Re: [Rd] row.names != rownames for data.frame?
On Mon, 1 May 2006, Seth Falcon wrote: > With a recent R 2.4 I notice the following: > > df <- data.frame(x=1:2) >> row.names(df) > [1] "1" "2" >> rownames(df) > [1] 1 2 > > This seems related to recent changes in the internal storage format of > the row names data for data frames. > > The man page for rownames says: > > For a data frame, 'rownames' and 'colnames' are equivalent to > 'row.names' and 'names' respectively. > > A number of Bioconductor packages seem to be relying on this. Interesting: nothing on CRAN did. Those are `equivalent' but not identical, but let's make them identical again. -- 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-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] optimize() and extrema at the interval bounds
Dear r-devels, by construction, optimize() only evaluates the objective function *inside* the bounds of argument 'interval'. It does not seem to be an 'extremely' rare case that extrema are attained *at* the bounds of argument 'interval' :-) It is fairly easy to write a wrapper to optimize() enforcing an evaluation of the objective function at these bounds, too, but wouldn't it be a good idea to a add an extra argument 'evalbounds' of optimize() defaulting to FALSE (behavior of optimize() as it is now), but which if TRUE does evaluate the objective at the bounds? I do not know how costly two extra evaluations are in general as to computation time at evaluation of optimize(), nor how many conflicts of unmatched arguments an extra argument to optimize() would cause; so consider this just as a proposal. Thank you for your attention, Peter __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Call trellis function in a function (PR#8827)
Full_Name: Fan
Version: 2.2.1
OS: Windows
Submission from: (NULL) (159.50.101.9)
Hello,
When I call trellis function (such as histogram, densityplot, etc.) in a
function,
the call seems being ignored (no graphics is drawing) if some other instructions
are placed afeter that call.
Here's an example:
y = rnorm(100*3)
b = sample(1:3,300,replace=T)
f = function()
{
densityplot(~y|b)
}
f1 = function()
{
densityplot(~y|b)
return(1)
}
f1() # this will not draw the histogram
f() # this will draw the histogram
Thanks in advance
Kind regards
--
Fan
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Re: [Rd] Call trellis function in a function (PR#8827)
On Tue, 2 May 2006 [EMAIL PROTECTED] wrote:
This is a FAQ:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-do-lattice_002ftrellis-graphics-not-work_003f
> Full_Name: Fan
> Version: 2.2.1
> OS: Windows
> Submission from: (NULL) (159.50.101.9)
>
>
> Hello,
>
> When I call trellis function (such as histogram, densityplot, etc.) in a
> function,
> the call seems being ignored (no graphics is drawing) if some other
> instructions
>
> are placed afeter that call.
>
> Here's an example:
>
> y = rnorm(100*3)
> b = sample(1:3,300,replace=T)
>
> f = function()
> {
> densityplot(~y|b)
> }
>
> f1 = function()
> {
> densityplot(~y|b)
> return(1)
> }
>
> f1() # this will not draw the histogram
> f() # this will draw the histogram
>
> Thanks in advance
> Kind regards
> --
> Fan
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: [EMAIL PROTECTED]
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[Rd] Force action in package install?
