[R] generating data

[Fred J.]

Hello
I am trying to generate data in say 2D x,y for a
circle. grid.circle {grid} does not do. any ides is
appreciated.

Thanks
F.J.

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RE: [R] generating data

[Lutz Prechelt]

Do you mean random data?
Generate polar coordinates (angle in range 0..2pi, radius in range 0..1)
and convert.

  Lutz

 -Original Message-
 From: [EMAIL PROTECTED] 
 [mailto:[EMAIL PROTECTED] On Behalf Of Fred J.
 Sent: Freitag, 7. Mai 2004 09:14
 To: r help
 Subject: [R] generating data
 
 
 Hello
 I am trying to generate data in say 2D x,y for a
 circle. grid.circle {grid} does not do. any ides is
 appreciated.
 
 Thanks
 F.J.
 
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[R] Problem (Bug?) with readLines on Suze

[Marc Mamin]

Hello,

I called readLines on  Suze 9.0 with a directory as parameter instead of a file.
R freezed for a very long time; this morning I could read following error message:

Error in readLines(paste(/home/,foo,/,sep=))  :  cannot allocate buffer in 
readLines


under W2K I get a more logical error (cannot open file)


(I'm still using R 1.8.1)

cheers,

Marc

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[R] sampling weights for lme

[alex pegucci]

Dear All,

I have a complex survey data with observations having differing
probabilities of selection into the sample. I would like to run a
linear mixed effects model and also to use weighting that takes this
into consideration. As far as I know, however, the weighting option for
the lme command from nlme package (or glmmPQL from MASS, for that
matter) is related to heteroscedasticity. Is there a sampling weights
option for these packages that I am not aware of? 

Regards,

Alex

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[R] Gaussian Hypergeometric Series _2F_1(a,b,c;z)

[Daniel Hoppe]

Dear all,

I am working on a small package which is supposed to provide evaluation
of the gaussian hypergeometric series. It will be based on the
Fortran-code by Robert Forrey. Does anyone beside me use this function
and would be willing to test the package or discuss requirements?

All the best,

Daniel

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Re: [R] Problem (Bug?) with readLines on Suze

[Prof Brian Ripley]

You asked R to read a binary file line-by-line, and it did its best.
Given that an incorrect operation resulted in an error message, it did 
reasonably well.

It looks to me as if end of directory is not being detected, and I'll dig 
deeper to see it that can be improved.

On Fri, 7 May 2004, Marc Mamin wrote:

 I called readLines on  Suze 9.0 with a directory as parameter instead of a file.
 R freezed for a very long time; this morning I could read following error message:
 
 Error in readLines(paste(/home/,foo,/,sep=))  :  cannot allocate buffer in 
 readLines
 
 
 under W2K I get a more logical error (cannot open file)

That's because on Windows a directory is not a text file.  We could 
probably add such a check on Unix.

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

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Re: [R] Gaussian Hypergeometric Series _2F_1(a,b,c;z)

[Robin Hankin]

Hi Daniel

try hypergeo in library(Davies)

best

rksh




Dear all,

I am working on a small package which is supposed to provide evaluation
of the gaussian hypergeometric series. It will be based on the
Fortran-code by Robert Forrey. Does anyone beside me use this function
and would be willing to test the package or discuss requirements?
All the best,

Daniel

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--
Robin Hankin
Uncertainty Analyst
Southampton Oceanography Centre
SO14 3ZH
tel +44(0)23-8059-7743
[EMAIL PROTECTED] (edit in obvious way; spam precaution)
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[R] Rterm

[Johannes SCHNITZLER]

Dear all,

 

Two questions regarding rterm

First:

C:\Program Files\R\rw1081\bin\rterm.exe --vanilla test.r --args Arg1
Arg2

worked for me so far with r Version 1081, to start a R script with the
given arguments.

 

With R1090

C:\Program Files\R\rw1090\bin\rterm.exe --vanilla test.r --args Arg1
Arg2

There is the error message: Rterm.exe is not a valid Win32 application

I tried on Windows 2000 and  XP

I couldn't find out what to change. 

 

Second:

I would like to set the working directory as well, in the same command,
when calling an r script with rterm.exe from the command line. 

Is there a way to do this?

 

Can somebody help me with these issues?

 

Thank you 

Johannes

 

 

  


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[R] svm question

[Frank Gerrit Zoellner]

Hi!

I have a questionaccording to classifing new examples from an already trained svm. I 
have tarined a svm (e1071 package) with a training set of 1526 examples.
Now I have another data set with 2163 examples and I want to use the already trained 
svm for prediction:

 pred-predict(a.svm,newdata);

Afterwards for further processessing I add further information to the results of teh 
classification from the original input (also 2163 x N matrix) 

result-as.data.frame(cbind(newdata[81:84],pred))

But I receive an error:

Error in data.frame(..., check.names = FALSE) : 
arguments imply differing number of rows: 2163, 1526

So I wonder why the svm is stick to a resultset of 1526 although I put in 2613 
examples? To my mind I thought that the classification/predictin depends on the length 
of the feature vector not on the number of examples? Or am I doing something wrong?

Thanks 
-- 
Frank G. Zoellner
AG Angewandte Informatik
Technische Fakultat
Universitat Bielefeld
phone: +49(0)521-106-2951
fax:   +49(0)521-106-2992
email: [EMAIL PROTECTED]

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Re: [R] Rterm

[Jason Turner]

 With R1090

 C:\Program Files\R\rw1090\bin\rterm.exe --vanilla test.r --args Arg1
 Arg2

 There is the error message: Rterm.exe is not a valid Win32 application

 I tried on Windows 2000 and  XP

 I couldn't find out what to change.

Weird.  Did you install in C:\Program Files\R\rw1090\?  On my XP machine,
it did, and rterm is valid.  The above works from a command prompt,
provided I wrap the executable path and name in quotes.  Failing that, is
it a corrupt binary install?

Here's the md5 of my (working) R-1.9.0, downloaded from CRAN (NOT the
patched version, and not built by me)

C:\Program Files\R\rw1090\bin md5sum.exe Rterm.exe
2565cd848bbd86b964624a0490352da2 *Rterm.exe

 I would like to set the working directory as well, in the same command,
 when calling an r script with rterm.exe from the command line.

 Is there a way to do this?

Inside R: setwd(your/path/here)  With the usual warning about using /
slashes, or \\ slashes (doubled).  I just stick with /.

Cheers

Jason

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[R] loess and as.POSIXct

[Wayne Jones]

Hi there fellow R-users, 

I have just upgraded to R version 1.9.0 from R version 1.7.1 for Windows. 

Im trying to use the loess smoother where the X-variable is an as.POSIXct
variable.
The following works fine with R1.7.1 but not with R1.9.0.

Here is the example:


dates-c('2003-08-03','2003-08-10','2003-08-17','2003-08-24','2003-08-31','2
003-09-07','2003-09-14','2003-09-21','2003-09-28','2003-10-05','2003-10-12',
'2003-10-19','2003-10-26','2003-11-02','2003-11-09','2003-11-16','2003-11-23
','2003-11-30','2003-12-07','2003-12-14','2003-12-21','2003-12-28','2004-01-
04','2004-01-11','2004-01-18','2004-01-25','2004-02-01','2004-02-08','2004-0
2-15','2004-02-22','2004-02-29','2004-03-07','2004-03-14','2004-03-21','2004
-03-28','2004-04-04','2004-04-11','2004-04-18','2004-04-25','2004-05-02')

length(dates)

strptime(dates,format=%Y-%m-%d)

length(strptime(dates,format=%Y-%m-%d))

my.df-data.frame(Sales=rnorm(40),Dates=as.POSIXct(strptime(dates,format=%Y
-%m-%d)))
my.df

loess(Sales~Dates,my.df)


I get the following error with version 1.9.0 
#Error: NA/NaN/Inf in foreign function call (arg 2)
#In addition: Warning messages: 
#1: longer object length
#is not a multiple of shorter object length in: cl == c(Date,
POSIXct, POSIXlt) 
#2: NAs introduced by coercion 

Can anyone help???



Dr Wayne R. Jones
Senior Statistician / Research Analyst
KSS Limited
St James's Buildings
79 Oxford Street
Manchester M1 6SS
Tel: +44(0)161 609 4084
Mob: +44(0)7810 523 713




KSS Ltd
Seventh Floor  St James's Buildings  79 Oxford Street  Manchester  M1 6SS  England
Company Registration Number 2800886
Tel: +44 (0) 161 228 0040   Fax: +44 (0) 161 236 6305
mailto:[EMAIL PROTECTED]http://www.kssg.com


The information in this Internet email is confidential and m...{{dropped}}

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[R] scores from multinomial logistic regression

[Jacqueline Hall]

Dear all,
 
I'm interested in extracting the score from multinomial logistic regression
models fit using multinom, to assess the stregth of assocation of the
parameter with the response (akin to the score from clogit/cox regression).
currently I'm using R 1.8.1.
Is there a function that will extract the score from a multinom object or
how i can get back to it? or from using glm?
I investigated the documention for Design but those functions seem to apply
to binary logistic.
 
