Nabble - R

Re: Random number generation

2008-05-13T02:55:33Z

On Behalf Of Esmail Bonakdarian wrote:
> ...
> What I read doesn't seem to be incorrect however (it may even
> have been an archived message here), the *language* itself
> does not seem to support block *comments*. Using conditional
> constructs, or an IDE/editor to achieve similar results is a
> work around - but not the same. I don't mean to nitpick, but
> as a computer scientist I see this as different :-)

For those using NEdit, the R block comment macro:

replace_in_selection("^","#","regex")

and the corresponding R block uncomment macro:

replace_in_selection("^#","","regex")

are both trivial. Just highlight the block and detonate the macro.

Jim

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From forum: R help

Re: test

2008-05-13T02:52:21Z

Tony Plate wrote:
> You probably should check this section in your R-help subscription
> options (via https://stat.ethz.ch/mailman/options/r-help/, I think):
>
>> Receive your own posts to the list?
>

Tony,

Like jt I too have it set to receive my own messages, but I too
don't see them. I wonder if it has to do with the fact that both
of us use gmail to post to the list?

In any case, regardless if we see them, they are getting posted,
which is what matters :)

Cheers,
Esmail

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From forum: R help

Re: Regular Expressions

2008-05-13T02:52:01Z

try this:

S <- c("World_is_beautiful", "one_two_three_four","My_book")

sapply(strsplit(S, "_"), tail, n = 2)[1, ]
# or
sapply(strsplit(S, "_"), function(x) x[length(x) - 1])

I hope it helps.

Best,
Dimitris

----
Dimitris Rizopoulos
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: "Shubha Vishwanath Karanth" <shubhak@...>
To: <r-help@...>
Sent: Tuesday, May 13, 2008 11:02 AM
Subject: [R] Regular Expressions

Hi R,

Again struck with regular expressions...

Suppose,

S=c("World_is_beautiful", "one_two_three_four","My_book")

I need to extract the last but one element of the strings. So, my
output should look like:

Ans=c("is","three","My")

gsub() can do this...but wondering how do I give the regular
expression....

Shubha Karanth | Amba Research

Ph +91 80 3980 8031 | Mob +91 94 4886 4510

Bangalore * Colombo * London * New York * San José * Singapore *
www.ambaresearch.com

This e-mail may contain confidential and/or privileged
i...{{dropped:13}}

--------------------------------------------------------------------------------

> ______________________________________________
> R-help@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

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From forum: R help

Re: array dimension changes with assignment

2008-05-13T02:44:55Z

>Why does the assignment of a 3178x93 object to >another 3178x93 object remove the dimension attribute?>> GT <- array(dim = c(6,nrow(InData),ncol(InSNPs)))>> dim(GT)>[1] 6 3178 93>> SNP1 <- InSNPs[InData[,"C1"],]>> dim(SNP1)>[1] 3178 93>> SNP2 <- InSNPs[InData[,"C2"],]>> dim(SNP2)>[1] 3178 93>> dim(pmin(SNP1,SNP2))>[1] 3178 93>> GT[1,,] <- pmin(SNP1,SNP2)>> dim(GT)>NULL # why??????????????????????????????????????>> GT[2,,] <- pmax(SNP1,SNP2)>Error in GT[2, , ] <- pmax(SNP1, SNP2) : incorrect number of .subscripts
---------------------------------------------------

My understanding is that an array is just a list with a dimension attribute, so first note that loosing the dim attribute is not a great loss. It does not represent an inefficiency.

But consider this code:
> GT <- array(dim = c(6,3178, 93) )> dim(GT)[1] 6 3178 93> > > SNP1 <-as.array(matrix(0,nrow=3178,ncol=93))> dim(SNP1)[1] 3178 93> > > > GT[1,,] <- SNP1> dim(GT)[1] 6 3178 93

Here what you wanted to happen happened just fine. So the question you might ask yourself is: what is different? And that leads to asking what class is the SNP1 object? If you can coerce into an array you probably can avoid the issue.

Jeremiah Rounds
Graduate Student
Utah State University
_________________________________________________________________
Get Free (PRODUCT) RED Emoticons, Winks and Display Pics.

[[alternative HTML version deleted]]

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From forum: R help

Re: Format integer

2008-05-13T02:40:55Z

Anh Tran wrote:
> Hi,
> What's one way to convert an integer to a string with preceding 0's?
> such that
> '13' becomes '00000000013'
> to be put into a string
>
> I've tried formatC, but they removes all the zeros and replace it with
> blanks

Hi,

try sprintf:

>i=13
> cat(sprintf("%05d\n", i))
00013
>

HTH,

Esmail

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From forum: R help

Re: fft: characteristic function to distribution

2008-05-13T02:22:25Z

Matthias Kohl was so kind and provided me the following lines in this issue:

library(distrEx)
chf <- function(t, D){
E(D, function(x){exp(1i*t*x)}, useApply = FALSE)
}

## Normalverteilung
D <- Norm()
t <- seq(-3, 3, by = 0.05)
chf.norm <- sapply(t, chf, D = D)
chf.exakt <- exp(-t^2/2)
chf.diff <- chf.norm - chf.exakt
plot(chf.diff)
abs(chf.diff)

This is nice BUT:
* Only built-in distributions can be used
* I want to understand the fft() function, instead here you used E()
of the distrEx package.

