date:20080523

Re: [R] 1501-511 Compilation failed for file ch2inv.f - R on AIX 5.2.

2008-05-23 Thread Prof Brian Ripley

Look like you need to use a Fortran compiler set to accept Fortran 77 
(which the R sources are).


We don't know what 'f95' is, and this is not really an R issue so please 
ask your sysadmins for help.


On Thu, 22 May 2008, Senthilkumaran wrote:



Hi,

While executing the make after successful configuration (./configure
--with-readline=no --without-iconv), the following error occurs:

mbf2n11s (Regatta) /saswork/R/R-2.7.0$ make
Target R is up to date.
Target R is up to date.
Target R is up to date.
Target R is up to date.
Target Makedeps is up to date.
Target libbz2.a is up to date.
Target Makedeps is up to date.
Target libpcre.a is up to date.
Target Makedeps is up to date.
Target libz.a is up to date.
Target Makedeps is up to date.
   f95   -g -c ch2inv.f -o ch2inv.o
ch2inv.f, line 1.2: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 2.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 3.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 4.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 5.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 6.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 7.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 7.39: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 8.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 9.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 9.41: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 10.8: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 11.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 12.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 13.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 13.38: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 14.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 15.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 16.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 17.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 18.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 18.32: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 19.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 20.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 21.2: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 22.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 23.3: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 24.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 25.3: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 26.3: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 27.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 28.3: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 29.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 30.3: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 30.30: 1515-018 (S) Incorrect character found in source at
line 30 in column 30.  Hexadecimal value of character is 7B.
ch2inv.f, line 30.39: 1515-018 (S) Incorrect character found in source at
line 30 in column 39.  Hexadecimal value of character is 7D.
ch2inv.f, line 31.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 32.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 33.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 34.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 35.3: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 36.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 37.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 38.3: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 39.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 40.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 41.3: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 42.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 43.3: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 44.0: 1515-010 (S) String is missing a closing delimiter.
Closing delimiter assumed at end of line.
ch2inv.f, line 44.4: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 45.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 46.3: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 47.3: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 48.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 49.0: 1515-010 (S) String is missing a closing delimiter.
Closing delimiter assumed at end of line.
ch2inv.f, line 49.3: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 50.3: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 51.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, 1515-002 (S) END card is missing.  One is assumed.
** _main   === End of Compilation 1 ===
ch2inv.f, line 53.7: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 54.6: 1514-050 (S) Specification statement is out of order.
Statement is ignored.
ch2inv.f, line 55.6: 1514-050 (S) Specification statement is out of order.
Statement is ignored.
ch2inv.f, line 56.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 57.6: 1514-050 (S) Specification statement is out of order.
Statement is ignored.
ch2inv.f, line 58.6: 1514-050 (S) Specification statement is out of order.
Statement is ignored.
ch2inv.f, line 59.1: 1515-019 (S) Syntax is incorrect.
ch2inv.f, line 66.11: 1515-025 (S) Only

Re: [R] Where to download BRugs

2008-05-23 Thread Prof Brian Ripley

install.packages(BRugs) still works on Windows -- the binaries have been 
moved to the CRAN extras collections.  If you want a direct URL


http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.7/BRugs_0.4-1.zip


On Thu, 22 May 2008, qqw wrote:



Hi all, I tried to follow an online tutorial to run openBUgs but the package
BRugs has been removed from R repository.

Could someone provide a link for where to download BRugs?

Thanks a lot!

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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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[R] Est. Component Size with AIC/BIC under Gamma Distribution

2008-05-23 Thread Edward Wijaya

Dear all,

I am trying to model number of samples from
a given series. The series are modelled according
Gamma function.

In order to estimate the # samples, I use BIC/AIC
with MLE (computed from dgamma function).

Here is the code I have.

__BEGIN__

mlogl - function( x_func, theta_func, samp) {
   # computing log_likelihood
return( - sum(dgamma(samp, shape = x_func, scale=theta_func, log = TRUE)))
}


find_bic - function(mll,smpl,k) {

  bic - (-2 * mll) + (k * log(length(smpl)))
  bic
}

find_aic - function(mll,smpl,k) {

  aic - (-2 * mll) + (k * 2)
  aic

}

mlogl_process - function(smpl,error,start ) {

# EM algorithm to estimate max loglikelihood
thetalast - 0
thetacurrent - start
theta - start
difference - start
thetaprocess - start
best - 0

while (difference  error) {
mlogl_out - nlm(mlogl, mean(smpl),  theta_func=thetacurrent, samp=smpl)
theta - mlogl_out$estimate
thetalast - thetacurrent
thetacurrent - theta
difference - abs(thetalast - thetacurrent)

# E-STEP
new_maxlogl - nlm(mlogl, mean(smpl),  theta_func=theta,  samp=smpl)

# M-STEP
if (new_maxlogl$minimum  best) {
   best - new_maxlogl$minimum

}
}
best
}

# main program

# my samples
vsamples- c(14.7, 18.8, 14, 15.9, 9.7, 12.8)

# initialize
start_ - 300
error_ - 0.001
thetastart - 1
k - 5

# compute AIC/BIC for k component

for (nofc in 1:k {
  cat(k = , nofc, \n)
  maxlogl - -(mlogl_process(vsamples,error_,thetastart))
  bic_k - find_bic(maxlogl,vsamples,nofc)
  aic_k - find_aic(maxlogl,vsamples,nofc)
  cat(BIC = , bic_k,  - AIC = , aic_k, - MLL= , maxlogl,\n)
}

__ END__

We finally expect to choose K with the smallest AIC/BIC
value.

However, the problem I have is that the AIC/BIC value is always
on the increase.

Can anybody advice what's wrong with my above approach?

Regards,
Edward

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[R] Re : How to import package into R script

2008-05-23 Thread justin bem

Read documentation carefully ! 
see ?library (e.g library(tseries)) 

 Justin BEM
BP 1917 YaoundÃ©
TÃ©l (237) 99597295
(237) 22040246



- Message d'origine 
De : Edward Wijaya [EMAIL PROTECTED]
Ã : r-help@r-project.org
EnvoyÃ© le : Vendredi, 23 Mai 2008, 4h23mn 06s
Objet : [R] How to import package into R script

Hi all,

What's the construct to import a built-in package
(e.g. ARIMA) into the R script.

I can't seem to find them in the documentation.

Regards,
Edward

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__


ble contre les messages non sollicitÃ©s 

[[alternative HTML version deleted]]

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[R] New version of ecological modeling software using R

2008-05-23 Thread Bio7


Dear R users,

Again with the hope that this application can also be useful for some R
users,
i like to announce a new Windows version of the ecological modeling software
Bio7.
In this release you can now easily transfer images from the well known image
analysis tool ImageJ to R or create images in ImageJ from a R matrix.

http://www.uni-bielefeld.de/biologie/Oekosystembiologie/bio7app/flashtut/imagetransfer.htm

Furthermore the interpretation of R scripts inside the RScript editor of
Bio7 is now much more stable and several methods have been added to the R
menu of Bio7.
In addition spatial data from R can now be visualized in a new available
OpenGL (Jogl) panel dynamically.

The software is available at:

http://www.uni-bielefeld.de/biologie/Oekosystembiologie/bio7app/index.html

With kind regards

M.Austenfeld



-- 
View this message in context: 
http://www.nabble.com/New-version-of-ecological-modeling-software-using-R-tp17419491p17419491.html
Sent from the R help mailing list archive at Nabble.com.

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[R] Some problems with Sweave

2008-05-23 Thread martin . gaston

Dear R users,
I'm working in a brief R-tutorial to a group of students. To make that I'm
using Sweave but I've got two problems:

First, I want show how R operates with the matrix type but, I write in the
.rnw document the code

echo=T,results=tex=
 matriz - matrix(vector,nrow=3,ncol=6)
 matriz
@

and after compilating the LaTex document I obtain in the pdf the next text

 matriz - matrix(vector, nrow = 3, ncol = 6)
 matriz
[,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 4 1 4 1 4 [2,] 2 5 2 5 2 5 [3,] 3 6 3
6 3 6

My question is, How must I do To obtain in the pdf somethin near to

 matriz - matrix(vector, nrow = 3, ncol = 6)
 matriz
 [,1] [,2] [,3] [,4] [,5] [,6]
[1,]141414
[2,]252525
[3,]363636

I`ve tought in xtable but the aspect is not as the R console.

On the other hand I want show the list type R-treatment, the problem here
is in the LaTex compilation
I write in the .rnwd document

echo=T,results=tex=
 lista - list(cadena='String',vector=c(1,1,1),logica=TRUE)
 lista$cadena
@

the Sweave call is ok, but when I compile the .tex document, It produces
errors caused by the $ simbols. Anybody knows how save this problem?

Thanks in advance,
Martín Gastón

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Re: [R] Re : How to import package into R script

2008-05-23 Thread martin . gaston

Before call library(package) it is needed install the package. To make
that, select Packages/InstallPkages... choose your nearest mirror and
select the package from the list and accept.

After that you can call library(tseries)
for example

Regards

El Vie, 23 de Mayo de 2008, 9:00, justin bem escribió:
 Read documentation carefully !
 see ?library (e.g library(tseries))

  Justin BEM
 BP 1917 YaoundÃ©
 TÃ©l (237) 99597295
 (237) 22040246



 - Message d'origine 
 De : Edward Wijaya [EMAIL PROTECTED]
 Ã : r-help@r-project.org
 EnvoyÃ© le : Vendredi, 23 Mai 2008, 4h23mn 06s
 Objet : [R] How to import package into R script

 Hi all,

 What's the construct to import a built-in package
 (e.g. ARIMA) into the R script.

 I can't seem to find them in the documentation.

 Regards,
 Edward

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


 __


 ble contre les messages non sollicitÃ©s

   [[alternative HTML version deleted]]

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


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[R] Strange julian and/or strptime

2008-05-23 Thread Kåre Edvardsen

Hi r-helpers...

Why do I get this strange huge jump of 36524 days when changing origin
from 1969-01-01 to 1968-12-31. It should still be close to zero! This
really messes up my calculations of follow-up times in my analyses.

 julian(strptime(010169, format = %d%m%y),origin =
as.Date(1969-01-01))
 Time difference of -0.0417 days

 julian(strptime(311268, format = %d%m%y),origin =
as.Date(1968-12-31))
 Time difference of 36524.96 days


Cheers,
Kare

[[alternative HTML version deleted]]

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Re: [R] plot 7 * 3 matrix on DIN A4 pdf

2008-05-23 Thread Uwe Ligges




[EMAIL PROTECTED] wrote:

Hello,

I want to plot 21 scatter plots in a 7*3 matrix on a single A4 page
(using mfcol). Below is an example, which -by and large- looks very
close to the desired result. But I do not get it to fill out the whole
page. If I specify the a different page size, the plots still do not
fill out the whole page.
Anybody an idea what to do? Maybe adjusting indvidiual plot size (if
so, how?). Or is there a neater command to create a matrix of
individual plots


Just specify width and height appropriately.

Uwe Ligges





Best,
Stefan



pdf(file='c:/matrix1.pdf',paper='a4',pagecentre=F)

x-c(rnorm(mean(100,mean=50,sd=10)),rnorm(mean(100,mean=50,sd=10)))
par(mfcol=c(7,3))
par(pch=19)
 par(pty=m) #s makes a square plot
 par(cex=.1)

 par(cex.axis=7)
 par(omi=c(1,1,1,1))
 axistick-c(0,10,20,30,40,50,60,70,80,90,100)
par(mar=c(3, 5, 0, 0) + 0.1)
plot(x,xlim=c(0,50),ylim=c(0,100),axes = FALSE)
axis(2,ylab='',at=axistick)
box(lty=1)
plot(x,xlim=c(0,50), ylim=c(0,100),axes = FALSE)
axis(2)
box(lty=1)
plot(x, xlim=c(0,50),ylim=c(0,100),axes = FALSE)
axis(2)
box(lty=1)
plot(x,xlim=c(0,50), ylim=c(0,100),axes = FALSE)
axis(2)
box(lty=1)
plot(x,xlim=c(0,50), ylim=c(0,100),axes = FALSE)
axis(2)
box(lty=1)
plot(x,xlim=c(0,50), ylim=c(0,100),axes = FALSE)
axis(2)
box(lty=1)
par(mar=c(3, 5 ,0, 0) + 0.1)
plot(x,xlim=c(0,50), ylim=c(0,100),axes = FALSE)
axis(2)
 axis(1,ylab='UAS_7')
 box(lty=1)

par(mar=c(3, 0, 0, 0) + 0.1)
plot(as.integer(Sex),GER_TOTAL,ylim=c(0,100),xlim=c(0,3),axes = FALSE,pch=12)
box(lty=1)
plot(x,ylim=c(0,100),xlim=c(0,3),axes = FALSE,pch=12)
box(lty=1)
plot(x,ylim=c(0,100),xlim=c(0,3),axes = FALSE,pch=12)
box(lty=1)
plot(x,ylim=c(0,100),xlim=c(0,3),axes = FALSE)
box(lty=1)
plot(x,ylim=c(0,100),xlim=c(0,3),axes = FALSE,pch=12)
box(lty=1)
plot(x,ylim=c(0,100),xlim=c(0,3),axes = FALSE,pch=12)
box(lty=1)
par(mar=c(3, 0, 0, 0) + 0.1)
plot(as.integer(Sex),GER_F6,ylim=c(0,100),xlim=c(0,3),axes = FALSE)
axis(1,at=c(1,2),ylab='Sex')
box(lty=1)

par(mar=c(3, 0, 0, 0) + 0.1)
plot(x,xlim=c(0,100),ylim=c(0,100),axes = FALSE,pch=12)
box(lty=1)
plot(x,xlim=c(0,100), ylim=c(0,100),axes = FALSE)
box(lty=1)
plot(x, xlim=c(0,100),ylim=c(0,100),axes = FALSE)
box(lty=1)
plot(x, xlim=c(0,100),ylim=c(0,100),axes = FALSE)
box(lty=1)
plot(x, xlim=c(0,100),ylim=c(0,100),axes = FALSE,pch=12)
box(lty=1)
plot(x, xlim=c(0,100),ylim=c(0,100),axes = FALSE)
box(lty=1)
par(mar=c(3, 0, 0, 0) + 0.1)
plot(x,xlim=c(0,100),ylim=c(0,100),axes = FALSE,pch=12)
box(lty=1)
axis(1,ylab='Sex')
dev.off()

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[R] [slightly off topic] Sweave with markdown

2008-05-23 Thread baptiste Auguié


DeaR list,

Has anyone tried to mix the Sweave paradigm with the Markdown[*] (and  
co.) syntax? Would this be hard to implement? My tiny understanding  
of Sweave is that one can define new drivers for the text part, while  
some functions that deal with the R code would not require any  
modification. Here's the reason I'm interested in Mardown for a driver.


