Re: [Rd] Problem in conditional looping

2008-06-27 Thread Mathieu Ribatet

Why don't you consider a "while" loop e.g.

while (Pij < 0)
##Then you resample according to your code

Nadeem Shafique a écrit :

Respected All,

I am writing a program in R and facing some problem with applying "if statment".

Program first draw random numbers from bivariate normal distribution
then compute variable say Pi and Pij from that sample and
then further computation
.
.
.
In some samples Pij is appearing with negitive sign and ultimately
resulted in an negative variance estimator.  Now i want to design the
program like this if the Pij is negative then go back and draw another
sample until we get a sample that produces positive Pij and then move
forward for further processing.

Best Regards,

Nadeem Shafique Butt

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[Rd] plot(type="l") disjoint between 100 and 101st datapoint

2008-06-27 Thread Richard Martin
Dear All:

We have been experiencing networking issues so I don't know if this
got through; I can't see it in the archive.  My sincere apologies if
this appears twice.

I may have found an unusual bug and am posting here to see if anyone
can reproduce it on their system. First of all, sessionInfo():

> sessionInfo()
R version 2.7.1 (2008-06-23)
i386-apple-darwin8.10.1

locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

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

The bug is in the plot() command; it does not draw the line between
the 100th and 101st point in a dataset when plotting in line mode
(type="l").

plot(1:102, type="l") reproduces the problem consistently on my
machine, on both png and quartz devices. The result of saving this to
the png device by the code below can be seen at
http://imagebin.ca/view/txKBk2M.html

> png(filename="disjoint.png")
> plot(1:102, type="l")
> dev.off()
quartz
2

I had a look through the archives but couldn't see any discussion of
this; apologies if I missed it. Is this purely a mac issue?
Unfortunately I don't have any other machines to test it on.

Kind regards,

Richard Martin




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Re: [Rd] plot(type="l") disjoint between 100 and 101st datapoint

2008-06-27 Thread Sklyar, Oleg (MI London)
I do not see any disjoint on 2.7.0 patched (r45879) or 2.8.0 devel
(r45830) on RHEL5 64bit.

Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED] 

> -Original Message-
> From: [EMAIL PROTECTED] 
> [mailto:[EMAIL PROTECTED] On Behalf Of Richard Martin
> Sent: 27 June 2008 12:38
> To: r-devel@r-project.org
> Subject: [Rd] plot(type="l") disjoint between 100 and 101st datapoint
> 
> Dear All:
> 
> We have been experiencing networking issues so I don't know 
> if this got through; I can't see it in the archive.  My 
> sincere apologies if this appears twice.
> 
> I may have found an unusual bug and am posting here to see if 
> anyone can reproduce it on their system. First of all, sessionInfo():
> 
> > sessionInfo()
> R version 2.7.1 (2008-06-23)
> i386-apple-darwin8.10.1
> 
> locale:
> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> 
> The bug is in the plot() command; it does not draw the line 
> between the 100th and 101st point in a dataset when plotting 
> in line mode (type="l").
> 
> plot(1:102, type="l") reproduces the problem consistently on 
> my machine, on both png and quartz devices. The result of 
> saving this to the png device by the code below can be seen 
> at http://imagebin.ca/view/txKBk2M.html
> 
> > png(filename="disjoint.png")
> > plot(1:102, type="l")
> > dev.off()
> quartz
> 2
> 
> I had a look through the archives but couldn't see any 
> discussion of this; apologies if I missed it. Is this purely 
> a mac issue?
> Unfortunately I don't have any other machines to test it on.
> 
> Kind regards,
> 
> Richard Martin
> 
> 
> 
> 
> --
> Contendere, Explorare, Invenire, et non Cedere
> 
> 
> 
> --
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> 
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Re: [Rd] plot(type="l") disjoint between 100 and 101st datapoint

2008-06-27 Thread Sklyar, Oleg (MI London)
No, it does not happen here and I tested other ranges as well.

Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED] 

> -Original Message-
> From: Richard Martin [mailto:[EMAIL PROTECTED] 
> Sent: 27 June 2008 15:32
> To: Sklyar, Oleg (MI London)
> Cc: r-devel@r-project.org
> Subject: Re: [Rd] plot(type="l") disjoint between 100 and 
> 101st datapoint
> 
> Hi Dr Sklyar,
> 
> This is interesting to know - I have just noticed that it 
> also happens every 100 points, there is another disjoint 
> between 200 and 201. I have attached a file showing this.
> 
> The file was created using the following code:
> 
> > png("disjoint2.png")
> > plot(1:210, type="l")
> > dev.off()
> 
> Regards,
> 
> Richard
> 
> 
> 
> 2008/6/27 Sklyar, Oleg (MI London) <[EMAIL PROTECTED]>:
> > I do not see any disjoint on 2.7.0 patched (r45879) or 2.8.0 devel
> > (r45830) on RHEL5 64bit.
> >
> > Dr Oleg Sklyar
> > Technology Group
> > Man Investments Ltd
> > +44 (0)20 7144 3803
> > [EMAIL PROTECTED]
> >
> >> -Original Message-
> >> From: [EMAIL PROTECTED]
> >> [mailto:[EMAIL PROTECTED] On Behalf Of Richard Martin
> >> Sent: 27 June 2008 12:38
> >> To: r-devel@r-project.org
> >> Subject: [Rd] plot(type="l") disjoint between 100 and 
> 101st datapoint
> >>
> >> Dear All:
> >>
> >> We have been experiencing networking issues so I don't 
> know if this 
> >> got through; I can't see it in the archive.  My sincere 
> apologies if 
> >> this appears twice.
> >>
> >> I may have found an unusual bug and am posting here to see 
> if anyone 
> >> can reproduce it on their system. First of all, sessionInfo():
> >>
> >> > sessionInfo()
> >> R version 2.7.1 (2008-06-23)
> >> i386-apple-darwin8.10.1
> >>
> >> locale:
> >> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
> >>
> >> attached base packages:
> >> [1] stats graphics  grDevices utils datasets  
> methods   base
> >>
> >> The bug is in the plot() command; it does not draw the 
> line between 
> >> the 100th and 101st point in a dataset when plotting in line mode 
> >> (type="l").
> >>
> >> plot(1:102, type="l") reproduces the problem consistently on my 
> >> machine, on both png and quartz devices. The result of 
> saving this to 
> >> the png device by the code below can be seen at 
> >> http://imagebin.ca/view/txKBk2M.html
> >>
> >> > png(filename="disjoint.png")
> >> > plot(1:102, type="l")
> >> > dev.off()
> >> quartz
> >> 2
> >>
> >> I had a look through the archives but couldn't see any 
> discussion of 
> >> this; apologies if I missed it. Is this purely a mac issue?
> >> Unfortunately I don't have any other machines to test it on.
> >>
> >> Kind regards,
> >>
> >> Richard Martin
> >>
> >>
> >>
> >>
> >> --
> >> Contendere, Explorare, Invenire, et non Cedere
> >>
> >>
> >>
> >> --
> >> Contendere, Explorare, Invenire, et non Cedere
> >>
> >> __
> >> R-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
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> >
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Re: [Rd] phyper hang (PR#11813)

2008-06-27 Thread maechler
> "MW" == Morten Welinder <[EMAIL PROTECTED]>
> on Thu, 26 Jun 2008 03:55:07 +0200 (CEST) writes:

MW> Full_Name: Morten Welinder
MW> Version: 
MW> OS: Linux
MW> Submission from: (NULL) (69.113.253.99)


MW> It appears that phyper hangs for insanely large x, such as the call

MW> phyper(1e67,0,0,0)

Yes.  I think it only happens for  (x, 0,0,0)  though.

MW> Adding something like this after the tail swap seems to cure that.

MW> if (x >= NR)
MW>return R_DT_1;

yes, and that also cures  phyper(1,0,0,0)  which gave NaN
instead of 1.
Is going to be fixed for R-devel and R-patched.

Thank you, Matt!

Martin Maechler, ETH Zurich

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Re: [Rd] plot(type="l") disjoint between 100 and 101st datapoint

2008-06-27 Thread Prof Brian Ripley
Please, this is specific to your device (since png() on MacOS defaults to 
quartz).  So discuss it on R-sig-mac.