Apart from this it was exactly what i was looking for: I know the
characteristic function and want to get the distribution. (My porposal
was to use fft(,inverse=T).)
Any help appreciated,
Thomas

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From forum: R help

Re: OS X / R.h

2008-05-13T02:06:05Z

On Tue, 13 May 2008, Adam Hinz wrote:

> Hey, I have a question about including the R framework in a file. I'm
> running OS X 10.5.2. When I attempt to use:
>
> #include <R/R.h>
>
> And compile I get the following error:
> /Library/Frameworks/R.framework/Headers/R.h:40:21: error: Rconfig.h:
> No such file or directory
> /Library/Frameworks/R.framework/Headers/R.h:41:57: error: R_ext/
> Arith.h: No such file or directory
> /Library/Frameworks/R.framework/Headers/R.h:42:50: error: R_ext/
> Boolean.h: No such file or directory
> /Library/Frameworks/R.framework/Headers/R.h:43:50: error: R_ext/
> Complex.h: No such file or directory
>
> What am I doing wrong?

Posting to multiple lists with insufficient information. This has already
been asked and answered on R-sig-mac -- see the thread beginning

https://stat.ethz.ch/pipermail/r-sig-mac/2008-May/004979.html

It would be nice to have some acknowledgement of help already received
....

>
> Thanks!
> Adam
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

--
Brian D. Ripley, ripley@...
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, UK Fax: +44 1865 272595

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From forum: R devel

Re: Unable to restore saved data in .RData (PR#11455)

2008-05-13T02:03:46Z

Sorry, there is nothing to reproduce here.

The pertinent error message is not the one you quote in your subject line
but

Error in file.exists(name) : unsupported conversion in 'filenameToWchar'

At face value that means that iconv does not know about your locale.
That's possible, but it does know about 'English'. If you can start R at
all, what does Sys.getlocale() give?

See what happens if you add LC_ALL=en to the target on the shortcut you
use to start R. That should force use of American English (it does for
me).

It's a long shot, but if that fails can you please try R-patched, binaries
available from

http://cran.r-project.org/bin/windows/base/rpatched.html

If the real error is something earlier, this might have solved it.

On Tue, 13 May 2008, ericwong001@... wrote:

> Full_Name: Eric Wong
> Version: 2.7

I presume you mean 2.7.0?

> OS: Windows XP SP2
> Submission from: (NULL) (203.198.252.239)
>
>
> I installed R software version 2.7 onto my computer (Windows XP SP2 English).
> The installation was smooth without problem.
>
> However, R program crashed with the following error message:
>
> Error in file.exists(name) : unsupported conversion in 'filenameToWchar'
> Fatal error: unable to restore saved data in .RData
>
> Can anyone provide a remedy to this? Many thanks in advance. Cheers.
>
> ______________________________________________
> R-devel@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

--
Brian D. Ripley, ripley@...
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, UK Fax: +44 1865 272595

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From forum: R devel

Regular Expressions

2008-05-13T02:02:31Z

Hi R,

Again struck with regular expressions...

Suppose,

S=c("World_is_beautiful", "one_two_three_four","My_book")

I need to extract the last but one element of the strings. So, my output should look like:

Ans=c("is","three","My")

gsub() can do this...but wondering how do I give the regular expression....

Shubha Karanth | Amba Research

Ph +91 80 3980 8031 | Mob +91 94 4886 4510

Bangalore * Colombo * London * New York * San José * Singapore * www.ambaresearch.com

This e-mail may contain confidential and/or privileged i...{{dropped:13}}

______________________________________________
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From forum: R help

Re: Permutations

2008-05-13T01:30:38Z

Hi Elke,

the matrix you are trying to create has 5^21 = 476837158203125 rows and 21 columns. I'm afraid Thierry's proposal with n=21 will not fit into memory. And the file you are writing is 5^21*5*8 bytes big, about 80108643 GB.

Perhaps you want to think a little more about what you are trying to achieve and, e.g., consider random sampling from the matrix?

In addition, look at your code: you append every single line to the output file, i.e., you open and close your file 5^21 = 476837158203125 times. File I/O always takes a lot of time. File I/O in a loop usually leads to slow execution.

HTH,
Stephan

ONKELINX, Thierry schrieb:

> Dear Elke,
>
> I think you need something like this. It's only for 3 variables, but I
> think you know how to expand it for more variables.
>
> mat <- expand.grid(a = 0:4, b = 0:4, c = 0:4)
> write.table(mat, file="C:/Documents and Settings/My
> Documents/permutations.txt",sep=";",col.names=FALSE, row.names=FALSE)
>
> HTH,
>
> Thierry