I've been orbiting around Sweave for several weeks, and while I  
understand the great value of this literate programming, I'm a bit  
put off by the technical aspect. I'm a LateX user, and a R user  
(you'd have guessed, albeit fairly novice), so the problem is not to  
get it working (i got some writings done with Sweave), but more of  
getting an efficient workflow. I find the LaTeX commands overly  
intruding in the middle of my R source code, plus the relatively slow  
compilation of latex makes it quite impractical for quick studies ( I  
once spent 20 minutes trying to get the graph to be at a sensible  
scale on the page).


As an alternative, I'm resorting to having a folder per study (I'm  
physicist, doing data analysis for optical spectroscopy), with one R  
file per analysis and a text file to keep track of the experimental  
conditions. When the data is really important / interesting, I've  
also tried to write a package: great for storing the data, functions  
and commands in a consistent manner (this works fine, but it cannot  
be a solution for quick trial experiments. Also, the figures cannot  
be included in the html doc as far as I know.)


I was considering some alternatives to Sweave, namely R2HTML and  
odfWeave, but in the former the source syntax is no less disturbing  
than LaTeX (although the zero compilation time is a plus), while for  
the latter I do not have a decent compatible editor (on a Mac, I  
tried Openoffice and Abiword but the fonts look like my handwriting  
for some obscure reason). Maybe I'll give it another shot at some  
stage, I just usually prefer plain text files.


Any input welcome,

Baptiste

[*]: http://en.wikipedia.org/wiki/Markdown

_

Baptiste Auguié

Physics Department
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK

Phone: +44 1392 264187

http://newton.ex.ac.uk/research/emag
http://projects.ex.ac.uk/atto

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Re: [R] 3D Area Diagram

2008-05-23 Thread Jim Lemon


AlGates wrote:

Thank you all for your help. I will check the packages you suggested asap and
maybe I find a good way to get a such a plot.

The picture I posted was only an example taken from the microsoft-website,
just to make clear what kind of diagram I am looking for. I know that one
part is hidden by the other and that it would be better to show it somehow
different.
The one I rather need, is something like this (scan from a book):
http://algates.de/Scan.jpg 
The only difference is the angle.

Hi Al,
You can get a 2D version of this with stackpoly in the plotrix package 
(v2.4-2) although if you really want 3D, I agree with Ben.


Jim

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Strange julian and/or strptime

2008-05-23 Thread Prof Brian Ripley


On my Linux box:


strptime(010169, format = %d%m%y)

[1] 1969-01-01

strptime(311268, format = %d%m%y)

[1] 2068-12-31


From the help page:


 '%y' Year without century (00-99). If you use this on input, which
  century you get is system-specific.  So don't!  Often values
  up to 69 (or 68) are prefixed by 20 and 70 (or 69) to 99 by
  19.

If all else fails, read the documentation (but the posting guide asks you 
to do that before posting).  Elsewhere on that help page it refers you to 
your OS documentation -- the posting guide asked for your OS 'at a 
minimum', but as you didn't follow it so we have no idea which you used.


On Fri, 23 May 2008, Kåre Edvardsen wrote:


Hi r-helpers...

Why do I get this strange huge jump of 36524 days when changing origin
from 1969-01-01 to 1968-12-31. It should still be close to zero! This
really messes up my calculations of follow-up times in my analyses.


julian(strptime(010169, format = %d%m%y),origin =

as.Date(1969-01-01))

Time difference of -0.0417 days



julian(strptime(311268, format = %d%m%y),origin =

as.Date(1968-12-31))

Time difference of 36524.96 days



Cheers,
Kare

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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)
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Re: [R] Where to download BRugs

2008-05-23 Thread qqw


Thanks, this works great! Thanks a lot!


aldi-2 wrote:
 
 Hi,
 
 I just installed it from
 http://cran.wustl.edu/bin/windows/contrib/2.7/BRugs_0.4-1.zip
 
 Change 2.7 to 2.6 and you get the older version.
 
 HTH,
 
 Aldi
 

 Thanks Aldi, do you know anywhere we could download previous package of
 BRugs? Do you have a copy which you could send to me? (I only found one
 old
 version on Splus site which is not usable under R2.6 :()
 Thanks!

 --
 View this message in context:
 http://www.nabble.com/Where-to-download-BRugs-tp17411410p17416516.html
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 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

 
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 PLEASE do read the posting guide
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[R] Create a data subset

2008-05-23 Thread MarySR


Hello,
I want to select same data of a data frame that has information of fish
catches:

 catch, vessel, trip, day, month, year

where trip is the fishing operation number done in each day by each vessel,
i.e. for each day, any vesel can have several register of catch
corresponding to each operation.
From this data frame I want to do:
1. Add the catches of all trip by vessel and day; then
2. Select rows corresponding to vessels that appear more than 120 days at
the year; then
3. Select rows corresponding to vessels that appear mode than 15 years
Does anyone know how to do that in R?

Thank you in advanced

Maria

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Re: [R] Some problems with Sweave

2008-05-23 Thread Charilaos Skiadas


Try results=verbatim instead of results=tex.

Haris Skiadas
Department of Mathematics and Computer Science
Hanover College


On May 23, 2008, at 4:16 AM, [EMAIL PROTECTED] wrote:


Dear R users,
I'm working in a brief R-tutorial to a group of students. To make  
that I'm

using Sweave but I've got two problems:

First, I want show how R operates with the matrix type but, I write  
in the

.rnw document the code

echo=T,results=tex=
 matriz - matrix(vector,nrow=3,ncol=6)
 matriz
@

and after compilating the LaTex document I obtain in the pdf the  
next text



matriz - matrix(vector, nrow = 3, ncol = 6)
matriz
[,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 4 1 4 1 4 [2,] 2 5 2 5 2 5  
[3,] 3 6 3

6 3 6

My question is, How must I do To obtain in the pdf somethin near to


matriz - matrix(vector, nrow = 3, ncol = 6)
matriz

 [,1] [,2] [,3] [,4] [,5] [,6]
[1,]141414
[2,]252525
[3,]363636

I`ve tought in xtable but the aspect is not as the R console.

On the other hand I want show the list type R-treatment, the  
problem here

is in the LaTex compilation
I write in the .rnwd document

echo=T,results=tex=
 lista - list(cadena='String',vector=c(1,1,1),logica=TRUE)
 lista$cadena
@

the Sweave call is ok, but when I compile the .tex document, It  
produces

errors caused by the $ simbols. Anybody knows how save this problem?

Thanks in advance,
Martín Gastón



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Re: [R] 3D Area Diagram

2008-05-23 Thread Patrick Connolly

On Thu, 22-May-2008 at 03:13PM -0700, AlGates wrote:


| The one I rather need, is something like this (scan from a book):
| http://algates.de/Scan.jpg 
| The only difference is the angle.

That one is even stranger.  There are two similar (but not parallel)
lines for imports and another two similar (but again not parallel)
lines for exports.  I can't see if there is anything systematic about
those small differences, and I suspect that there was meant to be
none -- just drawn by someone who didn't have a 45 deg set-square.  

Years ago I inherited some SPlus code which did, in fact, draw a plot
quite similar to that one (but without the inaccuracies).  I remember
it was quite lengthy and complicated, but I don't remember ever having
an inclination to use it for anything since R has so many easier and
better ways of visualizing data.

During the process of changing computer systems several times in the
intervening years, that code was something that went out with the old
faded photos.  Shame that. 

 Excel might have an option to do one like the import-export example.
If it does, it would be a lot easier than using R which has an
altogether different set of values.  If Excel doesn't do that type,
and it's *really* important to have such a plot, I'd be using grid
graphics which is almost infinitely flexible.  Only trouble is, by the
time you'd seen what you can do with grid, you'd likely find that you
no longer felt any urge to make such a plot.


best

-- 
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
   ___Patrick Connolly   
 {~._.~} Great minds discuss ideas
 _( Y )_Middle minds discuss events 
(:_~*~_:)Small minds discuss people  
 (_)-(_)   . Anon
  
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

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Re: [R] an unknown error message when using gamm function

2008-05-23 Thread Simon Wood

Could you try upgrading to the current version of mgcv, please? looking in the 
`changeLog' there were a couple of fixed problems that could be causing this.

On Wednesday 21 May 2008 16:14, Lung-Chang Chien wrote:
 The version is mgcv 1.3-27. Last night, I dropped out many arguments from
 my program to test which part
 might be the source of causing this error message, and found that the
 program works when just using corAR1().

 This program has no this kind of problem in the beginning, but doesn't work
 after I impute some missing data
 in PM10 and tmean by multiple imputation approach. Hope this information
 can also help identify the
 element of this problem.

 LC

  From: Simon Wood [EMAIL PROTECTED]
  To: r-help@r-project.org
  Date: Wed, 21 May 2008 08:55:02 +0100
  Subject: Re: [R] an unknown error message when using gamm function
  What version of mgcv are you using, please?
 
  On Wednesday 21 May 2008 06:16, Lung-Chang Chien wrote:
  Dear everyone,
 
  I'm encountering an unknown error message when using gamm function:
   fitoutput -
 
  gamm(cvd~as.factor(dow)+pm10+s

 (time,bs=cr,k=15,fx=TRUE)+s(tmean,bs=cr,k

 =7,fx=TRUE) +

 ,correlation=corAR1(form=~1|city),family=poisson,random=list(city=~pm10),da

 ta=mimp)
 
 
   Maximum number of PQL iterations:  20
  iteration 1
  iteration 2
  iteration 3
  iteration 4
  iteration 5
  iteration 6
  Error in `*tmp*`[[k]] : attempt to select less than one element
 
  I never saw this error message before, and there is also no related
  information about this error from the Internet. Hope some people who once
  encountered this problem can tell me what's wrong.
 
  Many thanks,
 
  LC

-- 
 Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
 +44 1225 386603  www.maths.bath.ac.uk/~sw283

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[R] Cleaning a time series

2008-05-23 Thread tolga . i . uzuner

Dear R Users,

Was wondering if anyone can give me pointers to functionality in R that 
can help clean a time series ? For example, some kind of 
package/functionality which identifies potential errors and takes some 
action, such as replacement by some suitable value (carry-forward, average 
of nearest, what have you) and reporting of errors identified.

I did search Google for R cran time series clean outlier and various 
permutations but did not come across anything.

Thanks,
Tolga

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Re: [R] colorspace package does not compile on ubuntu 7.04 32 bit

2008-05-23 Thread Mikhail Spivakov


Hi again,

I have managed to solve this problem myself - indeed, the trouble was with
the package being incompatible with gcc v4. 

Here what I've done - perhaps it's going to be useful for someone else:

1) installed gcc v3.4: sudo apt-get install gcc-3.4
2) opened .../R/etc/Makeconf (changing its access rights so it's no longer
read-only first)
3) changed all instances of gcc to gcc-3.4

I realise that this was perhaps quite a drastic measure and I could have
created a Makefile for the colorspace package specifically instead. But the
v4/v3 incompatibility is such a common problem that I decided to change this
once and for all - until new packages utilising some v4 - specific C code
appear out there..

