Re: [R] Block-diagonal matrix

[Robin Hankin]

Hi

adiag() from the magic package does what you want:

 > library(magic)
Loading required package: abind
 > a <- matrix(1,2,2)
 > b <- matrix(6,2,3)
 > adiag(a,b)
  [,1] [,2] [,3] [,4] [,5]
[1,]11000
[2,]11000
[3,]00666
[4,]00666
 >


HTH

rksh



On 1 Sep 2005, at 00:25, Caio Lucidius Naberezny Azevedo wrote:

> Dear R-users,
>
> Does anybody know how to construct a block-diagonal matrix (with  
> the blocks being different matrixs, concerning the dimension and  
> the values), without use loops ?
>
>
> Thanks all,
>
> Caio
>
>
>
> -
>
> [[alternative HTML version deleted]]
>
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--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
  tel  023-8059-7743

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[R] source(file) => file becomes readonly

[Hjellvik Vidar]

Hello,
when I work in R, I write code in a text file that I run with the 
"source(filename)" command. In R2.1.1 the file is read-only while the source 
command is executed. This was not the case in R2.0.1. Is this a bug-fix or is 
it possible not to have the file read-only when executed?
Best regards
Vidar

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[R] Robust Regression - LTS

[Kylie-Anne Richards]

Hi,

I am using robust regression, i.e. model.robust<-ltsreg(MXD~ORR,data=DATA).
My question:- is there any way to determine the Robust Multiple R-Squared
(as returned in the summary output in splus)? I found an equivalent model in
the rrcov package which included R-square, residuals etc in it's list of
components, but when I used this package the only results returned were
equivalent to the LTS reg in the MASS package, which obviously indicates
that the summary method does not work for this class of models. 

If required:

##The output for the LTS reg (MASS) using print and summary

Call:
lqs.formula(formula = MXD ~ ORR, data = DATA, method = "lts")

Coefficients:
(Intercept)ORR
  7.578e+082.533e+01

Scale estimates 1.333e+09 1.303e+09

  Length Class  Mode
crit 1   -none- numeric
sing 1   -none- character
coefficients 2   -none- numeric
bestone  2   -none- numeric
fitted.values 4899   -none- numeric
residuals 4899   -none- numeric
scale2   -none- numeric
terms3   terms  call
call 4   -none- call
xlevels  0   -none- list
model2   data.frame list



## The output for the LTS reg (rrcov) using print and summary
 
Coefficients:
Intercept  ORR
1.178e+09  2.387e+01

Scale estimate 1.722e+09

 Length Class  Mode
best 2451   -none- numeric
raw.coefficients2   -none- numeric
alpha   1   -none- numeric
quan1   -none- numeric
raw.scale   1   -none- numeric
raw.resid4899   -none- numeric
coefficients2   -none- numeric
scale   1   -none- numeric
resid4899   -none- numeric
lts.wt   4899   -none- numeric
crit1   -none- numeric
rsquared1   -none- numeric
residuals4899   -none- numeric
intercept   1   -none- logical
method  1   -none- character
RD   4899   -none- numeric
X9798   -none- numeric
Y4899   -none- numeric
fitted.values4899   -none- numeric

## The output for the LTS reg (SPLUS) using print and summary {What I am
wanting to achieve in R}

> model.robust<-ltsreg(MXD~ORR,data=DATA,na.action=na.exclude)
> print(model.robust)
Method:
Least Trimmed Squares Robust Regression. 

Call:
ltsreg(formula = MXD ~ ORR, data = DATA, na.action = na.exclude)

Coefficients:
 Intercept ORR 
 1.465502e+009 2.325200e+001

Scale estimate of residuals:  163900 

Total number of observations:  4899 

Number of observations that determine the LTS estimate:  4409 
> summary(model.robust)
Method:
[1] "Least Trimmed Squares Robust Regression."

Call:
ltsreg(formula = MXD ~ ORR, data = DATA, na.action = na.exclude)

Coefficients:
 Intercept ORR 
 1.465502e+009 2.325200e+001

Scale estimate of residuals: 163900 

Robust Multiple R-Squared: 0.4733 

Total number of observations:  4899 

Number of observations that determine the LTS estimate:  4409 

Residuals:
  Min.   1st Qu.Median   3rd Qu.  Max. 
 -228135629879   -1032103953-2313756371234533512   55539148696

Weights:
   01 
 588 4311




Thanks very much for any help you can offer. 

Kylie-Anne Richards

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Re: [R] "best" c++ matrix library?

[Ott Toomet]

Thanks for everyone who replied to my question.

I tried newmat myself, seems to be working well.  What I am interested in
is something like

* Fast element-wise operations.  You know, it may be slow in R.

* (Some) control over memory allocation.  I would like to specify when
  the matrix should not be copied.

* Compatibility with R.  At least the way how the matrix data is
  represented in memory should be the same as R has.  Otherwise, the
  data interchange may become slow and memory-consuming.

* And, of course, the basic matrix operations like multiplication,
  inverting, eigenvalues etc

I am using linux/gcc if that matters.

Best,
Ott
 | From: "Tuszynski, Jaroslaw W." <[EMAIL PROTECTED]>
 | Date: Wed, 31 Aug 2005 12:59:04 -0400
 | 
 | What kind of matrix operations do you need? 
 | 
 | Jarek
 | 
 | -Original Message-
 | From: [EMAIL PROTECTED]
 | [mailto:[EMAIL PROTECTED] On Behalf Of Ott Toomet
 | Sent: Wednesday, August 31, 2005 12:54 PM
 | To: r-help@stat.math.ethz.ch
 | Subject: [R] "best" c++ matrix library?
 | 
 | Hi folks,
 | 
 | I am planning to write some more time-consuming matrix manipulations in c++.
 | What is the experience with the existing c++ matrix libraries?  Do you have
 | some recommendations?  Are some libraries more compatible with R than the
 | others?
 | 
 | All suggestions welcome!
 | 
 | Best,
 | Ott

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[R] News from your Bank

[Clement]

Aeacides

[[alternative HTML version deleted]]

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Re: [R] "best" c++ matrix library?

[Romain Francois]

Le 01.09.2005 10:32, Ott Toomet a écrit :

>Thanks for everyone who replied to my question.
>
>I tried newmat myself, seems to be working well.  What I am interested in
>is something like
>
>* Fast element-wise operations.  You know, it may be slow in R.
>
>* (Some) control over memory allocation.  I would like to specify when
>  the matrix should not be copied.
>
>* Compatibility with R.  At least the way how the matrix data is
>  represented in memory should be the same as R has.  Otherwise, the
>  data interchange may become slow and memory-consuming.
>
>* And, of course, the basic matrix operations like multiplication,
>  inverting, eigenvalues etc
>
>I am using linux/gcc if that matters.
>
>Best,
>Ott
> | From: "Tuszynski, Jaroslaw W." <[EMAIL PROTECTED]>
> | Date: Wed, 31 Aug 2005 12:59:04 -0400
> | 
> | What kind of matrix operations do you need? 
> | 
> | Jarek
> | 
> | -Original Message-
> | From: [EMAIL PROTECTED]
> | [mailto:[EMAIL PROTECTED] On Behalf Of Ott Toomet
> | Sent: Wednesday, August 31, 2005 12:54 PM
> | To: r-help@stat.math.ethz.ch
> | Subject: [R] "best" c++ matrix library?
> | 
> | Hi folks,
> | 
> | I am planning to write some more time-consuming matrix manipulations in c++.
> | What is the experience with the existing c++ matrix libraries?  Do you have
> | some recommendations?  Are some libraries more compatible with R than the
> | others?
> | 
> | All suggestions welcome!
> | 
> | Best,
> | Ott
>  
>
Hello,

CPPLAPACK :  is a c++ wrapper for 
lapack routines.
It is not so complicated to use once you have blas and lapack installed.
I think it is much faster than newmat.

Romain

-- 
visit the R Graph Gallery : http://addictedtor.free.fr/graphiques
 ~ 
~~  Romain FRANCOIS - http://addictedtor.free.fr ~~
Etudiant  ISUP - CS3 - Industrie et Services   
~~http://www.isup.cicrp.jussieu.fr/  ~~
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~~   http://www.inria.fr/recherche/equipes/select.fr.html~~
 ~ 

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[R] standard deviation in barplots

[Knut Krueger]

Is there any function to plot the standard deviation with the barplots


_ _
  | Deviation
|---
| -|
|  |
|  |   Barplot
|  |
|  |
|  |


with regards
Knut Krueger

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Re: [R] standard deviation in barplots

[Sean Davis]

On 9/1/05 6:32 AM, "Knut Krueger" <[EMAIL PROTECTED]> wrote:

> Is there any function to plot the standard deviation with the barplots
> 
> 
>   _ _
> | Deviation
> |---
> | -|
> |  |
> |  |   Barplot
> |  |
> |  |
> |  |
> 
> 

I think barplot2 in the gregmisc (gplots) bundle will do that.

Sean

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Re: [R] Digest reading is tedious

[Martin Maechler]

Hi Trevor,

please excuse my late reply; your e-mail was sent when I started
travelling (to Seattle and the DSC and Bioconductor workshops there).

Also, I hope you don't mind if I follow this up on R-help, since
there, the thread started and this does related to it.

> "Trevor" == Trevor Hastie <[EMAIL PROTECTED]>
> on Thu, 11 Aug 2005 11:06:08 -0700 writes:

Trevor> Dear Martin I may still be doing something wrong.
Trevor> Here is what I see now in Mozilla Firefox (attached
Trevor> jpeg file of screen dump)

isn't that "Thunderbird" ?
"Firefox" the web browser, "Thunderbird" the mail client?

Trevor> This is still not the convenient layout I was
Trevor> envisaging.  Ideally one would have the usual list
Trevor> of contributions, with authors, and they would be
Trevor> clickable

I've now looked at your screen shot and agree this is really not
satisfactory.
{In my good old Emacs VM mail reader things are different: all
 is nice with a virtual mail folder of individual messages}

Hmm, I've checked :
The MIME type used for the whole digest is
 'Content-Type: multipart/digest'
and then 'Content-Type: message/rfc822'
for each individual message.

Since there *are* mail clients that nicely support these MIME
types, I wonder why thunderbird does not. 
I'd say this is clearly a deficiency in thunderbird;
or is it something you could optionally configure to it?

What are other readers' experiences with mailman mailing lists
in digest mode -- using "MIME" type delivery?

Regards,
Martin

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Re: [R] R environment

[Jean Eid]

Thank you all for the answers. I will look into both methods for doing so.

Jean

On Thu, 1 Sep 2005, Henrik Bengtsson wrote:

> Unfortunately Duncan's suggestion to restart is probably the only way to
> go here.  I've done similar thing myself too.  What I've learned was
> that it is clever to include a so called hot-patch mechanism in your
> code, which will load R source code found in a certain directory, say,
> "hot/", once in a while (easy if you have do interations) and at the end
> of the batch code. Here is the idea (typed out of my head):
>
> patchCode <- function(path="hot", pattern="[.]R$", removeAfter=FALSE, ...) {
>files <- list.files(pattern=pattern, path=path, full.names=TRUE);
>for (file in files) {
>  tryCatch({
># You don't want you patch code to kill you batch job,
># if you for instance have a typo.
>cat("Hot-path file: ", file, "\n");
>source(file);
># Remove the file afterwards? Especially useful if you only
># want to redefine functions, and patch once.  This way you
># can also see what files has successfully been source():ed.
>if (removeAfter)
>  file.remove(file);
>  }, error = function(ex) {
>cat("Ignored error when sourcing:\n");
>print(ex);
>  })
>}
> } # patchCode()
>
> Then in your batch code something like this:
>
> while (!converged) {
># Patch the code every iteration.
>patchCode(path="hot/", removeAfter=TRUE)
># The rest of your code here
> }
>
> # Put the code you want to call at the end, in a directory
> # of its own.
> patchCode(path="hot/onFinally/", removeAfter=TRUE)
> # End of your batch code
>
> Cheers
>
> Henrik
>
>
> Duncan Murdoch wrote:
> > Jean Eid wrote:
> >
> >>This is probably a weird question but I need to know if there is a way...
> >>
> >>I run an R batch job without saving the variables at each step to the
> >>disk.   Is there a way to invoke another session of R and link it to the
> >>same environment for read only.
> >>
> >>The problem is that I am running optim with every step getting the
> >>parameters into the global env using <<- However, I forgot to issue a
> >>save(list=ls(),...) right after so I can load and see how the parameters
> >>are changing. It's been couple of days and it is still running so I am
> >>hoping that I can invoke another session of R and link it to the
> >>environment of the batch session. Does this sound totally ridiculous ?
> >>
> >>it is a debian machine with R 2.1.1
> >
> >
> > If you happened to have compiled R with debug information, you might be
> > able to use gdb or another debugger to examine variables in the running
> > process, but you probably didn't, and it's probably easier to kill the
> > job, fix it, and start it again, than it would be to learn how to see
> > the active variables using gdb.
> >
> > Duncan Murdoch
> >
> > __
> > 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
> >
> >
>
>

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Re: [R] "best" c++ matrix library?

[Martin Maechler]

> "Romain" == Romain Francois <[EMAIL PROTECTED]>
> on Thu, 01 Sep 2005 11:19:59 +0200 writes:

Romain> Le 01.09.2005 10:32, Ott Toomet a écrit :
>> Thanks for everyone who replied to my question.
>> 
>> I tried newmat myself, seems to be working well.  What I
>> am interested in is something like
>> 
>> * Fast element-wise operations.  You know, it may be slow
>> in R.
>> 
>> * (Some) control over memory allocation.  I would like to
>> specify when the matrix should not be copied.
>> 
>> * Compatibility with R.  At least the way how the matrix
>> data is represented in memory should be the same as R
>> has.  Otherwise, the data interchange may become slow and
>> memory-consuming.
>> 
>> * And, of course, the basic matrix operations like
>> multiplication, inverting, eigenvalues etc
>> 
>> I am using linux/gcc if that matters.
>> 
>> Best, Ott | From: "Tuszynski, Jaroslaw W."
>> <[EMAIL PROTECTED]> | Date: Wed, 31 Aug 2005
>> 12:59:04 -0400
>> | 
>> | What kind of matrix operations do you need?
>> | 
>> | Jarek
>> | 
>> | -Original Message- | From:
>> [EMAIL PROTECTED] |
>> [mailto:[EMAIL PROTECTED] On Behalf Of
>> Ott Toomet | Sent: Wednesday, August 31, 2005 12:54 PM |
>> To: r-help@stat.math.ethz.ch | Subject: [R] "best" c++
>> matrix library?
>> | 
>> | Hi folks,
>> | 
>> | I am planning to write some more time-consuming matrix
>> manipulations in c++.  | What is the experience with the
>> existing c++ matrix libraries?  Do you have | some
>> recommendations?  Are some libraries more compatible with
>> R than the | others?
>> | 
>> | All suggestions welcome!
>> | 
>> | Best, | Ott
>> 
>> 
Romain> Hello,

Romain> CPPLAPACK :  is a
Romain> c++ wrapper for lapack routines.  It is not so
Romain> complicated to use once you have blas and lapack
Romain> installed.  I think it is much faster than newmat.