> Van: r-help-bounces@... [mailto:r-help-bounces@...]
> Namens Elke Moons
> Verzonden: dinsdag 13 mei 2008 9:49
> Aan: r-help@...
> Onderwerp: [R] Permutations
>
> Dear R-users,
>
>
>
>
>
> Is there an easy way to determine all possible vectors of length 21 with
> each entry having permutations from 0 to 4, instead of doing it like
> this?
> It really takes up too much time, and I am convinced that there exists
> something easier.
>
> Can you help me? Thank you in advance!
>
> Kind regards,
>
>
>
>
>
> Elke
>
>
>
> for (a in 0:4){
>
> for (b in 0:4){
>
> for (c in 0:4){
>
> for (d in 0:4){
>
> for (e in 0:4){
>
> for (f in 0:4){
>
> for (g in 0:4){
>
> for (h in 0:4){
>
> for (i in 0:4){
>
> for (j in 0:4){
>
> for (k in 0:4){
>
> for (l in 0:4){
>
> for (m in 0:4){
>
> for (n in 0:4){
>
> for (o in 0:4){
>
> for (p in 0:4){
>
> for (q in 0:4){
>
> for (r in 0:4){
>
> for (s in 0:4){
>
> for (u in 0:4){
>
> for (v in 0:4){
>
> vec<-list(a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,u,v)
>
> write.table(vec,file="C:/Documents and Settings/My
> Documents/permutations.txt",sep=";",col.names=FALSE, row.names=FALSE,
> append=TRUE)
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }
>
> }

--

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From forum: R help

Re: ggplot2: font size mismatch for pdf output

2008-05-13T01:29:34Z

If I do

> windows(width=6, height=5)

then the pdf plot is very good copy of what I see on screen. So the main
issue seems to be that you changed the device size when you asked for the
save. If you do that, you need to change 'pointsize' too -- but as you
changed the aspect ratio, you cannot make that work exactly.

There is a bug in ggsave() for bitmap devices: it computes the width and
height from 'dpi', but it fails to pass that information on to the
devices, which assume 72dpi. So what it actually asked for was a
8 x 6.67 inch plot at 72dpi. 72dpi would be a better default, as not all
of the many bitmap devices work correctly at other resolutions (and none
did prior to R 2.7.0).

If you want an accurate png copy of what you see on screen, use savePlot()
or the device menus. That copies the backing bitmap.

On Mon, 12 May 2008, Michael Friendly wrote:

> Sorry for not providing this in my initial posting.
> I'm using R version 2.7.0 (2008-04-22), on Win XP Pro.
>
> As I said, the .png output matched what I saw on screen.
> It was the .pdf output for which the font size was noticeably
> larger, enough to make the legend run off the screen.
>
> -Michael
>
> Prof Brian Ripley wrote:
>> What version of R and OS is this? Prior to R 2.7.0 there was little
>> attempt to match output dimensions from various devices, and one of the png
>> devices in 2.7.0 has an error in doing so, fixed in R-patched (see NEWS).
>>
>> On Mon, 12 May 2008, Michael Friendly wrote:
>>
>>> Hi
>>>
>>> In the following, the graph I see on the screen and the .png output
>>> coincide. However, in the .pdf file, the fonts seem to be scaled
>>> fairly larger, resulting in the label for the top legend disappearing.
>>> Is this an infelicity or bug, or is there something I've missed?
>>>
>>> More generally, how do I control the size of fonts used in legends
>>> and axis labels?
>>>
>>> library(car)
>>> library(ggplot2)
>>>
>>> qp <-qplot (education , income , shape=type , size=women , colour=prestige
>>> ,
>>> xlab="Education" , ylab="Income", data=Prestige)
>>> + scale_y_continuous(limits=c(NA, 20000))
>>
>> Hmm, you can't break the line before '+'.
>>
>>> qp + scale_size(to=c(1,8))
>>>
>>> ggsave(file="prestige-ggplot.png", width=6, height=5) # OK
>>> ggsave(file="prestige-ggplot.pdf", width=6, height=5) # fonts too large
>>
>> I would not expect you to be able to specify a smaller size without also
>> reducing 'pointsize'. E.g. dev.print() does so, but ggsave seems not to.
>>
>>> -Michael

--
Brian D. Ripley, ripley@...
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, UK Fax: +44 1865 272595

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From forum: R help

Re: (PR#11281) Bug in R 2.7 for over long lines (crasher+proposed fix!)

2008-05-13T01:25:09Z

On Tue, 13 May 2008, maechler@... wrote:

>>>>>> "BDR" == Prof Brian Ripley <ripley@...>
>>>>>> on Tue, 13 May 2008 07:32:43 +0100 (BST) writes:
>
> BDR> This example does not crash in R 2.7.0, R-patched nor
> BDR> R-devel (r45677) for me (x86_64 F8 Linux.) It also
> BDR> does not crash with the CRAN build of R 2.7.0 on
> BDR> Windows XP.
>
> Neither does it for me in R 2.7.0
> on two x86_64 Linux platforms:
> Ubuntu 8.04 and Redhat Enterprise 5.1

For the record, it does crash release 2.7.0 on a fully updated RHEL 5
ix86, on fully updated F7 ix86 (gdb "memory corruption"); on RHEL 4 ix86
gdb says: "double free or corruption" and points at

#0 0x003bc7a2 in _dl_sysinfo_int80 () from /lib/ld-linux.so.2
#1 0x00baa815 in raise () from /lib/tls/libc.so.6
#2 0x00bac279 in abort () from /lib/tls/libc.so.6
#3 0x00bdecca in __libc_message () from /lib/tls/libc.so.6
#4 0x00be555f in _int_free () from /lib/tls/libc.so.6
#5 0x00be593a in free () from /lib/tls/libc.so.6
#6 0x08169131 in Rf_yyparse () at gram.c:3041
#7 0x08169284 in R_Parse1 (status=0x0) at gram.c:3326
#8 0x08169362 in R_Parse (n=-1, status=0xbfffe9d8, srcfile=0x8b33820)
at gram.c:3447

This is of course only of historical interest, since 2.8.0 (2008-05-13
r45678) on RHEL 4 completes source("Features.R") repeatedly with no
apparent difficulty. So it was a 32-bit problem on some Linux systems.

