books like this backed by solid research might help counter such opposition. Hope this helps. Spencer Graves Armin Roehrl wrote: Dear R users, sorry for this general email and I am sure it has been asked way too many times. IT departements in big companies only want to support the big standards. Whatever big standards means apart from being expensive. We are in the process of trying to get a risk management project for a big conservative company in Germany. As part of the project we would use R to run simulations, but the company is afraid of R. 1) If anybody has any reference projects using R I can quote, please drop me an email. Best would be companies like Siemens, Allianz, Munich Re, Daimler Chrysler, Credit Suisse etc. 2) Are there any software companies around with R know-how and are interested in paid R-projects? The bigger the company, the better as this client seems to be scared of software companies with less than 200 developers. Thanks, -Armin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Thomas E Adams National Weather Service Ohio River Forecast Center 1901 South State Route 134 Wilmington, OH 45177 EMAIL: [EMAIL PROTECTED] VOICE: 937-383-0528 FAX:937-383-0033 __ R-help@stat.math.ethz.ch 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] Density Estimation
Pedro wrote: I have made a simple kernel density estimation by x - c(2,1,3,2,3,0,4,5,10,11,12,11,10) kde - density(x,n=100) Now I would like to know the estimated probability that a new observation falls into the interval 0x3. How can I integrate over the corresponding interval? In several R-packages for kernel density estimation I did not found a corresponding function. I could apply Simpson's Rule for integrating, but perhaps somebody knows a better solution. One possibility is to use splinefun(): spiffy - splinefun(kde$x,kde$y) integrate(spiffy,0,3) 0.2353400 with absolute error 2e-09 cheers, Rolf Turner [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] Density Estimation
Not a direct answer to your question, but if you use a logspline density estimate rather than a kernal density estimate then the logspline package will help you and it has built in functions for dlogspline, qlogspline, and plogspline that do the integrals for you. If you want to stick with the KDE, then you could find the area under each of the kernals for the range you are interested in (need to work out the standard deviation used from the bandwidth, then use pnorm for the default gaussian kernal), then just sum the individual areas. Hope this helps, Thanks a lot for your quick help! I think I will follow your first suggestion (logspline density estimation) instead of summing over the kernel areas because at the boundaries of the range truncated kernel areas can occur, so I think it is easier to do it with logsplines. Thanks again for your help!! Pedro -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Pedro Ramirez Sent: Wednesday, June 07, 2006 11:00 AM To: r-help@stat.math.ethz.ch Subject: [R] Density Estimation Dear R-list, I have made a simple kernel density estimation by x - c(2,1,3,2,3,0,4,5,10,11,12,11,10) kde - density(x,n=100) Now I would like to know the estimated probability that a new observation falls into the interval 0x3. How can I integrate over the corresponding interval? In several R-packages for kernel density estimation I did not found a corresponding function. I could apply Simpson's Rule for integrating, but perhaps somebody knows a better solution. Thanks a lot for help! Pedro _ __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] help with combination problem
hello: I have 3 data.frame objects. First df object: Of dim (149,31). Columns 2:31 are marked as T1..T14 and N1..N16. Name T1T2N1 T3 N2 N3 N4 T4 mu1 1010910 9 9 8 10 mu2 1111911 9 9 9 11 ... muN 1212911 9 9 8 12 Second df object: of Dim (5,31). Columns 2:31 are maked as T1...T14 and N1..N16. Name T1T2N1 T3 N2 N3 N4 T4 J1 2 3 20 222 21 29 3 J2 4 1 20 320 21 22 4 J3 3 1 33 131 31 33 3 ... JX 3 2 20 221 22 24 2 The column samples are identical in both first and second data frames. Third df object: of Dim (200,2). V1 V2 mu1:J1 -11 mu1:J100 -10.4 mu2:J31 11.3 mu2:J2 10.4 . . muN:JX 34.5 I want to create a combination of Ts and Ns. Where I want to subtract value of T-N in all combinations(225 combinations). Such as T1-N1,T1-N2,T1-N3,T1-N4,T1-N5...T14-N16 The rows should be the row pairs from 3rd dataframe. The final resultant matrix should look like the following: T1-N1 T1-N2 T1-N3 T1-N4 T1-N5...T14-N16 mu1 1(10-9) 1(10-9) 12 11 J100 -18(2-20) -20 -19 -27-20 -29 mu2 1 32 2 11 J2 -19 -21 -39-31-31 -28 I am a beginner level in R. I apologise for asking such a big question and subsequent help. I am unable to go forward as I have no idea as to how to do this. Could any one please help me. Thanks sri __ R-help@stat.math.ethz.ch 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 read hdf files under R?