Cheers
Mikhail



Mikhail Spivakov wrote:
 
 Hi everyone, 
 I am trying to install colorspace (needed as part of my favourite ggplot2)
 on R v 2.7.0 running under ubuntu 7.04. The package is provided as source
 files and the compilation fails as below.
 I suspect this might be a problem with gcc v3/v4 incompatibility (or
 anything else), but I don't really know how to resolve it. Any advice will
 be appreciated - or perhaps somebody has got this package compiled and
 could share the binaries?  
 Many thanks!
 Mikhail
 
 
 Mikhail Spivakov, PhD
 European Bioinformatics Institute
 European Molecular Biology Laboratory
 Germany/UK
 
 * Installing *source* package 'colorspace' ...
 ** libs
 gcc -std=gnu99 -I/usr/share/R/include  -fpic  -g -O2 -c colorspace.c
 -o colorspace.o
 In file included from colorspace.c:1:
 /usr/share/R/include/R.h:28:20: error: stdlib.h: No such file or directory
 /usr/share/R/include/R.h:29:19: error: stdio.h: No such file or directory
 In file included from
 /usr/lib/gcc/i486-linux-gnu/4.1.2/include/syslimits.h:7,
  from
 /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:11,
  from /usr/share/R/include/R.h:30,
  from colorspace.c:1:
 /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:122:61: error:
 limits.h: No such file or directory
 In file included from colorspace.c:1:
 /usr/share/R/include/R.h:32:18: error: math.h: No such file or directory
 /usr/share/R/include/R.h:33:19: error: errno.h: No such file or directory
 In file included from /usr/share/R/include/R.h:50,
  from colorspace.c:1:
 /usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or
 directory
 In file included from colorspace.c:2:
 /usr/share/R/include/Rinternals.h:770: error: expected declaration
 specifiers or ‘...’ before ‘FILE’
 /usr/share/R/include/Rinternals.h:773: error: expected declaration
 specifiers or ‘...’ before ‘FILE’
 colorspace.c: In function ‘gtrans’:
 colorspace.c:28: warning: implicit declaration of function ‘pow’
 colorspace.c:28: warning: incompatible implicit declaration of built-in
 function ‘pow’
 colorspace.c: In function ‘ftrans’:
 colorspace.c:36: warning: incompatible implicit declaration of built-in
 function ‘pow’
 colorspace.c: In function ‘g’:
 colorspace.c:92: warning: incompatible implicit declaration of built-in
 function ‘pow’
 colorspace.c: In function ‘LAB_to_XYZ’:
 colorspace.c:106: warning: incompatible implicit declaration of built-in
 function ‘pow’
 colorspace.c:114: warning: incompatible implicit declaration of built-in
 function ‘pow’
 colorspace.c:117: warning: incompatible implicit declaration of built-in
 function ‘pow’
 colorspace.c:123: warning: incompatible implicit declaration of built-in
 function ‘pow’
 colorspace.c: In function ‘f’:
 colorspace.c:132: warning: incompatible implicit declaration of built-in
 function ‘pow’
 colorspace.c: In function ‘XYZ_to_LAB’:
 colorspace.c:144: warning: incompatible implicit declaration of built-in
 function ‘pow’
 colorspace.c: In function ‘XYZ_to_HLAB’:
 colorspace.c:170: warning: implicit declaration of function ‘sqrt’
 colorspace.c:170: warning: incompatible implicit declaration of built-in
 function ‘sqrt’
 colorspace.c: In function ‘LAB_to_polarLAB’:
 colorspace.c:203: warning: implicit declaration of function ‘atan2’
 colorspace.c:203: warning: incompatible implicit declaration of built-in
 function ‘atan2’
 colorspace.c:207: warning: incompatible implicit declaration of built-in
 function ‘sqrt’
 colorspace.c: In function ‘polarLAB_to_LAB’:
 colorspace.c:216: warning: implicit declaration of function ‘cos’
 colorspace.c:216: warning: incompatible implicit declaration of built-in
 function ‘cos’
 colorspace.c:217: warning: implicit declaration of function ‘sin’
 colorspace.c:217: warning: incompatible implicit declaration of built-in
 function ‘sin’
 colorspace.c: In function ‘HSV_to_RGB’:
 colorspace.c:272: warning: implicit declaration of function ‘floor’
 colorspace.c:272: warning: incompatible implicit declaration of built-in
 function ‘floor’
 colorspace.c: In function ‘XYZ_to_LUV’:
 colorspace.c:311: warning: incompatible implicit declaration of built-in
 function ‘pow’
 colorspace.c: In function ‘LUV_to_XYZ’:

Re: [R] Some problems with Sweave

2008-05-23 Thread Andrew Robinson

Martin,

try omitting the results=tex argument.

Andrew

On Fri, May 23, 2008 at 10:16:33AM +0200, [EMAIL PROTECTED] wrote:
 Dear R users,
 I'm working in a brief R-tutorial to a group of students. To make that I'm
 using Sweave but I've got two problems:
 
 First, I want show how R operates with the matrix type but, I write in the
 .rnw document the code
 
 echo=T,results=tex=
  matriz - matrix(vector,nrow=3,ncol=6)
  matriz
 @
 
 and after compilating the LaTex document I obtain in the pdf the next text
 
  matriz - matrix(vector, nrow = 3, ncol = 6)
  matriz
 [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 4 1 4 1 4 [2,] 2 5 2 5 2 5 [3,] 3 6 3
 6 3 6
 
 My question is, How must I do To obtain in the pdf somethin near to
 
  matriz - matrix(vector, nrow = 3, ncol = 6)
  matriz
  [,1] [,2] [,3] [,4] [,5] [,6]
 [1,]141414
 [2,]252525
 [3,]363636
 
 I`ve tought in xtable but the aspect is not as the R console.
 
 On the other hand I want show the list type R-treatment, the problem here
 is in the LaTex compilation
 I write in the .rnwd document
 
 echo=T,results=tex=
  lista - list(cadena='String',vector=c(1,1,1),logica=TRUE)
  lista$cadena
 @
 
 the Sweave call is ok, but when I compile the .tex document, It produces
 errors caused by the $ simbols. Anybody knows how save this problem?
 
 Thanks in advance,
 Mart?n Gast?n
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

-- 
Andrew Robinson  
Department of Mathematics and StatisticsTel: +61-3-8344-6410
University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599
http://www.ms.unimelb.edu.au/~andrewpr
http://blogs.mbs.edu/fishing-in-the-bay/

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Re: [R] Pros and Cons of R

2008-05-23 Thread Neil Shephard


Installation under Gentoo is straightforward too (emerge dev-lang/R).

Updating has never really been a problem.  CRAN packages are rebuilt if
needed when updating R, and periodically all you need to do is fire up R and
use update.packages() to update any packages you've installed.

Another pro to consider is the cost, you can obtain R for free,
SAS/S-Plus/Stata all have licenses of some sort that require purchasing.

Neil
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Re: [R] Strange julian and/or strptime

2008-05-23 Thread Kåre Edvardsen

I'm on an Ubuntu Linux PC, and get the same wrong result as you.
I could not work out what the description of '%y' really ment, so I did
not realize this was operating system specific in this sense. Anyway,
I'll find a way to work around this bug.

Have a nice weekend,
Kare


On Fri, 2008-05-23 at 10:41 +0100, Prof Brian Ripley wrote:

 On my Linux box:
 
  strptime(010169, format = %d%m%y)
 [1] 1969-01-01
  strptime(311268, format = %d%m%y)
 [1] 2068-12-31
 
 From the help page:
 
   '%y' Year without century (00-99). If you use this on input, which
century you get is system-specific.  So don't!  Often values
up to 69 (or 68) are prefixed by 20 and 70 (or 69) to 99 by
19.
 
 If all else fails, read the documentation (but the posting guide asks you 
 to do that before posting).  Elsewhere on that help page it refers you to 
 your OS documentation -- the posting guide asked for your OS 'at a 
 minimum', but as you didn't follow it so we have no idea which you used.
 
 On Fri, 23 May 2008, Kåre Edvardsen wrote:
 
  Hi r-helpers...
 
  Why do I get this strange huge jump of 36524 days when changing origin
  from 1969-01-01 to 1968-12-31. It should still be close to zero! This
  really messes up my calculations of follow-up times in my analyses.
 
  julian(strptime(010169, format = %d%m%y),origin =
  as.Date(1969-01-01))
  Time difference of -0.0417 days
 
  julian(strptime(311268, format = %d%m%y),origin =
  as.Date(1968-12-31))
  Time difference of 36524.96 days
 
 
  Cheers,
  Kare
 
  [[alternative HTML version deleted]]
 
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  and provide commented, minimal, self-contained, reproducible code.
 
 

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Re: [R] Create a data subset

2008-05-23 Thread jim holtman

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

You should at least provide a sample of the data that you are working with
and what you might think the desired output should be.  It is difficult to
create sample data since you don't know what the user is really working
with.  It helps to get responses to questions.

On Fri, May 23, 2008 at 4:53 AM, MarySR [EMAIL PROTECTED] wrote:


 Hello,
 I want to select same data of a data frame that has information of fish
 catches:

 catch, vessel, trip, day, month, year

 where trip is the fishing operation number done in each day by each vessel,
 i.e. for each day, any vesel can have several register of catch
 corresponding to each operation.
 From this data frame I want to do:
 1. Add the catches of all trip by vessel and day; then
 2. Select rows corresponding to vessels that appear more than 120 days at
 the year; then
 3. Select rows corresponding to vessels that appear mode than 15 years
 Does anyone know how to do that in R?

 Thank you in advanced

 Maria

 --
 View this message in context:
 http://www.nabble.com/Create-a-data-subset-tp17420700p17420700.html
 Sent from the R help mailing list archive at Nabble.com.

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




-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?

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Re: [R] Strange julian and/or strptime

2008-05-23 Thread jim holtman

It is not a bug.

Y2K strikes again, a couple of years late.

On Fri, May 23, 2008 at 7:17 AM, Kåre Edvardsen [EMAIL PROTECTED] wrote:

 I'm on an Ubuntu Linux PC, and get the same wrong result as you.
 I could not work out what the description of '%y' really ment, so I did
 not realize this was operating system specific in this sense. Anyway,
 I'll find a way to work around this bug.

 Have a nice weekend,
 Kare


 On Fri, 2008-05-23 at 10:41 +0100, Prof Brian Ripley wrote:

  On my Linux box:
 
   strptime(010169, format = %d%m%y)
  [1] 1969-01-01
   strptime(311268, format = %d%m%y)
  [1] 2068-12-31
 
  From the help page:
 
'%y' Year without century (00-99). If you use this on input, which
 century you get is system-specific.  So don't!  Often values
 up to 69 (or 68) are prefixed by 20 and 70 (or 69) to 99 by
 19.
 
  If all else fails, read the documentation (but the posting guide asks you
  to do that before posting).  Elsewhere on that help page it refers you to
  your OS documentation -- the posting guide asked for your OS 'at a
  minimum', but as you didn't follow it so we have no idea which you used.
 
  On Fri, 23 May 2008, Kåre Edvardsen wrote:
 
   Hi r-helpers...
  
   Why do I get this strange huge jump of 36524 days when changing
 origin
   from 1969-01-01 to 1968-12-31. It should still be close to zero! This
   really messes up my calculations of follow-up times in my analyses.
  
   julian(strptime(010169, format = %d%m%y),origin =
   as.Date(1969-01-01))
   Time difference of -0.0417 days
  
   julian(strptime(311268, format = %d%m%y),origin =
   as.Date(1968-12-31))
   Time difference of 36524.96 days
  
  
   Cheers,
   Kare
  
   [[alternative HTML version deleted]]
  
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Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?

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[R] Evaluation conflict in combination of replicate() and rexp()as variable inside a function

2008-05-23 Thread Gerrit Eichner


Dear userRs,

playing around with combinations of replicate() and random number 
generating functions inside a self-defined wrapper function I encounterd 
a puzzling behaviour.


The following are intentionally simple (and rather nonsense-) examples to 
isolate the relevant aspects. Please, note the seemingly inconsistent 
behaviour for the second call of rdistr() (with distr = rexp) for which I 
have not found any explanation (yet):



rdistr - function( distr, ...) replicate( 1, distr( n = 1, ...))



rdistr( distr = rnorm)

[1] -0.8889223


rdistr( distr = rexp)

[1] NaN
Warning message:
In distr(n = 1, ...) : NAs produced


rdistr( distr = runif)

[1] 0.8444856


Trying to discover the reason for this observation, I looked into the code 
of replicate() and realized that this seems to be an issue of evaluation 
schemes (and maybe also of variable scoping), but I didn't delve deeper 
into it, yet. Can anybody more competent enlight me or give me a hint 
where to search, please? Thank you!


 Best regards  --  Gerrit

PS:


sessionInfo()

R version 2.6.2 (2008-02-08)
x86_64-unknown-linux-gnu

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

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

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17


-
AR Dr. Gerrit Eichner  Mathematical Institute
[EMAIL PROTECTED]   Justus-Liebig-University Giessen
Tel: +49-(0)641-99-32104  Arndtstr. 2, 35392 Giessen, Germany
Fax: +49-(0)641-99-32029   http://www.math.uni-giessen.de

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Re: [R] Pros and Cons of R

2008-05-23 Thread seanpor



Neil Shephard wrote:
 
 Another pro to consider is the cost, you can obtain R for free,
 SAS/S-Plus/Stata all have licenses of some sort that require purchasing.
 
 Neil
 

Which has the side effect of *not* restricting how many machines are
available for use or where; e.g. I was running big process a couple of
different times with different scenarios, so I just fired up a few un-used
machines and had them all running in parallel for the afternoon - no
installation issues as I was able to run it off the network drive (windows
as it happens).  If I was licence restricted this would not have been
possible.

Similarly I can do analyses at home on any machine or even if I'm visiting
somewhere else!

Regards
Sean

-- 
View this message in context: 
http://www.nabble.com/Pros-and-Cons-of-R-tp17407521p17424335.html
Sent from the R help mailing list archive at Nabble.com.

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Re: [R] Cleaning a time series

2008-05-23 Thread Gabor Grothendieck

The zoo package has six na.* routines for carrying values
forward, etc.

library(zoo)
?zoo

describes them.  Also see the vignettes.

On Fri, May 23, 2008 at 6:55 AM,  [EMAIL PROTECTED] wrote:
 Dear R Users,

 Was wondering if anyone can give me pointers to functionality in R that
 can help clean a time series ? For example, some kind of
 package/functionality which identifies potential errors and takes some
 action, such as replacement by some suitable value (carry-forward, average
 of nearest, what have you) and reporting of errors identified.

 I did search Google for R cran time series clean outlier and various
 permutations but did not come across anything.

 Thanks,
 Tolga

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Re: [R] [slightly off topic] Sweave with markdown

2008-05-23 Thread Gabor Grothendieck

You could check out the brew package:

https://stat.ethz.ch/pipermail/r-packages/2007/000327.html

On Fri, May 23, 2008 at 4:37 AM, baptiste Auguié [EMAIL PROTECTED] wrote:
 DeaR list,

 Has anyone tried to mix the Sweave paradigm with the Markdown[*] (and co.)
 syntax? Would this be hard to implement? My tiny understanding of Sweave is
 that one can define new drivers for the text part, while some functions that
 deal with the R code would not require any modification. Here's the reason
 I'm interested in Mardown for a driver.

 I've been orbiting around Sweave for several weeks, and while I understand
 the great value of this literate programming, I'm a bit put off by the
 technical aspect. I'm a LateX user, and a R user (you'd have guessed, albeit
 fairly novice), so the problem is not to get it working (i got some writings
 done with Sweave), but more of getting an efficient workflow. I find the
 LaTeX commands overly intruding in the middle of my R source code, plus the
 relatively slow compilation of latex makes it quite impractical for quick
 studies ( I once spent 20 minutes trying to get the graph to be at a
 sensible scale on the page).