Roger

>
> Martin
>
> BDR> On Tue, 13 May 2008, Soeren Sonnenburg wrote:
>
> >> On Mon, 2008-05-12 at 11:10 +0200,
> >> maechler@... wrote:
> >>> Hi Soeren,
> >>>>>>>> "SS" == Soeren Sonnenburg <bugreports@...> on
> >>>>>>>> Sat, 10 May 2008 05:32:14 +0000 writes:
> >>>
> SS> On Sat, 2008-04-26 at 09:38 +0200, Peter Dalgaard wrote:
> >>> >> bugreports@... wrote: > OK, I am just sending it
> >>> here >> too as it looks like r-devel@... > is
> >>> not the >> right place:
> >>> >>>
> >>> >> I think it was seen there too, just that noone got
> >>> around >> to reply. In R-bugs, there's a filing system
> >>> so that it >> won't be completely forgotten...
> >>>
> SS> Looks like no one cares about this :(
> >>>
> >>> Just "looks like" but it aint...
> >>>
> SS> What should I do now? I mean I pointed directly to the
> SS> bug and did show how it could be fixed....
> >>>
> >>> I'm not among the parse experts within R-core, but I
> >>> think the main problem with your report is that you talk
> >>> about a crash but do not provide "self-contained
> >>> reproducible" code to produce such a crash, but just the
> >>> assertion that you get crashes when working on R <->
> >>> Swig interaction. Can you construct simple R code
> >>> producing the crash?
> >>
> >> No. I put however difficult autogenerated (~800k big!) .R
> >> code that will crash R 2.7 at
> >> http://nn7.de/debugging/Features.R for everyone to enjoy
> >> :)
> >>
> >> Sourcing it will crash R2.7.0 (without my fix) but not
> >> 2.8.
> >>
> >> Soeren
> >>
> >> ______________________________________________
> >> R-devel@... 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: Roger.Bivand@...

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From forum: R devel

xirr...

2008-05-13T01:21:50Z

Hello.

A few weeks ago, I need to calculate the Internal Rate of Return for irregular intervals.

There is the package 'financial', with the function 'cashflow', calculating irr for regular intervals.
So I developed xirr, managing irregular intervals, that's accepting a vector of dates as xirr Excel function.

You can find the code at
http://albertosantini.blogspot.com/2008/01/xirr.html

#~ Title: XIRR Excel function simulation
#~
#~ Reference 1: How to manage irregular intervals - http://www.geocities.com/accessreddy/excel/xirr.htm
#~ Reference 2: How to calculate IRR manually - http://www.s-anand.net/Calculating_IRR_manually.html
#~
#~ Step 1: enter zeroes (0) against dates that do not have any cash outflow or inflows.
#~ Step 1bis: calculate IRR for these cash flow values using normal IRR function.
#~ Step 1tris: or using an iteractive approach as bisection method to find the NPV zeroes.
#~ Step 2: multiply this value of IRR by 365 to get annual IRR (since, these are daily cash flows).
#~ Step 3: refine using the formula =( 1+ R / 365) ^ 365 - 1), where R is the the value obtained in Step2.
#~

Regards,
Alberto Santini

From forum: R help

Re: Permutations

2008-05-13T01:15:49Z

Dear Elke,

I think you need something like this. It's only for 3 variables, but I
think you know how to expand it for more variables.

mat <- expand.grid(a = 0:4, b = 0:4, c = 0:4)
write.table(mat, file="C:/Documents and Settings/My
Documents/permutations.txt",sep=";",col.names=FALSE, row.names=FALSE)

HTH,

Thierry

------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
Thierry.Onkelinx@...
www.inbo.be

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey

-----Oorspronkelijk bericht-----
Van: r-help-bounces@... [mailto:r-help-bounces@...]
Namens Elke Moons
Verzonden: dinsdag 13 mei 2008 9:49
Aan: r-help@...
Onderwerp: [R] Permutations

Dear R-users,

Is there an easy way to determine all possible vectors of length 21 with
each entry having permutations from 0 to 4, instead of doing it like
this?
It really takes up too much time, and I am convinced that there exists
something easier.

Can you help me? Thank you in advance!