Apologies if I am missing something,
Many thanks in advance,
 
Jacqui Hall

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[R] contrasts in a type III anova

[David Jutier]

Hello,

I use a type III anova (car package) to analyse an unbalanced data design. I 
have two factors and I would have the effect of the interaction. I read that 
the result could be strongly influenced by the contrasts. I am really not an 
expert and I am not sure to understand indeed about what it is...

Consequently, I failed to properly used the fit.contrast function (gregmisc 
package) because I don't understand what the fonction need in the argument 
coeff.

The two factors are Y (Ya, Yb,..., Ye) and Auto (Auto1, Auto2,, Auto10)
The responses are binomial (counts in the matrice mat) and gaussian 
(variable tot). I use the glm procedure :

glm1 - glm (mat ~ y*auto, data, family=binomial)
glm2 - glm (tot ~ y*auto, data, family=gaussian)

Subsequently I use the Type III anova :

Anova (glm1, type=III)
Anova (glm2, type=III)

Using the contrast.treatment for both factors Y and Auto, R gives coherent 
results, but I really not sure that this contrasts are appropriate !

Thank's for your advices !
David

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RE: [R] Rterm

[Johannes SCHNITZLER]

Dear Jason,

Thank you very much, the first problem is solved. 
It was a corrupted file. After downloading a new version rterm works!

The second question:
I was trying to set the working directory while I'm calling a script
with Rterm.exe from the command line.
Something like
c:\Program Files\R\rw1090\bin\rterm.exe --vanilla workingdir=c:/data/
test.r --args Arg1 Arg2

Thank's again

Johannes



-Original Message-
From: Jason Turner [mailto:[EMAIL PROTECTED] 
Sent: 07 May 2004 12:15
To: Johannes SCHNITZLER
Cc: [EMAIL PROTECTED]
Subject: Re: [R] Rterm

 With R1090

 C:\Program Files\R\rw1090\bin\rterm.exe --vanilla test.r --args
Arg1
 Arg2

 There is the error message: Rterm.exe is not a valid Win32 application

 I tried on Windows 2000 and  XP

 I couldn't find out what to change.

Weird.  Did you install in C:\Program Files\R\rw1090\?  On my XP
machine,
it did, and rterm is valid.  The above works from a command prompt,
provided I wrap the executable path and name in quotes.  Failing that,
is
it a corrupt binary install?

Here's the md5 of my (working) R-1.9.0, downloaded from CRAN (NOT the
patched version, and not built by me)

C:\Program Files\R\rw1090\bin md5sum.exe Rterm.exe
2565cd848bbd86b964624a0490352da2 *Rterm.exe

 I would like to set the working directory as well, in the same
command,
 when calling an r script with rterm.exe from the command line.

 Is there a way to do this?

Inside R: setwd(your/path/here)  With the usual warning about using
/
slashes, or \\ slashes (doubled).  I just stick with /.

Cheers

Jason

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[R] x-axis tick mark labels running vertically

[Mohamed Abdolell]

I'm plotting obesity rates (y-axis) vs Public Health Unit (x-axis) for the 
province of Ontario and would like to have the Public Health Unit names appear 
vertically rather than the default, horizontally.

I'm actually using the 'barplot2' function in the {gregmisc} library ... I 
haven't been able to find a solution in either the barplot2 options or the 
general plotting options.

Any pointers would be appreciated.

- Mohamed

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[R] Start problem

[Bjørn Økland]

I had a well-working R 1.7, however, today the programme did not start, and I recieved 
an error message.
I have uninstalled the R 1.7, and then installed R 1.9.
Still it does not start, giving the error message Fatal error: invalid HOMEDRIVE.
How can I get it to work?

Bjorn Okland


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[R] help with histogram

[Martin Olivier]

Hi all,

I need some help with the function histogram. Let x be a vector.
The command hist(x,col=blue) gives an histogram for the vector x.
I would like to add some colors in the graphics such that the histogram is
red if abs(x)1.669 and blue otherwise...and what is the solution if I 
want to
change the  filling instead of the color

Thanks for your help,
Olivier
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Re: [R] x-axis tick mark labels running vertically

[Marc Schwartz]

On Fri, 2004-05-07 at 07:02, Mohamed Abdolell wrote:
 I'm plotting obesity rates (y-axis) vs Public Health Unit (x-axis) for the 
 province of Ontario and would like to have the Public Health Unit names appear 
 vertically rather than the default, horizontally.
 
 I'm actually using the 'barplot2' function in the {gregmisc} library ... I 
 haven't been able to find a solution in either the barplot2 options or the 
 general plotting options.
 
 Any pointers would be appreciated.
 
 - Mohamed


You need to adjust par(las) to alter the orientation of the of the
axis labels:

barplot2(1:4, names.arg = c(one, two, three, four), las = 2)

You can also use the axis() function separately:

barplot2(1:4)
axis(1, labels = c(one, two, three, four), las = 2)

Setting par(las = 2) rotates the axis labels so that they are
perpendicular to the axis.

See ?par for more information.

HTH,

Marc Schwartz

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R: [R] help with histogram

[Guazzetti Stefano]

Maybe you want something like:

x-rnorm(1000)
hist(x, breaks=100,
 col=ifelse(abs((hist(x, breaks=100, main=))$breaks)  1.669,
 4,2))

see also the density argument in ?hist
Stefano

 -Messaggio originale-
 Da: Martin Olivier [mailto:[EMAIL PROTECTED]
 Inviato: venerdì 7 maggio 2004 14.40
 A: r-help
 Oggetto: [R] help with histogram
 
 
 Hi all,
 
 I need some help with the function histogram. Let x be a vector.
 The command hist(x,col=blue) gives an histogram for the vector x.
 I would like to add some colors in the graphics such that the 
 histogram is
 red if abs(x)1.669 and blue otherwise...and what is the 
 solution if I 
 want to
 change the  filling instead of the color
 
 Thanks for your help,
 Olivier
 
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RE: [R] help with histogram

[Marc Mamin]

Hi,

you can use subset of data and superpose different histograms for each of them.

hth,

Marc

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Re: [R] Bluefish Editor with R

[Roger D. Peng]

I think you can download it here

http://bluefish.openoffice.nl/index.html

I used it once a while back and it's nice since it has built in 
support for R w/syntax highlighting.  But at this point I'm wedded to 
Emacs.

I thought it actually came bundled with a recent RedHat/Fedora Linux 
but now I can't find it

-roger

[EMAIL PROTECTED] wrote:
Dear List:
Somewhere in the R-Statistical Software website, I remember having read 
about using the opensource Bluefish editor with R. During a recent visit 
to the site, I could not find the link or reference. Also, when I 
searched the list archives 
(http://maths.newcastle.edu.au/~rking/R/about.html) for bluefish, the 
search returned no result.
Has anyone in the list used bluefish as an editor for writing R commands 
and functions? Are there any tutorials available?
TIA,
Arin Basu

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[R] Font and Color documentation

[Iyue Sung]

Hello R-ians,

  Could someone please point me to documentation on legal font and color
specifications (and other 'par' parameters); i.e. font=6 for Times New
Roman, col='Red', etc.?  Searches in ?par, MASS (1st ed.) and other
areas were unsuccessful. I thought I remember seeing it
before...somewhere.

Thanks,
Iyue

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RE: [R] sampling weights for lme

[Baskin, Robert]

 I would like to run a linear *mixed effects* model and also to use
(sample) weighting ...
I've been trying to do this for 2 decades :)

See
 9. Pfeffermann, D. , Skinner, C. J. , Holmes, D. J. , Goldstein, H. , and
Rasbash, J.  (1998), ``Weighting for unequal selection probabilities in
multilevel models (Disc: p41-56)'', Journal of the Royal Statistical
Society, Series B, Methodological, 60 , 23-40 

which refers back to:
29. Pfeffermann, D. , and LaVange, L.  (1989), ``Regression models for
stratified multi-stage cluster samples'', Analysis of Complex Surveys,
237-260 


If you don't like statistical papers, then see section 4.5 of 8. Korn,
Edward Lee , and Graubard, Barry I.  (1999), ``Analysis of health surveys'',
John Wiley  Sons (New York; Chichester)  They explain the idea of using
weights in a model fairly simply.