LAPACK is ``state of the art'' of numerical algebra.
Don't use anything else if you don't have to.

It's definitely *much* more ``compatible with R''
since we base almost all our matrix computations on LAPACK.
GNU octave and commercial Matlab are also entirely based on
LAPACK for the matrix computations.

I have no idea about the "CPP" (= c++) part in CPPLAPACK though.

The CRAN package 'Matrix' has several objectives, notably
*sparse* matrix computations.  But it also uses LAPACK for dense
matric computations, AFAIR also for a few things not available
(via LAPACK) in "core R".

Martin Maechler, ETH Zurich

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[R] ROracle under windows

[Laurent TESSIER]

Hello,
I’m currently working with Oracle under windows and I’d like to use the 
ROracle package which exists only for linux/unix. Is there any possibility to 
port this package under windows?


L. Tessier
[[alternative HTML version deleted]]

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[R] convex-polygon in scatter plot

[Zlatko Petrin]

Hello,

I am trying to draw a convex-polygon (envelope) connecting the outer points
(of a particular class) in a scatter plot

[which I want to do to illustrate the range of a particular type of samples
in an ordination plot].

Is there any function to plot this kind of polygon?

Kind regards
Zlatko Petrin

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Re: [R] convex-polygon in scatter plot

[Dr. Detlef Steuer]

Hi,


ever thought about using the built-in help of R?

try

> example(chull)

cu

detlef

On Thu, 1 Sep 2005 13:51:42 +0200
"Zlatko Petrin" <[EMAIL PROTECTED]> wrote:

> Hello,
> 
> I am trying to draw a convex-polygon (envelope) connecting the outer points
> (of a particular class) in a scatter plot
> 
> [which I want to do to illustrate the range of a particular type of samples
> in an ordination plot].
> 
> Is there any function to plot this kind of polygon?
> 
> Kind regards
> Zlatko Petrin
> 
> __
> R-help@stat.math.ethz.ch mailing list
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[R] Newbie help on dim

[Christian Prinoth]

Hi, if I do

Z<-rnorm(50)
Followed by
Dim(Z)
I get NULL. Is this correct? Shouldn't I get 50 instead?

TIA
Chris

DISCLAIMER:\ L'utilizzo non autorizzato del presente messagg...{{dropped}}

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Re: [R] Newbie help on dim

[Dimitris Rizopoulos]

yes it is correct! look at ?dim() for more info. In this case you need 
length(), i.e.,

Z <- rnorm(50)
length(Z)


I hope it helps.

Best,
Dimitris


Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/336899
Fax: +32/16/337015
Web: http://www.med.kuleuven.be/biostat/
 http://www.student.kuleuven.be/~m0390867/dimitris.htm



- Original Message - 
From: "Christian Prinoth" <[EMAIL PROTECTED]>
To: 
Sent: Thursday, September 01, 2005 2:00 PM
Subject: [R] Newbie help on dim


> Hi, if I do
>
> Z<-rnorm(50)
> Followed by
> Dim(Z)
> I get NULL. Is this correct? Shouldn't I get 50 instead?
>
> TIA
> Chris
>
> DISCLAIMER:\ L'utilizzo non autorizzato del presente 
> messagg...{{dropped}}
>
> __
> 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
>

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Re: [R] Newbie help on dim

[Andy Bunn]

Check out the "dim vs length for vectors" thread:

http://finzi.psych.upenn.edu/R/Rhelp02a/archive/50720.html

This thread goes through the bug-or-feature discussion which is always
entertaining from a socio-R perspective.

Also, note "Dim" with a capital D doesn't exist.

HTH, Andy


> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] Behalf Of Christian Prinoth
> Sent: Thursday, September 01, 2005 8:01 AM
> To: r-help@stat.math.ethz.ch
> Subject: [R] Newbie help on dim
>
>
> Hi, if I do
>
> Z<-rnorm(50)
> Followed by
> Dim(Z)
> I get NULL. Is this correct? Shouldn't I get 50 instead?
>
> TIA
> Chris
>
> DISCLAIMER:\ L'utilizzo non autorizzato del presente messagg...{{dropped}}
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
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> http://www.R-project.org/posting-guide.html
>

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Re: [R] ROracle under windows

[Uwe Ligges]

Laurent TESSIER wrote:

> Hello,
> I’m currently working with Oracle under windows and I’d like to use the 
> ROracle package which exists only for linux/unix. Is there any possibility to 
> port this package under windows?


It is ported, but perhaps you need some additional files:

See
http://stat.bell-labs.com/RS-DBI/download/index.html
for the binary package provided by David James and read the comments.

Uwe Ligges


> 
> L. Tessier
>   [[alternative HTML version deleted]]
> 
> 
> 
> 
> 
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Re: [R] Newbie help on dim

[Uwe Ligges]

Christian Prinoth wrote:

> Hi, if I do
> 
> Z<-rnorm(50)
> Followed by
> Dim(Z)
> I get NULL. Is this correct? Shouldn't I get 50 instead?


No, because Z has no dim attribute. ?dim tells you:

"For an array (and hence in particular, for a matrix) dim retrieves the 
dim attribute of the object. It is NULL or a vector of mode integer."

> TIA
> Chris
> 
> DISCLAIMER:\ L'utilizzo non autorizzato del presente messagg...{{dropped}}
> 
> __
> 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

Yes, PLEASE do read the posting guide! 
http://www.R-project.org/posting-guide.html


Uwe Ligges

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Re: [R] source(file) => file becomes readonly

[Uwe Ligges]

Hjellvik Vidar wrote:

> Hello,
> when I work in R, I write code in a text file that I run with the 
> "source(filename)" command. In R2.1.1 the file is read-only while the source 
> command is executed. This was not the case in R2.0.1. Is this a bug-fix or is 
> it possible not to have the file read-only when executed?

So you want to modify a file *while* it is executed?
Sounds dangerous to me, you may want to explain further...

BTW: Which OS are we talking about?

Uwe Ligges


> Best regards
> Vidar
> 
> __
> 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

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Re: [R] Newbie help on dim

[Chuck Cleland]

Should the Value: section of the help page read:

For an array (and hence in particular, for a matrix) dim retrieves the
dim attribute of the object. It is NULL for a vector of mode integer.

NOTE: for not or in the second sentence.

Uwe Ligges wrote:
> Christian Prinoth wrote:
> 
> 
>>Hi, if I do
>>
>>Z<-rnorm(50)
>>Followed by
>>Dim(Z)
>>I get NULL. Is this correct? Shouldn't I get 50 instead?
> 
> 
> 
> No, because Z has no dim attribute. ?dim tells you:
> 
> "For an array (and hence in particular, for a matrix) dim retrieves the 
> dim attribute of the object. It is NULL or a vector of mode integer."
> 
> 
>>TIA
>>Chris
>>
>>DISCLAIMER:\ L'utilizzo non autorizzato del presente messagg...{{dropped}}
>>
>>__
>>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
> 
> 
> Yes, PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
> 
> 
> Uwe Ligges
> 
> __
> 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
> 
> 

-- 
Chuck Cleland, Ph.D.
NDRI, Inc.
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 452-1424 (M, W, F)
fax: (917) 438-0894

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Re: [R] Dataset size in R

[Uwe Ligges]

[EMAIL PROTECTED] wrote:

> Dear listers,
> 
>  
> 
> I would like to know whether a maximum size is set for data sets in R.


Well, in theory, there are some limits re. size of some integers, but 
you are far away, as far as I understand.

In practice, you will somewhere hit the limit of available memory in 
your machine.


> I'm planning on analysing data sets which have 33 points for a
> sample. The response is from GCxGC output.


I don't understand this point:
How many observations and how many variables?


> Also, with data analysis, is there a time-cost saving by performing the
> analysis in Linux as against doing it in Windows XP?

Depends on the problem. For really huge data, you might want to use a 
"64bit machine", 64bit adressing for a single R process is (yet) only 
supported on Linux. If memory does not matter, Linux is sometimes a bit 
faster, but it depends also on other facts like using CPU optimized 
linear algebra systems such as ATLAS or Goto's BLAS.

Uwe Ligges



>  
> 
> Many thanks, Peter
> 
> 
>   [[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

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[R] Using non-gcc compilers with install.packages()

[Trond Hasle Amundsen]

Hi,

I have built R 2.1.1 on Solaris and OSF1, and used the operating
system's native compiler set. This worked fine. However, when I try
using install.packages() it insists on using g77 etc., which doesn't
exist on those systems.

How can I specify which compilers to use? What about other
compile-time options like LDFLAGS etc.?

NB! Please include me in the CC list, since I'm not a mailinglist
member.

PS. I really like perl's approach to module building. When building
perl modules, it defaults to the same compilers as perl was initially
built with. This seems like a sane approach also for R IMHO.

Cheers,

-- 
Trond Hasle Amundsen <[EMAIL PROTECTED]>
Center for Information Technology Services, University of Oslo

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Re: [R] Newbie help on dim

[Uwe Ligges]

Chuck Cleland wrote:

> Should the Value: section of the help page read:
> 
> For an array (and hence in particular, for a matrix) dim retrieves the
> dim attribute of the object. It is NULL for a vector of mode integer.
> 
> NOTE: for not or in the second sentence.

NO!!! The help page is correct!

The *value* is either NULL *or* a vector of mode integer.
It is always NULL for any vector without dim attribute (also for 
character vectors!):

  x <- "a"
  dim(x) # NULL
  dim(x) <- 1
  dim(x) # 1

Uwe Ligges




> Uwe Ligges wrote:
> 
>> Christian Prinoth wrote:
>>
>>
>>> Hi, if I do
>>>
>>> Z<-rnorm(50)
>>> Followed by
>>> Dim(Z)
>>> I get NULL. Is this correct? Shouldn't I get 50 instead?
>>
>>
>>
>>
>> No, because Z has no dim attribute. ?dim tells you:
>>
>> "For an array (and hence in particular, for a matrix) dim retrieves 
>> the dim attribute of the object. It is NULL or a vector of mode integer."
>>
>>
>>> TIA
>>> Chris
>>>
>>> DISCLAIMER:\ L'utilizzo non autorizzato del presente 
>>> messagg...{{dropped}}
>>>
>>> __
>>> 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
>>
>>
>>
>> Yes, PLEASE do read the posting guide! 
>> http://www.R-project.org/posting-guide.html
>>
>>
>> Uwe Ligges
>>
>> __
>> 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
>>
>>
>

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[R] VarCorr function for assigning random effects: was Question

[Doran, Harold]

If you are indeed using lme and not lmer then the needed function is
VarCorr(). However, 2 recommendations. First, this is a busy list and
better emails subject headers get better attention. Second, I would
recommend using lmer as it is much faster. However, VarCorr seems to be
incompatible with lmer and I do not know of another function to work
with lmer.

Hence, a better email subject header will attract the attention of
others *much* smarter than me!

I hope this helps,
Harold

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Mahmoud Torabi
Sent: Wednesday, August 31, 2005 9:51 PM
To: R-help@stat.math.ethz.ch
Cc: [EMAIL PROTECTED]
Subject: [R] Question

Dear Sir/Madam

I would be pleased if anybody can help me. I'm using linear mixed model
(lme) function.I'm doing some simulation in my research and need to be
assigned variance components values during of my program. Specifically,
when I use lme function, I can get some information by use summary() and
I can assign some valuse like variance of fixed parameters and variance
of random error term by using for example  varFix and sigma.But I don't
know how I can assign for variance of random effect.
I know in SPLUS we have command var.ran, how about R ?

Thanks alot.
M.Torabi

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Re: [R] R binaries, platform independent and Design of Experiments

[Uwe Ligges]

Nam-Ky Nguyen wrote:

> Dear Rexpert,
> 
> I would like to thank those who spend time  answering my email on the
> burning of a CD with all R binary files for Windows and Linux. I have
> tried a couple of suggestions but have not been successful. I will pass
> these suggestions to our system administrator and I am sure that he can
> sort them out.
> 
> I hope that the future version of R will be written in Java so that it is
> platform independent. This means there will be a single binary file for
> each new version of R. At the moment there are files for Windows, Mac OS,
> Fedora 1, 2, 3, 4, SUSE 9.1, 9.2, 9.3, etc.

Honestly ..
a) The sources are available and really easy to compile on all those 
operating systems.
b) You do NOT want to do numerical computations on software available in 
Java byte code.

> I also hope that the future of version of R include more DOE (Design of
> Experiments) modules. R will be more useful if it is not only a language

There are some packages availabe with tools for DOE, please check CRAN.
Further contributions from users who like to do DOE (like you!) are 
welocme, of course!

Uwe Ligges



> and environment for statistical computing and graphics, but also for
> design of experiments. I am toying with the idea of adding to R some
> modules of my Gendex DOE toolkit (http://designcomputing.net/gendex/). I
> learn from an Rexpert that the first step for this exercise is to convert
> my java code to C++.  As I do not know C++ (and life is short) please let
> me know whether there is an alternative way without this conversion and
> whether you can actively help me in this exercise.
> 
> Regards,

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Re: [R] Newbie help on dim

[Achim Zeileis]

On Thu, 01 Sep 2005 08:25:14 -0400 Chuck Cleland wrote:

> Should the Value: section of the help page read:
> 
> For an array (and hence in particular, for a matrix) dim retrieves the
> dim attribute of the object. It is NULL for a vector of mode integer.