Kind regards,

Elke

for (a in 0:4){

for (b in 0:4){

for (c in 0:4){

for (d in 0:4){

for (e in 0:4){

for (f in 0:4){

for (g in 0:4){

for (h in 0:4){

for (i in 0:4){

for (j in 0:4){

for (k in 0:4){

for (l in 0:4){

for (m in 0:4){

for (n in 0:4){

for (o in 0:4){

for (p in 0:4){

for (q in 0:4){

for (r in 0:4){

for (s in 0:4){

for (u in 0:4){

for (v in 0:4){

vec<-list(a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,u,v)

write.table(vec,file="C:/Documents and Settings/My
Documents/permutations.txt",sep=";",col.names=FALSE, row.names=FALSE,
append=TRUE)

}

}

}

}

}

}

}

}

}

}

}

}

}

}

}

}

}

}

}

}

}

____________________________

Elke Moons, PhD

Transportation Research Institute/

Instituut voor Mobiliteit (IMOB)

Wetenschapspark 1, bus 15

3590 Diepenbeek

BELGIUM

Tel. +32-11-26.91.26

Fax. +32-11-26.91.99

E-mail: elke.moons@...

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and provide commented, minimal, self-contained, reproducible code.

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From forum: R help

Re: (PR#11281) Bug in R 2.7 for over long lines

2008-05-13T00:50:24Z

On Tue, 2008-05-13 at 09:01 +0200, Martin Maechler wrote:

> >>>>> "BDR" =3D=3D Prof Brian Ripley <ripley@...>
> >>>>> on Tue, 13 May 2008 07:32:43 +0100 (BST) writes:
>=20
> BDR> This example does not crash in R 2.7.0, R-patched nor
> BDR> R-devel (r45677) for me (x86_64 F8 Linux.) It also
> BDR> does not crash with the CRAN build of R 2.7.0 on
> BDR> Windows XP.
>=20
> Neither does it for me in R 2.7.0=20
> on two x86_64 Linux platforms: =20
> Ubuntu 8.04 and Redhat Enterprise 5.1

=EF=BB=BFsource("http://nn7.de/debugging/Features.R")

crashes here on debian-sid (32bit x86 architecture).

@dirk: could you give it a go on some debian x86 and amd64 machine?

Soeren

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From forum: R devel

Re: (PR#11281) Bug in R 2.7 for over long lines

2008-05-13T00:50:01Z

>>>>> "SS" == Soeren Sonnenburg <r-ml@...>
>>>>> on Tue, 13 May 2008 08:17:23 +0200 writes:

SS> On Mon, 2008-05-12 at 08:39 -0400, Duncan Murdoch wrote:
>> On 5/10/2008 5:20 PM, bugreports@... wrote: > On Sat,
>> 2008-05-10 at 11:19 +0100, Prof Brian Ripley wrote: >>
>> You will see the current code is different, and your
>> 'fix' is not needed=20 >> nor applies in R-devel.
>> >
>> > would be nice...
>> >
>> >> You failed to provide an example to reproduce the
>> alleged bug, but the=20
>> >
>> > well the bug was obvious, I told that I can trigger it
>> and that the > proposed fix fixed it - no need to provide
>> an example.
>>
>> But it would be helpful to provide an example, so that we
>> can test the fix. As Brian told you, your fix was no
>> good: it was not against the current code.

SS> Well it was when I posted it 4 days after R 2.7.0 was
SS> released.

SS> And the bug was very obvious, I mean look at this
SS> (quoting from my original report):

SS> char *LongLine = (char *) malloc(nc);
SS> ...
SS> LongLine[nc] = '\0';

SS> note that LongLine is only nc chars long, so the LongLine[nc]='\0' might
SS> be an out of bounds write. the fix would be to do
SS> char *LongLine = (char *) malloc(nc+1);

Yes, you are right about this (first part of your report).

SS> Anyway an example that will crash R 2.7.0 is here
SS> http://nn7.de/debugging/Features.R .

>> >> issue does seem to be using lines beyond the
>> documented line length.
>> >
>> > exactly. one can crash R with too long lines.
>>
>> Then the bug is also in your code, for sending lines that
>> are too long. R shouldn't crash on user error, but
>> "don't do that" is an appropriate response.

SS> I would just like to see this bug in R fixed.

>> >> So it would have only affected people who did that
>> ....
>> >
>> > or use auto-generated code like e.g. swig produces.
>>
>> Then swig should be modified to produce valid code.

SS> Sure. That's what I am trying to achieve.

SS> [...]
>> > I don't intend to play with devel versions of R, I was
>> just trying to > get swig for R2.7 to work. Sorry that it
>> triggered a bug in R. =EF=BB=BFI w= > ill > try R2.7.1
>> when it is released and report back.
>>
>> If you aren't interested in being helpful by testing
>> fixes for your code, then I doubt if any of us are going
>> to go out of our way to help you with your errors.

SS> I still don't understand what I could have possibly
SS> done wrong in my initial post
SS> (http://article.gmane.org/gmane.comp.lang.r.devel/16243/)
SS> to cause this meta-discussion.

I think it was partly misunderstanding on both sides.

The bug *was* indeed fixed only a couple of hours after your report :

>> r45496 | ... | 2008-04-25 09:37:53 +0200 (Fri, 25 Apr 2008) |
>>
>> change long-standing out-by-one error for invalid input

I agree it would have been kind if we had thanked you
and had told you that the bug actually had been fixed.
Sometimes this if forgotten because of busy "schedules" ...
So let me give you late
** Thank you very much !! **
for the original bug report.

Martin Maechler, ETH Zurich

SS> But to put things in the right light. There is no bug in
SS> my code (this time). But in R. And I did not ask for
SS> help - to the contrary: I've pointed out a trivial to
SS> fix bug in R 2.7.0 and showed how it could be fixed.