And I would always recommend Rick's (us hillbillies gotta stick together:)
book:  5. Valliant, Richard , Dorfman, Alan H. , and Royall, Richard M.
(2000), ``Finite population sampling and inference: a prediction approach'',
John Wiley  Sons (New York; Chichester)  as a general fun read.

I didn't really answer your question but...
Bob



-Original Message-
From: alex pegucci [mailto:[EMAIL PROTECTED] 
Sent: Friday, May 07, 2004 4:03 AM
To: [EMAIL PROTECTED]
Subject: [R] sampling weights for lme

Dear All,

I have a complex survey data with observations having differing
probabilities of selection into the sample. I would like to run a
linear mixed effects model and also to use weighting that takes this
into consideration. As far as I know, however, the weighting option for
the lme command from nlme package (or glmmPQL from MASS, for that
matter) is related to heteroscedasticity. Is there a sampling weights
option for these packages that I am not aware of? 

Regards,

Alex

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[R] Anyone in need of fast evaluation of Gaussian Hypergeometric Series?

[Daniel Hoppe]

Dear all,

sorry for the repost, but I think that the subject line of my previous
posting did not really make my point clear. 

Is there anyone who would be interesting in testing and giving me
feedback about a package which evaluates the _2F_1 series and 
- is fast compared to the straightforward summation and
- is more precise especially near to the circle of convergence |z|~1?

If you are interested please send me a short note.

Daniel

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Re: [R] Rterm

[Jason Turner]

Johannes SCHNITZLER wrote:
The second question:
I was trying to set the working directory while I'm calling a script
with Rterm.exe from the command line.
Something like
c:\Program Files\R\rw1090\bin\rterm.exe --vanilla workingdir=c:/data/
test.r --args Arg1 Arg2
Not sure - if you could pass the working directory as an arg, then R can 
handle it from there - use the setwd() command.  What I usually do on 
Un*x-like systems is to cd to the directory first, then start the R run. 
 Something like

cd my favorite dir
R --vanilla ...
Since you're already specifying the absolute path for Rterm, the above 
should work...

Cheers

Jason

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Re: [R] scores from multinomial logistic regression

[Prof Brian Ripley]

What do you mean by the scores?

What multinom does is to fit probabilities (which you can extract by 
fitted()): the response is a discrete probability distribution.
There is an underlying linear predictor but

(a) it is K-dimensional and
(b) there is a degree of ambiguity, usually resolved by setting the 
predictor for one category to zero (but not in this code).

That linear predictor is only generated in the underlying C code.

On Fri, 7 May 2004, Jacqueline Hall wrote:

 Dear all,
  
 I'm interested in extracting the score from multinomial logistic regression
 models fit using multinom, to assess the stregth of assocation of the
 parameter with the response (akin to the score from clogit/cox regression).
 currently I'm using R 1.8.1.
 Is there a function that will extract the score from a multinom object or
 how i can get back to it? or from using glm?
 I investigated the documention for Design but those functions seem to apply
 to binary logistic.

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

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Re: [R] Rterm

[Prof Brian Ripley]

On Sat, 8 May 2004, Jason Turner wrote:

 Johannes SCHNITZLER wrote:
  The second question:
  I was trying to set the working directory while I'm calling a script
  with Rterm.exe from the command line.
  Something like
  c:\Program Files\R\rw1090\bin\rterm.exe --vanilla workingdir=c:/data/
  test.r --args Arg1 Arg2
 
 Not sure - if you could pass the working directory as an arg, then R can 
 handle it from there - use the setwd() command.  What I usually do on 
 Un*x-like systems is to cd to the directory first, then start the R run. 
   Something like
 
 cd my favorite dir
 R --vanilla ...
 
 Since you're already specifying the absolute path for Rterm, the above 
 should work...

That's the only way.  The `working directory' is the directory from which 
you launch an application (although you can fix that by a shortcut).  R 
looks in the working directory for several things, e.g. a .Rprofile file, 
before it ever runs any R code like setwd.  If that is not a problem you 
can use something like (from a decent shell)

(echo setwd(somewhere); cat test.r) | Rterm.exe --args Arg1

to make the first R code run change directories.  Or you can have at the 
top of test.r

setwd(Sys.getenv(WD))

and use 

Rterm.exe WD=c:/data  test.r --args Arg1 Arg2

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

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[R] How does the lm() function work?

[Phillip Good]

Does the lm() function use forward, backward, stepwise or some other method of 
multivariable regression?  Where can I look up the details?

Phillip Good
[[alternative HTML version deleted]]

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RE: [R] How does the lm() function work?

[Wayne Jones]

?step







-Original Message-
From: Phillip Good [mailto:[EMAIL PROTECTED]
Sent: 07 May 2004 15:19
To: [EMAIL PROTECTED]
Subject: [R] How does the lm() function work?


Does the lm() function use forward, backward, stepwise or some other method
of multivariable regression?  Where can I look up the details?

Phillip Good
[[alternative HTML version deleted]]

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KSS Ltd
Seventh Floor  St James's Buildings  79 Oxford Street  Manchester  M1 6SS  England
Company Registration Number 2800886
Tel: +44 (0) 161 228 0040   Fax: +44 (0) 161 236 6305
mailto:[EMAIL PROTECTED]http://www.kssg.com


The information in this Internet email is confidential and m...{{dropped}}

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Re: [R] How does the lm() function work?

[Roger D. Peng]

lm() itself does not implement any model selection procedures.  step() 
and stepAIC() in the MASS library do.

-roger

Phillip Good wrote:
Does the lm() function use forward, backward, stepwise or some other method of multivariable regression?  Where can I look up the details?

Phillip Good
[[alternative HTML version deleted]]
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RE: [R] generating data

[Huntsinger, Reid]

Keep in mind that the change of coordinates introduces a distortion; dxdy
becomes in polar coordinates rdrdtheta. So if you wanted a uniform
distribution on the disk you could generate theta uniform on [0,2pi] and r
from a distribution with density f(r)=2r on [0,1]. 

Reid Huntsinger

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Lutz Prechelt
Sent: Friday, May 07, 2004 3:43 AM
To: [EMAIL PROTECTED]
Subject: RE: [R] generating data


Do you mean random data?
Generate polar coordinates (angle in range 0..2pi, radius in range 0..1)
and convert.

  Lutz

 -Original Message-
 From: [EMAIL PROTECTED] 
 [mailto:[EMAIL PROTECTED] On Behalf Of Fred J.
 Sent: Freitag, 7. Mai 2004 09:14
 To: r help
 Subject: [R] generating data
 
 
 Hello
 I am trying to generate data in say 2D x,y for a
 circle. grid.circle {grid} does not do. any ides is
 appreciated.
 
 Thanks
 F.J.
 
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Re: [R] How does the lm() function work?

[Phillip Good]

Thank you.  I'll install the MASS library.

- Original Message -
From: Roger D. Peng [EMAIL PROTECTED]
To: Phillip Good [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Sent: Friday, May 07, 2004 7:28 AM
Subject: Re: [R] How does the lm() function work?


 lm() itself does not implement any model selection procedures.  step()
 and stepAIC() in the MASS library do.

 -roger

 Phillip Good wrote:
  Does the lm() function use forward, backward, stepwise or some other
method of multivariable regression?  Where can I look up the details?
 
  Phillip Good
  [[alternative HTML version deleted]]
 
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RE: [R] Rterm

[Johannes SCHNITZLER]

Thank you very much for the fast answers,

It work's very well

Johannes

-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] 
Sent: 07 May 2004 16:16
To: Jason Turner
Cc: Johannes SCHNITZLER; [EMAIL PROTECTED]
Subject: Re: [R] Rterm

On Sat, 8 May 2004, Jason Turner wrote:

 Johannes SCHNITZLER wrote:
  The second question:
  I was trying to set the working directory while I'm calling a script
  with Rterm.exe from the command line.
  Something like
  c:\Program Files\R\rw1090\bin\rterm.exe --vanilla
workingdir=c:/data/
  test.r --args Arg1 Arg2
 
 Not sure - if you could pass the working directory as an arg, then R
can 
 handle it from there - use the setwd() command.  What I usually do on 
 Un*x-like systems is to cd to the directory first, then start the R
run. 
   Something like
 
 cd my favorite dir
 R --vanilla ...
 
 Since you're already specifying the absolute path for Rterm, the above

 should work...