Nicolas Degallier wrote: Hi! I am trying to install in my R environment the rhdf5 package and library but it seems to have vanished from either the CRAN or BioConductors sites. Can you tell me where it would be possible to find it or any R library (or function) able to read hdf files? hf5 it is supposed to do this, but I haven't any success trying to open an .hdf (V5) file (i.e: pathfinderv5 sst data) I always get some data format problem message. So I use to search for a netcdf format for the data I want and input into R with the netCDF library (old but useful) BR, arv Sincerely, Nicolas Degallier UMR 7159 / IRD UR182 Laboratoire d'Océanographie et du Climat, Expérimentation et Approches Numériques (LOCEAN) Tour 45-55, 4e ét., case 100, 4 place Jussieu 75252 Paris Cedex 5 France tél: (33) 01 44 27 51 57 fax: (33) 01 44 27 38 05 E-mail: [EMAIL PROTECTED] Publications (anonymous ftp): ftp://ftp.lodyc.jussieu.fr/LOCEAN/ndelod __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- = Por favor, si me mandas correos con copia a varias personas, pon mi dirección de correo en copia oculta (CCO), para evitar que acabe en montones de sitios, eliminando mi privacidad, favoreciendo la propagación de virus y la proliferación del SPAM. Gracias. - If you send me e-mail which has also been sent to several other people, kindly mark my address as blind-carbon-copy (or BCC), to avoid its distribution, which affects my privacy, increases the likelihood of spreading viruses, and leads to more SPAM. Thanks. = __ R-help@stat.math.ethz.ch 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] Edit function
[Pikounis, Bill [CNTUS]]
view - function(x) {
warnopt - options()$warn
options(warn=-1)
on.exit({sink(); options(warn=warnopt)})
edit(x)
invisible()
}
I'm surprised by the necessity of sink(). Presuming it is necessary
indeed, the above could be simplified a bit like this (untested) code:
view - function(x) {
on.exit(sink())
invisible(suppressWarnings(edit(x)))
}
The documentation for suppressWarnings is not overly clear about if
the warn option is restored or not in case of error. It says:
'suppressWarnings' evaluates its expression in a context that
ignores all warnings.
My exegesis :-) for that sentence would be that the context does not
survive the error, and so, the warn option is not changed.