This statement is true, but less general than
  It is NULL or a vector of mode integer.
hence the latter is surely preferred.
Z

> NOTE: for not or in the second sentence.
> 
> Uwe Ligges wrote:
> > Christian Prinoth wrote:
> > 
> > 
> >>Hi, if I do
> >>
> >>Z<-rnorm(50)
> >>Followed by
> >>Dim(Z)
> >>I get NULL. Is this correct? Shouldn't I get 50 instead?
> > 

> > 
> > 
> > No, because Z has no dim attribute. ?dim tells you:
> > 
> > "For an array (and hence in particular, for a matrix) dim retrieves
> > the dim attribute of the object. It is NULL or a vector of mode
> > integer."
> > 
> > 
> >>TIA
> >>Chris
> >>
> >>DISCLAIMER:\ L'utilizzo non autorizzato del presente
> >messagg...{{dropped}}>
> >>__
> >>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
> > 
> > 
> > Yes, PLEASE do read the posting guide! 
> > http://www.R-project.org/posting-guide.html
> > 
> > 
> > Uwe Ligges
> > 
> > __
> > 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
> > 
> > 
> 
> -- 
> Chuck Cleland, Ph.D.
> NDRI, Inc.
> 71 West 23rd Street, 8th floor
> New York, NY 10010
> tel: (212) 845-4495 (Tu, Th)
> tel: (732) 452-1424 (M, W, F)
> fax: (917) 438-0894
> 
> __
> 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
>

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Re: [R] Using non-gcc compilers with install.packages()

[Roger Bivand]

On Thu, 1 Sep 2005, Trond Hasle Amundsen wrote:

> 
> Hi,
> 
> I have built R 2.1.1 on Solaris and OSF1, and used the operating
> system's native compiler set. This worked fine. However, when I try
> using install.packages() it insists on using g77 etc., which doesn't
> exist on those systems.
> 
> How can I specify which compilers to use? What about other
> compile-time options like LDFLAGS etc.?
> 
> NB! Please include me in the CC list, since I'm not a mailinglist
> member.
> 
> PS. I really like perl's approach to module building. When building
> perl modules, it defaults to the same compilers as perl was initially
> built with. This seems like a sane approach also for R IMHO.

Indeed, R is pretty sane. Fine tuning is conveniently carried out by
editing the config.site file in the root source directory; LDFLAGS are on
line 138 of the released 2.1.1 source. Which particular packages have you
found showing this behaviour?

> 
> Cheers,
> 
> 

-- 
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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Re: [R] Newbie help on dim

[Uwe Ligges]

Achim Zeileis wrote:

> On Thu, 01 Sep 2005 08:25:14 -0400 Chuck Cleland wrote:
> 
> 
>>Should the Value: section of the help page read:
>>
>>For an array (and hence in particular, for a matrix) dim retrieves the
>>dim attribute of the object. It is NULL for a vector of mode integer.
> 
> 
> This statement is true, but less general than
>   It is NULL or a vector of mode integer.
> hence the latter is surely preferred.

Z, in fact, it is not true:

  x <- integer(1)
  dim(x) <- 1
  typeof(x) # "integer"
  dim(x)# 1

Best,
Uwe




> Z
> 
> 
>>NOTE: for not or in the second sentence.
>>
>>Uwe Ligges wrote:
>>
>>>Christian Prinoth wrote:
>>>
>>>
>>>
Hi, if I do

Z<-rnorm(50)
Followed by
Dim(Z)
I get NULL. Is this correct? Shouldn't I get 50 instead?
>>>
> 
>>>
>>>No, because Z has no dim attribute. ?dim tells you:
>>>
>>>"For an array (and hence in particular, for a matrix) dim retrieves
>>>the dim attribute of the object. It is NULL or a vector of mode
>>>integer."
>>>
>>>
>>>
TIA
Chris

DISCLAIMER:\ L'utilizzo non autorizzato del presente
>>>
>>>messagg...{{dropped}}>
>>>
__
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
>>>
>>>
>>>Yes, PLEASE do read the posting guide! 
>>>http://www.R-project.org/posting-guide.html
>>>
>>>
>>>Uwe Ligges
>>>
>>>__
>>>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
>>>
>>>
>>
>>-- 
>>Chuck Cleland, Ph.D.
>>NDRI, Inc.
>>71 West 23rd Street, 8th floor
>>New York, NY 10010
>>tel: (212) 845-4495 (Tu, Th)
>>tel: (732) 452-1424 (M, W, F)
>>fax: (917) 438-0894
>>
>>__
>>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
>>

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Re: [R] source(file) => file becomes readonly

[Hjellvik Vidar]

The OS is Windows XP. 
I use to work on the file while it's executed and save changes continually. It 
doesn't seem to have any effect on the current execution. I just find it 
annoying not to be able to do it. It's not crucial, but if there is some easy 
way around it I would like to know

-Original Message-
From: Uwe Ligges [mailto:[EMAIL PROTECTED]
Sent: 1. september 2005 14:21
To: Hjellvik Vidar
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] source(file) => file becomes readonly


Hjellvik Vidar wrote:

> Hello,
> when I work in R, I write code in a text file that I run with the 
> "source(filename)" command. In R2.1.1 the file is read-only while the source 
> command is executed. This was not the case in R2.0.1. Is this a bug-fix or is 
> it possible not to have the file read-only when executed?

So you want to modify a file *while* it is executed?
Sounds dangerous to me, you may want to explain further...

BTW: Which OS are we talking about?

Uwe Ligges


> Best regards
> Vidar
> 
> __
> 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

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Re: [R] Using non-gcc compilers with install.packages()

[Trond Hasle Amundsen]

Roger Bivand <[EMAIL PROTECTED]> writes:

> On Thu, 1 Sep 2005, Trond Hasle Amundsen wrote:
>
>> 
>> Hi,
>> 
>> I have built R 2.1.1 on Solaris and OSF1, and used the operating
>> system's native compiler set. This worked fine. However, when I try
>> using install.packages() it insists on using g77 etc., which doesn't
>> exist on those systems.
>> 
>> How can I specify which compilers to use? What about other
>> compile-time options like LDFLAGS etc.?
>> 
>> NB! Please include me in the CC list, since I'm not a mailinglist
>> member.
>> 
>> PS. I really like perl's approach to module building. When building
>> perl modules, it defaults to the same compilers as perl was initially
>> built with. This seems like a sane approach also for R IMHO.
>
> Indeed, R is pretty sane. Fine tuning is conveniently carried out by
> editing the config.site file in the root source directory; LDFLAGS are on
> line 138 of the released 2.1.1 source. Which particular packages have you
> found showing this behaviour?

Hmm..

 - The following use correct c/c++ compilers, but fail to recognize
   this as as Solaris system and uses -fPIC instead of -KPIC for
   shared objects. They also use other gcc-specific options like
   '-O2':

  RandomFields
  geoR
  geoRglm
  rgl
  

 - The following packages try g77 without first checking if it
   exists. I did not specify the F77 variable when compiling R, since
   it found f77 by itself. If all I need is to re-compile with the F77
   variable set to 'f77', I won't mind.

  akima
  sm
  spatstat
  splancs

There are problably more.. these two problem seem to be consistent
across modules, but I can't be sure.

Cheers,

-- 
Trond Hasle Amundsen <[EMAIL PROTECTED]>
Center for Information Technology Services, University of Oslo

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Re: [R] standard deviation in barplots

[Knut Krueger]

Sean Davis schrieb:

>I think barplot2 in the gregmisc (gplots) bundle will do that.
>
>Sean
>
>  
>
Ok thank´s but I've got an error and do not found the solution:


ci.l
 [1] 304.09677 202.49907   0.0  63.14547   0.0   0.0   0.0
 [8]   0.0   0.0   0.0
ci.h
 [1] 633.50323 426.10093  45.12493 344.85453 196.19980 198.17632 208.96365
 [8]  76.49691   0.0   0.0
 xrow
 [1] 468.8 314.3  20.1 204.0  96.0  96.0 115.0  36.0   0.0   0.0
barplot2(xrow,plot.ci=TRUE,ci.l=ci.l,ci.h=ci.h)

Knut

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Re: [R] Newbie help on dim

[Achim Zeileis]

On Thu, 01 Sep 2005 14:44:53 +0200 Uwe Ligges wrote:

> Achim Zeileis wrote:
> 
> > On Thu, 01 Sep 2005 08:25:14 -0400 Chuck Cleland wrote:
> > 
> > 
> >>Should the Value: section of the help page read:
> >>
> >>For an array (and hence in particular, for a matrix) dim retrieves
> >the>dim attribute of the object. It is NULL for a vector of mode
> >integer.
> > 
> > 
> > This statement is true, but less general than
> >   It is NULL or a vector of mode integer.
> > hence the latter is surely preferred.
> 
> Z, in fact, it is not true:
> 
>   x <- integer(1)
>   dim(x) <- 1
>   typeof(x) # "integer"
>   dim(x)# 1

But then:
  is.vector(x) # FALSE
but let's not start nitpicking here.
Z

> Best,
> Uwe
> 
> 
> 
> 
> > Z
> > 
> > 
> >>NOTE: for not or in the second sentence.
> >>
> >>Uwe Ligges wrote:
> >>
> >>>Christian Prinoth wrote:
> >>>
> >>>
> >>>
> Hi, if I do
> 
> Z<-rnorm(50)
> Followed by
> Dim(Z)
> I get NULL. Is this correct? Shouldn't I get 50 instead?
> >>>
> > 
> >>>
> >>>No, because Z has no dim attribute. ?dim tells you:
> >>>
> >>>"For an array (and hence in particular, for a matrix) dim retrieves
> >>>the dim attribute of the object. It is NULL or a vector of mode
> >>>integer."
> >>>
> >>>
> >>>
> TIA
> Chris
> 
> DISCLAIMER:\ L'utilizzo non autorizzato del presente
> >>>
> >>>messagg...{{dropped}}>
> >>>
> __
> 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
> >>>
> >>>
> >>>Yes, PLEASE do read the posting guide! 
> >>>http://www.R-project.org/posting-guide.html
> >>>
> >>>
> >>>Uwe Ligges
> >>>
> >>>__
> >>>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
> >>>
> >>>
> >>
> >>-- 
> >>Chuck Cleland, Ph.D.
> >>NDRI, Inc.
> >>71 West 23rd Street, 8th floor
> >>New York, NY 10010
> >>tel: (212) 845-4495 (Tu, Th)
> >>tel: (732) 452-1424 (M, W, F)
> >>fax: (917) 438-0894
> >>
> >>__
> >>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
> >>
> 
> __
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> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
>

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[R] Spacing and margins in plot

[Jamieson Cobleigh]

If I use the following command to plot points:

plot(c(1,2,2,3,3,3), type="p", pch=20, ylab="Y Label", xlab="X Label", xaxt="n")

there is a large amount of space between the label "X Label" and the
actual x-axis.  If I change the xaxt="n" to xaxt="s", the label "X
Label" don't move at all.  Is there a way to get the label "X Label"
closer to the x-axis when xaxt="n"?



The plot I am generating is going to be included in a paper I am
writing.  I can cause the plot to be saved in a PDF file by doing the
following:

pdf("foo.pdf", width=5.5, height=4.25, onefile=FALSE)

plot(c(1,2,2,3,3,3), type="p", pch=20, ylab="Y Label", xlab="X Label", xaxt="n")

dev.off();

In the resulting file, there is a lot of whitespace around the graph,
particularly between the top line of the plot area and the top of the
page.  Since I am including these plots in a paper, I want them to be
as large as possible and not take up any extra space.  Is there a way
to get R to draw a plot that goes all the way to the margins of the
print area?

Jamie

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[R] Multivariate Skew Normal distribution

[Caio Lucidius Naberezny Azevedo]

Hi all,
 
Could anyone tell me if there is any package (or function) that generates 
values from a multivariate skew normal distribution?
 
Thanks all,
 
Caio


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[[alternative HTML version deleted]]

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Re: [R] standard deviation in barplots

[Knut Krueger]

I forgot the error message ...

Error in barplot2.default(xrow, plot.ci = TRUE, ci.l = ci.l, ci.h = ci.h) :
confidence interval values are missing

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Re: [R] Using non-gcc compilers with install.packages()

[Roger Bivand]

On Thu, 1 Sep 2005, Trond Hasle Amundsen wrote:

> Roger Bivand <[EMAIL PROTECTED]> writes:
> 
> > On Thu, 1 Sep 2005, Trond Hasle Amundsen wrote:
> >
> >> 
> >> Hi,
> >> 
> >> I have built R 2.1.1 on Solaris and OSF1, and used the operating
> >> system's native compiler set. This worked fine. However, when I try
> >> using install.packages() it insists on using g77 etc., which doesn't
> >> exist on those systems.
> >> 
> >> How can I specify which compilers to use? What about other
> >> compile-time options like LDFLAGS etc.?
> >> 
> >> NB! Please include me in the CC list, since I'm not a mailinglist
> >> member.
> >> 
> >> PS. I really like perl's approach to module building. When building
> >> perl modules, it defaults to the same compilers as perl was initially
> >> built with. This seems like a sane approach also for R IMHO.
> >
> > Indeed, R is pretty sane. Fine tuning is conveniently carried out by
> > editing the config.site file in the root source directory; LDFLAGS are on
> > line 138 of the released 2.1.1 source. Which particular packages have you
> > found showing this behaviour?
> 
> Hmm..
> 
>  - The following use correct c/c++ compilers, but fail to recognize
>this as as Solaris system and uses -fPIC instead of -KPIC for
>shared objects. They also use other gcc-specific options like
>'-O2':
> 
>   RandomFields
>   geoR
>   geoRglm
>   rgl
>   
> 
>  - The following packages try g77 without first checking if it
>exists. I did not specify the F77 variable when compiling R, since
>it found f77 by itself. If all I need is to re-compile with the F77
>variable set to 'f77', I won't mind.
> 
>   akima
>   sm
>   spatstat
>   splancs
> 
> There are problably more.. these two problem seem to be consistent
> across modules, but I can't be sure.

OK. When installing packages, the settings in the R_HOME/etc/Makeconf file 
are used, unless over-ridden by a src/Makevars file in the source package. 
Since I maintain splancs, I know that it does not have a src/Makevars 
file. That means that you are getting the R_HOME/etc/Makeconf settings 
generated at compile time. Can you confirm that your R_HOME/etc/Makeconf 
file has the compile time settings?