Try a different device (you do have several of those on your system!) 
including a different version of png().


I think it is related to the fix for excessively slow plotting in 2.7.0, 
but I'm not near my Mac.


On Fri, 27 Jun 2008, Richard Martin wrote:


Dear All:

We have been experiencing networking issues so I don't know if this
got through; I can't see it in the archive.  My sincere apologies if
this appears twice.

I may have found an unusual bug and am posting here to see if anyone
can reproduce it on their system. First of all, sessionInfo():


sessionInfo()

R version 2.7.1 (2008-06-23)
i386-apple-darwin8.10.1

locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

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

The bug is in the plot() command; it does not draw the line between
the 100th and 101st point in a dataset when plotting in line mode
(type="l").

plot(1:102, type="l") reproduces the problem consistently on my
machine, on both png and quartz devices. The result of saving this to
the png device by the code below can be seen at
http://imagebin.ca/view/txKBk2M.html


png(filename="disjoint.png")
plot(1:102, type="l")
dev.off()

quartz
   2

I had a look through the archives but couldn't see any discussion of
this; apologies if I missed it. Is this purely a mac issue?
Unfortunately I don't have any other machines to test it on.

Kind regards,

Richard Martin




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University of Oxford, Tel:  +44 1865 272861 (self)
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Re: [Rd] plot(type="l") disjoint between 100 and 101st datapoint

2008-06-27 Thread Richard Martin
Dear Prof. Ripley,

Thanks for your advice; indeed, plotting with cairo is not disjointed
and therefore this is a quartz issue. I will inquire further on sig
mac.

Have a nice weekend,

Regards,

Richard Martin

2008/6/27 Prof Brian Ripley <[EMAIL PROTECTED]>:
> Please, this is specific to your device (since png() on MacOS defaults to
> quartz).  So discuss it on R-sig-mac.
>
> Try a different device (you do have several of those on your system!)
> including a different version of png().
>
> I think it is related to the fix for excessively slow plotting in 2.7.0, but
> I'm not near my Mac.
>
> On Fri, 27 Jun 2008, Richard Martin wrote:
>
>> Dear All:
>>
>> We have been experiencing networking issues so I don't know if this
>> got through; I can't see it in the archive.  My sincere apologies if
>> this appears twice.
>>
>> I may have found an unusual bug and am posting here to see if anyone
>> can reproduce it on their system. First of all, sessionInfo():
>>
>>> sessionInfo()
>>
>> R version 2.7.1 (2008-06-23)
>> i386-apple-darwin8.10.1
>>
>> locale:
>> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>>
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>>
>> The bug is in the plot() command; it does not draw the line between
>> the 100th and 101st point in a dataset when plotting in line mode
>> (type="l").
>>
>> plot(1:102, type="l") reproduces the problem consistently on my
>> machine, on both png and quartz devices. The result of saving this to
>> the png device by the code below can be seen at
>> http://imagebin.ca/view/txKBk2M.html
>>
>>> png(filename="disjoint.png")
>>> plot(1:102, type="l")
>>> dev.off()
>>
>> quartz
>>   2
>>
>> I had a look through the archives but couldn't see any discussion of
>> this; apologies if I missed it. Is this purely a mac issue?
>> Unfortunately I don't have any other machines to test it on.
>>
>> Kind regards,
>>
>> Richard Martin
>>
>>
>>
>>
>> --
>> Contendere, Explorare, Invenire, et non Cedere
>>
>>
>>
>> --
>> Contendere, Explorare, Invenire, et non Cedere
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
> --
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> 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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[Rd] RBGL not compiling on Debian Lenny with c++ (Debian 4.3.1-2) 4.3.1

2008-06-27 Thread Mark Kimpel
I've just installed Debian Lenny and RBGL fails compilation with the
following errors (sessionInfo() follows).

* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/home/mkimpel/R_HOME/R-patched/R-build/lib64/R/include
-I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c bbc.cpp -o bbc.o
In file included from /usr/include/c++/4.3/ext/hash_set:64,
 from boostIncl/boost/graph/adjacency_list.hpp:22,
 from RBGL.hpp:26,
 from bbc.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:32:2: warning:
#warning This file includes at least one deprecated or antiquated
header which may be removed without further notice at a future date.
Please use a non-deprecated interface with equivalent functionality
instead. For a listing of replacement headers and interfaces, consult
the file backward_warning.h. To disable this warning use
-Wno-deprecated.
In file included from boostIncl/boost/graph/dijkstra_shortest_paths.hpp:19,
 from boostIncl/boost/graph/betweenness_centrality.hpp:14,
 from bbc.cpp:2:
boostIncl/boost/pending/relaxed_heap.hpp: In member function 'size_t
boost::relaxed_heap::log_base_2(size_t)':
boostIncl/boost/pending/relaxed_heap.hpp:101: error: 'CHAR_BIT' was
not declared in this scope
make: *** [bbc.o] Error 1

> sessionInfo()
R version 2.7.1 Patched (2008-06-26 r45997)
x86_64-unknown-linux-gnu

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

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

other attached packages:
[1] graph_1.18.1

loaded via a namespace (and not attached):
[1] cluster_1.11.11 tcltk_2.7.1 tools_2.7.1

-- 
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN 46074

(317) 490-5129 Work, & Mobile & VoiceMail
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Re: [Rd] RBGL not compiling on Debian Lenny with c++ (Debian 4.3.1-2) 4.3.1

2008-06-27 Thread Kasper Daniel Hansen

Hi Mark

This issue (I think) was recently discussed on the BioC list. The  
upshot of that conversation was that Boost (not RBGL) has a problem  
with GCC 4.3. You'll need to fix the headers of boost which is rather  
simple, there is a fix in the Bioconductor thread.


Kasper

On Jun 27, 2008, at 9:14 AM, Mark Kimpel wrote:


I've just installed Debian Lenny and RBGL fails compilation with the
following errors (sessionInfo() follows).

* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/home/mkimpel/R_HOME/R-patched/R-build/lib64/R/include
-I/usr/local/include   -IboostIncl  -fpic  -g -O2 -c bbc.cpp -o bbc.o
In file included from /usr/include/c++/4.3/ext/hash_set:64,
from boostIncl/boost/graph/adjacency_list.hpp:22,
from RBGL.hpp:26,
from bbc.cpp:1:
/usr/include/c++/4.3/backward/backward_warning.h:32:2: warning:
#warning This file includes at least one deprecated or antiquated
header which may be removed without further notice at a future date.
Please use a non-deprecated interface with equivalent functionality
instead. For a listing of replacement headers and interfaces, consult
the file backward_warning.h. To disable this warning use
-Wno-deprecated.
In file included from boostIncl/boost/graph/ 
dijkstra_shortest_paths.hpp:19,
from boostIncl/boost/graph/ 
betweenness_centrality.hpp:14,

from bbc.cpp:2:
boostIncl/boost/pending/relaxed_heap.hpp: In member function 'size_t
boost::relaxed_heap::log_base_2(size_t)':
boostIncl/boost/pending/relaxed_heap.hpp:101: error: 'CHAR_BIT' was
not declared in this scope
make: *** [bbc.o] Error 1


sessionInfo()

R version 2.7.1 Patched (2008-06-26 r45997)
x86_64-unknown-linux-gnu

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


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

other attached packages:
[1] graph_1.18.1

loaded via a namespace (and not attached):
[1] cluster_1.11.11 tcltk_2.7.1 tools_2.7.1

--
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN 46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)

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[Rd] unexpected lining up of labels in axis(4,hadj=1) (PR#11836)

2008-06-27 Thread rene . locher
Full_Name: Rene Locher
Version:  2.7.1
OS: i386-pc-mingw32
Submission from: (NULL) (160.85.231.140)


Here is the example:

par(las=1,mar=rep(4,4))
plot(c(-1000,1000),axes=FALSE)
box()
axis(4,hadj=1)
## axis labels are positioned in an awkward way

## I would expect to see label positions like here:
axis(4,hadj=1,mgp=c(3,3,0))

These are my sessionInfos:
R version 2.7.1 (2008-06-23) 
i386-pc-mingw32 

locale:
LC_COLLATE=German_Switzerland.1252;LC_CTYPE=German_Switzerland.1252;LC_MONETARY=German_Switzerland.1252;LC_NUMERIC=C;LC_TIME=German_Switzerland.1252

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

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Re: [Rd] plot(type="l") disjoint between 100 and 101st datapoint

2008-06-27 Thread Richard Martin
Hi Dr Sklyar,

This is interesting to know - I have just noticed that it also happens
every 100 points, there is another disjoint between 200 and 201. I
have attached a file showing this.