--
François Pinard http://pinard.progiciels-bpi.ca
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[R] decideTests extraction of p-values
Hello all, Here is the code that I am using for finding differentially expressed genes. #Normalization library(affy) library(Biobase) library(limma) library(gcrma) pd-read.phenoData(file.txt,header=TRUE,row.names=1,as.is=TRUE,sep=\t) Data - ReadAffy(filenames=pData(pd)$FileName,phenoData=pd) print(Data) eset - gcrma(Data) write.exprs(eset, file=decide-test.6-6-06.txt) #Linear Model pData(eset) targets-pData(eset) model.matrix(~ -1 +factor(targets$Target,levels=unique(targets$Target))) design - model.matrix(~ -1 + factor(targets$Target,levels=unique(targets$Target))) unique(targets$Target) colnames(design) - unique(targets$Target) ncol(design) numParameters - ncol(design) colnames(design) parameterNames - colnames(design) design fit - lmFit(eset,design=design) names(fit) contrastNames -c(paste(parameterNames[2],parameterNames[1],sep=-), paste(parameterNames[3],parameterNames[1],sep=-), paste(parameterNames[4],parameterNames[1],sep=-), paste(parameterNames[5],parameterNames[1],sep=-), paste(parameterNames[6],parameterNames[1],sep=-), paste(parameterNames[7],parameterNames[1],sep=-)) contrastsMatrix - matrix(c( -1,1,0,0,0,0,0, -1,0,1,0,0,0,0, -1,0,0,1,0,0,0, -1,0,0,0,1,0,0, -1,0,0,0,0,1,0, -1,0,0,0,0,0,1),nrow=ncol(design)) rownames(contrastsMatrix) - parameterNames colnames(contrastsMatrix) - contrastNames contrastsMatrix fit2 - contrasts.fit(fit,contrasts=contrastsMatrix) names(fit2) #ebayes fit2 - eBayes(fit2) names(fit2) numGenes - nrow([EMAIL PROTECTED]) #decideTest results - decideTests(fit2,method=nestedF,p=0.05); write.fit(fit2, results, data.txt, adjust=BH); Is there any way for getting the adjusted p-values from the decideTests method ? Thanks, Vijay [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] bootstrap data from groups
I am not sure I understand what you want to do, but maybe some of this
will be helpful. I first generate some data that should resemble yours:
dat-expand.grid(Region=1:3, Species=1:4, Sex=c(M,F))
dat-do.call(rbind,lapply(1:10,function(x) dat))
dat$Bodysize-rnorm(nrow(dat),10,2)
Now what the following piece of code does is this: it samples 4 of the
10 individuals in each of the 24 subsets (region*species*sex) and
creates a new data frame with 96 cases. It then computes the mean of
bodysize in each of the subsets. The whole thing is done 100 times, the
results are put in a data frame. We end up with 100 bootstrapped means
for the 24 subsets.
groupmeans-sapply(1:100, function(z) {
dat.rs-do.call(rbind,
lapply(split(dat,list(dat$Region,dat$Species,dat$Sex)),
function(x) x[sample(10, 4, replace=TRUE),]))
aggregate(dat.rs$Bodysize,
list(dat.rs$Region,dat.rs$Species,dat.rs$Sex),
mean)$x
}
)
tmp-aggregate(dat$Bodysize,
list(dat$Region,dat$Species,dat$Sex),mean)
rownames(groupmeans)-apply(tmp[,1:3],1,paste,collapse=)
Now we can compute the mean and sd of the means by group:
apply(groupmeans,1,mean)
11M 21M 31M 12M 22M 32M
13M 23M
9.353095 9.267570 9.907933 10.992796 9.575841 10.412816 9.646964
9.433724
33M 14M 24M 34M 11F 21F
31F 12F
10.750797 9.083630 10.573421 9.615743 10.267587 10.231126 9.329375
10.799071
22F 32F 13F 23F 33F 14F
24F 34F
9.355510 10.555705 9.919161 10.277103 9.335649 9.339544 10.023688
9.755115
apply(groupmeans,1,sd)
11M 21M 31M 12M 22M 32M
13M 23M
0.7720758 1.5301540 1.0973516 0.8970237 1.0492995 0.9460970 0.5362957
1.1106675
33M 14M 24M 34M 11F 21F
31F 12F
0.5333081 0.9259341 0.8198624 0.8061832 0.8466780 0.7052473 0.9857680
1.1057607
22F 32F 13F 23F 33F 14F
24F 34F
0.8272433 1.2614559 1.2377154 1.0958545 0.9213648 0.9985215 1.1131870
1.0572494
Milton Cezar schrieb:
Hi R-friends.
I have a mammalŽs dataset looking like:
Region Species Sex Bodysize
1 Sp1 M 10.2
1 Sp1 M 12.1
1 Sp1 M 9.1
...