> 
> Cheers,
> 
> 

-- 
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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Re: [R] standard deviation in barplots

[Marc Schwartz]

On Thu, 2005-09-01 at 15:00 +0200, Knut Krueger wrote:
> 
> Sean Davis schrieb:
> 
> >I think barplot2 in the gregmisc (gplots) bundle will do that.
> >
> >Sean
> >
> >  
> >
> Ok thank´s but I've got an error and do not found the solution:
> 
> 
> ci.l
>  [1] 304.09677 202.49907   0.0  63.14547   0.0   0.0   0.0
>  [8]   0.0   0.0   0.0
> ci.h
>  [1] 633.50323 426.10093  45.12493 344.85453 196.19980 198.17632 208.96365
>  [8]  76.49691   0.0   0.0
>  xrow
>  [1] 468.8 314.3  20.1 204.0  96.0  96.0 115.0  36.0   0.0   0.0
> barplot2(xrow,plot.ci=TRUE,ci.l=ci.l,ci.h=ci.h)
> 
> Knut


Presumably, you are getting:

> barplot2(xrow, plot.ci = TRUE, ci.l = ci.l, ci.h = ci.h)
Error in barplot2.default(xrow, plot.ci = TRUE, ci.l = ci.l, ci.h =
ci.h) : 
confidence interval values are missing



There is an error in your function call. The argument 'ci.h' is
incorrect, as it should be 'ci.u'. Thus, use:


ci.l <- c(304.09677, 202.49907, 0.0, 63.14547,
  0.0, 0.0, 0.0, 0.0,
  0.0, 0.0)

ci.u <- c(633.50323, 426.10093, 45.12493, 344.85453,
  196.19980, 198.17632, 208.96365, 76.49691,
  0.0, 0.0)

xrow <- c(468.8, 314.3, 20.1, 204.0, 96.0, 96.0,
  115.0, 36.0, 0.0, 0.0)

barplot2(xrow, plot.ci = TRUE, ci.l = ci.l, ci.u = ci.u)


HTH,

Marc Schwartz

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Re: [R] Using non-gcc compilers with install.packages()

[Uwe Ligges]

Trond Hasle Amundsen wrote:

> Roger Bivand <[EMAIL PROTECTED]> writes:
> 
> 
>>On Thu, 1 Sep 2005, Trond Hasle Amundsen wrote:
>>
>>
>>>Hi,
>>>
>>>I have built R 2.1.1 on Solaris and OSF1, and used the operating
>>>system's native compiler set. This worked fine. However, when I try
>>>using install.packages() it insists on using g77 etc., which doesn't
>>>exist on those systems.
>>>
>>>How can I specify which compilers to use? What about other
>>>compile-time options like LDFLAGS etc.?
>>>
>>>NB! Please include me in the CC list, since I'm not a mailinglist
>>>member.
>>>
>>>PS. I really like perl's approach to module building. When building
>>>perl modules, it defaults to the same compilers as perl was initially
>>>built with. This seems like a sane approach also for R IMHO.
>>
>>Indeed, R is pretty sane. Fine tuning is conveniently carried out by
>>editing the config.site file in the root source directory; LDFLAGS are on
>>line 138 of the released 2.1.1 source. Which particular packages have you
>>found showing this behaviour?
> 
> 
> Hmm..
> 
>  - The following use correct c/c++ compilers, but fail to recognize
>this as as Solaris system and uses -fPIC instead of -KPIC for
>shared objects. They also use other gcc-specific options like
>'-O2':
> 
>   RandomFields
>   geoR
>   geoRglm
>   rgl
>   
> 
>  - The following packages try g77 without first checking if it
>exists. I did not specify the F77 variable when compiling R, since
>it found f77 by itself. If all I need is to re-compile with the F77
>variable set to 'f77', I won't mind.
> 
>   akima
>   sm
>   spatstat
>   splancs
> 
> There are problably more.. these two problem seem to be consistent
> across modules, but I can't be sure.


So these are package related problems.
Can you please let the corresponding package authors know and ask them 
to fix their packages.

Uwe Ligges


> Cheers,
>

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[R] default height width of graphs

[[EMAIL PROTECTED]]

hy all,

When i plot under R it generates a 440x440px image, is it possible to modify 
and increase this ?


thks all
guillaume.

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Re: [R] standard deviation in barplots

[Uwe Ligges]

Knut Krueger wrote:

> 
> Sean Davis schrieb:
> 
> 
>>I think barplot2 in the gregmisc (gplots) bundle will do that.
>>
>>Sean
>>
>> 
>>
> 
> Ok thank´s but I've got an error and do not found the solution:
> 
> 
> ci.l
>  [1] 304.09677 202.49907   0.0  63.14547   0.0   0.0   0.0
>  [8]   0.0   0.0   0.0
> ci.h
>  [1] 633.50323 426.10093  45.12493 344.85453 196.19980 198.17632 208.96365
>  [8]  76.49691   0.0   0.0
>  xrow
>  [1] 468.8 314.3  20.1 204.0  96.0  96.0 115.0  36.0   0.0   0.0
> barplot2(xrow,plot.ci=TRUE,ci.l=ci.l,ci.h=ci.h)


It is called ci.u, not ci.h!

Uwe Ligges


> Knut
> 
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
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Re: [R] standard deviation in barplots

[Knut Krueger]

>
>There is an error in your function call. The argument 'ci.h' is
>incorrect, as it should be 'ci.u'. Thus, use:
>
>  
>
... I think I will need glasses 


Tank's a lot Knut

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Re: [R] default height width of graphs

[Uwe Ligges]

[EMAIL PROTECTED] wrote:

> hy all,
> 
> When i plot under R it generates a 440x440px image, is it possible to modify 
> and increase this ?


What device are we talking about?
See the corresponding help file, maybe starting at ?Devices

Uwe Ligges


> 
> thks all
> guillaume.
> 
> __
> R-help@stat.math.ethz.ch mailing list
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Re: [R] Spacing and margins in plot

[Uwe Ligges]

Jamieson Cobleigh wrote:

> If I use the following command to plot points:
> 
> plot(c(1,2,2,3,3,3), type="p", pch=20, ylab="Y Label", xlab="X Label", 
> xaxt="n")
> 
> there is a large amount of space between the label "X Label" and the
> actual x-axis.  If I change the xaxt="n" to xaxt="s", the label "X
> Label" don't move at all.  Is there a way to get the label "X Label"
> closer to the x-axis when xaxt="n"?
> 
> 
> 
> The plot I am generating is going to be included in a paper I am
> writing.  I can cause the plot to be saved in a PDF file by doing the
> following:
> 
> pdf("foo.pdf", width=5.5, height=4.25, onefile=FALSE)
> 
> plot(c(1,2,2,3,3,3), type="p", pch=20, ylab="Y Label", xlab="X Label", 
> xaxt="n")
> 
> dev.off();
> 
> In the resulting file, there is a lot of whitespace around the graph,
> particularly between the top line of the plot area and the top of the
> page.  Since I am including these plots in a paper, I want them to be
> as large as possible and not take up any extra space.  Is there a way
> to get R to draw a plot that goes all the way to the margins of the
> print area?
> 
> Jamie

For the size of margins see ?par and its argument "mar", for the 
position of the x-axis label, add it in a separate call to title() and 
specify the "line" where to add the text as in:

   par(mar = c(1, 4, 0, 0) + 0.1)
   plot(c(1,2,2,3,3,3), type="p", pch=20, ylab="Y Label",
   xlab="", xaxt="n")
   title(xlab="X Label", line=0)


Uwe Ligges

> __
> R-help@stat.math.ethz.ch mailing list
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Re: [R] Using non-gcc compilers with install.packages()

[Trond Hasle Amundsen]

Roger Bivand <[EMAIL PROTECTED]> writes:

> On Thu, 1 Sep 2005, Trond Hasle Amundsen wrote:
>
>> Roger Bivand <[EMAIL PROTECTED]> writes:
>> 
>> > On Thu, 1 Sep 2005, Trond Hasle Amundsen wrote:
>> >
>> >> 
>> >> Hi,
>> >> 
>> >> I have built R 2.1.1 on Solaris and OSF1, and used the operating
>> >> system's native compiler set. This worked fine. However, when I try
>> >> using install.packages() it insists on using g77 etc., which doesn't
>> >> exist on those systems.
>> >> 
>> >> How can I specify which compilers to use? What about other
>> >> compile-time options like LDFLAGS etc.?
>> >> 
>> >> NB! Please include me in the CC list, since I'm not a mailinglist
>> >> member.
>> >> 
>> >> PS. I really like perl's approach to module building. When building
>> >> perl modules, it defaults to the same compilers as perl was initially
>> >> built with. This seems like a sane approach also for R IMHO.
>> >
>> > Indeed, R is pretty sane. Fine tuning is conveniently carried out by
>> > editing the config.site file in the root source directory; LDFLAGS are on
>> > line 138 of the released 2.1.1 source. Which particular packages have you
>> > found showing this behaviour?
>> 
>> Hmm..
>> 
>>  - The following use correct c/c++ compilers, but fail to recognize
>>this as as Solaris system and uses -fPIC instead of -KPIC for
>>shared objects. They also use other gcc-specific options like
>>'-O2':
>> 
>>   RandomFields
>>   geoR
>>   geoRglm
>>   rgl
>>   
>> 
>>  - The following packages try g77 without first checking if it
>>exists. I did not specify the F77 variable when compiling R, since
>>it found f77 by itself. If all I need is to re-compile with the F77
>>variable set to 'f77', I won't mind.
>> 
>>   akima
>>   sm
>>   spatstat
>>   splancs
>> 
>> There are problably more.. these two problem seem to be consistent
>> across modules, but I can't be sure.
>
> OK. When installing packages, the settings in the R_HOME/etc/Makeconf file 
> are used, unless over-ridden by a src/Makevars file in the source package. 
> Since I maintain splancs, I know that it does not have a src/Makevars 
> file. That means that you are getting the R_HOME/etc/Makeconf settings 
> generated at compile time. Can you confirm that your R_HOME/etc/Makeconf 
> file has the compile time settings?

Aha. This explains everything. At our site, we use a software
distribution and build system that classifies files a certain way. For
text files, the Linux version is used, for no other reason than that
the Linux compile server is the master of the cluster. This system
does not recognize files that look different on different
architectures. If it's a text file, it's considered architecture
independent and only one version (in our case, the one built on Linux)
is kept.

I'll rebuild R on all architectures, and flag the contents of
R_HOME/etc as architecture dependent so that the correct version is
kept. That way, module building shouldn't give me more problems.

Thanks for your quick and valuable input. You deserve a cold beer :)

Cheers,

-- 
Trond Hasle Amundsen <[EMAIL PROTECTED]>
Gruppe for basis systemdrift (BSD), SAPP, USIT

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[R] 3d cube with labels along axes

[jonne]

Hi R-users,

I would like to draw a cube with a grid on it and labels along all
three axes. I have trouble printing the labels correctly. My
best attempt is described below.
   Can somebody explain me how I can change the 0,20,40,80,100
along the x axis into character vectors like
"no", "light", "intermediate", "severe" ?

x <- seq(0, 100, length=10)
#x <- c("no", "light", "intermediate", "severe")
y <- x
f <- function(x,y) { numeric(length=100) + 5 }
z <- outer(x, y, f)

P <- persp(x, y, z, theta=30, phi=30, zlim=c(-10,10), ticktype="detailed")

text3d(0, 0, -10, "Hello world", P)

Thanks in advance,
Jonne.

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Re: [R] Spacing and margins in plot

[Earl F. Glynn]

This technote explains the margin area (mar) and how to modify it to control
white space around a graphic:
http://research.stowers-institute.org/efg/R/Graphics/Basics/mar-oma/index.htm

When you have multiple figures on a graphic, you may also want to learn to
control the outer margin area (oma), which is also explained.

AFAIK, the only way to get the axis label "closer" to the axis is to
suppress the actual axis labels and use the mtext command to display
alternative text where you want it.  For example, look at the blue text in
Figure 2B (at the above link)  that is between the axis label and the axis.
This blue text is at line=2, when the axis labels are at line=3.

efg
Bioinformatics
Stowers Institute

"Jamieson Cobleigh" <[EMAIL PROTECTED]> wrote in message
news:[EMAIL PROTECTED]
> If I use the following command to plot points:
>
> plot(c(1,2,2,3,3,3), type="p", pch=20, ylab="Y Label", xlab="X Label",
xaxt="n")
>
> there is a large amount of space between the label "X Label" and the
> actual x-axis.  If I change the xaxt="n" to xaxt="s", the label "X
> Label" don't move at all.  Is there a way to get the label "X Label"
> closer to the x-axis when xaxt="n"?
>
> The plot I am generating is going to be included in a paper I am
> writing.  I can cause the plot to be saved in a PDF file by doing the
> following:
>
> pdf("foo.pdf", width=5.5, height=4.25, onefile=FALSE)
>
> plot(c(1,2,2,3,3,3), type="p", pch=20, ylab="Y Label", xlab="X Label",
xaxt="n")
>
> dev.off();
>
> In the resulting file, there is a lot of whitespace around the graph,
> particularly between the top line of the plot area and the top of the
> page.  Since I am including these plots in a paper, I want them to be
> as large as possible and not take up any extra space.  Is there a way
> to get R to draw a plot that goes all the way to the margins of the
> print area?

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Re: [R] Statistics with R

[vincent]

Hi Vincent,
I regularly have a look at your web site.
Very big thanks and bravo for this very useful work.
(Just a little remark, why not let the french html
version fully available on line, (findable by google, etc)
This would/could be useful to promote R for french peoples ?)
Many thanks.
Vincent

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Re: [R] Spacing and margins in plot

[Jamieson Cobleigh]

That worked and gave me enough information so to make it look exactly
the way I want.

Thanks!

Jamie

On 9/1/05, Chuck Cleland <[EMAIL PROTECTED]> wrote:
> How about this:
> 
> par(mar=c(2,4,1,1))
> 
> plot(c(1,2,2,3,3,3), type="p", pch=20, ylab="Y Label", xlab="", xaxt="n")
> 
> mtext(side=1, line=0.5, "X Label")
> 
> hope it helps,
> 
> Chuck
> 
> Jamieson Cobleigh wrote:
> > If I use the following command to plot points:
> >
> > plot(c(1,2,2,3,3,3), type="p", pch=20, ylab="Y Label", xlab="X Label", 
> > xaxt="n")
> >
> > there is a large amount of space between the label "X Label" and the
> > actual x-axis.  If I change the xaxt="n" to xaxt="s", the label "X
> > Label" don't move at all.  Is there a way to get the label "X Label"
> > closer to the x-axis when xaxt="n"?
> >
> >
> >
> > The plot I am generating is going to be included in a paper I am
> > writing.  I can cause the plot to be saved in a PDF file by doing the
> > following:
> >
> > pdf("foo.pdf", width=5.5, height=4.25, onefile=FALSE)
> >
> > plot(c(1,2,2,3,3,3), type="p", pch=20, ylab="Y Label", xlab="X Label", 
> > xaxt="n")
> >
> > dev.off();
> >
> > In the resulting file, there is a lot of whitespace around the graph,
> > particularly between the top line of the plot area and the top of the
> > page.  Since I am including these plots in a paper, I want them to be
> > as large as possible and not take up any extra space.  Is there a way
> > to get R to draw a plot that goes all the way to the margins of the
> > print area?
> >
> > Jamie
> >
> > __
> > 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
> >
> >
> 
> --
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> NDRI, Inc.
> 71 West 23rd Street, 8th floor
> New York, NY 10010
> tel: (212) 845-4495 (Tu, Th)
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[R] Spacing and margins in lattice...

[Jamieson Cobleigh]

Similar to my last question, I want to tighten up the spacing and
margins in a plot I am doing with lattice.

Here are the commands I'm using:

data <- data.frame(x=c(1:3, 1:3), y=c(1:3, 1:3*2),
cat=c("foo","foo","foo","bar", "bar","bar"))

xyplot(panel=panel.superpose, y~x, data=data, groups=cat, type="b",
scales=list(tck=c(2,0), axs="r", cex=c(1,0)))

I know that par(mar=c(2,2,1,1)) would do what I want with plot.  Is
there something similar for xyplot/lattice that can reduce the size of
the margins of the plot?