 As an alternative, I'm resorting to having a folder per study (I'm
 physicist, doing data analysis for optical spectroscopy), with one R file
 per analysis and a text file to keep track of the experimental conditions.
 When the data is really important / interesting, I've also tried to write a
 package: great for storing the data, functions and commands in a consistent
 manner (this works fine, but it cannot be a solution for quick trial
 experiments. Also, the figures cannot be included in the html doc as far as
 I know.)

 I was considering some alternatives to Sweave, namely R2HTML and odfWeave,
 but in the former the source syntax is no less disturbing than LaTeX
 (although the zero compilation time is a plus), while for the latter I do
 not have a decent compatible editor (on a Mac, I tried Openoffice and
 Abiword but the fonts look like my handwriting for some obscure reason).
 Maybe I'll give it another shot at some stage, I just usually prefer plain
 text files.

 Any input welcome,

 Baptiste

 [*]: http://en.wikipedia.org/wiki/Markdown

 _

 Baptiste Auguié

 Physics Department
 University of Exeter
 Stocker Road,
 Exeter, Devon,
 EX4 4QL, UK

 Phone: +44 1392 264187

 http://newton.ex.ac.uk/research/emag
 http://projects.ex.ac.uk/atto

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[R] Advise in R- plotting graphs

2008-05-23 Thread Jason Lee

Hi

I have a data table matrix,data which looks like below:-
 V1V2  V3
1 -6382.719 -1096.554 6998994
2 -some values-
3 -some values-
4 -some values-
5  -some values-

Querying dim of data gives me 3 columns and 5 rows.

And currently I want to plot V1 against V2 with the condition that I
want to mark(color) the point(row 5) on the graph. This is so i could see
some triangle shape thing on the graph for row 5.

I couldnt recall how I could use repo() to change the line 5 to some value
to differentiate with others. And then using PCH for the color.

Please advise. Thanks.

-jason

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Re: [R] Advise in R- plotting graphs

2008-05-23 Thread jim holtman

try this:

x - matrix(runif(15, 100, 300), ncol=3)
plot(x[,1], x[,2], type='l')
points(x[5,1], x[5,2], pch=17, cex=3, col='red')  # plot point #5

On Fri, May 23, 2008 at 8:50 AM, Jason Lee [EMAIL PROTECTED] wrote:

 Hi

 I have a data table matrix,data which looks like below:-
 V1V2  V3
 1 -6382.719 -1096.554 6998994
 2 -some values-
 3 -some values-
 4 -some values-
 5  -some values-

 Querying dim of data gives me 3 columns and 5 rows.

 And currently I want to plot V1 against V2 with the condition that I
 want to mark(color) the point(row 5) on the graph. This is so i could see
 some triangle shape thing on the graph for row 5.

 I couldnt recall how I could use repo() to change the line 5 to some value
 to differentiate with others. And then using PCH for the color.

 Please advise. Thanks.

 -jason

[[alternative HTML version deleted]]

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-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?

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Re: [R] [slightly off topic] Sweave with markdown

2008-05-23 Thread Max Kuhn

On Fri, May 23, 2008 at 4:37 AM, baptiste Auguié [EMAIL PROTECTED] wrote:

 (although the zero compilation time is a plus), while for the latter I do
 not have a decent compatible editor (on a Mac, I tried Openoffice and
 Abiword but the fonts look like my handwriting for some obscure reason).
 Maybe I'll give it another shot at some stage, I just usually prefer plain
 text files.

Try using NeoOffice or the development version of OpenOffice. The new
version (3.0) of OpenOffice is better integrated into OS X and should
probably do the trick

   http://download.openoffice.org/3.0beta/

It is beta, but it has been pretty stable for me.

Max

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[R] van der Corput sequences

2008-05-23 Thread Alberto Monteiro

In package fOptions, there are functions that generate
Halton sequences. 

The van der Corput sequence for base 2 is a particular case
of the Halton sequence generated by:

n - 8 # anything here...
x - runif.halton(n, 1)

In fact, x - runif.halton(n, dim) will generate the van der Corput
sequences for the base b as the i-th prime number in x[,i].

(in other words, if I want the van der Corput sequence for
base b = 5, I do x - runif.halton(n, 3) and take x[,3]).

However, it's possible to have van der Corput sequences for
non-prime basis, like (for b = 10):

0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.01, 0.11, 0.21, 0.31, 0.41, 
0.51, 0.61, 0.71, 0.81, 0.91, 0.02, 0.12, 0.22, 0.32,  

Is there any R function that generates those sequences?

Alberto Monteiro

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Re: [R] extracting columns from a list

2008-05-23 Thread N. Lapidus

Hi Mohamed

Try:
lapply (NameOfYourList, function (dat, NumCol) dat[,NumCol], c(12,13))

But there must be a shorter way to write this.

Nael


On Fri, May 23, 2008 at 3:37 PM, mohamed nur anisah 
[EMAIL PROTECTED] wrote:

 Dear all,

  i have 2 lists of data with each of the list contain 14 columns. How am i
 going to extract column 12 and 13 from each of the list ?? and can i combine
 my extracted columns to form a single list. Attach with are my data. Your
 coorperation is highly appreciated. Many thanks

  Regards,
   Anisah


 [[1]]
   CS(O)   id no.anchor   ref loc.start  loc.end CS(O).size CS(O)ref.density
 tested loc.start  loc.end breakp.start breakp.end den of anchor
 1 CS  2.0 3 mmu19   6465196  6978022 512826
  6  cfa18  55567952 55782336  6978022699273428
 2 CS  3.057 mmu19   6992734 102499663257232
 17  cfa18  55792632 57688808 10249966   1027743025
 3 CS  4.021 mmu19  10277430 10955201 61
 31  cfa18  57721864 58419812 10955201   1100852636
 4 CS  5.0 2 mmu19  11008526 11045352  36826
 54  cfa18  58462088 58518608 11045352   1131686532
 5 CS  6.0 7 mmu19  11316865 11814604 497739
 14  cfa21  53902028 53514536 11814604   1193722837
 6 CS  7.014 mmu19  11937228 138476331910405
  7  cfa18  40111560 41204940 13847633   1451509117
 7 CS  8.0 3 mmu19  14515091 160227701507679
  2   cfa1  82195232 83511824 16022770   16199850 5
 8 CS  9.025 mmu19  16199850 236258567426006
  3   cfa1  83903856 90638880 23625856   2375455414
 9 CS 10.033 mmu19  23754554 296761925921638
  6   cfa1  90773872 96913624 29676192   2976391816
 10CS 11.0 6 mmu19  29763918 30164446 400528
 15  cfa11  29919668 30510776 30164446   30611872 8
 11CS 12.019 mmu19  30611872 345583123946440
  5  cfa26  38767664 41958808 34558312   3473440415
 12   CSO 13.173 mmu19  34734404 440096169275212
  8  cfa28   7343952 15872122 44009616   4408825621
 13   CSO 13.271 mmu19  44088256 535826329494376
  7  cfa28  15923283 24830712 53582632   5365479614

 [[2]]
   CS(O)   id no.anchor  ref loc.start   loc.end CS(O).size CS(O)ref.density
 tested loc.start   loc.end breakp.start breakp.end den of anchor
 1CSO  2.1 4 mmuX   7311438   7428353 116915
 34   cfaX  41732964  41660008  7428353835693216
 2CSO  2.241 mmuX   8356932  20225456   11868524
  3   cfaX  32299338  41540632 20225456   2064158413
 3CSO  2.3 8 mmuX  20641584  33046200   12404616
  1   cfaX  91770240  94412912 33046200   3317518815
 4CSO  3.173 mmuX  33175188  57970280   24795092
  3   cfaX  94538728 114133200 57970280   64939220 3
 5CSO  3.229 mmuX  64939220  700112805072060
  6   cfaX 119319152 124625688 70011280   7003978432
 6 CS  4.021 mmuX  70039784  70677328 637544
 33   cfaX 124652504 125280776 70677328   7124127229
 7CSO  5.1 2 mmuX  71241272  71362456 121184
 17   cfaX 125764816 125872960 71362456   7142557614
 8CSO  6.1 4 mmuX  71425576  71824776 399200
 10   cfaX 125917392 126261784 71824776   73894168 6
 9CSO  6.2 2 mmuX  73894168  74014744 120576
 17   cfaX   6363930   1898656 74014744   7470540811
 10   CSO  6.317 mmuX  74705408  90487648   15782240
  1   cfaX  32034930  19573208 90487648   9122816010
 11   CSO  6.449 mmuX  91228160 1010581929830032
  5   cfaX  51733740  61930260101058192  101967264 9
 12CS  7.0 3 mmuX 101967264 102176888 209624
 14   cfaX  62797768  63194052102176888  10223004011
 13   CSO  8.1 2 mmuX 102230040 102409592 179552
 11   cfaX  63307688  63460248102409592  103123352 9
 14   CSO  8.216 mmuX 103123352 1105914647468112
  2   cfaX  63896752  71000280110591464  116044144 2
 15CS  9.0 2 mmuX 116044144 116407200 363056
  6   cfaX  71543016  71752808116407200  118512328 1
 16CS 10.024 mmuX 118512328 131185424   12673096
  2   cfaX  72291072  79468544131185424  13161668820
 17CS 11.0 8 mmuX 131616688 132395992 779304
 10   cfaX  79821128  80586408132395992  13246176017
 18CS 12.021 mmuX 132461760 1375643685102608
  4   cfaX  80674704  85936464137564368  13792777612
 19   CSO 13.114 mmuX 137927776 1427167524788976
  3   cfaX  86288848  90933784142716752  145888160 5
 20   CSO 13.2

Re: [R] extracting columns from a list

2008-05-23 Thread N. Lapidus

I forgot to answer to the last part of your question.
I think what you call a list is actually an element of a list, right?
If so, the command you want depends on the way you want to combine these
elements.

For example, the following lines will extract columns 12 and 13 of any
array-like element of your list and bind them into columns of a same array
(if all your elements have the same number of rows).

List2 - lapply (NameOfYourList, function (dat, NumCol) dat[,NumCol],
c(12,13))
Array2 - do.call (cbind, List2)

If you meant something else by 'combine, please be more explicit.

Nael





On Fri, May 23, 2008 at 3:54 PM, N. Lapidus [EMAIL PROTECTED] wrote:

 Hi Mohamed

 Try:
 lapply (NameOfYourList, function (dat, NumCol) dat[,NumCol], c(12,13))

 But there must be a shorter way to write this.

 Nael


 On Fri, May 23, 2008 at 3:37 PM, mohamed nur anisah 
 [EMAIL PROTECTED] wrote:

 Dear all,

  i have 2 lists of data with each of the list contain 14 columns. How am i
 going to extract column 12 and 13 from each of the list ?? and can i combine
 my extracted columns to form a single list. Attach with are my data. Your
 coorperation is highly appreciated. Many thanks

  Regards,
   Anisah


 [[1]]
   CS(O)   id no.anchor   ref loc.start  loc.end CS(O).size
 CS(O)ref.density tested loc.start  loc.end breakp.start breakp.end den of
 anchor
 1 CS  2.0 3 mmu19   6465196  6978022 512826
  6  cfa18  55567952 55782336  6978022699273428
 2 CS  3.057 mmu19   6992734 102499663257232
 17  cfa18  55792632 57688808 10249966   1027743025
 3 CS  4.021 mmu19  10277430 10955201 61
 31  cfa18  57721864 58419812 10955201   1100852636
 4 CS  5.0 2 mmu19  11008526 11045352  36826
 54  cfa18  58462088 58518608 11045352   1131686532
 5 CS  6.0 7 mmu19  11316865 11814604 497739
 14  cfa21  53902028 53514536 11814604   1193722837
 6 CS  7.014 mmu19  11937228 138476331910405
  7  cfa18  40111560 41204940 13847633   1451509117
 7 CS  8.0 3 mmu19  14515091 160227701507679
  2   cfa1  82195232 83511824 16022770   16199850 5
 8 CS  9.025 mmu19  16199850 236258567426006
  3   cfa1  83903856 90638880 23625856   2375455414
 9 CS 10.033 mmu19  23754554 296761925921638
  6   cfa1  90773872 96913624 29676192   2976391816
 10CS 11.0 6 mmu19  29763918 30164446 400528
 15  cfa11  29919668 30510776 30164446   30611872 8
 11CS 12.019 mmu19  30611872 345583123946440
  5  cfa26  38767664 41958808 34558312   3473440415
 12   CSO 13.173 mmu19  34734404 440096169275212
  8  cfa28   7343952 15872122 44009616   4408825621
 13   CSO 13.271 mmu19  44088256 535826329494376
  7  cfa28  15923283 24830712 53582632   5365479614

 [[2]]
   CS(O)   id no.anchor  ref loc.start   loc.end CS(O).size
 CS(O)ref.density tested loc.start   loc.end breakp.start breakp.end den of
 anchor
 1CSO  2.1 4 mmuX   7311438   7428353 116915
 34   cfaX  41732964  41660008  7428353835693216
 2CSO  2.241 mmuX   8356932  20225456   11868524
  3   cfaX  32299338  41540632 20225456   2064158413
 3CSO  2.3 8 mmuX  20641584  33046200   12404616
  1   cfaX  91770240  94412912 33046200   3317518815
 4CSO  3.173 mmuX  33175188  57970280   24795092
  3   cfaX  94538728 114133200 57970280   64939220 3
 5CSO  3.229 mmuX  64939220  700112805072060
  6   cfaX 119319152 124625688 70011280   7003978432
 6 CS  4.021 mmuX  70039784  70677328 637544
 33   cfaX 124652504 125280776 70677328   7124127229
 7CSO  5.1 2 mmuX  71241272  71362456 121184
 17   cfaX 125764816 125872960 71362456   7142557614
 8CSO  6.1 4 mmuX  71425576  71824776 399200
 10   cfaX 125917392 126261784 71824776   73894168 6
 9CSO  6.2 2 mmuX  73894168  74014744 120576
 17   cfaX   6363930   1898656 74014744   7470540811
 10   CSO  6.317 mmuX  74705408  90487648   15782240
  1   cfaX  32034930  19573208 90487648   9122816010
 11   CSO  6.449 mmuX  91228160 1010581929830032
  5   cfaX  51733740  61930260101058192  101967264 9
 12CS  7.0 3 mmuX 101967264 102176888 209624
 14   cfaX  62797768  63194052102176888  10223004011
 13   CSO  8.1 2 mmuX 102230040 102409592 179552
 11   cfaX  63307688  63460248102409592  103123352 9
 14   CSO  8.216 mmuX 103123352 1105914647468112
  2   cfaX  63896752  71000280110591464  116044144

Re: [R] Fit a sine to data

2008-05-23 Thread Juan Manuel Barreneche

i guess nls or gnls should work

JM

El Viernes, 23 de Mayo de 2008 10:47, Zroutik Zroutik escribió:
 Dear R-users,

 I'd like to fit a sine function to my data. The result should have a format
 (and thus the formula, too)

 y ~ a + sin(x+b)

 where y and x are vectors, and a and b are (yet) unknown values.