I have three regions, four species and the body size of 10 individual. IŽd
like to do a bootstrap resample (100 resamples) of 4 of 10 individuals for
each Region, Species and Sex and compute de means and S.D. for the
combinations Regions-Species-Sex.
How can I do that?
Thanks a lot,
Miltinho
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[R] simplier way to import txt time-series data
Hello much more experienced R-users, I have got a txt - file which contains data formated like this: MM DD HH data1 data2 ... data31 2002 12 01 01 0.002 0.003 ... 312.0 The single columns are divided by at least one space. Is their an easy and fast way to make R understand that the first 4 columns are year month day and hour to recognize it as time series data. The time series are not complete. Single hours could be missing. Thanks a lot for answering my question. I just cannot believe that it is a big problem for R to handle this clean format while it even imports data from excel-files. Greatings Jan __ R-help@stat.math.ethz.ch 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 crashes on quantreg
I was trying quantreg package, lm1 - lm(y~x) rq1 - rq(y~x) plot(summary(rq1)) #then got a warning says singular value, etc. but this line can be omited plot(lm1) #crash here It happened every time on my PC, Windows XP Pro Serv. Pack 1, Pentium(4) 3.00G. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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 crashes on quantreg
I forgot to mention my R version is 2.3.1 and quantreg is the most updated too. On 6/7/06, Mu Tian [EMAIL PROTECTED] wrote: I was trying quantreg package, lm1 - lm(y~x) rq1 - rq(y~x) plot(summary(rq1)) #then got a warning says singular value, etc. but this line can be omited plot(lm1) #crash here It happened every time on my PC, Windows XP Pro Serv. Pack 1, Pentium(4) 3.00G. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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 crashes on quantreg
Since the crash occurs plotting the lm object it is unclear what this has to do with quantreg, but maybe you could explain 1. what you mean by crash, 2. something about x,y, This is best addressed to the maintainer of the package rather than to R-help, provided, of course, that it is really a question about quantreg. url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Champaign, IL 61820 On Jun 7, 2006, at 2:32 PM, Mu Tian wrote: I was trying quantreg package, lm1 - lm(y~x) rq1 - rq(y~x) plot(summary(rq1)) #then got a warning says singular value, etc. but this line can be omited plot(lm1) #crash here It happened every time on my PC, Windows XP Pro Serv. Pack 1, Pentium(4) 3.00G. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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 crashes on quantreg
Without y and x we cannot reproduce this. PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html On Wed, 7 Jun 2006, Mu Tian wrote: I forgot to mention my R version is 2.3.1 and quantreg is the most updated too. It has a version number, which the posting guide tells you how to find. On 6/7/06, Mu Tian [EMAIL PROTECTED] wrote: I was trying quantreg package, lm1 - lm(y~x) rq1 - rq(y~x) plot(summary(rq1)) #then got a warning says singular value, etc. but this line can be omited plot(lm1) #crash here It happened every time on my PC, Windows XP Pro Serv. Pack 1, Pentium(4) 3.00G. [[alternative HTML version deleted]] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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 crashes on quantreg
I attached the data file here. I restarted the PC but it still happens. It says a memory address could not be written. I am not sure it is a problem of R or quantreg but I plot without problems before I load quantreg. Thank you. Tian On 6/7/06, Prof Brian Ripley [EMAIL PROTECTED] wrote: Without y and x we cannot reproduce this. PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html On Wed, 7 Jun 2006, Mu Tian wrote: I forgot to mention my R version is 2.3.1 and quantreg is the most updated too. It has a version number, which the posting guide tells you how to find. On 6/7/06, Mu Tian [EMAIL PROTECTED] wrote: I was trying quantreg package, lm1 - lm(y~x) rq1 - rq(y~x) plot(summary(rq1)) #then got a warning says singular value, etc. but this line can be omited plot(lm1) #crash here It happened every time on my PC, Windows XP Pro Serv. Pack 1, Pentium(4) 3.00G. [[alternative HTML version deleted]] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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] Using data=x or subset=y in user-defined functions
Dear list members,
In some of my functions, I attach the data internally to allow subset
commands or to specify a data frame. This works well except for cases
where there is a masking conflict (which returns a warning). I see
some alternative listed in ?attach, but I'm not sure which of them do
what I'd like. Any suggestions?