That's the only way.  The `working directory' is the directory from
which 
you launch an application (although you can fix that by a shortcut).  R 
looks in the working directory for several things, e.g. a .Rprofile
file, 
before it ever runs any R code like setwd.  If that is not a problem you

can use something like (from a decent shell)

(echo setwd(somewhere); cat test.r) | Rterm.exe --args Arg1

to make the first R code run change directories.  Or you can have at the

top of test.r

setwd(Sys.getenv(WD))

and use 

Rterm.exe WD=c:/data  test.r --args Arg1 Arg2

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

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RE: [R] contrasts in a type III anova

[John Fox]

Dear David,

The short answer is that in a two-way ANOVA (or an analogous generalized
linear model), the test for the interaction doesn't depend upon the contrast
type, and is identical for Type-II and Type-III (and, indeed, Type-I
-- i.e., sequential) tests. It's the main-effect tests that depend upon
contrast type (for Type-III tests), and for which Type-II and Type-III
tests differ. There's a longer answer in the book with which the car package
is associated (and a longer one still in my Applied Regression text, as well
as other places).

I hope this helps,
 John

 -Original Message-
 From: [EMAIL PROTECTED] 
 [mailto:[EMAIL PROTECTED] On Behalf Of David Jutier
 Sent: Friday, May 07, 2004 6:20 AM
 To: [EMAIL PROTECTED]
 Subject: [R] contrasts in a type III anova
 
 Hello,
 
 I use a type III anova (car package) to analyse an 
 unbalanced data design. I have two factors and I would have 
 the effect of the interaction. I read that the result could 
 be strongly influenced by the contrasts. I am really not an 
 expert and I am not sure to understand indeed about what it is...
 
 Consequently, I failed to properly used the fit.contrast 
 function (gregmisc
 package) because I don't understand what the fonction need in 
 the argument coeff.
 
 The two factors are Y (Ya, Yb,..., Ye) and Auto (Auto1, 
 Auto2,, Auto10) The responses are binomial (counts in the 
 matrice mat) and gaussian (variable tot). I use the glm 
 procedure :
 
 glm1 - glm (mat ~ y*auto, data, family=binomial)
 glm2 - glm (tot ~ y*auto, data, family=gaussian)
 
 Subsequently I use the Type III anova :
 
 Anova (glm1, type=III)
 Anova (glm2, type=III)
 
 Using the contrast.treatment for both factors Y and Auto, R 
 gives coherent results, but I really not sure that this 
 contrasts are appropriate !
 
 Thank's for your advices !
 David
 
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Re: [R] How does the lm() function work?

[Martin Maechler]

 Phillip == Phillip Good [EMAIL PROTECTED]
 on Fri, 7 May 2004 07:40:15 -0700 writes:

Phillip Thank you.  I'll install the MASS library.

Two things:

- it's the MASS   package 

- if library(MASS)  does not work for you,
  you have either a very old version of R, or a broken one.
  In both cases, rather re-install R than trying to install
  MASS.

  But I assume you just didn't know that  
  library(MASS)
  would work for you.

Regards,
Martin

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[R] Re: R web interfaces

[Nathan Whitehouse]

Hi,
 
 I don't see any replies to this, but it does seem
 quite a good idea, 
 especially as the existing information (eg in the
 FAQ) is rather thin 
 and probably incomprehensible to most.  I have no
 time to do it myself, 
 though.

  Someone in this lab(Andrew Young, Chad Shaw or I)
would be willing to put together a page.  I think it's
a good way to collect a lot of current development.
 
 
 I look forward to meeting you there.

  I think circumstances will prevent me from going,
which I'm disappointed about.
  
  That said, both the PI of our lab and another guy
will be there(Chad Shaw  Andrew Young).  They will be
very keen to discuss stuff more.
  Best, 
  Nathan 

 Cheers,
 David
 


=
Nathan Whitehouse
Statistics/Programming
Baylor College of Medicine
Houston, TX, USA
[EMAIL PROTECTED]
work: 1-713-798-9029
cell:1-512-293-5840

http://rho-project.org: rho- open source web services for R.
http://franklin.imgen.bcm.tmc.edu: Shaw laboratory, bcm.

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Re: [R] help with histogram

[Martin Maechler]

 Guazzetti == Guazzetti Stefano [EMAIL PROTECTED]
 on Fri, 7 May 2004 14:45:22 +0200 writes:

Guazzetti Maybe you want something like:

Guazzetti x-rnorm(1000)
Guazzetti hist(x, breaks=100,
Guazzetticol=ifelse(abs((hist(x, breaks=100, main=))$breaks)  1.669,
Guazzetti4,2))

Guazzetti see also the density argument in ?hist

very good!

Even slightly better {not calling  hist() twice} is

 x - rnorm(1000)
 hx - hist(x, breaks=100,plot=FALSE)
 plot(hx, col=ifelse(abs(hx$breaks)  1.669, 4, 2))

Regards, Martin

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[R] Re: Sessioned R web interfaces

[Nathan Whitehouse]

Frank,

  Both RZope and Rho solve this problem.  
  
  RZope
(http://www.analytics.washington.edu/statcomp/projects/rzope/)solves
it by using *nix's fork command, which takes as much
time as a memcopy.  
 
  Rho(http://rho-project.org) solves it by maintaining
a pool of idling R processes, which it maintains
active  can pull to do a calculation immediately.

  Both of these are pretty immediate  allow
multistep/session calculations.(As compared to CGI
stuff)

  cheers,
  Nathan

Here's a related question:  Do any of the mentioned
R-web interfaces
(Rweb, R-Online, CGIwithR, RSPerl) support reusing the
same R process,
eliminating the startup overhead?  This would be
useful to me as well.

Currently I use such a method on my computing cluster:
 All 40 
compute nodes run an R process/compute server that
listens at a socket 
for
any 
connection and subsequent commands from another
computer. 
When the master process disconnects, the R processes
go back to 
listening
at the socket.  Connecting to the R compute servers
this way
takes  2 milliseconds rather than the typical ~2
second R startup 
time.

Thanks for any tips.

-Frank

=
Nathan Whitehouse
Statistics/Programming
Baylor College of Medicine
Houston, TX, USA
[EMAIL PROTECTED]
work: 1-713-798-9029
cell:1-512-293-5840

http://rho-project.org: rho- open source web services for R.
http://franklin.imgen.bcm.tmc.edu: Shaw laboratory, bcm.

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RE: [R] scores from multinomial logistic regression

[Jacqueline Hall]

Hi,

Sorry for not making this clear,

By score I meant the score from the score test, for assessing the addition
of a new variable to the model. (first derivative of the log likeihood/
information matrix, the ratio (score)having a chi squared distribution of
appropriate df)

I'm looking for something similar/appropraite for logistic regression, my
outcome (response) variable has 4 categories (hence the interest in
multinom), the covariates are continuous.

Thanks again,

Jacqui

-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] 
Sent: 07 May 2004 15:07
To: Jacqueline Hall
Cc: [EMAIL PROTECTED]
Subject: Re: [R] scores from multinomial logistic regression


What do you mean by the scores?

What multinom does is to fit probabilities (which you can extract by 
fitted()): the response is a discrete probability distribution. There is an
underlying linear predictor but

(a) it is K-dimensional and
(b) there is a degree of ambiguity, usually resolved by setting the 
predictor for one category to zero (but not in this code).

That linear predictor is only generated in the underlying C code.

On Fri, 7 May 2004, Jacqueline Hall wrote:

 Dear all,
  
 I'm interested in extracting the score from multinomial logistic 
 regression models fit using multinom, to assess the stregth of 
 assocation of the parameter with the response (akin to the score from 
 clogit/cox regression). currently I'm using R 1.8.1. Is there a 
 function that will extract the score from a multinom object or how i 
 can get back to it? or from using glm? I investigated the documention 
 for Design but those functions seem to apply to binary logistic.

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

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[R] randomForests and Y-scrambling on a small synthetic dataset

[clayton . springer]

Dear r-help,


The following dataset (generated with perl) has 10 observations of 100 
dependant variables (integers drawn uniformly
from [1:9]) which is split evenly between two classes..