 The data sets (vectors x and y) are OK, and I can do a simple lm fitting
 lm(y~x), or lm(y~I(sin(2*pi*x/360))), succesfully  My issue is that I'm not
 able to do the optional linear shift in x (e.g. x+b). What other
 possibilities should I use instead of lm? I looked searched the R-seek for
 terms: fit, sine, lm, and combinations, but I could not find anything
 useful. Anybody would be so kind and point me to the right direction where
 I can find other fitting possibilities?

 Thank you for listening and kind answers upfront.

 Regards,
 Milan

   [[alternative HTML version deleted]]

 __
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Re: [R] Pros and Cons of R

2008-05-23 Thread Roland Rau


Monica Pisica wrote:

- You can save scripts, but not *.exe.


If you want to contrast R with statistical packages like SPSS or Stata 
(and if your audience has rather a background in those than in general 
purpose languages), I think this is not really a problem unless I missed 
something recently about the capabilities of SPSS or Stata.


Best,
Roland

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Re: [R] extracting columns from a list

2008-05-23 Thread Vincent Goulet


Le ven. 23 mai à 09:37, mohamed nur anisah a écrit :


Dear all,

 i have 2 lists of data with each of the list contain 14 columns.


No, you have one list with two elements; each is a 14-column data frame.


How am i going to extract column 12 and 13 from each of the list ??


Let's call your list 'x'. Then

lapply(x, [, c(12, 13))

or, better yet,

lapply(x, [, c(breakp.start, breakp.end))

if I counted your columns correctly.


and can i combine my extracted columns to form a single list.


You mean a single data frame? Given that the number of rows is not the  
same in both elements, no. If they were, using sapply() instead of  
lapply() would do the trick.


HTH   Vincent

Attach with are my data. Your coorperation is highly appreciated.  
Many thanks


 Regards,
 Anisah

[[1]]
  CS(O)   id no.anchor   ref loc.start  loc.end CS(O).size  
CS(O)ref.density tested loc.start  loc.end breakp.start breakp.end  
den of anchor
1 CS  2.0 3 mmu19   6465196  6978022  
5128266  cfa18  55567952 55782336  6978022 
699273428
2 CS  3.057 mmu19   6992734 10249966 
3257232   17  cfa18  55792632 57688808 10249966
1027743025
3 CS  4.021 mmu19  10277430 10955201  
61   31  cfa18  57721864 58419812 10955201
1100852636
4 CS  5.0 2 mmu19  11008526 11045352   
36826   54  cfa18  58462088 58518608 11045352
1131686532
5 CS  6.0 7 mmu19  11316865 11814604  
497739   14  cfa21  53902028 53514536 11814604
1193722837
6 CS  7.014 mmu19  11937228 13847633 
19104057  cfa18  40111560 41204940 13847633
1451509117
7 CS  8.0 3 mmu19  14515091 16022770 
15076792   cfa1  82195232 83511824 16022770
16199850 5
8 CS  9.025 mmu19  16199850 23625856 
74260063   cfa1  83903856 90638880 23625856
2375455414
9 CS 10.033 mmu19  23754554 29676192 
59216386   cfa1  90773872 96913624 29676192
2976391816
10CS 11.0 6 mmu19  29763918 30164446  
400528   15  cfa11  29919668 30510776 30164446
30611872 8
11CS 12.019 mmu19  30611872 34558312 
39464405  cfa26  38767664 41958808 34558312
3473440415
12   CSO 13.173 mmu19  34734404 44009616 
92752128  cfa28   7343952 15872122 44009616
4408825621
13   CSO 13.271 mmu19  44088256 53582632 
94943767  cfa28  15923283 24830712 53582632
5365479614


[[2]]
  CS(O)   id no.anchor  ref loc.start   loc.end CS(O).size  
CS(O)ref.density tested loc.start   loc.end breakp.start breakp.end  
den of anchor
1CSO  2.1 4 mmuX   7311438   7428353  
116915   34   cfaX  41732964  41660008  7428353 
835693216
2CSO  2.241 mmuX   8356932  20225456
118685243   cfaX  32299338  41540632 20225456
2064158413
3CSO  2.3 8 mmuX  20641584  33046200
124046161   cfaX  91770240  94412912 33046200
3317518815
4CSO  3.173 mmuX  33175188  57970280
247950923   cfaX  94538728 114133200 57970280
64939220 3
5CSO  3.229 mmuX  64939220  70011280 
50720606   cfaX 119319152 124625688 70011280
7003978432
6 CS  4.021 mmuX  70039784  70677328  
637544   33   cfaX 124652504 125280776 70677328
7124127229
7CSO  5.1 2 mmuX  71241272  71362456  
121184   17   cfaX 125764816 125872960 71362456
7142557614
8CSO  6.1 4 mmuX  71425576  71824776  
399200   10   cfaX 125917392 126261784 71824776
73894168 6
9CSO  6.2 2 mmuX  73894168  74014744  
120576   17   cfaX   6363930   1898656 74014744
7470540811
10   CSO  6.317 mmuX  74705408  90487648
157822401   cfaX  32034930  19573208 90487648
9122816010
11   CSO  6.449 mmuX  91228160 101058192 
98300325   cfaX  51733740  61930260101058192   
101967264 9
12CS  7.0 3 mmuX 101967264 102176888  
209624   14   cfaX  62797768  63194052102176888   
10223004011
13   CSO  8.1 2 mmuX 102230040 102409592  
179552   11   cfaX  63307688  63460248102409592   
103123352 9
14   CSO  8.216 mmuX 103123352 110591464 
74681122   cfaX  63896752  71000280110591464

[R] Preparing high quality figures with tiff as end result

2008-05-23 Thread Gustaf Rydevik

Hi all,

I'm currently preparing some figures that will be submitted to PloS One.
In their guidelines they state that they will only accept figures in
tiff or eps format, with the warning that eps figures will be
converted to tiff format ( see
http://www.plosone.org/static/figureGuidelines.action ).

Because of this conversion, I figured I'd generate tiff-format figures
from the beginning.
However, a number of issues cropped up:
1) using

library(Cairo)
CairoTIFF(test.tif)

I get  Sorry, this Cairo was compiled without tiff support.. I tried
finding out how to recompile Cairo, but got lost in a lot of confusing
talk about GTK+, downloaded dll files that I didn't know how to use
etc.

so I turned to plain tiff(), and

2) R started crashing on me.The following code

tiff(test.tif)
plot(rnorm(100))
dev.off()

,crashes R (i.e R GUI has encountered a problem and needs to
close...) every third time or so.
When it does work, the resulting output is not too pretty.

So I turned to using postscript files. However, Plos One requires that
fonts be embedded into the figure.
embedFonts()  works for this, but the result is that text becomes
low-res bitmaps, and I don't know how to solve this.

So basically my question is: How should I go about generating graphics
that will look as nice as possible given the above constraints?

Many thanks in advance,

Gustaf




-- 
Gustaf Rydevik, M.Sci.
tel: +46(0)703 051 451
address:Essingetorget 40,112 66 Stockholm, SE
skype:gustaf_rydevik

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

Re: [R] Preparing high quality figures with tiff as end result

2008-05-23 Thread Gustaf Rydevik

On Fri, May 23, 2008 at 4:40 PM, Gustaf Rydevik
[EMAIL PROTECTED] wrote:
 Hi all,

 I'm currently preparing some figures that will be submitted to PloS One.
 In their guidelines they state that they will only accept figures in
 tiff or eps format, with the warning that eps figures will be
 converted to tiff format ( see
 http://www.plosone.org/static/figureGuidelines.action ).

 Because of this conversion, I figured I'd generate tiff-format figures
 from the beginning.
 However, a number of issues cropped up:
 1) using

 library(Cairo)
 CairoTIFF(test.tif)

 I get  Sorry, this Cairo was compiled without tiff support.. I tried
 finding out how to recompile Cairo, but got lost in a lot of confusing
 talk about GTK+, downloaded dll files that I didn't know how to use
 etc.

 so I turned to plain tiff(), and

 2) R started crashing on me.The following code

 tiff(test.tif)
 plot(rnorm(100))
 dev.off()

 ,crashes R (i.e R GUI has encountered a problem and needs to
 close...) every third time or so.
 When it does work, the resulting output is not too pretty.

 So I turned to using postscript files. However, Plos One requires that
 fonts be embedded into the figure.
 embedFonts()  works for this, but the result is that text becomes
 low-res bitmaps, and I don't know how to solve this.

 So basically my question is: How should I go about generating graphics
 that will look as nice as possible given the above constraints?

 Many thanks in advance,

 Gustaf


Oh, and before anyone bites my head of, I forgot the following:


 sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-mingw32

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

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

other attached packages:
[1] RWinEdt_1.8-0 Cairo_1.4-2


, and  I'm using windows XP professional


again, many thanks in advance
/Gustaf


-- 
Gustaf Rydevik, M.Sci.
tel: +46(0)703 051 451
address:Essingetorget 40,112 66 Stockholm, SE
skype:gustaf_rydevik

__
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[R] Percentages for categorical data by group

2008-05-23 Thread Economics Guy

I can think of several ways to blunt force hard code what I want but I
imagine there is a command or two that can be easily combined to do this:

I have a data frame with about 23000 observations. There first variable is
the group to which the observation belongs (about 500 different groups). The
second variable is a response for each observation that is a 1,2,3,4 or 5. I
want to be able to calculate the percentage of each group that choose each
response. For example I want to know what percentage of group 1 (which may
have a value of 34456) choose response 1 and so on.

Here is some code I wrote that generates a data frame like the one I have.

pop - matrix(1:10)
groupIDs - sample(pop,500)
groupVar - sample(groupIDs,23000,replace=TRUE)
responseVar - sample(1:5,23000,replace=TRUE)

example.data - data.frame(groupVar,responseVar)

Is there a fast way to calculate these percentages beyond writing loops to
manually count the responses for each of the groups?

Thanks,

EG

[[alternative HTML version deleted]]

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[R] Line Breaks and Axis breaks..

2008-05-23 Thread Megan J Bellamy

Hello all,

I have two questions. One probably has a very simple answer but I have checked 
the FAQ, other websites and still have not found an  answer. I am new to using 
R. My very simple question is how to do line breaks when creating an axis title 
(xlab) ? I have a few that are too long and they get cut off... I found on the 
internet the /n function but I think I must be using it incorrectly because 
it is not working.

My second question is: after inserting an axis break using the following code, 
how to I adjust the scales on either side of that axis break? This is for a 
boxplot graph. See attachment... there is an outlier under CLI 5 that can't be 
seen as a result.

install.packages(plotrix)
axis.break(axis=1, breakpos=NULL, bgcol=white, breakcol=black, style=gap, 
brw=0.02)

Thank you very much in advance!
Megan Bellamy

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

Re: [R] Fit a sine to data

2008-05-23 Thread Peter Dalgaard

Juan Manuel Barreneche wrote:
 i guess nls or gnls should work
   
Yes. Notice though that this is really a linear problem because of the
trigonometric identity

sin(x+b) = cos(b) * sin(x) + sin(b) * cos(x)

which means that you can reparametrize c*sin(x+b) (you forgot the
multiplier, did you not?) as

A*sin(x)+B*cos(x)

It is easy to invert the reparametrization if you notice that A^2 + B^2
= c^2, but it may be expedient to use the nonlinear functions to get
confidence itervals for a,b,c.
 JM

 El Viernes, 23 de Mayo de 2008 10:47, Zroutik Zroutik escribió:
   
 Dear R-users,

 I'd like to fit a sine function to my data. The result should have a format
 (and thus the formula, too)

 y ~ a + sin(x+b)

 where y and x are vectors, and a and b are (yet) unknown values.

 The data sets (vectors x and y) are OK, and I can do a simple lm fitting
 lm(y~x), or lm(y~I(sin(2*pi*x/360))), succesfully  My issue is that I'm not
 able to do the optional linear shift in x (e.g. x+b). What other
 possibilities should I use instead of lm? I looked searched the R-seek for
 terms: fit, sine, lm, and combinations, but I could not find anything
 useful. Anybody would be so kind and point me to the right direction where
 I can find other fitting possibilities?

 Thank you for listening and kind answers upfront.

 Regards,
 Milan

  [[alternative HTML version deleted]]

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

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


-- 
   O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
~~ - ([EMAIL PROTECTED])  FAX: (+45) 35327907

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

Re: [R] Line Breaks and Axis breaks..

2008-05-23 Thread Doran, Harold

plot(1:10, xlab='Hi Megan,  \n Is this what you want?') 

 -Original Message-
 From: [EMAIL PROTECTED] 
 [mailto:[EMAIL PROTECTED] On Behalf Of Megan J Bellamy
 Sent: Friday, May 23, 2008 10:56 AM
 To: r-help@r-project.org
 Subject: [R] Line Breaks and Axis breaks..