Below is how I've been setting up my functions:
eg.function - function(x, data=NULL, subset=NULL, ...) {
# Set up environment
on.exit(detach(data))
attach(data)
if(!is.null(subset)) {
data-subset(data,subset)
detach(data)
attach(data)
}
subset = NULL
# Function body here
output - x
return(output)
}
Thanks!
Manuel
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Re: [R] R crashes on quantreg
On Wed, 7 Jun 2006, roger koenker wrote: Since the crash occurs plotting the lm object it is unclear what this has to do with quantreg, but maybe you could explain 1. what you mean by crash, 2. something about x,y, This is best addressed to the maintainer of the package rather than to R-help, provided, of course, that it is really a question about quantreg. Agreed, but just so R-help knows how to solve such problems, I ran this under valgrind (see `Writing R Extensions') and got rq1 - rq(y~x) ==7870== Invalid write of size 8 ==7870==at 0x9ED8BDE: rqbr_ (rqbr.f:309) ... ==7870== Address 0x92162A0 is 12,248 bytes inside a block of size 12,288 free'd ==7870==at 0x49055DD: free (vg_replace_malloc.c:235) ==7870==by 0x53D64A: build_trtable (regex.c:9618) ==7870==by 0x53AEB4: transit_state (regex.c:8393) ==7870==by 0x538977: check_matching (regex.c:7318) ==7870==by 0x537E89: re_search_internal (regex.c:7007) ==7870==by 0x53EF3D: Rregexec (regex.c:10440) ==7870==by 0x438AAF: do_gsub (character.c:1127) and it seems object lm1 has been trashed and you soon get a segfault. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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] Using data=x or subset=y in user-defined functions
I suggest you investigate with().
On Wed, 7 Jun 2006, Manuel Morales wrote:
Dear list members,
In some of my functions, I attach the data internally to allow subset
commands or to specify a data frame. This works well except for cases
where there is a masking conflict (which returns a warning). I see
some alternative listed in ?attach, but I'm not sure which of them do
what I'd like. Any suggestions?
Below is how I've been setting up my functions:
eg.function - function(x, data=NULL, subset=NULL, ...) {
# Set up environment
on.exit(detach(data))
attach(data)
if(!is.null(subset)) {
data-subset(data,subset)
detach(data)
attach(data)
}
subset = NULL
# Function body here
output - x
return(output)
}
Thanks!
Manuel
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--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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[R] bootstrapping
hi.
i'm a statistics student and studying bootstrap in R.
i'm trying to draw bootstrap samples from a sample, using the following R
code:
*boot = numeric(200)*
* {for (i in 1:200)*
* boot [i] = (sample(data,replace=T))}*
i obtain 200 samples but all of them are the same.
i want to obtain different samples. what should i do? can you please help me
if possible.
thank you.