First I show some work, and then ask two questions at the end.

 data - read.table (rf_input.dat)
 library (randomForest)
# if we do randomForest one time it looks like this:

 rf - randomForest (factor(V101) ~. ,data=data)
 rf$confusion
  1 2 class.error
1 5 5 0.5
2 4 6 0.4

# now we do it 100 times 

 
tnum - numeric()

for (i in 1:100) { MT - data$V101
   MT.rf - randomForest (factor(MT) ~ . ,data =data[-c(101)])
   number - as.integer (summary ( predict(MT.rf) == MT)[3] )
   tnum - c(tnum,number)
}

+ + + + + + +  

# and this distribution of results (about 13 correct out of 20) 
  quantile (tnum,probs = seq (0,1,0.1),na.rm = T)
  0%  10%  20%  30%  40%  50%  60%  70%  80%  90% 100% 
   9   11   12   12   13   13   13   14   14   15   17 

# now lets permute (re-randomize?) the classes and repeat 1000 times: 

 library (gregmisc)
tnum - numeric()

for (i in 1:1000) { MT - permute (data$V101)
   MT.rf - randomForest (factor(MT) ~ . ,data =data[-c(101)])
   number - as.integer (summary ( predict(MT.rf) == MT)[3] )
   tnum - c(tnum,number)
}

# I get these results: the average is about 8 correct (out of 20) with 13 
correct being at about
# the 95% confidence level

 quantile (tnum,probs = seq (0,1,0.1),na.rm = T)
  0%  10%  20%  30%  40%  50%  60%  70%  80%  90% 100% 
   14567889   10   12   18 
  quantile (tnum,probs = seq (0.9,1,0.01),na.rm = T)
 90%  91%  92%  93%  94%  95%  96%  97%  98%  99% 100% 
  12   12   12   12   12   13   13   14   14   15   18 



My two questions:

Question 1: Naively I might have expected to get 10/20 for the Y-scrambled 
examples, but instead I got 8/20.  Why is that?
(Persumably has something to do with the randomForest only training on 2/3 
of the examples.)

Question 2: With my Y scrambling exercise I seem to have demonstrated that 
the original dataset was not random. But yet it
is random by construction. Is this just a fluke, or is something wrong 
with my protocol?

thanks in advance,

Clayton__
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RE: [R] scores from multinomial logistic regression

[Prof Brian Ripley]

Note the coxph docs call these `efficient scores', which helps. However,
what the `score' part of a coxph object gives is not the score for the
addition of a new variable, but for the addition of all the variables, as
I understand it. (You could do repeated fits using init=, but that's not
what you said.)

I am not aware of a good way to do that even for a glm. (Smart people
could make add1.lm do it, I guess.) I would just do likelihood ratio tests
since computation time is unlikely to be an issue these days.


On Fri, 7 May 2004, Jacqueline Hall wrote:

 Hi,
 
 Sorry for not making this clear,
 
 By score I meant the score from the score test, for assessing the addition
 of a new variable to the model. (first derivative of the log likeihood/
 information matrix, the ratio (score)having a chi squared distribution of
 appropriate df)
 
 I'm looking for something similar/appropraite for logistic regression, my
 outcome (response) variable has 4 categories (hence the interest in
 multinom), the covariates are continuous.
 
 Thanks again,
 
 Jacqui
 
 -Original Message-
 From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] 
 Sent: 07 May 2004 15:07
 To: Jacqueline Hall
 Cc: [EMAIL PROTECTED]
 Subject: Re: [R] scores from multinomial logistic regression
 
 
 What do you mean by the scores?
 
 What multinom does is to fit probabilities (which you can extract by 
 fitted()): the response is a discrete probability distribution. There is an
 underlying linear predictor but
 
 (a) it is K-dimensional and
 (b) there is a degree of ambiguity, usually resolved by setting the 
 predictor for one category to zero (but not in this code).
 
 That linear predictor is only generated in the underlying C code.
 
 On Fri, 7 May 2004, Jacqueline Hall wrote:
 
  Dear all,
   
  I'm interested in extracting the score from multinomial logistic 
  regression models fit using multinom, to assess the stregth of 
  assocation of the parameter with the response (akin to the score from 
  clogit/cox regression). currently I'm using R 1.8.1. Is there a 
  function that will extract the score from a multinom object or how i 
  can get back to it? or from using glm? I investigated the documention 
  for Design but those functions seem to apply to binary logistic.
 
 

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

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Re: [R] Font and Color documentation

[Prof Brian Ripley]

This is R-specific, and R was but a glimmer of the eye when MASS (1st ed) 
was written in 1992/3.  pp. 79-84 of the current edition does have the 
information.

I think all the information you ask for is in ?par, or that points to the 
appropriate place.

Fonts are device specific.  ?par says

 'font' An integer which specifies which font to use for text.  If
  possible, device drivers arrange so that 1 corresponds to
  plain text, 2 to bold face, 3 to italic and 4 to bold italic.

and BTW, font 5 is always a symbol font.  To go beyond that you need to 
look at the documentation of the device you use.  Many devices (e.g. x11, 
windows, postscript, pdf) allow you to map fonts to those numbers.

There is a whole section on `Color Specification' in ?par, which says 
colors() gives all the known colour names, and valid numbers are from 0 to 
the size of the palette.


On Fri, 7 May 2004, Iyue Sung wrote:

   Could someone please point me to documentation on legal font and color
 specifications (and other 'par' parameters); i.e. font=6 for Times New
 Roman, col='Red', etc.?  Searches in ?par, MASS (1st ed.) and other
 areas were unsuccessful. I thought I remember seeing it
 before...somewhere.

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

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[R] Quantile of a function

[José Fernando Silva]

I have a simple doubt:
I have a function, say:
 
test - function (theta) {
return (theta^2) }
 
I can use:
integrate (test,0,1)
to obtain the area under de function.
Can I do the opposite? I`d like to give the lower limit and the area I need as 
arguments, in order to get the upper limit. In other words, I`d like to obtain the 
quantile of the function (the lower limit could be 0, for example).
Thank you in advance.
 



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Re: [R] Start problem

[Uwe Ligges]

Bjørn Økland wrote:

I had a well-working R 1.7, however, today the programme did not start, and I recieved 
an error message.
I have uninstalled the R 1.7, and then installed R 1.9.
Still it does not start, giving the error message Fatal error: invalid HOMEDRIVE.
How can I get it to work?
Bjorn Okland

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Either try out r-patched or look in the R-help archives for the string 
Fatal error: invalid HOMEDRIVE. There were several discussions (and 
hints for a workaround) about that bug introduced by Microsoft's 
security patch.

Uwe Ligges

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[R] rpart for CART with weights/priors

[Carolin Strobl]

Hi,
I have a technical question about rpart:
according to Breiman et al. 1984, different costs for misclassification in
CART can be modelled 
either by means of modifying the loss matrix or by means of using different
prior probabilities for the classes, 
which again should have the same effect as using different weights for the
response classes.

What I tried was this:

library(rpart)
data(kyphosis)

#fit1 from original unweighted data set
fit1 - rpart(Kyphosis ~ Age + Number + Start, data=kyphosis)

#modify loss matrix
loss-matrix(c(0,1,2,0),nrow=2,ncol=2)

#   true class?
#[,1] [,2]
#[1,]02 
#[2,]10 predicted class?


#modify priors
prior=c(1/3,2/3)

fit2- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis,
parms=list(loss=loss))
fit3 - rpart(Kyphosis ~ Age + Number + Start, data=kyphosis,
parms=list(prior=prior))

fit2
fit3

par(mfrow=c(2,1))
plot(fit2)
text(fit2,use.n=T)
plot(fit3)
text(fit3,use.n=T)

#lead to similar but not identical trees (similar topology but different
cutoff points), 
#while all other combinations (even complete reversion, i.e. preference for
the other class) 
#lead to totally different trees...

#third approach using weights:
#sorting of data to design weight vector
ind-order(kyphosis[,1])
kyphosis1-kyphosis[ind,]

summary(kyphosis1[,1])
weight-c(rep(1,64),rep(2,17))
summary(as.factor(weight))

fit4 - rpart(Kyphosis ~ Age + Number + Start, data=kyphosis1,
weights=weight)

#leads to result very similar to fit2 with
loss-matrix(c(0,1,2,0),nrow=2,ncol=2)
#(same tree and cutoff points, but slightly different probabilities, maybe
numerical artefact?)

fit4
plot(fit4)
text(fit4,use.n=T)

#doule check with inverse loss matrix

loss-matrix(c(0,1,2,0),nrow=2,ncol=2,byrow=T)
fit2- rpart(Kyphosis ~ Age + Number + Start, data=kyphosis,
parms=list(loss=loss))

weight-c(rep(2,64),rep(1,17))
fit4 - rpart(Kyphosis ~ Age + Number + Start, data=kyphosis1,
weights=weight)

fit2
fit4
#also same except for probabilities yprob

I don't see 
1. why the approach using prior probabilities doesn't work
2. what causes the differences in predicted probabilities in the weights
approach

Any idea? Thank You! C.

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Re: [R] Quantile of a function

[Uwe Ligges]

José Fernando Silva wrote:

I have a simple doubt:
I have a function, say:
 
test - function (theta) {
return (theta^2) }
 
I can use:
integrate (test,0,1)
to obtain the area under de function.
Can I do the opposite? I`d like to give the lower limit and the area I need as arguments, in order to get the upper limit. In other words, I`d like to obtain the quantile of the function (the lower limit could be 0, for example).
Thank you in advance.
 