 Hello all,

 I have two questions. One probably has a very simple answer 
 but I have checked the FAQ, other websites and still have not 
 found an  answer. I am new to using R. My very simple 
 question is how to do line breaks when creating an axis title 
 (xlab) ? I have a few that are too long and they get cut 
 off... I found on the internet the /n function but I think 
 I must be using it incorrectly because it is not working.

 My second question is: after inserting an axis break using 
 the following code, how to I adjust the scales on either side 
 of that axis break? This is for a boxplot graph. See 
 attachment... there is an outlier under CLI 5 that can't be 
 seen as a result.

 install.packages(plotrix)
 axis.break(axis=1, breakpos=NULL, bgcol=white, 
 breakcol=black, style=gap, brw=0.02)

 Thank you very much in advance!
 Megan Bellamy

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

[R] Question about Runuran (Triangular Distribution)

2008-05-23 Thread Alberto Monteiro

The Runuran package includes a simulation for the Triangular Distribution,
urtriang. But I didn't find an analogue of the q* functions (rnorm - qnorm,
runif - qunif), that would invert the CDF (?uqtriang).

Are there any such functions?

Alberto Monteiro

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Re: [R] Percentages for categorical data by group

2008-05-23 Thread Marc Schwartz


on 05/23/2008 09:51 AM Economics Guy wrote:

I can think of several ways to blunt force hard code what I want but I
imagine there is a command or two that can be easily combined to do this:

I have a data frame with about 23000 observations. There first variable is
the group to which the observation belongs (about 500 different groups). The
second variable is a response for each observation that is a 1,2,3,4 or 5. I
want to be able to calculate the percentage of each group that choose each
response. For example I want to know what percentage of group 1 (which may
have a value of 34456) choose response 1 and so on.

Here is some code I wrote that generates a data frame like the one I have.

pop - matrix(1:10)
groupIDs - sample(pop,500)
groupVar - sample(groupIDs,23000,replace=TRUE)
responseVar - sample(1:5,23000,replace=TRUE)

example.data - data.frame(groupVar,responseVar)

Is there a fast way to calculate these percentages beyond writing loops to
manually count the responses for each of the groups?

Thanks,

EG


Using:

  table(example.data)

will give you a cross tabulation of the counts of your ResponseVar by 
each groupVar.


  prop.table(table(example.data), 1)

will give you a row-wise proportion (0 - 1) of the counts of ResponseVar 
for each groupVar. If you want percentages (0 - 100):


   prop.table(table(example.data), 1) * 100


See ?table and ?prop.table for more information.

HTH,

Marc Schwartz

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Re: [R] Question about Runuran (Triangular Distribution)

2008-05-23 Thread Yasir Kaheil


Please refer to: qtriangle function in VGAM library

thanks
y



Alberto Monteiro wrote:
 
 The Runuran package includes a simulation for the Triangular Distribution,
 urtriang. But I didn't find an analogue of the q* functions (rnorm -
 qnorm,
 runif - qunif), that would invert the CDF (?uqtriang).
 
 Are there any such functions?
 
 Alberto Monteiro
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
 
 


-
Yasir H. Kaheil
Catchment Research Facility
The University of Western Ontario 

-- 
View this message in context: 
http://www.nabble.com/Question-about-Runuran-%28Triangular-Distribution%29-tp17427688p17428151.html
Sent from the R help mailing list archive at Nabble.com.

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[R] problem using embedded R

2008-05-23 Thread Lobanov, Victor S. [PRDUS]

I have a peculiar problem with an application that uses embedded R. The
application comes with its own copy of R installation and it sets up
correct environment path for the process during the startup. However,
when I execute R code that loads an additional package (e.g.
library(XYZ)), the environment path gets reset to the system's default
value, which renders R unusable. I wonder if anyone had experienced a
similar problem and knows how to fix it?

Victor


[[alternative HTML version deleted]]

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Re: [R] Fit a sine to data

2008-05-23 Thread apjaworski

Milan,

This is a fairly standard trick.  Let us generalize your equation slightly:

y ~ a + c*sin(x+b)

so the amplitude of the sine wave is adjustable (otherwise, you assume (or
know) that the amplitude is 1).  Then

y ~ a + c*sin(b)*cos(x) + c*cos(b)*sin(x)

or

y ~ b0 + b1*x1 + b2*x2

which is a linear regression form that you can do using the lm function.
After you get b0, b1 and b2 you do

a = b0
b1^2 + b2^2 = c^2*(sin^2(b) + cos^2(b)) = c^2   c = sqrt(b1^2 + b2^2)
b1/b2 = tan(b)    b = arctan(b1/b2)

Hope this helps,

Andy


__
Andy Jaworski
518-1-01
Process Laboratory
3M Corporate Research Laboratory
-
E-mail: [EMAIL PROTECTED]
Tel:  (651) 733-6092
Fax:  (651) 736-3122


   
 Zroutik Zroutik 
 [EMAIL PROTECTED] 
 m To 
 Sent by:  r-help@r-project.org
 [EMAIL PROTECTED]  cc 
 project.org   
   Subject 
   [R] Fit a sine to data  
 05/23/2008 08:49  
 AM
   
   
   
   




Dear R-users,

I'd like to fit a sine function to my data. The result should have a format
(and thus the formula, too)

y ~ a + sin(x+b)

where y and x are vectors, and a and b are (yet) unknown values.

The data sets (vectors x and y) are OK, and I can do a simple lm fitting
lm(y~x), or lm(y~I(sin(2*pi*x/360))), succesfully  My issue is that I'm not
able to do the optional linear shift in x (e.g. x+b). What other
possibilities should I use instead of lm? I looked searched the R-seek for
terms: fit, sine, lm, and combinations, but I could not find anything
useful. Anybody would be so kind and point me to the right direction where
I
can find other fitting possibilities?

Thank you for listening and kind answers upfront.

Regards,
Milan

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Re: [R] automation of R? running an R script at a certain time each night?

2008-05-23 Thread Felipe Carrillo

Hi:
Edward, were you able to automate the process? if so,
do you mind giving me a hint on how you did it? I am
facing the same problem. I created a batch file which
it runs fine using the task scheduler but only opens
Tinn-R and R but it doesn't execute my script.
My task scheduler executes everyday at 8:00 am
This is my batch file:
@echo off
Start  C:\Program Files\R\R-2.7.0\bin\Rgui.exe
 start  C:\Documents and
settings\Desktop\Software\MyScript.r

What am I missing?


--- Edward Wijaya [EMAIL PROTECTED] wrote:

 You might try cron job under Windows.
 
 http://drupal.org/node/31506
 
 HTH.
 
 - Edward
 
 On Thu, May 22, 2008 at 8:51 AM, Thomas Pujol
 [EMAIL PROTECTED] wrote:
  I am using R in a Windows environment.
 
  I store my data in a Microsoft SQL database that
 gets updated automatically nightly.  Once my SQL db
 is updated, I wish to automatically run an R
 script
 
  Any tips on good ways to approach this task?
 
  Is there an easy way to launch an R script using
 the Windows or other scheduler? Can I have an
 R-script run every hour, and within the script check
 to determine if my database is updated, and proceed
 only if it is updated?
 
 
 [[alternative HTML version deleted]]
 
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 reproducible code.
 
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained,
 reproducible code.
 


 Felipe D. Carrillo
  Fishery Biologist
  Department of the Interior
  US Fish  Wildlife Service
  California, USA

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Re: [R] Percentages for categorical data by group

2008-05-23 Thread Michael Conklin

tapply(example.data$responseVar,example.data$groupVar,function(x){prop.t
able(table(x))})

Michael Conklin

Chief Methodologist - Advanced Analytics

 

MarketTools, Inc.

6465 Wayzata Blvd. Suite 170

Minneapolis, MN 55426 

Tel: 952.417.4719 | Mobile:612.201.8978

[EMAIL PROTECTED]

 

MarketTools(r)http://www.markettools.com

 

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delete the original and any copies from your system. Thank you for your
cooperation.

 


-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Economics Guy
Sent: Friday, May 23, 2008 9:52 AM
To: [EMAIL PROTECTED]
Subject: [R] Percentages for categorical data by group

I can think of several ways to blunt force hard code what I want but I
imagine there is a command or two that can be easily combined to do
this:

I have a data frame with about 23000 observations. There first variable
is
the group to which the observation belongs (about 500 different groups).
The
second variable is a response for each observation that is a 1,2,3,4 or
5. I
want to be able to calculate the percentage of each group that choose
each
response. For example I want to know what percentage of group 1 (which
may
have a value of 34456) choose response 1 and so on.

Here is some code I wrote that generates a data frame like the one I
have.

pop - matrix(1:10)
groupIDs - sample(pop,500)
groupVar - sample(groupIDs,23000,replace=TRUE)
responseVar - sample(1:5,23000,replace=TRUE)

example.data - data.frame(groupVar,responseVar)

Is there a fast way to calculate these percentages beyond writing loops
to
manually count the responses for each of the groups?

Thanks,

EG

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Re: [R] Preparing high quality figures with tiff as end result

2008-05-23 Thread Prof Brian Ripley


Try bitmap(): this produces PostScript and converts with ghostscript.

BTW, everything (including text) in TIFF files *is* 'low-res bitmaps' by 
definition, so you cannot avoid this.  Anti-aliasing *may* help, and the 
bitmap() device in R-devel supports it.


On Fri, 23 May 2008, Gustaf Rydevik wrote:


Hi all,

I'm currently preparing some figures that will be submitted to PloS One.
In their guidelines they state that they will only accept figures in
tiff or eps format, with the warning that eps figures will be
converted to tiff format ( see
http://www.plosone.org/static/figureGuidelines.action ).

Because of this conversion, I figured I'd generate tiff-format figures
from the beginning.
However, a number of issues cropped up:
1) using

library(Cairo)
CairoTIFF(test.tif)

I get  Sorry, this Cairo was compiled without tiff support.. I tried
finding out how to recompile Cairo, but got lost in a lot of confusing
talk about GTK+, downloaded dll files that I didn't know how to use
etc.

so I turned to plain tiff(), and

2) R started crashing on me.The following code

tiff(test.tif)
plot(rnorm(100))
dev.off()

,crashes R (i.e R GUI has encountered a problem and needs to
close...) every third time or so.
When it does work, the resulting output is not too pretty.


Which means what?


So I turned to using postscript files. However, Plos One requires that
fonts be embedded into the figure.
embedFonts()  works for this, but the result is that text becomes
low-res bitmaps, and I don't know how to solve this.

So basically my question is: How should I go about generating graphics
that will look as nice as possible given the above constraints?

Many thanks in advance,

Gustaf




--
Gustaf Rydevik, M.Sci.
tel: +46(0)703 051 451
address:Essingetorget 40,112 66 Stockholm, SE
skype:gustaf_rydevik

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



--
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] Boxplot width

2008-05-23 Thread Antje


Hi there,

assume that you have data with different sampling like

d1 - rnorm(100)
d2 - rnorm(150)

now, I'd like to create two boxplots in one graph but each plot located at the 
sampling number at the x-axis. This, I can do with at


l - list(d1,d2)
boxplot(l, at=c(length(d1), length(d2)), xlim=c(0,200) )

but both plots are very thin and I'd like to increase the width of the plot.
I tried width but probably I do it wrong.

Can anybody help me?

Antje

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Re: [R] automation of R? running an R script at a certain time each night?

2008-05-23 Thread Felipe Carrillo

Thank you Prof Ripley


--- Prof Brian Ripley [EMAIL PROTECTED] wrote:

 On Fri, 23 May 2008, Felipe Carrillo wrote:
 
  Hi:
  Edward, were you able to automate the process? if
 so,
  do you mind giving me a hint on how you did it? I
 am
  facing the same problem. I created a batch file
 which
  it runs fine using the task scheduler but only
 opens
  Tinn-R and R but it doesn't execute my script.
  My task scheduler executes everyday at 8:00 am
  This is my batch file:
  @echo off
  Start  C:\Program Files\R\R-2.7.0\bin\Rgui.exe
  start  C:\Documents and
  settings\Desktop\Software\MyScript.r
 
  What am I missing?
 
 Rscript[.exe]
 
 You don't want (I presume) to run a GUI to execute a
 script.


 Felipe D. Carrillo
  Fishery Biologist
  Department of the Interior
  US Fish  Wildlife Service
  California, USA

__
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Re: [R] Preparing high quality figures with tiff as end result

2008-05-23 Thread Prof Brian Ripley

One bit you didn't tell us was that the journal asks for 600dpi TIFF 
files, but you also forgot to tell R that.


Try bitmap(type=tifflzw, res=600) -- you probably will not need 
anti-aliasing.


On Fri, 23 May 2008, Prof Brian Ripley wrote:


Try bitmap(): this produces PostScript and converts with ghostscript.

BTW, everything (including text) in TIFF files *is* 'low-res bitmaps' by 
definition, so you cannot avoid this.  Anti-aliasing *may* help, and the 
bitmap() device in R-devel supports it.


On Fri, 23 May 2008, Gustaf Rydevik wrote:


Hi all,

I'm currently preparing some figures that will be submitted to PloS One.
In their guidelines they state that they will only accept figures in
tiff or eps format, with the warning that eps figures will be
converted to tiff format ( see
http://www.plosone.org/static/figureGuidelines.action ).

Because of this conversion, I figured I'd generate tiff-format figures
from the beginning.
However, a number of issues cropped up:
1) using

library(Cairo)
CairoTIFF(test.tif)

I get  Sorry, this Cairo was compiled without tiff support.. I tried
finding out how to recompile Cairo, but got lost in a lot of confusing
talk about GTK+, downloaded dll files that I didn't know how to use
etc.

so I turned to plain tiff(), and

2) R started crashing on me.The following code

tiff(test.tif)
plot(rnorm(100))
dev.off()

,crashes R (i.e R GUI has encountered a problem and needs to
close...) every third time or so.
When it does work, the resulting output is not too pretty.