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Re: [R] R crashes on quantreg
R-help doesn't foward attached data files like this, but Brian kindly forwarded it to me. You need to restrict X so that it is full rank, it now has rank 19 and column dimension 29 (with intercept). See for example svd(cbind(1,x)). I'll add some better checking for this, but it will basically amount to setting singular.ok = FALSE in lm() and forcings users to do the rank reduction themselves. url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Champaign, IL 61820 On Jun 7, 2006, at 3:05 PM, Mu Tian wrote: I attached the data file here. I restarted the PC but it still happens. It says a memory address could not be written. I am not sure it is a problem of R or quantreg but I plot without problems before I load quantreg. Thank you. Tian On 6/7/06, Prof Brian Ripley [EMAIL PROTECTED] wrote: Without y and x we cannot reproduce this. PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html On Wed, 7 Jun 2006, Mu Tian wrote: I forgot to mention my R version is 2.3.1 and quantreg is the most updated too. It has a version number, which the posting guide tells you how to find. On 6/7/06, Mu Tian [EMAIL PROTECTED] wrote: I was trying quantreg package, lm1 - lm(y~x) rq1 - rq(y~x) plot(summary(rq1)) #then got a warning says singular value, etc. but this line can be omited plot(lm1) #crash here It happened every time on my PC, Windows XP Pro Serv. Pack 1, Pentium(4) 3.00G. [[alternative HTML version deleted]] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] bootstrapping
2006/6/7, Recep Aykaya [EMAIL PROTECTED]:
hi.
i'm a statistics student and studying bootstrap in R.
i'm trying to draw bootstrap samples from a sample, using the following R
code:
*boot = numeric(200)*
* {for (i in 1:200)*
* boot [i] = (sample(data,replace=T))}*
i obtain 200 samples but all of them are the same.
i want to obtain different samples. what should i do? can you please help
me
if possible.
thank you.
[[alternative HTML version deleted]]
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Hi,
I think you have forgotten an parameter of the sample function. Indeed the
help page give these information:
sample(x, size, replace = FALSE, prob = NULL)
size: non-negative integer giving the number of items to choose
By default 'size' is equal to 'length(x)' so that 'sample(x)'
generates a random permutation of the elements of 'x' (or '1:x').
Therefore try to add the number of observed values with this:
nb=100 #the number of values for each sample
boot = c()
for (i in 1:200)
boot [i] = mean(sample(x=data,size=nb,replace=TRUE)) # if you try to
estimate the mean
--
Clément Viel
Student in Polytech-Lille's engineering school
http://www.polytech-lille.fr
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Re: [R] simplier way to import txt time-series data
Try this which reads in the data as a data frame and appends a chron variable datetime: Lines - MM DD HH data1 data2 2002 12 01 01 0.002 0.003 DF - read.table(textConnection(Lines), header = TRUE) library(chron) DF$datetime - with(DF, chron(paste(MM, DD, , sep = /)) + HH/24) DF On 6/7/06, Jan Schwanbeck [EMAIL PROTECTED] wrote: Hello much more experienced R-users, I have got a txt - file which contains data formated like this: MM DD HH data1 data2 ... data31 2002 12 01 01 0.002 0.003 ... 312.0 The single columns are divided by at least one space. Is their an easy and fast way to make R understand that the first 4 columns are year month day and hour to recognize it as time series data. The time series are not complete. Single hours could be missing. Thanks a lot for answering my question. I just cannot believe that it is a big problem for R to handle this clean format while it even imports data from excel-files. Greatings Jan __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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 do this simple integration?
Hello,
I have a simple function in the form as follows:
f-function(x){sum(v^x)}
where v is a vector. I was trying to integrate f using the command
I-integrate(f,0,1)
However, this will not work and seems that the reason is to use
integrate, the f must be a function that with input and output of same
length. Anyone can point out which command should I use in order to
compute this type of integration(such as a function involve sum(), prod(),
etc.)?
Thank you.
Jianing
--
There are three kinds of lies: lies, damned lies, and Statistics.
---Benjamin Disraeli
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Re: [R] [OFF] The best tool for a space-temporal analyses?