Thanks!

Jamie

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Re: [R] Spacing and margins in plot

[Chris Wallace]

"Earl F. Glynn" <[EMAIL PROTECTED]> writes:

> AFAIK, the only way to get the axis label "closer" to the axis is to
> suppress the actual axis labels and use the mtext command to display
> alternative text where you want it.  For example, look at the blue text in
> Figure 2B (at the above link)  that is between the axis label and the axis.
> This blue text is at line=2, when the axis labels are at line=3.

how about
plot(..., xlab="")
title(xlab="label text", line=2)

?

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[R] making self-starting function for nls

[Bill Shipley]

Hello.  Following pages 342-347 of Pinheiro & Bates, I am trying to
write a self-starting nonlinear function (a non-rectagular hyperbola) to
be used in nonlinear least squares regression (and eventually for a
mixed model).  When I use the getInitial function for my self-starting
function I get the following error message:

 

> getInitial(photo~NRhyperbola(Irr,theta,Am,alpha,Rd),dat)

Error in tapply(y, x, mean, na.rm = TRUE) : 

arguments must have same length

 

Since I do not explicitly call tapply in my function that makes
NRhyperbola a self-starting function (called NRhyperbolaInit, see
below), I assume that the error is coming from within the mCall function
but I can't figure out where or how.

 

Would someone who has successfully done this be willing to look at my
code and see where the problem arises?

 

> NRhyperbolaInit

function(mCall,LHS,data) 

{

xy<-sortedXyData(mCall[["x"]],LHS,data)

if(nrow(xy)<3){

 stop("Too few unique irradiance values")

}

theta<-0.75

Rd<-min(xy[,"y"])

Am<-max(xy[,"y"]) + abs(Rd)

if(sum(xy[,"x"]<50)>3)alpha<-coef(lm(y~x,data=xy,subset=x<50))[2]

if(sum(xy[,"x"]<50)<=3)alpha<-0.07

value<-c(theta,Am,alpha,Rd)

names(value)<-mCall[c("theta","Am","alpha","Rd")]

value

}

 

Bill Shipley

[EMAIL PROTECTED]

 
http://callisto.si.usherb.ca:8080/bshipley/

 


[[alternative HTML version deleted]]

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[R] Matrices with a single column

[Crispin Miller]

Hi,
I've got a quick question about what happens when indexing into matrices
with a single column. I was wondering if anyone can help ...
 
For example:
> x <- matrix(1:10)

> y <- cbind(x,x)

> x[4:6,]

[1] 4 5 6

> y[4:6,]

   [,1] [,2]

[1,] 4 4

[2,] 5 5

[3,] 6 6

> class(x[4:6,])

[1] "integer"

> class(y[4:6,])

[1] "matrix"

It seems that R is returning the results of indexing into a matrix with
one column as a vector rather than a matrix?

Does anyone have a good way of preventing this from happening?

cheers,

crispin
 


 
This email is confidential and intended solely for the use o...{{dropped}}

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Re: [R] Multivariate Skew Normal distribution

[Ruben Roa]

> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] Behalf Of Caio Lucidius
> Naberezny Azevedo
> Sent: 01 September 2005 12:09
> To: Help mailing list - R
> Subject: [R] Multivariate Skew Normal distribution
> 
> 
> Hi all,
>  
> Could anyone tell me if there is any package (or function) 
> that generates values from a multivariate skew normal distribution?
>  
> Thanks all,
>  
> Caio

Try
RSiteSearch("multivariate normal skew") 
I tried and 39 messages turned up.
R.

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Re: [R] Matrices with a single column

[Huntsinger, Reid]

There's an optional "drop" argument to the indexing operations, which is by
default TRUE. You just want 

> x[4:6,,drop=FALSE]
 [,1]
[1,]4
[2,]5
[3,]6

Reid Huntsinger

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Crispin Miller
Sent: Thursday, September 01, 2005 10:54 AM
To: R-help@stat.math.ethz.ch
Subject: [R] Matrices with a single column


Hi,
I've got a quick question about what happens when indexing into matrices
with a single column. I was wondering if anyone can help ...
 
For example:
> x <- matrix(1:10)

> y <- cbind(x,x)

> x[4:6,]

[1] 4 5 6

> y[4:6,]

   [,1] [,2]

[1,] 4 4

[2,] 5 5

[3,] 6 6

> class(x[4:6,])

[1] "integer"

> class(y[4:6,])

[1] "matrix"

It seems that R is returning the results of indexing into a matrix with
one column as a vector rather than a matrix?

Does anyone have a good way of preventing this from happening?

cheers,

crispin
 


 
This email is confidential and intended solely for the use o...{{dropped}}

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Re: [R] Multivariate Skew Normal distribution

[Ted Harding]

On 01-Sep-05 Caio Lucidius Naberezny Azevedo wrote:
> Hi all,
>  
> Could anyone tell me if there is any package (or function) that
> generates values from a multivariate skew normal distribution?
>  
> Thanks all,
>  
> Caio

Hello, Caio

Please tell us what you mean by "skew normal distribution".

Since normal (i.e. gaussian) distributions are not skew, you
presumably mean something different from what you said, so
unless we understand this more clearly  it is unlikely that
anyone can make a suggestion which would meet your needs.

With best wishes,
Ted.



E-Mail: (Ted Harding) <[EMAIL PROTECTED]>
Fax-to-email: +44 (0)870 094 0861
Date: 01-Sep-05   Time: 15:02:37
-- XFMail --

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Re: [R] Matrices with a single column

[Uwe Ligges]

Crispin Miller wrote:

> Hi,
> I've got a quick question about what happens when indexing into matrices
> with a single column. I was wondering if anyone can help ...
>  
> For example:
> 
>>x <- matrix(1:10)
> 
> 
>>y <- cbind(x,x)
> 
> 
>>x[4:6,]
> 
> 
> [1] 4 5 6
> 
> 
>>y[4:6,]
> 
> 
>[,1] [,2]
> 
> [1,] 4 4
> 
> [2,] 5 5
> 
> [3,] 6 6
> 
> 
>>class(x[4:6,])
> 
> 
> [1] "integer"
> 
> 
>>class(y[4:6,])
> 
> 
> [1] "matrix"
> 
> It seems that R is returning the results of indexing into a matrix with
> one column as a vector rather than a matrix?
> 
> Does anyone have a good way of preventing this from happening?

Yes, the argument "drop":

x[4:6,,drop=FALSE]

Uwe Ligges

> cheers,
> 
> crispin
>  
> 
> 
>  
> This email is confidential and intended solely for the use o...{{dropped}}
> 
> __
> R-help@stat.math.ethz.ch mailing list
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> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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Re: [R] Spacing and margins in lattice...

[Sundar Dorai-Raj]

Jamieson Cobleigh wrote:
> Similar to my last question, I want to tighten up the spacing and
> margins in a plot I am doing with lattice.
> 
> Here are the commands I'm using:
> 
> data <- data.frame(x=c(1:3, 1:3), y=c(1:3, 1:3*2),
> cat=c("foo","foo","foo","bar", "bar","bar"))
> 
> xyplot(panel=panel.superpose, y~x, data=data, groups=cat, type="b",
> scales=list(tck=c(2,0), axs="r", cex=c(1,0)))
> 
> I know that par(mar=c(2,2,1,1)) would do what I want with plot.  Is
> there something similar for xyplot/lattice that can reduce the size of
> the margins of the plot?
> 
> Thanks!
> 
> Jamie
> 

Hi, Jamie,

Will the following work for you?

library(lattice)
data <- data.frame(x = c(1:3, 1:3), y = c(1:3, 1:3*2),
cat = c("foo","foo","foo","bar", "bar","bar"))

trellis.par.set(theme = col.whitebg())

lw <- list(left.padding = list(x = 0, units = "inches"))
lw$right.padding <- list(x = -0.1, units = "inches")
lh <- list(bottom.padding = list(x = 0, units = "inches"))
lh$top.padding <- list(x = -0.2, units = "inches")

lattice.options(layout.widths = lw, layout.heights = lh)
xyplot(y ~ x, data, groups = cat, type="b")

HTH,

--sundar

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Re: [R] Matrices with a single column

[Crispin Miller]

Thanks everyone!

Crispin
 


 
This email is confidential and intended solely for the use o...{{dropped}}

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Re: [R] Spacing and margins in plot

[Earl F. Glynn]

"Chris Wallace" <[EMAIL PROTECTED]> wrote in message
news:[EMAIL PROTECTED]

> how about
> plot(..., xlab="")
> title(xlab="label text", line=2)

Yes, Chris, I like your idea, especially when I can "fix" both X and Y axes
at the same time:

  plot(0, xlab="",ylab="")
  title(xlab="X axis", ylab="Y axis", line=2)

I'd prefer a way to set the axis title line at the same time I change the
mar parameters, but it's not a big deal.

Thanks.
efg

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Re: [R] making self-starting function for nls

[Douglas Bates]

On 9/1/05, Bill Shipley <[EMAIL PROTECTED]> wrote:
> Hello.  Following pages 342-347 of Pinheiro & Bates, I am trying to
> write a self-starting nonlinear function (a non-rectagular hyperbola) to
> be used in nonlinear least squares regression (and eventually for a
> mixed model).  When I use the getInitial function for my self-starting
> function I get the following error message:

> > getInitial(photo~NRhyperbola(Irr,theta,Am,alpha,Rd),dat)
> 
> Error in tapply(y, x, mean, na.rm = TRUE) :
> 
> arguments must have same length
> 
> Since I do not explicitly call tapply in my function that makes
> NRhyperbola a self-starting function (called NRhyperbolaInit, see
> below), I assume that the error is coming from within the mCall function
> but I can't figure out where or how.

My guess is that it is occuring in the call to sortedXyData but I
won't be able to tell for sure without test data.

One of the things that sortedXyData does is to average the y values
for replicated x values.  It seems that in the call the lengths of the
x and y arguments are different.

> 
> 
> 
> Would someone who has successfully done this be willing to look at my
> code and see where the problem arises?
> 
> 
> 
> > NRhyperbolaInit
> 
> function(mCall,LHS,data)
> 
> {
> 
> xy<-sortedXyData(mCall[["x"]],LHS,data)
> 
> if(nrow(xy)<3){
> 
>  stop("Too few unique irradiance values")
> 
> }
> 
> theta<-0.75
> 
> Rd<-min(xy[,"y"])
> 
> Am<-max(xy[,"y"]) + abs(Rd)
> 
> if(sum(xy[,"x"]<50)>3)alpha<-coef(lm(y~x,data=xy,subset=x<50))[2]
> 
> if(sum(xy[,"x"]<50)<=3)alpha<-0.07
> 
> value<-c(theta,Am,alpha,Rd)
> 
> names(value)<-mCall[c("theta","Am","alpha","Rd")]
> 
> value
> 
> }
> 
> 
> 
> Bill Shipley
> 
> [EMAIL PROTECTED]
> 
>  
> http://callisto.si.usherb.ca:8080/bshipley/
> 
> 
> 
> 
> [[alternative HTML version deleted]]
> 
> __
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Re: [R] VarCorr function for assigning random effects: was Question

[Douglas Bates]

On 9/1/05, Doran, Harold <[EMAIL PROTECTED]> wrote:
> If you are indeed using lme and not lmer then the needed function is
> VarCorr(). However, 2 recommendations. First, this is a busy list and
> better emails subject headers get better attention. Second, I would
> recommend using lmer as it is much faster. However, VarCorr seems to be
> incompatible with lmer and I do not know of another function to work
> with lmer.

I hope that VarCorr is compatible with lmer.  It is intended to be

> library(lme4)
Loading required package: Matrix
Loading required package: lattice
> example(VarCorr)

VarCrr> (fm2 <- lmer(Reaction ~ Days + (1 | Subject) + (0 + 
Days | Subject), sleepstudy))
Linear mixed-effects model fit by REML
Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 
   Data: sleepstudy 
  AIC  BIClogLik MLdeviance REMLdeviance
 1753.669 1769.634 -871.8346   1752.047 1743.669
Random effects:
 Groups   NameVariance Std.Dev.
 Subject  (Intercept) 627.571  25.0514 
 Subject  Days 35.858   5.9881 
 Residual 653.584  25.5653 
# of obs: 180, groups: Subject, 18; Subject, 18

Fixed effects:
Estimate Std. Error  DF t value  Pr(>|t|)
(Intercept) 251.4051 6.8854 178 36.5128 < 2.2e-16 ***
Days 10.4673 1.5596 178  6.7117 2.480e-10 ***
---
Signif. codes:  0 $-1òø***òù 0.001 òø**òù 0.01 òø*òù 0.05 òø.òù 0.1 òø òù 1 

VarCrr> VarCorr(fm2)
 Groups   NameVariance Std.Dev.
 Subject  (Intercept) 627.571  25.0514 
 Subject  Days 35.858   5.9881 
 Residual 653.584  25.5653 

What may have occurred is that you had the nlme package loaded after
the lme4 (actually the important package is Matrix which gets loaded
by lme4) package was loaded.  The VarCorr generic in nlme would mask
the VarCorr generic in the Matrix package.

> 
> Hence, a better email subject header will attract the attention of
> others *much* smarter than me!
> 
> I hope this helps,
> Harold
> 
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Mahmoud Torabi
> Sent: Wednesday, August 31, 2005 9:51 PM
> To: R-help@stat.math.ethz.ch
> Cc: [EMAIL PROTECTED]
> Subject: [R] Question
> 
> Dear Sir/Madam
> 
> I would be pleased if anybody can help me. I'm using linear mixed model
> (lme) function.I'm doing some simulation in my research and need to be
> assigned variance components values during of my program. Specifically,
> when I use lme function, I can get some information by use summary() and
> I can assign some valuse like variance of fixed parameters and variance
> of random error term by using for example  varFix and sigma.But I don't
> know how I can assign for variance of random effect.
> I know in SPLUS we have command var.ran, how about R ?


The development version of the Matrix package, available at

https://svn.r-project.org/R-packages/trunk/Matrix

and soon to be Matrix_0.98-6 has a "simulate" method for lmer objects
that may be of interest to you.

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[R] post hoc analysis after anova

[Mahdi Osman]

Dear list,

This is a simple question but I spent an hour on it without success. So I
sorry to bother you.

 I fit a linear model "lm" and then did "anova". 


My idea is to run multiple pairwise comparision for  several factor
variables (f1, f2, f3, f4 each with its own levels, say "0", "1", "3" etc
)at the same time and get statistics for each factor's levels. The
statistics I want is just the basic one such as mean standard error.

I tried the "pairwise.t.test", but I could not do what I wnated to.

I was wondering if anyone has idea about how I can accopmlish this task?