SS> The problem is that I am not really an R user, but just
SS> wanted to support the R community by porting shogun to R
SS> in the hope that it may be useful for some. To achieve
SS> this I am fixing bugs in the R swig interface generator
SS> and now also R. So the detour I am taking here is
SS> massive and I have not received any help (except from
SS> Dirk so far).

SS> So if possible lets stay focused on the bug: Dirk helped
SS> me to get the R from svn-trunk (it says R 2.8 at
SS> startup) to compile and voila, sourcing the code from
SS> above does not generate any crashes anymore. So the
SS> rewrite of gram.c fixes it I guess.

SS> Soeren

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From forum: R devel

Permutations

2008-05-13T00:49:20Z

Dear R-users,

Is there an easy way to determine all possible vectors of length 21 with
each entry having permutations from 0 to 4, instead of doing it like this?
It really takes up too much time, and I am convinced that there exists
something easier.

Can you help me? Thank you in advance!

Kind regards,

Elke

for (a in 0:4){

for (b in 0:4){

for (c in 0:4){

for (d in 0:4){

for (e in 0:4){

for (f in 0:4){

for (g in 0:4){

for (h in 0:4){

for (i in 0:4){

for (j in 0:4){

for (k in 0:4){

for (l in 0:4){

for (m in 0:4){

for (n in 0:4){

for (o in 0:4){

for (p in 0:4){

for (q in 0:4){

for (r in 0:4){

for (s in 0:4){

for (u in 0:4){

for (v in 0:4){

vec<-list(a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,u,v)

write.table(vec,file="C:/Documents and Settings/My
Documents/permutations.txt",sep=";",col.names=FALSE, row.names=FALSE,
append=TRUE)

}

}

}

}

}

}

}

}

}

}

}

}

}

}

}

}

}

}

}

}

}

____________________________

Elke Moons, PhD

Transportation Research Institute/

Instituut voor Mobiliteit (IMOB)

Wetenschapspark 1, bus 15

3590 Diepenbeek

BELGIUM

Tel. +32-11-26.91.26

Fax. +32-11-26.91.99

E-mail: elke.moons@...

[[alternative HTML version deleted]]

______________________________________________
R-help@... mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

From forum: R help

Re: (PR#11281) Bug in R 2.7 for over long lines (crasher+proposed fix!)

2008-05-13T00:45:12Z

2008/5/13 <maechler@...>:

I get a segfault.

> sessionInfo()
R version 2.7.0 (2008-04-22)
i686-pc-linux-gnu

locale:
LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=C;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

$ uname -r
2.6.22-14-generic

--
Antonio, Fabio Di Narzo
Ph.D. student at
Department of Statistical Sciences
University of Bologna, Italy

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From forum: R devel

Re: Left censored responses in mixed effects models(II)

2008-05-13T00:45:03Z

Dear Bert,
you can also translate in nlme, as I'm trying to do, the approach of
Thiébaut and *Gadda( *Mixed models for longitudinal left-censored
repeated measures. Computer Methods and Programs in Biomedicine 74
<http://www.informatik.uni-trier.de/%7Eley/db/journals/cmpb/cmpb74.html#ThiebautJ04>(3):
<javascript:void(0)>(2004)) written in nlmixed(SAS)
Giovanni
Bert Gunter ha scritto:

> Dear R Fellow-Travellers:
>
> What is your recommended way of dealing with a left-censored response
> (non-detects) in (linear Gaussian) mixed effects models?
>
> Specifics: Response is a numeric positive measurement (of volume, actually);
> but when it falls below some unknown and slightly random value (depending on
> how the sample is prepared and measured), it cannot be measured and is
> recorded as 0.
>
> There is some statistical literature on this, but I was unable to find
> anything that appeared to me to implement a strategy in any R package. If it
> matters, I am less interested in inference than in removing possible bias in
> estimation.
>
> Feel free to respond off-list if you feel that this would not be of general
> interest.
>
> Cheers,
>
> Bert Gunter
> Genentech
>
> ______________________________________________
> R-help@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
>

--
dr. Giovanni Parrinello
Department of Biotecnologies
Medical Statistics Unit
University of Brescia
Viale Europa, 11 25123 Brescia
email: parrinel@...
Phone: +390303717528
Fax: +390303717488

______________________________________________
R-help@... mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

From forum: R help

Re: Left censored responses in mixed effects models

2008-05-13T00:37:36Z

Dear Bert,
a solution is the 'package'
censre3 by Hughes JP
Reference: Hughes JP: Mixed effects models with censored data with
application to HIV RNA levels. Biometrics, 55:625-629, 1999.