Have you tried RSiteSearch(spatial ecology)? I just got 47 hits from that. Some of them might be relevant to your question. If that fails, you might consider providing this group with the math behind the automata models you are considering. I might expect them to be expressed in terms of Markov chain (or Markov random field) probability models with parameters to be estimated. The standard statistical approach is to consider a sequence of different models, with at least some of them nested, with increasing numbers of parameters and levels of complexity. We then estimate the parameters to maximize the likelihood (= probability of what was observed given the data). Testing typically assumes that 2*log(likelihood ratio) is approximately chi-square, with additional precision given by simulation if desired. Hope this helps. Spencer Graves Ronaldo Reis-Jr. wrote: Hi, I try to make an analyses to discover what is the time that an area begin to have spacial autocorrelation. And after, what is the number of individuals responsible for this autocorrelation. The main idea is to discover if exist a contamination of a quadrat from others quadrats and how is the population needed to make this contamination. This is very common to use automata to simulate this situation. But I try to make a more statistical approach. I'm studing about, but I dont know the tool for testing examples. I make an example just for tests: Geodata - data.frame(X=rep(rep(c(1:10), (rep(10,10))),5),Y=rep(c(1:10),50),Abund=c(1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 2, 0, 0, 2, 0, 0, 3, 0, 0, 2, 0, 0, 1, 2, 0, 0, 2, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 3, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 5, 0, 0, 2, 0, 0, 0, 0, 2, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 4, 0, 0, 0, 0, 5, 0, 2, 0, 0, 0, 0, 3, 0, 0, 2, 0, 0, 0, 0, 1, 0, 0, 0, 2, 3, 0, 0, 3, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 2, 0, 0, 4, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 2, 10, 0, 0, 3, 0, 0, 0, 0, 3, 3, 4, 2, 0, 0, 0, 1, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 3, 0, 3, 0, 0, 0, 0, 4, 0, 2, 1, 0, 0, 3, 0, 0, 0, 2, 0, 1, 4, 0, 0, 4, 0, 0, 4, 0, 0, 0, 0, 0, 4, 0, 0, 0, 0, 0, 3, 0, 0, 5, 0, 0, 0, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 0, 0, 0, 0, 0, 4, 10, 15, 0, 0, 4, 0, 0, 0, 0, 8, 11, 9, 0, 0, 0, 0, 0, 0, 0, 1, 5, 3, 0, 0, 0, 0, 0, 4, 0, 0, 0, 0, 4, 0, 4, 0, 0, 0, 0, 5, 0, 0, 2, 0, 0, 0, 0, 2, 0, 0, 1, 0, 5, 0, 0, 5, 0, 0, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 0, 6, 0, 0, 0, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 10, 15, 20, 0, 0, 0, 0, 0, 0, 4, 13, 16, 13, 0, 0, 0, 0, 0, 0, 5, 8, 8, 10, 0, 0, 0, 0, 0, 0, 1, 2, 3, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),Time=rep(c(1:5),rep(100,5))) X and Y are coordinates, Abund is the number of individuals and Time is the date of observation. In this example the population grows from an vertice, and after 10 individuals it contaminates your neighbors. I need ideas about the best approach and R's tools for this problem. I'm studing this question in these books: W.N. Venables, B.D. Ripley. 2003. Modern Applied Statistics with S. Springer; 4 edition (September 2, 2003). 512 pages. Crawley, M. J. 2002. Statistical Computing: An Introduction to Data Analysis using S-Plus. John Wiley Sons; 1st edition (May 15, 2002). 772 pages. Diggle, Peter J. 2003. Statistical Analysis of Spatial Point Patterns (2nd ed.), Arnold, London. Ripley, B.D. Spatial Statistics Spatial Ecology Thanks for all __ R-help@stat.math.ethz.ch 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 analyze the following data?--anxious for the result
Dear friends, I have a dataset: response var--y, class var-group, and the third variable-x. I want to test whether there is statistical significance bewteen group for y with the controlled x. First, i want to use analysis of covariance in SAS, but i found that y isn't noramal and can't become normal through transformation. Under that condition, what should i do using R / SAS? Any suggestions are great appreciate! -- Kind Regards,Zhi Jie,Zhang ,PHDDepartment of EpidemiologySchool of Public HealthFudan UniversityTel:86-21-54237149 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