Thanks a lot for your tips and help


Greetings



Mahdi

-- 
---
Mahdi Osman (PhD)
E-mail: [EMAIL PROTECTED]

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[R] axis of plot

[[EMAIL PROTECTED]]

hy,

I need to have the 0 on the bottom left corner of the graph being joined , not 
with this little hole between x axis and y axis...

I've saw this question with the answer one time but i'm unable to find it 
again..


thks.
guillaume

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Re: [R] VarCorr function for assigning random effects: was Question

[Doran, Harold]

You are correct, VarCorr IS compatible with lmer. It must be what you state 
below. I should have saved the message but VarCorr() complained that I was not 
dealing with an lme() object. I had multiple packages (nlme, Matrix, mlmRev, 
among others) in the search path. 

 
On 9/1/05, Doran, Harold <[EMAIL PROTECTED]> wrote:
> If you are indeed using lme and not lmer then the needed function is 
> VarCorr(). However, 2 recommendations. First, this is a busy list and 
> better emails subject headers get better attention. Second, I would 
> recommend using lmer as it is much faster. However, VarCorr seems to 
> be incompatible with lmer and I do not know of another function to 
> work with lmer.

I hope that VarCorr is compatible with lmer.  It is intended to be



> library(lme4)
Loading required package: Matrix
Loading required package: lattice
> example(VarCorr)

VarCrr> (fm2 <- lmer(Reaction ~ Days + (1 | Subject) + (0 +
Days | Subject), sleepstudy))
Linear mixed-effects model fit by REML
Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 
   Data: sleepstudy 
  AIC  BIClogLik MLdeviance REMLdeviance
 1753.669 1769.634 -871.8346   1752.047 1743.669
Random effects:
 Groups   NameVariance Std.Dev.
 Subject  (Intercept) 627.571  25.0514 
 Subject  Days 35.858   5.9881 
 Residual 653.584  25.5653 
# of obs: 180, groups: Subject, 18; Subject, 18

Fixed effects:
Estimate Std. Error  DF t value  Pr(>|t|)
(Intercept) 251.4051 6.8854 178 36.5128 < 2.2e-16 ***
Days 10.4673 1.5596 178  6.7117 2.480e-10 ***
---
Signif. codes:  0 $-1òø***òù 0.001 òø**òù 0.01 òø*òù 0.05 òø.òù 0.1 òø òù 1 

VarCrr> VarCorr(fm2)
 Groups   NameVariance Std.Dev.
 Subject  (Intercept) 627.571  25.0514 
 Subject  Days 35.858   5.9881 
 Residual 653.584  25.5653 

What may have occurred is that you had the nlme package loaded after the lme4 
(actually the important package is Matrix which gets loaded by lme4) package 
was loaded.  The VarCorr generic in nlme would mask the VarCorr generic in the 
Matrix package.

> 
> Hence, a better email subject header will attract the attention of 
> others *much* smarter than me!
> 
> I hope this helps,
> Harold
> 
> -Original Message-
> From: [EMAIL PROTECTED] 
> [mailto:[EMAIL PROTECTED] On Behalf Of Mahmoud Torabi
> Sent: Wednesday, August 31, 2005 9:51 PM
> To: R-help@stat.math.ethz.ch
> Cc: [EMAIL PROTECTED]
> Subject: [R] Question
> 
> Dear Sir/Madam
> 
> I would be pleased if anybody can help me. I'm using linear mixed 
> model
> (lme) function.I'm doing some simulation in my research and need to be 
> assigned variance components values during of my program. 
> Specifically, when I use lme function, I can get some information by 
> use summary() and I can assign some valuse like variance of fixed 
> parameters and variance of random error term by using for example  
> varFix and sigma.But I don't know how I can assign for variance of random 
> effect.
> I know in SPLUS we have command var.ran, how about R ?


The development version of the Matrix package, available at

https://svn.r-project.org/R-packages/trunk/Matrix

and soon to be Matrix_0.98-6 has a "simulate" method for lmer objects that may 
be of interest to you.

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Re: [R] axis of plot

[Marc Schwartz (via MN)]

On Thu, 2005-09-01 at 16:58 +0100, [EMAIL PROTECTED] wrote:
> hy,
> 
> I need to have the 0 on the bottom left corner of the graph being
> joined , not with this little hole between x axis and y axis...
> 
> I've saw this question with the answer one time but i'm unable to find
> it again..
> 
> 
> thks.
> guillaume

See 'xaxs' and 'yaxs' in ?par:

plot(1:5, xaxs = "i", yaxs = "i", xlim = c(0, 5), ylim = c(0, 5))

By default, both are set to "r", which adds +/- 4% to the range of each
axis.

HTH,

Marc Schwartz

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[R] controlling where *.Rout gets printed. Possible?

[Paul Johnson]

OK, my journey to make lab machines automagically install & update all 
desirable R packages is nearing an end!  The only question I have now is 
this: How can I control where the system prints the *.Rout file that is 
created automatically when the R batch program runs.  In "man R" I don't 
find any information about it.  When the cron job runs "R_installAll.sh" 
(see below), I'd like to re-direct it to someplace that ordinary users 
can read.

Here's the shell script I will schedule with cron

R_installAll.sh --
#!/bin/bash
R CMD BATCH /usr/local/bin/R_installAll.R
--

And here's the R program

-R_installAll.R-

# Paul Johnson  2005-08-31
# This should update and then install all packages, except for
# ones I exclude because they don't work or we don't want them.


options(repos = "http://lib.stat.cmu.edu/R/CRAN/";)

update.packages(ask=F)
theNew <- new.packages()
failPackages <- 
c("BRugs","GDD","gtkDevice","gap","gnomeGUI","mimR","ncdf","pathmix","rcdd","rgdal","rpvm",
"Rmpi","RQuantLib","RMySQL", 
"RNetCDF","RODBC","ROracle","RScaLAPACK","rsprng","RWinEdt","taskPR")

shouldFail <- theNew %in% failPackages

install.packages( theNew[!shouldFail],dependencies=T)


# VGAM is not in CRAN yet, but Zelig wants it.
# install.packages("VGAM", CRAN="http://www.stat.auckland.ac.nz/~yee";);


update.packages(CRAN="http://www.stat.auckland.ac.nz/~yee";)
--




-- 
Paul E. Johnson   email: [EMAIL PROTECTED]
Dept. of Political Sciencehttp://lark.cc.ku.edu/~pauljohn
1541 Lilac Lane, Rm 504
University of Kansas  Office: (785) 864-9086
Lawrence, Kansas 66044-3177   FAX: (785) 864-5700

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[R] access to on.exit expressions in parent frames?

[jhallman]

In R, sys.on.exit() retrieves the expression stored for use by 'on.exit' in
the function currently being evaluated.  In S, you get the list of expressions
for the current frame and its parents.  Is there any way I can do the same in
R?  If not, can this be added?  Maybe 'sys.on.exit' could take a frame number
or environment as an argument.

Jeff

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Re: [R] controlling where *.Rout gets printed. Possible?

[Uwe Ligges]

Paul Johnson wrote:

> OK, my journey to make lab machines automagically install & update all 
> desirable R packages is nearing an end!  The only question I have now is 
> this: How can I control where the system prints the *.Rout file that is 
> created automatically when the R batch program runs.  In "man R" I don't 
> find any information about it.  When the cron job runs "R_installAll.sh" 
> (see below), I'd like to re-direct it to someplace that ordinary users 
> can read.

But you find help in
   R CMD BATCH --help
which tells you:
   "Usage: R CMD BATCH [options] infile [outfile]"

Hence simply call R by something like
   R CMD BATCH /usr/local/bin/R_installAll.R /path/to/R_installAll.Result


Uwe Ligges


> Here's the shell script I will schedule with cron
> 
> R_installAll.sh --
> #!/bin/bash
> R CMD BATCH /usr/local/bin/R_installAll.R
> --
> 
> And here's the R program
> 
> -R_installAll.R-
> 
> # Paul Johnson  2005-08-31
> # This should update and then install all packages, except for
> # ones I exclude because they don't work or we don't want them.
> 
> 
> options(repos = "http://lib.stat.cmu.edu/R/CRAN/";)
> 
> update.packages(ask=F)
> theNew <- new.packages()
> failPackages <- 
> c("BRugs","GDD","gtkDevice","gap","gnomeGUI","mimR","ncdf","pathmix","rcdd","rgdal","rpvm",
> "Rmpi","RQuantLib","RMySQL", 
> "RNetCDF","RODBC","ROracle","RScaLAPACK","rsprng","RWinEdt","taskPR")
> 
> shouldFail <- theNew %in% failPackages
> 
> install.packages( theNew[!shouldFail],dependencies=T)
> 
> 
> # VGAM is not in CRAN yet, but Zelig wants it.
> # install.packages("VGAM", CRAN="http://www.stat.auckland.ac.nz/~yee";);
> 
> 
> update.packages(CRAN="http://www.stat.auckland.ac.nz/~yee";)
> --
> 
> 
> 
>

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Re: [R] Spacing and margins in lattice...

[Jamieson Cobleigh]

That did the trick.

Thanks!

Jamie

On 9/1/05, Sundar Dorai-Raj <[EMAIL PROTECTED]> wrote:
> 
> 
> Jamieson Cobleigh wrote:
> > Similar to my last question, I want to tighten up the spacing and
> > margins in a plot I am doing with lattice.
> >
> > Here are the commands I'm using:
> >
> > data <- data.frame(x=c(1:3, 1:3), y=c(1:3, 1:3*2),
> > cat=c("foo","foo","foo","bar", "bar","bar"))
> >
> > xyplot(panel=panel.superpose, y~x, data=data, groups=cat, type="b",
> > scales=list(tck=c(2,0), axs="r", cex=c(1,0)))
> >
> > I know that par(mar=c(2,2,1,1)) would do what I want with plot.  Is
> > there something similar for xyplot/lattice that can reduce the size of
> > the margins of the plot?
> >
> > Thanks!
> >
> > Jamie
> >
> 
> Hi, Jamie,
> 
> Will the following work for you?
> 
> library(lattice)
> data <- data.frame(x = c(1:3, 1:3), y = c(1:3, 1:3*2),
> cat = c("foo","foo","foo","bar", "bar","bar"))
> 
> trellis.par.set(theme = col.whitebg())
> 
> lw <- list(left.padding = list(x = 0, units = "inches"))
> lw$right.padding <- list(x = -0.1, units = "inches")
> lh <- list(bottom.padding = list(x = 0, units = "inches"))
> lh$top.padding <- list(x = -0.2, units = "inches")
> 
> lattice.options(layout.widths = lw, layout.heights = lh)
> xyplot(y ~ x, data, groups = cat, type="b")
> 
> HTH,
> 
> --sundar
>

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[R] SpatStat Kest - Error Message help

[DrakeGis]

Hi I'm working with the function Kest in the package SpatStat (under LINUX
with R 2.1.0). In order to evaluate the statistical significance of my
point pattern I'm doing 999 Montecarlo replications. The script that use
the Kest function runs OK for most of the different point patterns that I
have but for a particular point pattern, which have only 17 points, it
runs until the 34th iteration and then I receive this message:

Error in "[<-"(`*tmp*`, index, value = NULL) :
incompatible types (1000) in subassignment type fix
Execution halted

  Do you have any idea about what could be the cause of this ? Thanks in
advance

D.






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[R] Strange build message: request help w/resolving

[Zajd, John]

Greetings,
 
I am attempting to build a R package, however the build fails and the
following message is ouput:
 
C:\ConstellaGroup\EPA\RAGG\package>R CMD BUILD --binary --force RAGG
* checking for file 'RAGG/DESCRIPTION' ... OK
* preparing 'RAGG':
* checking DESCRIPTION meta-information ... ERROR
Error in if (regexpr(dep_regexp, dep) == -1) { :
missing value where TRUE/FALSE needed
Execution halted


The DESCRIPTION file is as follows:

Package: RAGG

Title: Aggregation Tool for CMAQ gridded model data

Version: 1.5

Date: 2004-08-23

Author: Nathan Shackles <[EMAIL PROTECTED]>, ported from SAS code
written by Renee Jaramillo <[EMAIL PROTECTED]>

Description: The RAGG package performs aggregation of gridded CMAQ model
data. The pacakge reads event data from Models3 IO-API files and outputs the
aggregated annual data in Models3 IO-API file(s). 

Aggegation came about as a means to provide CMAQ-based estimates of total
annual deposition and average annual concentrations. CMAQ is an episodic
model requiring detailed meteorological and emissions inputs. Because of the
extensive inputs and the time required to run CMAQ, it would be
cost-prohibitive to simulate an entire year to estimate annual quantities.
Aggregation formulas group events into clusters with similar 850-mb windflow
patters to create annual estimates.

Maintainer: Nathan Shackles <[EMAIL PROTECTED]>

Depends: Models3

License: GPL version 2 or newer

Any help that can be provided is appreciated.

Thank you,

John Zajd

 

 

 


[[alternative HTML version deleted]]

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Re: [R] Strange build message: request help w/resolving

[Uwe Ligges]

Zajd, John wrote:

> Greetings,
>  
> I am attempting to build a R package, however the build fails and the
> following message is ouput:
>  
> C:\ConstellaGroup\EPA\RAGG\package>R CMD BUILD --binary --force RAGG
> * checking for file 'RAGG/DESCRIPTION' ... OK
> * preparing 'RAGG':
> * checking DESCRIPTION meta-information ... ERROR
> Error in if (regexpr(dep_regexp, dep) == -1) { :
> missing value where TRUE/FALSE needed
> Execution halted
> 
> 
> The DESCRIPTION file is as follows:
> 
> Package: RAGG
> 
> Title: Aggregation Tool for CMAQ gridded model data
> 
> Version: 1.5
> 
> Date: 2004-08-23
> 
> Author: Nathan Shackles <[EMAIL PROTECTED]>, ported from SAS code
> written by Renee Jaramillo <[EMAIL PROTECTED]>
> 
> Description: The RAGG package performs aggregation of gridded CMAQ model
> data. The pacakge reads event data from Models3 IO-API files and outputs the
> aggregated annual data in Models3 IO-API file(s). 
> 
> Aggegation came about as a means to provide CMAQ-based estimates of total
> annual deposition and average annual concentrations. CMAQ is an episodic
> model requiring detailed meteorological and emissions inputs. Because of the
> extensive inputs and the time required to run CMAQ, it would be
> cost-prohibitive to simulate an entire year to estimate annual quantities.
> Aggregation formulas group events into clusters with similar 850-mb windflow
> patters to create annual estimates.
> 
> Maintainer: Nathan Shackles <[EMAIL PROTECTED]>
> 
> Depends: Models3
> 
> License: GPL version 2 or newer
> 
> Any help that can be provided is appreciated.

One obvious point:
Continuation lines should begin with a white space (such as a tab). See 
the Writing R Extensions manual for more details.