If you really want to do it numerically (assuming your function is much 
more complex and the exmaple one), try e.g.

solveit - function (quant, foo, lw, area) {
   (integrate(foo, lw, quant)$value - area)^2
}
optimize(solveit, c(0, 100),
foo = function(theta) theta^2, lw = 0, area = 0.95)
Uwe Ligges






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[R] cannot allocate vector of length 1072693248

[David L. Van Brunt, Ph.D.]

Well, I've done everything I can think of the make the code more efficient,
but it seems (if I read this error message correctly) that I'm running out
of memory on what should be small data set.

Here's the sequence:

A vector of 30 possible identifiers
For each value, query a MySQL database to pull in 80 or so records
Run a few different random Forests on those data
Print the results as I go
rm() all the objects created in the loop, including all the old data
Next value, to repeat for each identifier.


Round the 3rd time through the loop, I get kicked out with:

Error in as.vector(data) : cannot allocate vector of length 1072693248

This is on Mac OS X, which is UNIX-based (from freeBSD, as I understand it),
so I haven't set anything special with the memory at startup. But then, I
only have 80 observations running through at a time, so it doesn't seem like
there should be a memory issue.

Any ideas?

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Re: [R] cannot allocate vector of length 1072693248

[Prof Brian Ripley]

I think it is more likely that you have a bug.  Probably you have run out 
of address space, as that's almost 4Gb if an integer and 8Gb if real.

Can you do options(error=dump.frames) and debugger() after the error 
message and try to find out what `data' is and what size it is.

On Fri, 7 May 2004, David L. Van Brunt, Ph.D. wrote:

 Well, I've done everything I can think of the make the code more efficient,
 but it seems (if I read this error message correctly) that I'm running out
 of memory on what should be small data set.
 
 Here's the sequence:
 
 A vector of 30 possible identifiers
 For each value, query a MySQL database to pull in 80 or so records
 Run a few different random Forests on those data
 Print the results as I go
 rm() all the objects created in the loop, including all the old data
 Next value, to repeat for each identifier.
 
 
 Round the 3rd time through the loop, I get kicked out with:
 
 Error in as.vector(data) : cannot allocate vector of length 1072693248
 
 This is on Mac OS X, which is UNIX-based (from freeBSD, as I understand it),
 so I haven't set anything special with the memory at startup. But then, I
 only have 80 observations running through at a time, so it doesn't seem like
 there should be a memory issue.
 
 Any ideas?
 
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-- 
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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Re: [R] cgi/servlets/httpd in R

[wwsprague]

Samuelson, Frank* wrote:


Currently I use such a method on my computing cluster:  All 40 
compute nodes run an R process/compute server that listens at a socket for
any 
connection and subsequent commands from another computer. 
When the master process disconnects, the R processes go back to listening
at the socket.  Connecting to the R compute servers this way
takes  2 milliseconds rather than the typical ~2 second R startup time.
Your solution seems what I am looking for, actually.  Questions:

1.  How do you communicate with an R process?  I can only think of 
embedded code like SQL in Perl.

2.  How do you find an R node that is open?

2.5  You are haveing cgi scripts connect to the R processes, right?  Or 
are the R processes available for another purpose?

3.  How much of your code are you willing to share :)?  We are 
interested in making demographic analysis tools available online 
(life-table-ish stuff to start with, then as much as we can get grant 
money for).

W

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Re: [R] cannot allocate vector of length 1072693248

[David L. Van Brunt, Ph.D.]

Thanks for the suggestion. If there's a bug in my code, I can't find it.

The code runs successfully several times through. And I have only a few
lines, but repeated in blocks with a few tweaks to make different
predictions each time.

If I comment out a line that preceeds a crash, it will run a little longer
before giving up next time. So it is as if something is slowly filling up
through each run, and is accumulating.

But I do rm() all the objects created inside of the for loop, and then
gc() before the loop is finished, also.

So I'm stumped.

When I called the debugger, the last item shown was the vector line, so I
chose that option and typed ls()... It had only mode and x. The value
of mode was any, and when I tried to display x, I expected a slew of
data but instead R crashed.

Don't know if that's informative or not!

On 5/7/04 11:42, Prof Brian Ripley [EMAIL PROTECTED] wrote:

 I think it is more likely that you have a bug.  Probably you have run out
 of address space, as that's almost 4Gb if an integer and 8Gb if real.
 
 Can you do options(error=dump.frames) and debugger() after the error
 message and try to find out what `data' is and what size it is.
 
 On Fri, 7 May 2004, David L. Van Brunt, Ph.D. wrote:
 
 Well, I've done everything I can think of the make the code more efficient,
 but it seems (if I read this error message correctly) that I'm running out
 of memory on what should be small data set.
 
 Here's the sequence:
 
 A vector of 30 possible identifiers
 For each value, query a MySQL database to pull in 80 or so records
 Run a few different random Forests on those data
 Print the results as I go
 rm() all the objects created in the loop, including all the old data
 Next value, to repeat for each identifier.
 
 
 Round the 3rd time through the loop, I get kicked out with:
 
 Error in as.vector(data) : cannot allocate vector of length 1072693248
 
 This is on Mac OS X, which is UNIX-based (from freeBSD, as I understand it),
 so I haven't set anything special with the memory at startup. But then, I
 only have 80 observations running through at a time, so it doesn't seem like
 there should be a memory issue.
 
 Any ideas?
 
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-- 
David L. Van Brunt, Ph.D.
Outlier Consulting  Development
mailto: [EMAIL PROTECTED]

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Re: [R] cgi/servlets/httpd in R

[Joe Conway]

[EMAIL PROTECTED] wrote:
Your solution seems what I am looking for, actually.  Questions:
FWIW, another possible option if your data is stored in an RDBMS is 
Postgres with PL/R; see:
  http://www.joeconway.com/plr/

As of Postgres 7.4 you can preload and initialize libraries at 
postmaster start, which means that each forked database backend includes 
a fully initialized copy of libR.

If you are interested, there is some information available regarding how 
to use this with PHP to generate online charts here:
http://www.joeconway.com/oscon-pres-2003-1.pdf

HTH,

Joe

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Re: [R] I have some problem about save and open

[Sean Davis]

If you want to save the workspace to a file, type:

save.image(filename)

To load the file, type:

load(filename)

The save that you do when you exit R saves by default to a (typically)
hidden file called .Rdata.  If you start R in a directory with a .Rdata
file in it, R will load that file automatically.

Sean
- Original Message -
From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Monday, May 03, 2004 10:32 PM
Subject: [R] I have some problem about save and open


 Hello R-help

 I use R program on linux.
 and when I would like to quick R, then I type q()
 after than has question Save workspace image? [y/n/c]:
 when I ans y , why not to ask about name of file.
 and when I would like to open last file , how can I do?
 thanks for your help.
 and sorry if my English not so good. I'm Thai people and I know
 English a little.
 Mathinee

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[R] dump.frames in non-interactive mode

[Vadim Ogranovich]

Hi,
 
recover() resorts to dump.frames() when called in non-interactive
sessions. However dump.frames() still puts the dump into last.dump
object and not into a file, which brings the question of how to get hold
of the object once the session terminates.
 
I guess the supposed answer is that last.dump is saved in .Rdata once R
exits. However I find it more convenient on day-to-day basis to use
--no-save --no-restore options and avoid .Rdata. So my question is how
to best set a hook, in say .Rprofile, so that in non-interactive mode
(and only in it) last.dump (and only it) will be saved in a file upon
exit from R.
 
Thanks,
Vadim

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Re: [R] dump.frames in non-interactive mode

[Prof Brian Ripley]

On Fri, 7 May 2004, Vadim Ogranovich wrote:

 recover() resorts to dump.frames() when called in non-interactive
 sessions. However dump.frames() still puts the dump into last.dump
 object and not into a file, which brings the question of how to get hold
 of the object once the session terminates.

This is discussed in the help file for dump.frames ...

 If 'dump.frames' is installed as the error handler, execution will
 continue even in non-interactive sessions. See the examples for
 how to dump and then quit.

 I guess the supposed answer is that last.dump is saved in .Rdata once R
 exits. However I find it more convenient on day-to-day basis to use
 --no-save --no-restore options and avoid .Rdata. So my question is how
 to best set a hook, in say .Rprofile, so that in non-interactive mode
 (and only in it) last.dump (and only it) will be saved in a file upon
 exit from R.

dump.frames has parameters to do exactly this.

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

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Re: [R] generating data

[Giovanni Petris]

 Hello
 I am trying to generate data in say 2D x,y for a
 circle.

I think data are usually collected...