Which means what?


So I turned to using postscript files. However, Plos One requires that
fonts be embedded into the figure.
embedFonts()  works for this, but the result is that text becomes
low-res bitmaps, and I don't know how to solve this.

So basically my question is: How should I go about generating graphics
that will look as nice as possible given the above constraints?

Many thanks in advance,

Gustaf




--
Gustaf Rydevik, M.Sci.
tel: +46(0)703 051 451
address:Essingetorget 40,112 66 Stockholm, SE
skype:gustaf_rydevik

__
R-help@r-project.org mailing list
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http://www.R-project.org/posting-guide.html

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



--
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



--
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] problem using embedded R

2008-05-23 Thread Prof Brian Ripley


All the usual questions:

What OS?
What version of R?
What is meant by 'environment path'?  (The environment of a process is not 
a path.)


I have a hunch that if this is Windows = XP it was solved in R 2.7.0. 
Otherwise the footer of this message applies.


On Fri, 23 May 2008, Lobanov, Victor S. [PRDUS] wrote:


I have a peculiar problem with an application that uses embedded R. The
application comes with its own copy of R installation and it sets up
correct environment path for the process during the startup. However,
when I execute R code that loads an additional package (e.g.
library(XYZ)), the environment path gets reset to the system's default
value, which renders R unusable. I wonder if anyone had experienced a
similar problem and knows how to fix it?

Victor


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



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

Re: [R] automation of R? running an R script at a certain time each night?

2008-05-23 Thread Tony Plate


Felipe Carrillo wrote:

Hi:
Edward, were you able to automate the process? if so,
do you mind giving me a hint on how you did it? I am
facing the same problem. I created a batch file which
it runs fine using the task scheduler but only opens
Tinn-R and R but it doesn't execute my script.
My task scheduler executes everyday at 8:00 am
This is my batch file:
@echo off
Start  C:\Program Files\R\R-2.7.0\bin\Rgui.exe
 start  C:\Documents and
settings\Desktop\Software\MyScript.r

What am I missing?


Looks to me that the batch file above starts up the R GUI, 
and opens an editor, so it sounds like it is doing exactly 
what you're asking it to.


Here's how I can get R to run as a scheduled task in Windows XP:

Create a new Scheduled Task with the following in the 
Run: box:

C:\Rbuild\R-2.6.2\bin\Rcmd.exe BATCH c:/Temp/Rtest.R

Then schedule it how I want it to run.  Here's the contents 
of my .R file and the output:


$ cat c:/Temp/Rtest.R
cat(file=c:/Temp/Rtest.txt, date(), \n, append=TRUE)

$ cat c:/Temp/Rtest.txt
Fri May 23 10:34:22 2008
Fri May 23 10:34:50 2008
Fri May 23 10:40:01 2008

(I'm sure there are dozens of other ways of doing this, but 
the above worked for me.)


-- Tony Plate




--- Edward Wijaya [EMAIL PROTECTED] wrote:


You might try cron job under Windows.

http://drupal.org/node/31506

HTH.

- Edward

On Thu, May 22, 2008 at 8:51 AM, Thomas Pujol
[EMAIL PROTECTED] wrote:

I am using R in a Windows environment.

I store my data in a Microsoft SQL database that

gets updated automatically nightly.  Once my SQL db
is updated, I wish to automatically run an R
script

Any tips on good ways to approach this task?

Is there an easy way to launch an R script using

the Windows or other scheduler? Can I have an
R-script run every hour, and within the script check
to determine if my database is updated, and proceed
only if it is updated?


   [[alternative HTML version deleted]]

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http://www.R-project.org/posting-guide.html

and provide commented, minimal, self-contained,

reproducible code.
__
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PLEASE do read the posting guide
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reproducible code.




 Felipe D. Carrillo
  Fishery Biologist
  Department of the Interior
  US Fish  Wildlife Service
  California, USA

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Re: [R] Alternatives to rJava and JRI

2008-05-23 Thread Tobias Verbeke


Roy Mendelssohn wrote:
I do not know if this is better as we are just starting to look into 
it (and better is in the eye of the beholder) but look at:


http://tolstoy.newcastle.edu.au/R/e3/help/07/11/4253.html

in the archives.  The link to the software is 
http://www.ebi.ac.uk/microarray-srv/frontendapp/


The new website (with all current information)
is at

http://www.biocep.net

It is still very actively developed and
there will be a tutorial at useR!2008
as well as a presentation.

Cf.

http://www.statistik.uni-dortmund.de/useR-2008//tutorials/chine.html

HTH,
Tobias



HTH,

-Roy M.

On May 22, 2008, at 12:50 PM, Munir, Danish wrote:



Has anyone come across any alternatives to rJava and JRI? Are they any
good? Better perhaps?

Please give your reasons.

Thanks,
Danish
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**
The contents of this message do not reflect any position of the U.S. 
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Environmental Research Division   
Southwest Fisheries Science Center

1352 Lighthouse Avenue
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e-mail: [EMAIL PROTECTED] (Note new e-mail address)
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Re: [R] problem using embedded R

2008-05-23 Thread Lobanov, Victor S. [PRDUS]

It is Windows 2000 still... I use latest version of R 2.7.0. There is a
system environment variable PATH that lists directories where system
looks for dlls when needed. Each running process can modify this
environment variable, but changes apply to this process only. Instead of
modifying system settings, my application simply sets correct R_HOME and
PATH (e.g. c:\MyApp\R\bin) when it starts so that R can load supporting
dlls such as lapack.dll. However, after I load a package and check
process PATH, it is reset to the original system setting and all my
modifications are lost.

-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] 
Sent: Friday, May 23, 2008 12:46 PM
To: Lobanov, Victor S. [PRDUS]
Cc: r-help@r-project.org
Subject: Re: [R] problem using embedded R


All the usual questions:

What OS?
What version of R?
What is meant by 'environment path'?  (The environment of a process is
not 
a path.)

I have a hunch that if this is Windows = XP it was solved in R 2.7.0. 
Otherwise the footer of this message applies.

On Fri, 23 May 2008, Lobanov, Victor S. [PRDUS] wrote:

 I have a peculiar problem with an application that uses embedded R. 
 The application comes with its own copy of R installation and it sets 
 up correct environment path for the process during the startup. 
 However, when I execute R code that loads an additional package (e.g. 
 library(XYZ)), the environment path gets reset to the system's default

 value, which renders R unusable. I wonder if anyone had experienced a 
 similar problem and knows how to fix it?

 Victor


   [[alternative HTML version deleted]]

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


-- 
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] 1501-511 Compilation failed for file ch2inv.f - R on AIX 5.2.

2008-05-23 Thread Senthilkumaran Ramaiyan

Hi,
Thanks for the response. 
We do have a IBM XL Fortran Enterprise Edition for AIX, V11.1 coupled with IBM 
XL C/C++ Enterprise Edition for AIX, V9.0 specifically on our IBM-AIX 5.2 
system for the 'R' software.
The 'f95' represents Fortran 95 compiler and I presume the 'R' sources can be 
compiled with 'f95' compiler too. Any thoughts?
 
Thanks,
Senthil



- Original Message 
From: Prof Brian Ripley [EMAIL PROTECTED]
To: Senthilkumaran [EMAIL PROTECTED]
Cc: r-help@r-project.org
Sent: Friday, May 23, 2008 1:39:16 AM
Subject: Re: [R] 1501-511 Compilation failed for file ch2inv.f - R on AIX 5.2.

Look like you need to use a Fortran compiler set to accept Fortran 77 
(which the R sources are).

We don't know what 'f95' is, and this is not really an R issue so please 
ask your sysadmins for help.

On Thu, 22 May 2008, Senthilkumaran wrote:


 Hi,

 While executing the make after successful configuration (./configure
 --with-readline=no --without-iconv), the following error occurs:

 mbf2n11s (Regatta) /saswork/R/R-2.7.0$ make
 Target R is up to date.
 Target R is up to date.
 Target R is up to date.
 Target R is up to date.
 Target Makedeps is up to date.
 Target libbz2.a is up to date.
 Target Makedeps is up to date.
 Target libpcre.a is up to date.
 Target Makedeps is up to date.
 Target libz.a is up to date.
 Target Makedeps is up to date.
        f95  -g -c ch2inv.f -o ch2inv.o
 ch2inv.f, line 1.2: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 2.1: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 3.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 4.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 5.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 6.1: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 7.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 7.39: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 8.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 9.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 9.41: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 10.8: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 11.1: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 12.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 13.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 13.38: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 14.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 15.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 16.1: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 17.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 18.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 18.32: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 19.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 20.1: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 21.2: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 22.1: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 23.3: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 24.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 25.3: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 26.3: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 27.1: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 28.3: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 29.1: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 30.3: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 30.30: 1515-018 (S) Incorrect character found in source at
 line 30 in column 30.  Hexadecimal value of character is 7B.
 ch2inv.f, line 30.39: 1515-018 (S) Incorrect character found in source at
 line 30 in column 39.  Hexadecimal value of character is 7D.
 ch2inv.f, line 31.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 32.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 33.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 34.1: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 35.3: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 36.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 37.1: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 38.3: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 39.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 40.1: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 41.3: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 42.1: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 43.3: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 44.0: 1515-010 (S) String is missing a closing delimiter.
 Closing delimiter assumed at end of line.
 ch2inv.f, line 44.4: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 45.1: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 46.3: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 47.3: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 48.1: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 49.0: 1515-010 (S) String is missing a closing delimiter.
 Closing delimiter assumed at end of line.
 ch2inv.f, line 49.3: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 50.3: 1515-019 (S) Syntax is incorrect.
 ch2inv.f, line 51.1: 1515-019 (S) Syntax is incorrect.

Re: [R] Alternatives to rJava and JRI

2008-05-23 Thread Munir, Danish

Thanks a lot everyone. These seem like very useful resources. I will
check all of these out, and hopefully provide feedback so others can
benefit too.

-Original Message-
From: Tobias Verbeke [mailto:[EMAIL PROTECTED] 
Sent: Friday, May 23, 2008 1:03 PM
To: Roy Mendelssohn
Cc: Munir, Danish; r-help@r-project.org
Subject: Re: [R] Alternatives to rJava and JRI

Roy Mendelssohn wrote:
 I do not know if this is better as we are just starting to look into

 it (and better is in the eye of the beholder) but look at:

 http://tolstoy.newcastle.edu.au/R/e3/help/07/11/4253.html

 in the archives.  The link to the software is 
 http://www.ebi.ac.uk/microarray-srv/frontendapp/

The new website (with all current information)
is at

http://www.biocep.net

It is still very actively developed and
there will be a tutorial at useR!2008
as well as a presentation.

Cf.

http://www.statistik.uni-dortmund.de/useR-2008//tutorials/chine.html

HTH,
Tobias

 HTH,

 -Roy M.

 On May 22, 2008, at 12:50 PM, Munir, Danish wrote:

 Has anyone come across any alternatives to rJava and JRI? Are they
any
 good? Better perhaps?

 Please give your reasons.

 Thanks,
 Danish
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communication is for information purposes only and should not be regarded as an 
offer to sell or as a solicitation of an offer to buy any financial product, an 
official confirmation of any transaction, or as an official statement of Lehman 
Brothers.  Email transmission cannot be guaranteed to be secure or error-free.  
Therefore, we do not represent that this information is complete or accurate 
and it should not be relied upon as such.  All information is subject to change 
without notice.

IRS Circular 230 Disclosure:
Please be advised that any discussion of U.S. tax matters contained within this 
communication (including any attachments) is not intended or written to be used 
and cannot be used for the purpose of (i) avoiding U.S. tax related penalties 
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or matter addressed herein.

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[R] IDE

2008-05-23 Thread Alexandra Almeida

People,

I'm a ubunto user and I used to write my scipts in Java Gui for R, but it
is a very slow tool to run my scripts...
Do you know some efficient IDE for R?
Thank!!!

Alexandra Almeida


-- 
Alexandra R M de Almeida

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[R] Colspan rowspan

2008-05-23 Thread Arshavir


Hi,

What's the best way to build tables with multiple sets of column/row  
headings, each spanning 1 or more cols/rows, similar to the colspan/ 
rowspan options in HTML.


I am using Sweave but couldn't find an option to do this in xtable. I  
can obviously build it by hand, just wanted to make sure there wasn't  
an easier way.


Thanks.

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[R] GARCH-like

2008-05-23 Thread Renato Costa

I need to change the code of Garch to the FCGARCH (a  non-linear
multi-regime GARCH).
I don't know nothing about R.
I'd like to know how can I get the code of the garch in order to change it
and make the fit for the FC-GARCH.
Any non-linear code will be helpfull because if doesn't help in the
programming it helps in getting familiar with R.

Thank you

Renato

-- 
PhD Student Renato Alencar Adelino da Costa ([EMAIL PROTECTED])
Department of Electrical Engineering (Mathematical Finance)
Pontifical Catholic University (PUC-Rio)
Rua Marques de Sao Vicente, 225, Sala 604L
Gavea CEP: 22453-900
Rio de Janeiro
BRASIL
tel.:55-21-3527-1205

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Re: [R] Percentages for categorical data by group

2008-05-23 Thread Economics Guy

Thanks Michael that works!

Now I am having a problem getting the results into a format I can use.

prop.table generates a contingency table that I tried to turn into a data
frame I could graph from with as.data.frame() however the results are not a
true data.frame. The rows have commas between some of the elements and
trying to look at a column results in the original contingency table being
displayed.

This is what I have:

pop - matrix(1:10)
groupIDs - sample(pop,500)
groupVar - sample(groupIDs,23000,replace=TRUE)
responseVar - sample(1:5,23000,replace=TRUE)

example.data - data.frame(groupVar,responseVar)

data.table -
tapply(example.data$responseVar,example.data$groupVar,function(x){prop.table(table(x))})

example.data.frame - as.data.frame(data.table)

But the example.data.frame object is not a true data frame, and I am not
sure how to get it into a format I can graph.