Uwe Ligges


> Thank you,
> 
> John Zajd
> 
>  
> 
>  
> 
>  
> 
> 
>   [[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

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Re: [R] label *on the side* in conditional lattice plots?

[Deepayan Sarkar]

On 8/31/05, Maciej Kalisiak <[EMAIL PROTECTED]> wrote:
> I'm doing bwplot(x ~ y | z, ...) with lattice, but would like the
> z-labels to appear to the *side* of each bwplot, rather than on top...
> is this possible?  

Not currently (it's on my TODO list).

Deepayan

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Re: [R] Linux Standalone Server Suggestions for R

[bogdan romocea]

Most powerful in what way? Quite a lot depends on the jobs you're going to run.
- To run CPU-bound jobs, more CPUs is better. (Even though R doesn't
do threading, you can manually split some CPU-bound jobs in several
parts and run them simultaneously.) Apart from multiple CPUs and
hyperthreading, check the new dual-core CPUs.
- To run very large jobs, more memory is better. You can easily spend
most of your money on memory. Get the fastest one.
- You should get 64-bit CPUs, otherwise you won't be able to run very
large jobs (search the list for details).

I would suggest that you buy a configuration that can handle more CPUs
and memory than you think you need now (say, at least 4 max CPUs and
16 GB max memory), then keep on adding more memory and CPUs as your
needs change.
hth,
b.


> -Original Message-
> From: Jia-Shing So [mailto:[EMAIL PROTECTED] 
> Sent: Wednesday, August 31, 2005 10:03 PM
> To: r-help@stat.math.ethz.ch
> Cc: Phuoc Hong
> Subject: [R] Linux Standalone Server Suggestions for R
> 
> 
> Hi All,
> 
> My group is  looking for any suggestions on what to purchase to  
> achieve the most powerful number crunching system that $50k 
> can buy.   
> The main application that will be used is R so input on what 
> hardware  
> benefits R most will be appreciated.  The requirements are 
> that it be  
> a single standalone server (i.e. not a cluster solution), and 
> it that  
> must be able to run unix/linux.  If anyone has any experience/ 
> suggestions regarding the following questions that would also be  
> greatly appreciated.
> 
> AMD vs Intel chips, especially 64-bit versions of the two?
> Using Itanium/Opterons and if so how much of a performance boost did  
> you achieve vs other 64-bit chip sets?
> Also, does anyone know if there is an upper thresh hold on much  
> memory R can use?
> 
> Thanks in advance for any help and suggestions,
> 
> Jia-Shing So
> Programmer Analyst
> Biostatistics and Bioinformatics Lab
> University of California, San Diego
> 
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
>

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[R] png scaling problem

[Knut Krueger]

scaling<-4
xywidth<-480
resolution<-150
png(filename = "c:/r/anschluss/plots/4.png", width = xywidth*scaling, 
height = xywidth*scaling,pointsize = 12, bg = "white", res = 
resolution*scaling)
..

barplot(xrow,col = barcolors,cex.axis=scaling, ylab="mean time till attachment 
in sec",cex.lab=1.2*scaling) 

I tried to scale the barplot but there is one strange result:
scaling=1
http://biostatistic.de/temp/1.png--- the ylab is ok

scaling=2
http://biostatistic.de/temp/2.png--- the ylab is not ok

scaling=4
http://biostatistic.de/temp/4.png--- the ylab is terrible

is there any better solution to scale the resolution and the width/height?


with regards
Knut

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Re: [R] png scaling problem

[Marc Schwartz (via MN)]

On Thu, 2005-09-01 at 21:51 +0200, Knut Krueger wrote:
> scaling<-4
> xywidth<-480
> resolution<-150
> png(filename = "c:/r/anschluss/plots/4.png", width = xywidth*scaling, 
> height = xywidth*scaling,pointsize = 12, bg = "white", res = 
> resolution*scaling)
> ..
> 
> barplot(xrow,col = barcolors,cex.axis=scaling, ylab="mean time till 
> attachment in sec",cex.lab=1.2*scaling) 
> 
> I tried to scale the barplot but there is one strange result:
> scaling=1
> http://biostatistic.de/temp/1.png--- the ylab is ok
> 
> scaling=2
> http://biostatistic.de/temp/2.png--- the ylab is not ok
> 
> scaling=4
> http://biostatistic.de/temp/4.png--- the ylab is terrible
> 
> is there any better solution to scale the resolution and the width/height?
> 
> 
> with regards
> Knut

Probably a better first question is, why are you using a bitmapped
graphics format if you need the image to be re-scaled? In general,
bitmapped graphics do not resize well, though if you have a specific
need and know a target image size, you can adjust various parameters to
look decent. Are you going to view these images in a web browser, where
you are concerned with display size and resolution?

>From your e-mail headers it appears you are on Windows. If you need a
re-sizable graphic, use a vector based format such as wmf/emf,
especially if you need the graphics embedded in a Windows application
such as Word or Powerpoint. This is the default format under Windows
when copying and pasting a graphic between applications. You can then,
fairly freely, resize the image in the target application as you may
require.

If you are going to print the graphic directly or include it in a
document for printing (as opposed to just viewing it), then use PDF or
Postscript. The latter in EPS format, can be imported into many Windows
applications like Word, including the generation of a preview image.
However, they don't look good for direct use in presentations (unless
you print to a PS file and then convert to PDF for viewing).

See ?Devices for more information.

With a better idea of how you plan to use the graphic(s), we can offer
more specific recommendations on how to proceed.

Marc Schwartz

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[R] transparency?

[ivo_welch-rstat8303]

dear R wizards:

I am getting to play more and more with fun fonts (irony warning).  I 
now know that I can safely use my TeXtext encoding with the postscript 
device, but not with the pdf device.  Unfortunately, I believe that the 
postscript device does not support translucent colors---or is there a 
version parameter (like the version="1.4" that I need with the pdf 
device) that would permit the use of translucent colors?

Right now, it seems that my choice either TeX encoding or translucence? 
  [there turns out to be another reason why I prefer the pdf to the 
postscript device.  ps2pdf13 seems to lose the bounding box, at least 
sometimes.  it seems to like to create one page and one page only.]

And let me add---thank you very mcuh paul murrell and brian ripley for 
helping me figure out how to get the lucida fonts to work under R.  
highly appreciated.

Regards,

/iaw

---
ivo welch


Suggestion to the R graphics folks:

* Why is R's default device pdf v1.1 ?  this was Acrobat version 2.0, 
isn't it?  we are now at version 7.  wouldn't it be useful to make the 
default 1.4 at this point?  acrobat version 5.0 would seem a reasonable 
default assumption these days.

* There is a bug (R segfaults) when afm files are not found.

* When something does not work, such as encoding that is not supported, 
it would be nice to print a warning.

   --- I should also email this to the ghostscript 7.07 folks.  If 
there is no Fontmap, they silently replace fonts.
 It is wonderful that they do replace, but they should print 
a warning " Font xyz not found, thus replacing
it with Font abs."

The lack of good errors made it doubly hard to figure out the workings, 
and without the help of the aforementioned two angels, I would not have 
had a chance to figure it out.

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[R] Request: in savePlot, type="eps"

[Mike Prager]

Platform: Windows
R version: 2.1.1

This is a request that in the savePlot function, type="eps" be included 
in the next release. This would be an alias for type="ps" but with a 
different file extension.

Rationale:  The current version of R outputs excellent EPS files.  It is 
strictly correct to call these Postscript files, as EPS is a subset of 
PS.  However, on Windows, files are often distinguished by the file 
extension, and users may have different applications associated with the 
different extensions.  It would be nice to be able to save EPS files 
with the EPS extension.

I realize that this can be accomplished with

file.rename(paste(fn,".ps",sep=""), paste(fn,".eps",sep=""))

but saving directly would be more convenient.

Thanks for considering it.

...Mike Prager

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Re: [R] Linux Standalone Server Suggestions for R

[Pikounis, Bill [CNTUS]]

Jia-Shing,
I missed your original message, but would like to reiterate Bogdan's
comments and suggestions.

In a former life, a colleague of mine led the way for us to construct a
"small farm" of Opteron servers that all had 2 AMD64 CPU's, SUSE Enterprise
Server OS, and the ability to have up to 16GB RAM. We experimented with
clustering them but that was not successful, and for practical purposes, not
necessary. Penguin computing (http://www.penguincomputing.com) provided us
very reliable products, solutions, and service, and I am sure there are
other vendors just as capable. As Bogdan mentioned, search the r-help
archives for various discussions on this over the past few years.

With $50K US, you likely will come up more computing power than you can
dream of (for now at least :-). That can get you multiple 16GB 2CPU
machines, I believe.

Good luck!

Hope that helps,
Bill

---
Bill Pikounis, PhD
Nonclinical Statistics
Centocor, Inc.

> -Original Message-
> From: bogdan romocea [mailto:[EMAIL PROTECTED]
> Sent: Thursday, September 01, 2005 2:54 PM
> To: [EMAIL PROTECTED]
> Cc: R-help@stat.math.ethz.ch
> Subject: Re: [R] Linux Standalone Server Suggestions for R
> 
> 
> Most powerful in what way? Quite a lot depends on the jobs 
> you're going to run.
>   - To run CPU-bound jobs, more CPUs is better. (Even 
> though R doesn't
> do threading, you can manually split some CPU-bound jobs in several
> parts and run them simultaneously.) Apart from multiple CPUs and
> hyperthreading, check the new dual-core CPUs.
>   - To run very large jobs, more memory is better. You 
> can easily spend
> most of your money on memory. Get the fastest one.
>   - You should get 64-bit CPUs, otherwise you won't be 
> able to run very
> large jobs (search the list for details).
> 
> I would suggest that you buy a configuration that can handle more CPUs
> and memory than you think you need now (say, at least 4 max CPUs and
> 16 GB max memory), then keep on adding more memory and CPUs as your
> needs change.
> hth,
> b.
> 
> 
> > -Original Message-
> > From: Jia-Shing So [mailto:[EMAIL PROTECTED] 
> > Sent: Wednesday, August 31, 2005 10:03 PM
> > To: r-help@stat.math.ethz.ch
> > Cc: Phuoc Hong
> > Subject: [R] Linux Standalone Server Suggestions for R
> > 
> > 
> > Hi All,
> > 
> > My group is  looking for any suggestions on what to purchase to  
> > achieve the most powerful number crunching system that $50k 
> > can buy.   
> > The main application that will be used is R so input on what 
> > hardware  
> > benefits R most will be appreciated.  The requirements are 
> > that it be  
> > a single standalone server (i.e. not a cluster solution), and 
> > it that  
> > must be able to run unix/linux.  If anyone has any experience/ 
> > suggestions regarding the following questions that would also be  
> > greatly appreciated.
> > 
> > AMD vs Intel chips, especially 64-bit versions of the two?
> > Using Itanium/Opterons and if so how much of a performance 
> boost did  
> > you achieve vs other 64-bit chip sets?
> > Also, does anyone know if there is an upper thresh hold on much  
> > memory R can use?
> > 
> > Thanks in advance for any help and suggestions,
> > 
> > Jia-Shing So
> > Programmer Analyst
> > Biostatistics and Bioinformatics Lab
> > University of California, San Diego
> > 
> > __
> > 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
> 

[[alternative HTML version deleted]]

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[R] Need help understanding/resolving build error message

[Zajd, John]

Can someone provide help to resolve this build failure?
 
Thank you,
John Zajd 
 

C:\ConstellaGroup\EPA\RAGG\package>rcmd check RAGG
* checking for working latex ... OK
* using log directory 'C:/ConstellaGroup/EPA/RAGG/package/RAGG.Rcheck'
* using R version 2.1.0, 2005-04-18
* checking for file 'RAGG/DESCRIPTION' ... OK
* this is package 'RAGG' version '1.5'
* checking if this is a source package ... OK
 
installing R.css in C:/ConstellaGroup/EPA/RAGG/package/RAGG.Rcheck
 

-- Making package RAGG 
  adding build stamp to DESCRIPTION
Error in if (regexpr(dep_regexp, dep) == -1) { :
missing value where TRUE/FALSE needed
Execution halted
make[2]: *** [frontmatter] Error 1
make[1]: *** [all] Error 2
make: *** [pkg-RAGG] Error 2
*** Installation of RAGG failed ***
 
Removing 'C:/ConstellaGroup/EPA/RAGG/package/RAGG.Rcheck/RAGG'
 ERROR
Installation failed.

[[alternative HTML version deleted]]

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Re: [R] Multivariate Skew Normal distribution

[David Scott]

On Thu, 1 Sep 2005 [EMAIL PROTECTED] wrote:

> On 01-Sep-05 Caio Lucidius Naberezny Azevedo wrote:
>> Hi all,
>>
>> Could anyone tell me if there is any package (or function) that
>> generates values from a multivariate skew normal distribution?
>>
>> Thanks all,
>>
>> Caio
>
> Hello, Caio
>
> Please tell us what you mean by "skew normal distribution".
>
> Since normal (i.e. gaussian) distributions are not skew, you
> presumably mean something different from what you said, so
> unless we understand this more clearly  it is unlikely that
> anyone can make a suggestion which would meet your needs.
>
Actually Ted it is perfectly clear. There are modifications of the normal 
(more than one approach) which incorporate skewness.

There is a very nice package by Azzellini called sn which deals with this 
and with the skew t.

A different version of the skew t is given in the package skewt. This is 
univariate only.

There also appear to be some skew normal and skew t tools in RMetrics (in 
FSeries and fPortfolio).

What is not clear is why Caio keeps asking the same question when I 
emailed him the name of the package yesterday.

David Scott
_
David Scott Department of Statistics, Tamaki Campus
The University of Auckland, PB 92019
AucklandNEW ZEALAND
Phone: +64 9 373 7599 ext 86830 Fax: +64 9 373 7000
Email:  [EMAIL PROTECTED]


Graduate Officer, Department of Statistics

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[R] More block diagonal matrix construction code

[Berton Gunter]

Folks:

In answer to a query, Andy Liaw recently submitted some code to construct a
block diagonal matrix. For what seemed a fairly straightforward task, the
code seemed a little "overweight" to me (that's an American stock analyst's
term, btw), so I came up with a slightly cleaner version (with help from
Andy):

bdiag<-function(...){
mlist<-list(...)
## handle case in which list of matrices is given
if(length(mlist)==1)mlist<-unlist(mlist,rec=FALSE)
csdim<-rbind(c(0,0),apply(sapply(mlist,dim),1,cumsum ))
ret<-array(0,dim=csdim[length(mlist)+1,])
add1<-matrix(rep(1:0,2),nc=2)
for(i in seq(along=mlist)){
indx<-apply(csdim[i:(i+1),]+add1,2,function(x)x[1]:x[2])
  ## non-square matrix
if(is.null(dim(indx)))ret[indx[[1]],indx[[2]]]<-mlist[[i]]
## square matrix
else ret[indx[,1],indx[,2]]<-mlist[[i]]
}
ret
}

I doubt that there's any noticeable practical performance difference, of
course.