GP

-- 

 __
[  ]
[ Giovanni Petris [EMAIL PROTECTED] ]
[ Department of Mathematical Sciences  ]
[ University of Arkansas - Fayetteville, AR 72701  ]
[ Ph: (479) 575-6324, 575-8630 (fax)   ]
[ http://definetti.uark.edu/~gpetris/  ]
[__]

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[R] Lattice xyplot - problem trying to produce multiple output files with a 'for' loop

[richard . kittler]

I am stuck on trying to get the Lattice xyplot to output a separate PNG file each time 
through my 'for' loop.  The files get produced but are empty.

Here is the code.  I'm running 1.9 on Windows.  BTW is there a more efficient way of 
creating the separate output files than looping over the levels and subsetting? 

.
lev - levels(ds$TR)

for (byvar in lev) {

 file.png - paste(u:/data/R/Scatter_CTY_HWY_CO_TR, byvar,  .png, sep=)

 trellis.device( device=png, file=file.png, 
 width=1000, height=1000, pointsize=20, bg=transparent )

 ds1 - subset(ds, TR == byvar, select=c(CTY, HWY, CO))

 xyplot( ds1$CTY ~ ds1$HWY, groups=ds1$CO,
auto.key=list(space=right), ylab=CTY, xlab=HWY)

 dev.off()

}
.

--Rich

Richard Kittler 
AMD TDG
408-749-4099

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Re: [R] Lattice xyplot - problem trying to produce multiple output files with a 'for' loop

[Sundar Dorai-Raj]

[EMAIL PROTECTED] wrote:

I am stuck on trying to get the Lattice xyplot to output a separate PNG file each time through my 'for' loop.  The files get produced but are empty.

Here is the code.  I'm running 1.9 on Windows.  BTW is there a more efficient way of creating the separate output files than looping over the levels and subsetting? 

.
lev - levels(ds$TR)
for (byvar in lev) {

 file.png - paste(u:/data/R/Scatter_CTY_HWY_CO_TR, byvar,  .png, sep=)

 trellis.device( device=png, file=file.png, 
 width=1000, height=1000, pointsize=20, bg=transparent )

 ds1 - subset(ds, TR == byvar, select=c(CTY, HWY, CO))

 xyplot( ds1$CTY ~ ds1$HWY, groups=ds1$CO,
auto.key=list(space=right), ylab=CTY, xlab=HWY)
 dev.off()

}
.
--Rich

Richard Kittler 
AMD TDG
408-749-4099

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See the FAQ.

you have to wrap the xyplot call with a print. I.e.

for(...) {
  ...
  print(xyplot(...))
  ...
}
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[R] Invalid HOMEDRIVE

[Jim Stimson]

Attempting to install the most recent R on a Windows/XP machine, I get 
what appears to be a normal (completely default) installation. Then when 
I attempt to load rgui I get the fatal error message: Invalid HOMEDRIVE. 
Any explanation of the error or suggestions of fixes to files or 
registry would be appreciated.

--
Jim Stimson
Email: [EMAIL PROTECTED]
Web: http://www.unc.edu/~jstimson
Phone: (919) 962-0428  Fax: (919) 962-0432  Home: (919) 968-0942
Department of Political Science
University of North Carolina at Chapel Hill
Chapel Hill, NC 27599-3265
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[R] plotting planes and lines in wireframe()

[wwsprague]

Hi R-helpers

I would like to plot some planes which are perpendicular to the x-y 
plane, such as x=y.  Is there a way to do this in wireframe?  I realize 
that I am not plotting a function of x, y since there are infinite 
number of z's that satisfy the above relation  Hmm...

Somewhat related, I would also like to plot a line in 3 d space...

Finally, if you are feeling really brave, I am interested in doing all 
of this based on sums generating vectors (I know there is a linear 
algebra term for this) -- ie generate the plane based on c_1*v_1 + 
c_2*v_2 for c_1 and c_2 in reals.

Thanks again to all you helpful folks!
W
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[R] Error compiling ROracle on Windows 2000

[mark . threefoot]

Hello,

I am trying to compile ROracle _0.5-4 under R 1.9.0 without much success.  I am 
running Windows 2000 SP4, Visual C++ 6.0 SP6, and Oracle client 9.2.0.1.0.  I was able 
to run the pre-compiled version of ROracle_0.5-2 under R 1.7.1, but does not work on R 
1.8.1 or R 1.9.0.  Here is the output from nmake:

C:\Program Files\R\rw1090\library\ROracle\srcnmake

Microsoft (R) Program Maintenance Utility   Version 6.00.9782.0
Copyright (C) Microsoft Corp 1988-1998. All rights reserved.

cl /IC:\\Program Files\\R\\rw1090\\src\\include /MT /Ox /D MSVC /D 
WIN32 /c RS-DBI.c
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 12.00.8804 for 80x86
Copyright (C) Microsoft Corp 1984-1998. All rights reserved.

RS-DBI.c
cl /IC:\\Program Files\\R\\rw1090\\src\\include /MT /Ox /D MSVC /D 
WIN32 /c RS-Oracle.c
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 12.00.8804 for 80x86
Copyright (C) Microsoft Corp 1984-1998. All rights reserved.

RS-Oracle.c
NMAKE : fatal error U1073: don't know how to make '\src\\gnuwin32\\Rdll.lib'
Stop.

Here is a copy of my Makefile:

R_HOME = C:\\Program Files\\R\\rw1090
ORACLE_HOME = C:\\oracle\\oracle92
SRC  = RS-DBI.h RS-DBI.c RS-Oracle.h RS-Oracle.pc S4R.h
RLIB = $(R_HOME)\\src\\gnuwin32\\Rdll.lib
OBJ  = RS-DBI.obj RS-Oracle.obj 

##
## The Oracle ProC/C++ precompiler and options we need (these have worked
## on Linux, Solaris, and Windows 2000).
##

PROC=proc  ## this is the ProC/C++ executable
CODE=ANSI_C## the following are ProC/C++ options
MODE=ORACLE
PARSE=NONE ## don't do any C parse
LINES=false## use true for debugging

ROracle.dll:  $(OBJ) $(RLIB)
(cd $(R_HOME)\\src\\gnuwin32  lib /def:R.exp /out:Rdll.lib)
link /dll /def:ROracle.def /out:ROracle.dll 
$(ORACLE_HOME)\\precomp\\lib\\orasql9.lib *.obj $(R_HOME)\\src\\gnuwin32\\Rdll.lib 

RS-DBI.obj: RS-DBI.h RS-DBI.c S4R.h
cl /I$(R_HOME)\\src\\include /MT /Ox /D MSVC /D WIN32 /c RS-DBI.c

RS-Oracle.obj: RS-Oracle.h RS-Oracle.c S4R.h
cl /I$(R_HOME)\\src\\include /MT /Ox /D MSVC /D WIN32 /c RS-Oracle.c

RS-Oracle.c: RS-Oracle.h RS-Oracle.pc 
$(PROC) CODE=$(CODE) MODE=$(MODE) INCLUDE=$(R_HOME)/include \
PARSE=$(PARSE) LINES=$(LINES) RS-Oracle.pc
force-Rdll.lib:
(cd $(R_HOME)\\src\\gnuwin32  lib /def:R.exp /out:Rdll.lib)
clean:
rm -f $(OBJ) *.a *.d *.rc 
clobber:
rm -f $(RLIB) $(OBJ) RS-Oracle.c *.a *.d *.rc *.dll 

Thanks for your help,
Mark

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[R] re-ordering a vector by name

[Liaw, Andy]

Dear R-help,

Let's say `x1' and `x2' are very long vectors (length=5e5, say) with same
set of names but in different order.  If I want to sort `x2' in the order of
`x1', I would do 

  x2[names(x1)]

but the amount of time that takes is quite prohibitive!  Does anyone have
any suggestion on a more efficient way to do this?

If the two vectors are exactly the same length (as I said above), sorting
both by names would probably be the fastest.  However, if the two vectors
differ in length (and the names for the shorter one are a subset of names of
the longer one) then that doesn't work...

Best,
Andy

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RE: [R] re-ordering a vector by name

[Huntsinger, Reid]

I suspect three causes for slowness:

1) possibly names are lot of overhead (string compares, lookup, etc).
2) maybe it's just memory, in which case you could loop over chunks of the
names(x1) vector
3) you're basically asking for the permutation taking names(x2) into
names(x1) and then applying it to x2. The first step is a sort but perhaps
the indexing code doesn't optimize that.