I'd like to substitute the Subversion revision number for a string in a package man page every time the package is installed or built. I can assume it is being installed or built from a Subversion working copy. I tried putting a target that depends on FORCE into Makefile or Makevars in the src directory, but it is not being built. What sort of make magic do I need, and where do I put it in order to get R CMD INSTALL to run my code? Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] normal random number generator in R
Hi, I am trying to figure out how normal random number generator works in R. As I look at .../src/nmath/snorm.c file, I find the default algorithm is inverse CDF method. In more detail, instead of directly using uniform value by unif_rand(), snorm function will first get a sum by adding unif_rand() and 2^27*unif_rand(), then divide it by 2^27 and transfer it to qnorm5() function for inverting. Only a short comment for this operation is available in the source: /* unif_rand() alone is not of high enough precision */ Just curious why this operation is needed? Is it a general algorithm for inverse CDF method, or simply unif_rand() in R returns float precision? Thanks Tib __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Installation problem of R.app GUI 1.15 for R 2.3.0 (PR#8828)
Full_Name: Pan Du Version: 2.3.0 OS: Mac OS X 10.4.6 Submission from: (NULL) (165.124.152.227) Hi, I just downloaded the latest R2.3.0 for Mac. When I tried to install R.app GUI 1.15, it told me "You cannot install R GUI for Mac OS X on this volume. Requires Mac OS X 10.4.4 or higher." But actually I am using Mac OS X 10.4.6, which is higher than 10.4.4. Is there anyone knows what the problem is? BTW, all other packages were installed smoothly. Thanks a lot! Best, Pan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] normal random number generator in R
On Tue, 2 May 2006, Tibshirani wrote: > Hi, > > I am trying to figure out how normal random number generator works in R. As I > look at .../src/nmath/snorm.c file, I find the default algorithm is inverse > CDF method. In more detail, instead of directly using uniform value by > unif_rand(), snorm function will first get a sum by adding unif_rand() and > 2^27*unif_rand(), then divide it by 2^27 and transfer it to qnorm5() function > for inverting. Only a short comment for this operation is available in the > source: > /* unif_rand() alone is not of high enough precision */ > > Just curious why this operation is needed? Is it a general algorithm for > inverse CDF method, or simply unif_rand() in R returns float precision? unif_rand() returns a uniform over about 2^31 distinct doubles, and that gives granularity in the far tails of a normal. It is a known (at least to me) trick for improving the accuracy of inversion. -- 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-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Histogram to pdf file (PR#8829)
Full_Name: Ksawery Version: 2.30 OS: WinXp Submission from: (NULL) (195.150.76.2) The bug apears when I'm trying to save, for example histogram into PDF file.I'm using Polish language, and while in R letters are correct, in PDF file I have some strange one... __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Installation problem of R.app GUI 1.15 for R 2.3.0 (PR#8828)
Pan, On May 2, 2006, at 12:34 PM, [EMAIL PROTECTED] wrote: > I just downloaded the latest R2.3.0 for Mac. When I tried to > install R.app GUI 1.15, it told me "You cannot install R GUI for > Mac OS X on this volume. Requires Mac OS X 10.4.4 or higher." But > actually I am using Mac OS X 10.4.6, which is higher than 10.4.4. > Is there anyone knows what the problem is? BTW, all other packages > were installed smoothly. Thanks a lot! > Indeed there is a bug in that PackageMaker that causes the individual installer for Packages/R-GUI.pkg to fail (SpecType should be plist not bundle). Please use the regular R package instead (R.mpkg) - that should work. FWIW: If R.app is all you want, you may in fact just get it from the nightly page ( http://R.research.att.com ), because as it appears it has an important bug fix: http://R.research.att.com/R-GUI-3114-2.3-Deployment.dmg Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Force action in package install?
On May 2, 2006, at 12:09 PM, Duncan Murdoch wrote: > I tried putting a target that depends on FORCE into Makefile or > Makevars in the src directory, but it is not being built. What > sort of make magic do I need, and where do I put it in order to get > R CMD INSTALL to run my code? > I don't think that's supported at all. I have successfully used this VeryUglyHack(TM) in the package's Makevars: OBJECTS=dummy.o real1.o real2.o dummy.o: myExtraTarget echo "" > dummy.c $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -c dummy.c -o $@ where real1.o and real2.o are real object files that have corresponding sources and dummy.c is a non-existent file thus forcing make to use my extra target. This hack exploits the fact that SHLIB will let Makevars override the objects list (the above is not the exact application I use, but the essence of the idea). I agree that it would be great to add something like $(EXTRA_TARGETS) to SHLIB such that Makevars can define extra targets. Back to your original problem, though, I never build packages directly from development sources (didn't we have a discussion about this recently?) for the reasons discussed - IMHO it's much better to have a script build the package tar ball, stamping files as necessary. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Force action in package install?