Giovanni

Don MacQueen ha scritto:

> I assume you've looked at the NADA package(?) While I don't believe it
> goes as far as dealing the mixed effects models, it might give you a
> starting point, and possibly some additional references.
>
> -Don
>
> At 9:08 AM -0700 5/12/08, Bert Gunter wrote:
>> Dear R Fellow-Travellers:
>>
>> What is your recommended way of dealing with a left-censored response
>> (non-detects) in (linear Gaussian) mixed effects models?
>>
>> Specifics: Response is a numeric positive measurement (of volume,
>> actually);
>> but when it falls below some unknown and slightly random value
>> (depending on
>> how the sample is prepared and measured), it cannot be measured and is
>> recorded as 0.
>>
>> There is some statistical literature on this, but I was unable to find
>> anything that appeared to me to implement a strategy in any R
>> package. If it
>> matters, I am less interested in inference than in removing possible
>> bias in
>> estimation.
>>
>> Feel free to respond off-list if you feel that this would not be of
>> general
>> interest.
>>
>> Cheers,
>>
>> Bert Gunter
>> Genentech
>>
>> ______________________________________________
>> R-help@... mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>

From forum: R help

Re: ggplot2: font size mismatch for pdf output

2008-05-13T00:18:04Z

What you can do is change the parameter "pointsize" when creating the
device. See ?pdf. It will change the size of all texts (labels, legend,
title...) at the same time. I tried it with png, it works quite well
(provided you use the latest versions of everything, including cairo, I
think).

Xavier

hadley wickham a écrit :

>> More generally, how do I control the size of fonts used in legends
>> and axis labels?
>>
>
> There is no general way (yet) - it is on my customisation to do list,
> which I hope to make progress on over summer.
>
> Hadley
>
>

--
Xavier Chardon
Thésard Institut de l'élevage / INRA
Projet ACTA "modélisation environnementale des systèmes bovins et porcins"

xavier.chardon@...
xavier.chardon@...
02 23 48 50 91

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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From forum: R help

Compare columns

2008-05-13T00:08:03Z

Dear R-users,

I have the following 2 files;

A

V1 V2
A 1
A 2
A 3
A 4
B 1
B 4
C 1
C 3
D 4

B

V1 V2
process1 1
process2 2
process3 3
process4 4

I want to get this output

C
V1 V2 V3
A 1 process1
A 2 process2
A 3 process3
A 4 process4
B 1 process1
B 4 process4
C 1 process1
C 3 process3
D 4 process4

I want to compare A$V2 with B$V2, if it is the same, then append B$V1 to A.

Any tips are highly appreciated. TQVM!

--
Suhaila Zainudin
PhD Candidate
Universiti Teknologi Malaysia

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

From forum: R help

Re: (PR#11281) Bug in R 2.7 for over long lines (crasher+proposed fix!)

2008-05-13T00:05:13Z

>>>>> "BDR" == Prof Brian Ripley <ripley@...>
>>>>> on Tue, 13 May 2008 07:32:43 +0100 (BST) writes:

BDR> This example does not crash in R 2.7.0, R-patched nor
BDR> R-devel (r45677) for me (x86_64 F8 Linux.) It also
BDR> does not crash with the CRAN build of R 2.7.0 on
BDR> Windows XP.

Neither does it for me in R 2.7.0
on two x86_64 Linux platforms:
Ubuntu 8.04 and Redhat Enterprise 5.1

Martin

BDR> On Tue, 13 May 2008, Soeren Sonnenburg wrote:

>> On Mon, 2008-05-12 at 11:10 +0200,
>> maechler@... wrote:
>>> Hi Soeren,
>>>>>>>> "SS" == Soeren Sonnenburg <bugreports@...> on
>>>>>>>> Sat, 10 May 2008 05:32:14 +0000 writes:
>>>
SS> On Sat, 2008-04-26 at 09:38 +0200, Peter Dalgaard wrote:
>>> >> bugreports@... wrote: > OK, I am just sending it
>>> here >> too as it looks like r-devel@... > is
>>> not the >> right place:
>>> >>>
>>> >> I think it was seen there too, just that noone got
>>> around >> to reply. In R-bugs, there's a filing system
>>> so that it >> won't be completely forgotten...
>>>
SS> Looks like no one cares about this :(
>>>
>>> Just "looks like" but it aint...
>>>
SS> What should I do now? I mean I pointed directly to the
SS> bug and did show how it could be fixed....
>>>
>>> I'm not among the parse experts within R-core, but I
>>> think the main problem with your report is that you talk
>>> about a crash but do not provide "self-contained
>>> reproducible" code to produce such a crash, but just the
>>> assertion that you get crashes when working on R <->
>>> Swig interaction. Can you construct simple R code
>>> producing the crash?
>>
>> No. I put however difficult autogenerated (~800k big!) .R
>> code that will crash R 2.7 at
>> http://nn7.de/debugging/Features.R for everyone to enjoy
>> :)
>>
>> Sourcing it will crash R2.7.0 (without my fix) but not
>> 2.8.
>>
>> Soeren
>>
>> ______________________________________________
>> R-devel@... mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>

--
Brian D. Ripley, ripley@...
BDR> Professor of Applied Statistics,
BDR> http://www.stats.ox.ac.uk/~ripley/ University of
BDR> Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road,
BDR> +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865
BDR> 272595

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From forum: R devel

Re: is.category

2008-05-12T23:53:07Z

Applejus <ielkhoury <at> gmail.com> writes:

>
>
> Hello,
>
> Could someone tell me what the SPLUS "is.category" function do and what is
> its equivalent in R?
> Thank you, I couldn't find any help elsewhere...
>
>

If you Web search for "splus help" or similar, you will find, among others,

http://www.uni-muenster.de/ZIV/Mitarbeiter/BennoSueselbeck/s-html/shelp.html

and there under "is.category"

"Creates or tests for categorical objects (vectors with a "levels" attribute).
This function is deprecated; factor or ordered are now preferred."