The file was created using the following code:

> png("disjoint2.png")
> plot(1:210, type="l")
> dev.off()

Regards,

Richard



2008/6/27 Sklyar, Oleg (MI London) <[EMAIL PROTECTED]>:
> I do not see any disjoint on 2.7.0 patched (r45879) or 2.8.0 devel
> (r45830) on RHEL5 64bit.
>
> Dr Oleg Sklyar
> Technology Group
> Man Investments Ltd
> +44 (0)20 7144 3803
> [EMAIL PROTECTED]
>
>> -Original Message-
>> From: [EMAIL PROTECTED]
>> [mailto:[EMAIL PROTECTED] On Behalf Of Richard Martin
>> Sent: 27 June 2008 12:38
>> To: r-devel@r-project.org
>> Subject: [Rd] plot(type="l") disjoint between 100 and 101st datapoint
>>
>> Dear All:
>>
>> We have been experiencing networking issues so I don't know
>> if this got through; I can't see it in the archive.  My
>> sincere apologies if this appears twice.
>>
>> I may have found an unusual bug and am posting here to see if
>> anyone can reproduce it on their system. First of all, sessionInfo():
>>
>> > sessionInfo()
>> R version 2.7.1 (2008-06-23)
>> i386-apple-darwin8.10.1
>>
>> locale:
>> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>>
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>>
>> The bug is in the plot() command; it does not draw the line
>> between the 100th and 101st point in a dataset when plotting
>> in line mode (type="l").
>>
>> plot(1:102, type="l") reproduces the problem consistently on
>> my machine, on both png and quartz devices. The result of
>> saving this to the png device by the code below can be seen
>> at http://imagebin.ca/view/txKBk2M.html
>>
>> > png(filename="disjoint.png")
>> > plot(1:102, type="l")
>> > dev.off()
>> quartz
>> 2
>>
>> I had a look through the archives but couldn't see any
>> discussion of this; apologies if I missed it. Is this purely
>> a mac issue?
>> Unfortunately I don't have any other machines to test it on.
>>
>> Kind regards,
>>
>> Richard Martin
>>
>>
>>
>>
>> --
>> Contendere, Explorare, Invenire, et non Cedere
>>
>>
>>
>> --
>> Contendere, Explorare, Invenire, et non Cedere
>>
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>>
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Re: [Rd] unexpected lining up of labels in axis(4, hadj=1) (PR#11840)

2008-06-27 Thread ripley
Please explain (I am quoting the FAQ) how you 'are sure you know for
certain what it ought to have done'.  Please quote and give exact 
references to the documentation that led you to expect what you expected 
(but did not actually describe).

I would have expected it to work as documented using the default value 
mgp=c(3,1,0), and that is what I see when I run the example.  As far as I 
can see this is the result of not wanting what you actually asked for.


On Fri, 27 Jun 2008, [EMAIL PROTECTED] wrote:

> Full_Name: Rene Locher
> Version:  2.7.1
> OS: i386-pc-mingw32
> Submission from: (NULL) (160.85.231.140)
>
>
> Here is the example:
>
> par(las=1,mar=rep(4,4))
> plot(c(-1000,1000),axes=FALSE)
> box()
> axis(4,hadj=1)
> ## axis labels are positioned in an awkward way
>
> ## I would expect to see label positions like here:
> axis(4,hadj=1,mgp=c(3,3,0))
>
> These are my sessionInfos:
> R version 2.7.1 (2008-06-23)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=German_Switzerland.1252;LC_CTYPE=German_Switzerland.1252;LC_MONETARY=German_Switzerland.1252;LC_NUMERIC=C;LC_TIME=German_Switzerland.1252
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
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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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