On May 2, 2006, at 4:25 PM, Simon Urbanek wrote: > > On May 2, 2006, at 12:09 PM, Duncan Murdoch wrote: > >> I tried putting a target that depends on FORCE into Makefile or >> Makevars in the src directory, but it is not being built. What >> sort of make magic do I need, and where do I put it in order to >> get R CMD INSTALL to run my code? >> > > I don't think that's supported at all. I have successfully used > this VeryUglyHack(TM) in the package's Makevars: > Oops - I just realized that it's a huge overkill for what you described (the application actually did matter - it involved generated c files). The generated files force make to re-make the target unconditionally when using phony target, but that's another story. Sorry for the noise - feel free to delete it :). Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] cannot use fanny in package cluster (PR#8830)
Full_Name: Guan-Hua Huang
Version: 2.0.1
OS: Linux
Submission from: (NULL) (140.113.114.123)
I install the package cluster by using install.packages("cluster"). After
install it, it runs fine for function clara, but it does not work for function
fanny. I did the following things:
library(cluster)
set.seed(21)
x <- rbind(cbind(rnorm(10, 0, 0.5), rnorm(10, 0, 0.5)),
cbind(rnorm(15, 5, 0.5), rnorm(15, 5, 0.5)),
cbind(rnorm( 3,3.2,0.5), rnorm( 3,3.2,0.5)))
.proctime00 <- proc.time()
(fannyx <- fanny(x, 2))
and got the following messages:
Error in .Fortran("fanny", as.integer(n), as.integer(jp), k, x2, dis = dv, ;
Fortran function name not in DLL for package cluster
Any help.
Guan-Hua
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Re: [Rd] cannot use fanny in package cluster (PR#8830)
[EMAIL PROTECTED] wrote:
> Full_Name: Guan-Hua Huang
> Version: 2.0.1
> OS: Linux
> Submission from: (NULL) (140.113.114.123)
>
>
> I install the package cluster by using install.packages("cluster"). After
> install it, it runs fine for function clara, but it does not work for function
> fanny. I did the following things:
>
> library(cluster)
> set.seed(21)
> x <- rbind(cbind(rnorm(10, 0, 0.5), rnorm(10, 0, 0.5)),
>cbind(rnorm(15, 5, 0.5), rnorm(15, 5, 0.5)),
>cbind(rnorm( 3,3.2,0.5), rnorm( 3,3.2,0.5)))
> .proctime00 <- proc.time()
> (fannyx <- fanny(x, 2))
>
> and got the following messages:
>
> Error in .Fortran("fanny", as.integer(n), as.integer(jp), k, x2, dis = dv, ;
> Fortran function name not in DLL for package cluster
>
> Any help.
>
> Guan-Hua
>
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If this is a bug, then with your installation of the package, but NOT
with R nor with the package.
Please read the FAQs what a bug is and how to report it (check with a
***recent*** version of R first!).
Uwe Ligges
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Re: [Rd] Histogram to pdf file (PR#8829)
[EMAIL PROTECTED] wrote: > Full_Name: Ksawery > Version: 2.30 Currently we have R-2.3.0. 2.30 will be released in October 2019, if R core does not manage to get R-3.0.0 out some day before. > OS: WinXp > Submission from: (NULL) (195.150.76.2) > > > The bug apears when I'm trying to save, for example histogram into PDF > file.I'm > using Polish language, and while in R letters are correct, in PDF file I have > some strange one... Which bug? Please read the FAQs what a bug is and how to report it. I'd highly recommend to *ask* a question on R-help how to solve your problem rather than claiming there is a bug without giving a reproducible example that helps to fix it. Uwe Ligges > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