Hans Werner

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From forum: R help

Re: (PR#11281) Bug in R 2.7 for over long lines (crasher+proposed

2008-05-12T23:35:16Z

This example does not crash in R 2.7.0, R-patched nor R-devel (r45677) for
me (x86_64 F8 Linux.) It also does not crash with the CRAN build of R
2.7.0 on Windows XP.

On Tue, 13 May 2008, Soeren Sonnenburg wrote:

> On Mon, 2008-05-12 at 11:10 +0200, maechler@... wrote:
>> Hi Soeren,
>>>>>>> "SS" == Soeren Sonnenburg <bugreports@...>
>>>>>>> on Sat, 10 May 2008 05:32:14 +0000 writes:
>>
>> SS> On Sat, 2008-04-26 at 09:38 +0200, Peter Dalgaard wrote:
>> >> bugreports@... wrote: > OK, I am just sending it here
>> >> too as it looks like r-devel@... > is not the
>> >> right place:
>> >>>
>> >> I think it was seen there too, just that noone got around
>> >> to reply. In R-bugs, there's a filing system so that it
>> >> won't be completely forgotten...
>>
>> SS> Looks like no one cares about this :(
>>
>> Just "looks like" but it aint...
>>
>> SS> What should I do now? I mean I pointed directly to the
>> SS> bug and did show how it could be fixed....
>>
>> I'm not among the parse experts within R-core, but I think the
>> main problem with your report is that
>> you talk about a crash but do not provide "self-contained
>> reproducible" code to produce such a crash, but just the
>> assertion that you get crashes when working on R <-> Swig
>> interaction.
>> Can you construct simple R code producing the crash?
>
> No. I put however difficult autogenerated (~800k big!) .R code that will
> crash R 2.7 at http://nn7.de/debugging/Features.R for everyone to
> enjoy :)
>
> Sourcing it will crash R2.7.0 (without my fix) but not 2.8.
>
> Soeren
>
> ______________________________________________
> R-devel@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

From forum: R devel

Re: (PR#11281) Bug in R 2.7 for over long lines

2008-05-12T23:17:23Z

On Mon, 2008-05-12 at 08:39 -0400, Duncan Murdoch wrote:

> On 5/10/2008 5:20 PM, bugreports@... wrote:
> > On Sat, 2008-05-10 at 11:19 +0100, Prof Brian Ripley wrote:
> >> You will see the current code is different, and your 'fix' is not needed=20
> >> nor applies in R-devel.
> >
> > would be nice...
> >
> >> You failed to provide an example to reproduce the alleged bug, but the=20
> >
> > well the bug was obvious, I told that I can trigger it and that the
> > proposed fix fixed it - no need to provide an example.
>
> But it would be helpful to provide an example, so that we can test the
> fix. As Brian told you, your fix was no good: it was not against the
> current code.

Well it was when I posted it 4 days after R 2.7.0 was released.

And the bug was very obvious, I mean look at this (quoting from my
original report):

char *LongLine = (char *) malloc(nc);
...
LongLine[nc] = '\0';

note that LongLine is only nc chars long, so the LongLine[nc]='\0' might
be an out of bounds write. the fix would be to do
char *LongLine = (char *) malloc(nc+1);

Anyway an example that will crash R 2.7.0 is here
http://nn7.de/debugging/Features.R .

> >> issue does seem to be using lines beyond the documented line length.
> >
> > exactly. one can crash R with too long lines.
>
> Then the bug is also in your code, for sending lines that are too long.
> R shouldn't crash on user error, but "don't do that" is an appropriate
> response.

I would just like to see this bug in R fixed.

> >> So it would have only affected people who did that ....
> >
> > or use auto-generated code like e.g. swig produces.
>
> Then swig should be modified to produce valid code.

Sure. That's what I am trying to achieve.

[...]
> > I don't intend to play with devel versions of R, I was just trying to
> > get swig for R2.7 to work. Sorry that it triggered a bug in R. =EF=BB=BFI w=
> > ill
> > try R2.7.1 when it is released and report back.
>
> If you aren't interested in being helpful by testing fixes for your
> code, then I doubt if any of us are going to go out of our way to help
> you with your errors.

I still don't understand what I could have possibly done wrong
in my initial
post (http://article.gmane.org/gmane.comp.lang.r.devel/16243/)
to cause this meta-discussion.

But to put things in the right light. There is no bug in my code (this
time). But in R. And I did not ask for help - to the contrary: I've
pointed out a trivial to fix bug in R 2.7.0 and showed how it could be
fixed.

The problem is that I am not really an R user, but just wanted to
support the R community by porting shogun to R in the hope that it may
be useful for some. To achieve this I am fixing bugs in the R swig
interface generator and now also R. So the detour I am taking here is
massive and I have not received any help (except from Dirk so far).

So if possible lets stay focused on the bug: Dirk helped me to get the R
from svn-trunk (it says R 2.8 at startup) to compile and voila, sourcing
the code from above does not generate any crashes anymore. So the
rewrite of gram.c fixes it I guess.

Soeren

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