Reid Huntsinger
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Liaw, Andy
Sent: Friday, May 07, 2004 5:16 PM
To: [EMAIL PROTECTED]
Subject: [R] re-ordering a vector by name


Dear R-help,

Let's say `x1' and `x2' are very long vectors (length=5e5, say) with same
set of names but in different order.  If I want to sort `x2' in the order of
`x1', I would do 

  x2[names(x1)]

but the amount of time that takes is quite prohibitive!  Does anyone have
any suggestion on a more efficient way to do this?

If the two vectors are exactly the same length (as I said above), sorting
both by names would probably be the fastest.  However, if the two vectors
differ in length (and the names for the shorter one are a subset of names of
the longer one) then that doesn't work...

Best,
Andy

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Re: [R] cgi/servlets/httpd in R

[A.J. Rossini]

Samuelson, Frank* [EMAIL PROTECTED] writes:

 Here's a related question:  Do any of the mentioned R-web interfaces
 (Rweb, R-Online, CGIwithR, RSPerl) support reusing the same R process,
 eliminating the startup overhead?  This would be useful to me as well.

Greg Warnes' RSOAP allows you to pre-start a pool of processes to
eliminate this under light/moderate load.

It's on my lab group's WWW page.

best,
-tony

-- 
[EMAIL PROTECTED]http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN  Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
FHCRC  (M/W): 206-667-7025 FAX=206-667-4812 | use Email

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Re: [R] Invalid HOMEDRIVE

[Jason Turner]

Jim Stimson wrote:
Attempting to install the most recent R on a Windows/XP machine, I get 
what appears to be a normal (completely default) installation. Then when 
I attempt to load rgui I get the fatal error message: Invalid HOMEDRIVE. 
Any explanation of the error or suggestions of fixes to files or 
registry would be appreciated.

1) Follow the instructions in the posting guide, which asks you to 
search the archives before posting (saves us both time).

2) From there, you'll find
https://www.stat.math.ethz.ch/pipermail/r-help/2004-April/048397.html
Short answer - it's a bug introduced by a Microsoft critical update (out 
with the old bugs, in with the new!).

Cheers

Jason

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Re: [R] re-ordering a vector by name

[Sundar Dorai-Raj]

Liaw, Andy wrote:

Dear R-help,

Let's say `x1' and `x2' are very long vectors (length=5e5, say) with same
set of names but in different order.  If I want to sort `x2' in the order of
`x1', I would do 

  x2[names(x1)]

but the amount of time that takes is quite prohibitive!  Does anyone have
any suggestion on a more efficient way to do this?
If the two vectors are exactly the same length (as I said above), sorting
both by names would probably be the fastest.  However, if the two vectors
differ in length (and the names for the shorter one are a subset of names of
the longer one) then that doesn't work...
Best,
Andy
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Hi Andy,
  Using match seems to be *much* faster:
R x1 - 1:1; names(x1) - 1:1
R x2 - 1:1; names(x2) - 1:1
R system.time(x3 - x1[names(x2)])
[1] 1.88 0.00 1.88   NA   NA
R system.time(x4 - x1[match(names(x1), names(x2))])
[1] 0.01 0.00 0.01   NA   NA
R all.equal(x3, x4)
[1] TRUE
R
This should also work if x1 and x2 are of diffent lengths.

--sundar

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Re: [R] plotting planes and lines in wireframe()

[Deepayan Sarkar]

On Friday 07 May 2004 16:07, [EMAIL PROTECTED] wrote:
 Hi R-helpers

 I would like to plot some planes which are perpendicular to the x-y
 plane, such as x=y.  Is there a way to do this in wireframe?  I
 realize that I am not plotting a function of x, y since there are
 infinite number of z's that satisfy the above relation  Hmm...

Well, from R 1.9.0 onwards wireframe can draw arbitrary 3-D parametric 
surfaces (spheres and such) with a formula of the form z ~ x * y where 
x, y and z are all matrices. A plane is a very trivial application of 
this, e.g.:

x - matrix(rep(1:10, 10), 10)
y - x
z - matrix(rep(1:10, each = 10), 10)
wireframe(z ~ x * y)

Of course, you are probably not interested in only this plane, in which 
case things may not be as easy, since (1) formally there's no way to 
specify multiple surfaces with this usage and (2) wireframe doesn't do 
hidden surface removal, so intersecting surfaces are messed up. But in 
many cases you can probably make do with a fine mesh and some 
innovative use of NA's. e.g. (continuing the earlier example):

xx - cbind(x, NA, x)
yy - cbind(y+50, NA, y^2)
zz - cbind(z, NA, z)
wireframe(zz ~ xx * yy)

 Somewhat related, I would also like to plot a line in 3 d space...

That's also easy, e.g. cloud(1:3 ~ 3:1 * 1:3) (there seems to be bug 
with just 2 points, I'll fix that in the next release). To do this in a 
wireframe plot you would probably use the panel function 
panel.3dscatter. What's not easy, however, when you are combining 
planes and lines, is to make sure that the appropriate parts of the 
line are hidden.

 Finally, if you are feeling really brave, I am interested in doing
 all of this based on sums generating vectors (I know there is a
 linear algebra term for this) -- ie generate the plane based on
 c_1*v_1 + c_2*v_2 for c_1 and c_2 in reals.

You mean the span of v_1 and v_2 ? Very easy with the approach outlined 
above. Visualize a rectangular grid on the c_1-c_2 plane determining 
the ranges of c_1 and c_2. Let's say the ranges are c1 and c2, e.g., c1 
= c2 = seq(0, 1, length = 11). Next, evaluate the values of c1 and c2 
on this grid as matrices:

tmp = expand.grid(c1 = c1, c2 = c2)
mc1 = matrix(tmp$c1, length(c1))
mc2 = matrix(tmp$c2, length(c1))

Next evaluate the corresponding points on your plane:

x = v1[1] * mc1 + v2[1] * mc2
y = v1[2] * mc1 + v2[2] * mc2
z = v1[3] * mc1 + v2[3] * mc2

and plot them

wireframe(z ~ x * y)

If you don't like the distortion, you could use a wide range of c1 and 
c2 and then use appropriate x/y/zlim.

Deepayan

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RE: [R] re-ordering a vector by name

[Liaw, Andy]

 From: Sundar Dorai-Raj 
 
 Liaw, Andy wrote:
 
  Dear R-help,
  
  Let's say `x1' and `x2' are very long vectors (length=5e5, 
 say) with same
  set of names but in different order.  If I want to sort 
 `x2' in the order of
  `x1', I would do 
  
x2[names(x1)]
  
  but the amount of time that takes is quite prohibitive!  
 Does anyone have
  any suggestion on a more efficient way to do this?
  
  If the two vectors are exactly the same length (as I said 
 above), sorting
  both by names would probably be the fastest.  However, if 
 the two vectors
  differ in length (and the names for the shorter one are a 
 subset of names of
  the longer one) then that doesn't work...
  
  Best,
  Andy
 
 Hi Andy,

 Using match seems to be *much* faster:
 
 R x1 - 1:1; names(x1) - 1:1
 R x2 - 1:1; names(x2) - 1:1
 R system.time(x3 - x1[names(x2)])
 [1] 1.88 0.00 1.88   NA   NA
 R system.time(x4 - x1[match(names(x1), names(x2))])
 [1] 0.01 0.00 0.01   NA   NA
 R all.equal(x3, x4)
 [1] TRUE
 R
 
 This should also work if x1 and x2 are of diffent lengths.
 
 --sundar

Sundar,

Thanks very much for the tip!  However, I think the arguments in match() is
backward:

 n = 1e4
 x1 = sample(n)
 x2 = sample(n)
 names(x1) = sample(n)
 names(x2) = sample(n)
 system.time(x3 - x1[names(x2)])
[1] 5.71 0.00 6.02   NA   NA
 system.time(x4 - x1[match(names(x1),names(x2))])
[1] 0.03 0.00 0.03   NA   NA
 all.equal(x3, x4)
[1] Names: 9997 string mismatches   Mean relative  difference:
0.669837
 names(x3[1:5])
 [1] 5391 9927 6499 1863 8287
 names(x4[1:5])
 [1] 2560 9914 6348 1291 5718
 system.time(x4 - x1[match(names(x2),names(x1))])
[1] 0.03 0.00 0.03   NA   NA
 names(x4[1:5])
 [1] 5391 9927 6499 1863 8287
 all.equal(x3, x4)
[1] TRUE

[Admittedly this is why I rarely use match():  I get mixed up easily.]

Reid: It isn't a memory problem.  For vectors of length 6e5, I killed the R
process after more than 5 hours on an Opteron 248.  The R process was taking
up about 114MB of RAM, out of 8GB in the box.  I'm rather surprised that
such seemingly simple operation would take so long, especially when sorting
such vectors is very fast.  What am I missing?

Best,
Andy

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