The strategy is entirely basic: just get the right indices for replacement
of the arguments into a matrix of 0's of the right dimensions. About the
only thing to notice is that the apply() construction returns either a list
or matrix depending on whether a matrix is square or not (a subtlety that
tripped me up in my first version of this code).

I would be pleased if this stimulated others to come up with cleverer/more
elegant approaches that they would share, as it's the sort of thing that
I'll learn from and find useful.

Cheers to all,

Bert Gunter

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Re: [R] Pseudo-Voigt fit

[Spencer Graves]

  I haven't seen a reply to this question, so I will attempt a few 
remarks in spite of some confusion about what you are asking.

  1.  The function to use for parameter estimation depends on ths 
structure of the data.  My all-around preference for many purposes is 
for "optim", but I've used "nls", "fitdistr" (in the MASS package) and 
others in different circumstances.

  2.  If you are doing nonlinear estimation with, e.g., optim, I 
suggest you request "hessian=TRUE".  The eigenvalues of the hessian will 
tell you if it is ill conditioned.  If it is, you might consider 
reparameterizing the model.

  3.  I try to avoid using reserved words like "c".  R can often 
determine what you want from the context, but there are exceptions.  I 
try to avoid that problem by testing a name at a command prompt before I 
use it.  If it returns, "object not found", I'm fine;  if not, I try 
something different.

  4.  Following the posting guide! 
"http://www.R-project.org/posting-guide.html"; can on average increase 
the likelihood that you will receive helpful suggestions quickly.  (I've 
learned that people rarely respond to my incoherent screams;  when they 
do, it's rarely helpful.  I've reluctantly learned that there is often 
no substutute for reading the [EMAIL PROTECTED] manual.)

  I'd be shocked if this answered your question, but I hope it is 
helpful nonetheless.

  spencer graves

[EMAIL PROTECTED] wrote:

> Hi, I am sorry for this question, but I am trying to speed up an
> application
> I will need to fit many x-y data sets (input from text files) to
> 4-parameter Pseudo-Voigt peak function.
> Until now I used SigmaPlot macro to do it (enclosed just in case...)
> 
> peaksign(q) = if(total(q)>q[1], 1, -1)
> xatymin(q,r) = xatymax(q,max(r)-r)
> [Parameters]
> a = if(peaksign(y)>0, max(y), min(y)) ''Auto {{previous: 60.8286}}
> b = fwhm(x,abs(y))/2 ''Auto {{previous: 0.656637}}
> c = .5 ''Auto {{previous: 6.82973e-010}}
> x0 = if(peaksign(y)>0, xatymax(x,y), xatymin(x,y)) ''Auto {{previous:
> 3.19308}}
> 
> 
> [Equation]
> f = a*(c*(1/(1+((x-x0)/b)^2))+(1-c)*exp(-0.5*((x-x0)/b)^2))
> 
> fit f to y
> 
>  (manageable for ~100), but it looks like the next project would need to
> process ~1000 member sets.
> 
> I am not as familiar with R to find the right info (although I can use R in
> general).
> 
> I am also nearly sure that there should be a solution to this task "out
> there" ready to be modified...
> 
> Could you be so kind and direct me please to the right package or web-site
> with examples?
> 
> Thank you very much
> 
> 
> 
> Dr. Petr Pancoska
> Department of Pathology
> SUNY Stony Brook, NY 11794
> phone:  (631)-444-3030
> 
> **
> 
> This e- mail message, including any attachments,
> is for the sole use of the intended recipient(s) and may
> contain confidential and privileged information.
> Any unauthorized review, use, disclosure or distribution is prohibited.
> If you are not the intended recipient, please contact the sender
> by e-mail and destroy all copies of the original.
> 
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-- 
Spencer Graves, PhD
Senior Development Engineer
PDF Solutions, Inc.
333 West San Carlos Street Suite 700
San Jose, CA 95110, USA

[EMAIL PROTECTED]
www.pdf.com 
Tel:  408-938-4420
Fax: 408-280-7915

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Re: [R] Defining an ex-gaussian PDF

[Spencer Graves]

  1.  I just got 10 hits from 'RSiteSearch("convolution of exponential 
and normal")', at least two of which look like they might interest you.

  2.  I similarly got 27 hits from 'RSiteSearch("convolution 
distribution")', several of which mention the "distr" package, which you 
might find useful.

  3.  I doubt if this solves your problem, but I hope you find it 
useful.  If you have other questions for this list, I encourage you to 
PLEASE do read the posting guide! 
"http://www.R-project.org/posting-guide.html";.  It can increase the 
chances that you will get a useful reply quickly.

  spencer graves

Michael Kubovy wrote:

> How does one define PDFs as yet undefined in R, such as the ex- 
> gaussian, the sum of two RVs, one exponential, one Gaussian? The PDF  
> would then be the convolution of an exponential PDF, dexp(), and a  
> normal, dnorm().
> 
> Kindly cc me in your reply to r-help.
> 
> Thanks,
> 
> 
> _
> Professor Michael Kubovy
> University of Virginia
> Department of Psychology
> USPS: P.O.Box 400400Charlottesville, VA 22904-4400
> Parcels:Room 102Gilmer Hall
>  McCormick RoadCharlottesville, VA 22903
> Office:B011+1-434-982-4729
> Lab:B019+1-434-982-4751
> Fax:+1-434-982-4766
> WWW:http://www.people.virginia.edu/~mk9y/
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-help@stat.math.ethz.ch mailing list
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> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

-- 
Spencer Graves, PhD
Senior Development Engineer
PDF Solutions, Inc.
333 West San Carlos Street Suite 700
San Jose, CA 95110, USA

[EMAIL PROTECTED]
www.pdf.com 
Tel:  408-938-4420
Fax: 408-280-7915

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[R] partial association model

[0034058]

my last post was filtered,so I post it again with another title.

If I do not make a mistake,the partial association model is an 
extension of log-linear model.I read a papers which gives an example 
of it.(Sloane and Morgan,1996,An Introduction to Categorical Data 
Analysis,Annual Review of Sociology.22:351-375) Can R fit such partial 
association model?

ps:Another somewhat off-topic question.What's the motivations to use 
log-linear model?Or why use log-linear model?I learn the log-linear 
model butI still do not master the the advantage of the model.thank 
you!

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Re: [R] png scaling problem

[Knut Krueger]

>Probably a better first question is, why are you using a bitmapped
>graphics format if you need the image to be re-scaled? 
>
I need a 1000 dpi tif file in a size of appr. 10 to 10 cm for applied 
animal behaviour science:
http://authors.elsevier.com/GuideForAuthors.html?PubID=503301&dc=GFA

images to one of the following formats (Note the resolution requirements 
for line drawings, halftones, and
line/halftone combinations given below.):
EPS: Vector drawings. Embed the font or save the text as "graphics".
TIFF: Colour or greyscale photographs (halftones): always use a minimum 
of 300 dpi.
TIFF: Bitmapped line drawings: use a minimum of 1000 dpi.
TIFF: Combinations bitmapped line/half-tone (colour or greyscale): a 
minimum of 500 dpi is required.
DOC, XLS or PPT: If your electronic artwork is created in any of these 
Microsoft Office applications please
supply "as is".

I tired the Postscript file but the file is double heigh as width i do 
not know why.
The problem was already discussed in the tread: [R] High resolution plots

I have to send the images possibly yesterday and I am looking fo a 
suitable solution since two months now.
I tired gsview with converting to all possible Tiff formats but the 
images appear not in color and in a strange black and white way
Some readers are able to read it  (Windows Image view) other not and I 
do not know which reader the journal will use :-(
And the ylab is too small ...

http://biostatistic.de/temp/1.tif 
http://biostatistic.de/temp/2.tif 
http://biostatistic.de/temp/3.tif 
http://biostatistic.de/temp/4.tif 





>In general,
>bitmapped graphics do not resize well, though if you have a specific
>need and know a target image size, you can adjust various parameters to
>look decent. Are you going to view these images in a web browser, where
>you are concerned with display size and resolution?
>
>>From your e-mail headers it appears you are on Windows. If you need a
>re-sizable graphic, use a vector based format such as wmf/emf,
>especially if you need the graphics embedded in a Windows application
>such as Word or Powerpoint. This is the default format under Windows
>when copying and pasting a graphic between applications. You can then,
>fairly freely, resize the image in the target application as you may
>require.
>
>If you are going to print the graphic directly or include it in a
>document for printing (as opposed to just viewing it), then use PDF or
>Postscript.
>

Ok there is a second description for the file format :-(
http://authors.elsevier.com/ArtworkInstructions.html?dc=AI2
there are pdf formats welcome but with defined conditions:

Maybe anybody could give me a hint to get the files in the recommendet 
format.
I will ask them immediately which whether the pdf is allowed or not, 
becaus they have two different instruction sites :-(

Regards Knut

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Re: [R] png scaling problem

[Gabor Grothendieck]

If you have not already tried it try creating a fig file:

xfig("myfile.fig")
plot(1:10)
dev.off()

and then using the fig2dev utility (find it via google) to convert it to a tiff:

fig2dev -L tiff myfile.fig > myfile.tiff


On 9/2/05, Knut Krueger <[EMAIL PROTECTED]> wrote:
> 
> 
> 
> >Probably a better first question is, why are you using a bitmapped
> >graphics format if you need the image to be re-scaled?
> >
> I need a 1000 dpi tif file in a size of appr. 10 to 10 cm for applied
> animal behaviour science:
> http://authors.elsevier.com/GuideForAuthors.html?PubID=503301&dc=GFA
> 
> images to one of the following formats (Note the resolution requirements
> for line drawings, halftones, and
> line/halftone combinations given below.):
> EPS: Vector drawings. Embed the font or save the text as "graphics".
> TIFF: Colour or greyscale photographs (halftones): always use a minimum
> of 300 dpi.
> TIFF: Bitmapped line drawings: use a minimum of 1000 dpi.
> TIFF: Combinations bitmapped line/half-tone (colour or greyscale): a
> minimum of 500 dpi is required.
> DOC, XLS or PPT: If your electronic artwork is created in any of these
> Microsoft Office applications please
> supply "as is".
> 
> I tired the Postscript file but the file is double heigh as width i do
> not know why.
> The problem was already discussed in the tread: [R] High resolution plots
> 
> I have to send the images possibly yesterday and I am looking fo a
> suitable solution since two months now.
> I tired gsview with converting to all possible Tiff formats but the
> images appear not in color and in a strange black and white way
> Some readers are able to read it  (Windows Image view) other not and I
> do not know which reader the journal will use :-(
> And the ylab is too small ...
> 
> http://biostatistic.de/temp/1.tif
> http://biostatistic.de/temp/2.tif
> http://biostatistic.de/temp/3.tif
> http://biostatistic.de/temp/4.tif
> 
> 
> 
> 
> 
> >In general,
> >bitmapped graphics do not resize well, though if you have a specific
> >need and know a target image size, you can adjust various parameters to
> >look decent. Are you going to view these images in a web browser, where
> >you are concerned with display size and resolution?
> >
> >>From your e-mail headers it appears you are on Windows. If you need a
> >re-sizable graphic, use a vector based format such as wmf/emf,
> >especially if you need the graphics embedded in a Windows application
> >such as Word or Powerpoint. This is the default format under Windows
> >when copying and pasting a graphic between applications. You can then,
> >fairly freely, resize the image in the target application as you may
> >require.
> >
> >If you are going to print the graphic directly or include it in a
> >document for printing (as opposed to just viewing it), then use PDF or
> >Postscript.
> >
> 
> Ok there is a second description for the file format :-(
> http://authors.elsevier.com/ArtworkInstructions.html?dc=AI2
> there are pdf formats welcome but with defined conditions:
> 
> Maybe anybody could give me a hint to get the files in the recommendet
> format.
> I will ask them immediately which whether the pdf is allowed or not,
> becaus they have two different instruction sites :-(
> 
> Regards Knut
> 
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

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Re: [R] post hoc analysis after anova

[Dieter Menne]

Mahdi Osman  gmx.net> writes:

> 
>  I fit a linear model "lm" and then did "anova". 
> 
> My idea is to run multiple pairwise comparision for  several factor

Package multcomp helps you here, and also protects you against overdoing it.

Dieter

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[R] Calculating Goodman-Kurskal's gamma using delta method

[Wuming Gong]

Dear list, 

I have a problem on calculating the standard error of
Goodman-Kurskal's gamma using delta method. I exactly follow the
method and forumla described in Problem 3.27 of Alan Agresti's
Categorical Data Analysis (2nd edition). The data I used is also from
the job satisfaction vs. income example from that book.

job <- matrix(c(1, 3, 10, 6, 2, 3, 10, 7, 1, 6, 14, 12, 0, 1, 9, 11),
nrow = 4, ncol = 4, byrow = TRUE, dimnames = list(c("< 15,000",
"15,000 - 25,000", "25,000 - 40,000", "> 40,000"), c("VD", "LD", "MS",
"VS")))

The following code is for calculating gamma value, which is consistent
with the result presented in section 2.4.5 of that book.

C <- 0
D <- 0
for (i in 1:nrow(job)){
for (j in 1:ncol(job)){
pi_c <- 0
pi_d <- 0
for (h in 1:nrow(job)){
for (k in 1:ncol(job)){
if ((h > i & k > j) | (h < i & k < j)){
pi_c <- pi_c + job[h, k]/sum(job)
}

if ((h > i & k < j) | (h < i & k > j)){
pi_d <- pi_d + job[h, k]/sum(job)
}
}
}

C <- C + job[i, j] * pi_c
D <- D + job[i, j] * pi_d
}
}
gamma <- (C - D) / (C + D) # gamma = 0.221 for this example.

The following code is for calculating stardard error of gamma.
sigma.squared <- 0
for (i in 1:nrow(job)){
for (j in 1:ncol(job)){
pi_c <- 0
pi_d <- 0
for (h in 1:nrow(job)){
for (k in 1:ncol(job)){
if ((h > i & k > j) | (h < i & k < j)){
pi_c <- pi_c + job[h, k]/sum(job)
}

if ((h > i & k < j) | (h < i & k > j)){
pi_d <- pi_d + job[h, k]/sum(job)
}
}
}
phi <- 4 * (pi_c * D - pi_d * C) / (C + D)^2

sigma.squared <- sigma.squared + phi^2
}   
}

se <- (sigma.squared/sum(job))^.5 # 0.00748, which is different from
the SE 0.117 given in section 3.4.3 of that book.

I am not able to figure out what is the problem with my code... Could
anyone point out what the problem is?

Thanks.

Wuming

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