On Fri, May 23, 2008 at 11:33 AM, Michael Conklin 
[EMAIL PROTECTED] wrote:

 tapply(example.data$responseVar,example.data$groupVar,function(x){prop.t
 able(table(x))})

 Michael Conklin

 Chief Methodologist - Advanced Analytics





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

Re: [R] Boxplot width

2008-05-23 Thread Jorge Ivan Velez

Hi Antje,

Try this:

d1 - rnorm(100)
d2 - rnorm(150)
boxplot(c(d1,d2) ~ rep(c(1,2),c(100,150)),col=c(4:5))

HTH,

Jorge


On Fri, May 23, 2008 at 11:52 AM, Antje [EMAIL PROTECTED] wrote:

 Hi there,

 assume that you have data with different sampling like

 d1 - rnorm(100)
 d2 - rnorm(150)

 now, I'd like to create two boxplots in one graph but each plot located at
 the sampling number at the x-axis. This, I can do with at

 l - list(d1,d2)
 boxplot(l, at=c(length(d1), length(d2)), xlim=c(0,200) )

 but both plots are very thin and I'd like to increase the width of the
 plot.
 I tried width but probably I do it wrong.

 Can anybody help me?

 Antje

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 R-help@r-project.org mailing list
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 PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Percentages for categorical data by group

2008-05-23 Thread Jorge Ivan Velez

Hi there,
Try this:


do.call(rbind,data.table)


HTH,

Jorge



On Fri, May 23, 2008 at 1:31 PM, Economics Guy [EMAIL PROTECTED]
wrote:

 Thanks Michael that works!

 Now I am having a problem getting the results into a format I can use.

 prop.table generates a contingency table that I tried to turn into a data
 frame I could graph from with as.data.frame() however the results are not a
 true data.frame. The rows have commas between some of the elements and
 trying to look at a column results in the original contingency table being
 displayed.

 This is what I have:

 pop - matrix(1:10)
 groupIDs - sample(pop,500)
 groupVar - sample(groupIDs,23000,replace=TRUE)
 responseVar - sample(1:5,23000,replace=TRUE)

 example.data - data.frame(groupVar,responseVar)

 data.table -

 tapply(example.data$responseVar,example.data$groupVar,function(x){prop.table(table(x))})

 example.data.frame - as.data.frame(data.table)

 But the example.data.frame object is not a true data frame, and I am not
 sure how to get it into a format I can graph.


 On Fri, May 23, 2008 at 11:33 AM, Michael Conklin 
 [EMAIL PROTECTED] wrote:

  tapply(example.data$responseVar,example.data$groupVar,function(x){prop.t
  able(table(x))})
 
  Michael Conklin
 
  Chief Methodologist - Advanced Analytics
 
 
 
 

 [[alternative HTML version deleted]]

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

Re: [R] Pros and Cons of R

2008-05-23 Thread GREGOR Brian J

Monica, here are some other Pros to consider about R:

1) IMHO, the most important reason for using R is that expressed by John
Chambers as the aim of the S language: to turn ideas into software,
quickly and faithfully. The broad capabilities of R facilitate the
integration of data maintenance and cleaning, exploratory data analysis,
model estimation, model implementation, model calibration, model
application, and the reporting and display of model outputs. This has
tremendous productivity advantages. For example, I was able to meet a
tight timeline for developing a regional land use model because R
allowed me to easily move through the steps of model development from
data analysis to implementation. I even found that I could do some
geographical operations that could not be done using our GIS software.
In addition, all of the model outputs (including a very many maps) were
produced with R. Once you learn how to use R in this way, you will find
it takes less time to program the outputs in R than to produce them in
GIS. R yields productivity advantages in smaller ways too. We've
developed a number of small applications to solve GIS or other problems
that could not be solved as easily using other tools. Moreover, once
they have been solved using R, the solutions are easily automated or
recycled in other contexts.

2) R facilitates documentation and replication. Previous to using R, we
did our data analysis and implemented our models in a variety of
platforms. For example, Access, Excel, SPSS and Stata were all
previously used in household survey data processing and analysis. This
was a documentation nightmare. All the steps can be done using R instead
and documentation can be easily included in the scripts. If care is
taken to use good naming conventions that emphasize readability, the
scripts can be largely self documenting. This also facilitates group
work. 

Since we started using R in our work, we have been able to greatly
increase our modeling capabilities and output with no increase in
staffing.

Brian Gregor, P.E.
Senior Transportation Analyst
Oregon Department of Transportation
Transportation Planning Analysis Unit
555 13th Street NE
Salem, OR 97301
503-986-4120



Message: 22
Date: Thu, 22 May 2008 16:00:10 +
From: Monica Pisica [EMAIL PROTECTED]
Subject: [R] Pros and Cons of R
To: r-help@r-project.org
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=Windows-1252


Hi,

I am doing a very informal presentation for my office about R
capabilities to deal with and analyze spatial data, display data and
maps, and connections with GIS. I've used in my presentation info from
the CRAN, the spatial Task view, and the more striking graphics examples
from http://addictedtor.free.fr/graphiques/thumbs.php and NCEAS
http://www.nceas.ucsb.edu/scicomp/GISSeminar/UseCases/MapProdWithRGraphi
cs/OneMapProdWithRGraphics.html together with examples of my own work.

I am finishing with pros and cons about R and I am wondering if you can
come up with other examples, or comments. Here they are:

Pros:

- R is a programming environment well suited for statistical analysis.
- R is open source and cross platforms (Windows, Mac, Linux).
- Fortran, C (C++), and Python wrappers are in place.
- Deals well with spatial data, has a robust graphical interface and
has an active user group list / forum.
- External packages for R are almost daily increasing, most of them
based on published up-to-date books and peer-reviewed articles.
- R related books ? quite a few ?.

Cons:

- R has a very steep learning curve.
- There is no perfect ?beginner? book.
- Experience with other programming languages is a plus / minus.
- You can save scripts, but not *.exe.
- It is updated several times a year (good) but there are no up-grades.
- It seems that it is hard to install correctly under Linux.
- Everything you want to do is a command line, minimal GUI.
- Memory management problems (depends on your OS), especially when
displaying big images at high resolution or working with huge matrices
(hundreds of Mb).

Also i am wondering if R works under 64 bit computers and if it takes
advantage of it.

Thanks,

Monica 

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

Re: [R] Percentages for categorical data by group

2008-05-23 Thread Economics Guy

I appreciate all the help.  The trouble is that in my real data set each
group does not always have an observation that choose each response. This
results in some of the rows returned from prop.table() to be shorter than
others so I get:

Warning message:
In function (..., deparse.level = 1)  :
  number of columns of result is not a multiple of vector length (arg 8)

Is there a way to tell rbind() or do.call() to treat missing values as zero
or make prop.table() include the zero proportions?



On Fri, May 23, 2008 at 1:59 PM, Phil Spector [EMAIL PROTECTED]
wrote:

 EG -
Thanks for the reproducible example!

When I run your code, and check the class of the result from tapply(), I
 see that it is an
 array, and using dim(), I see it's an array
 of length 500.  How big is each element?

  table(sapply(res,length))


  5
 500

 So each piece is the same length.  That means we could
 make a 500x5 matrix as follows:

 do.call(rbind,res)
   - Phil Spector
 Statistical Computing Facility
 Department of Statistics
 UC Berkeley
 [EMAIL PROTECTED]








[[alternative HTML version deleted]]

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

Re: [R] Pros and Cons of R

2008-05-23 Thread Antonio_Paredes

Yes, but R is not a spectator sport and that is the beauty of it.




GREGOR Brian J [EMAIL PROTECTED] 
Sent by: [EMAIL PROTECTED]
05/23/2008 01:00 PM

To
r-help@r-project.org
cc

Subject
Re: [R] Pros and Cons of R






Monica, here are some other Pros to consider about R:

1) IMHO, the most important reason for using R is that expressed by John
Chambers as the aim of the S language: to turn ideas into software,
quickly and faithfully. The broad capabilities of R facilitate the
integration of data maintenance and cleaning, exploratory data analysis,
model estimation, model implementation, model calibration, model
application, and the reporting and display of model outputs. This has
tremendous productivity advantages. For example, I was able to meet a
tight timeline for developing a regional land use model because R
allowed me to easily move through the steps of model development from
data analysis to implementation. I even found that I could do some
geographical operations that could not be done using our GIS software.
In addition, all of the model outputs (including a very many maps) were
produced with R. Once you learn how to use R in this way, you will find
it takes less time to program the outputs in R than to produce them in
GIS. R yields productivity advantages in smaller ways too. We've
developed a number of small applications to solve GIS or other problems
that could not be solved as easily using other tools. Moreover, once
they have been solved using R, the solutions are easily automated or
recycled in other contexts.

2) R facilitates documentation and replication. Previous to using R, we
did our data analysis and implemented our models in a variety of
platforms. For example, Access, Excel, SPSS and Stata were all
previously used in household survey data processing and analysis. This
was a documentation nightmare. All the steps can be done using R instead
and documentation can be easily included in the scripts. If care is
taken to use good naming conventions that emphasize readability, the
scripts can be largely self documenting. This also facilitates group
work. 

Since we started using R in our work, we have been able to greatly
increase our modeling capabilities and output with no increase in
staffing.

Brian Gregor, P.E.
Senior Transportation Analyst
Oregon Department of Transportation
Transportation Planning Analysis Unit
555 13th Street NE
Salem, OR 97301
503-986-4120



Message: 22
Date: Thu, 22 May 2008 16:00:10 +
From: Monica Pisica [EMAIL PROTECTED]
Subject: [R] Pros and Cons of R
To: r-help@r-project.org
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=Windows-1252


Hi,

I am doing a very informal presentation for my office about R
capabilities to deal with and analyze spatial data, display data and
maps, and connections with GIS. I've used in my presentation info from
the CRAN, the spatial Task view, and the more striking graphics examples
from http://addictedtor.free.fr/graphiques/thumbs.php and NCEAS
http://www.nceas.ucsb.edu/scicomp/GISSeminar/UseCases/MapProdWithRGraphi
cs/OneMapProdWithRGraphics.html together with examples of my own work.

I am finishing with pros and cons about R and I am wondering if you can
come up with other examples, or comments. Here they are:

Pros:

- R is a programming environment well suited for statistical analysis.
- R is open source and cross platforms (Windows, Mac, Linux).
- Fortran, C (C++), and Python wrappers are in place.
- Deals well with spatial data, has a robust graphical interface and
has an active user group list / forum.
- External packages for R are almost daily increasing, most of them
based on published up-to-date books and peer-reviewed articles.
- R related books ? quite a few ?.

Cons:

- R has a very steep learning curve.
- There is no perfect ?beginner? book.
- Experience with other programming languages is a plus / minus.
- You can save scripts, but not *.exe.
- It is updated several times a year (good) but there are no up-grades.
- It seems that it is hard to install correctly under Linux.
- Everything you want to do is a command line, minimal GUI.
- Memory management problems (depends on your OS), especially when
displaying big images at high resolution or working with huge matrices
(hundreds of Mb).

Also i am wondering if R works under 64 bit computers and if it takes
advantage of it.

Thanks,

Monica 

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


[[alternative HTML version deleted]]

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Re: [R] 3D Area Diagram

2008-05-23 Thread John Kane


--- Patrick Connolly [EMAIL PROTECTED]
wrote:

 On Thu, 22-May-2008 at 03:13PM -0700, AlGates wrote:
 
 
 | The one I rather need, is something like this
 (scan from a book):
 | http://algates.de/Scan.jpg 
 | The only difference is the angle.
 
 That one is even stranger.  There are two similar
 (but not parallel)
 lines for imports and another two similar (but again
 not parallel)
 lines for exports.  

I think the question here is Does the graph show two
lines or four lines of data?  I think it probably
onlyl shows two. The apparent two lines for imports
and for exports is almost certainly chart junk. 



I can't see if there is anything
 systematic about
 those small differences, and I suspect that there
 was meant to be
 none -- just drawn by someone who didn't have a 45
 deg set-square.  
 
 Years ago I inherited some SPlus code which did, in
 fact, draw a plot
 quite similar to that one (but without the
 inaccuracies).  I remember
 it was quite lengthy and complicated, but I don't
 remember ever having
 an inclination to use it for anything since R has so
 many easier and
 better ways of visualizing data.
 
 During the process of changing computer systems
 several times in the
 intervening years, that code was something that went
 out with the old
 faded photos.  Shame that. 
 
  Excel might have an option to do one like the
 import-export example.
 If it does, it would be a lot easier than using R
 which has an
 altogether different set of values.  If Excel
 doesn't do that type,
 and it's *really* important to have such a plot, I'd
 be using grid
 graphics which is almost infinitely flexible.  Only
 trouble is, by the
 time you'd seen what you can do with grid, you'd
 likely find that you
 no longer felt any urge to make such a plot.
 
 
 best
 
 -- 

~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
   
___Patrick Connolly   
  {~._.~}   Great minds discuss ideas
  _( Y )_  Middle minds discuss events 
 (:_~*~_:)  Small minds discuss people  
  (_)-(_) . Anon
 

~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
 
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Re: [R] Pros and Cons of R

2008-05-23 Thread John Kane

I even carry a copy of R on a USB so that I can do a
bit of work on a machine that does not have it
installed.  It's a bit slow and one would not want to
do anything major with it but it's handy to show
someone a quick graph or check something when far from
the office.

--- seanpor [EMAIL PROTECTED] wrote:

 
 
 Neil Shephard wrote:
  
  Another pro to consider is the cost, you can
 obtain R for free,
  SAS/S-Plus/Stata all have licenses of some sort
 that require purchasing.
  
  Neil
  
 
 Which has the side effect of *not* restricting how
 many machines are
 available for use or where; e.g. I was running big
 process a couple of
 different times with different scenarios, so I just
 fired up a few un-used
 machines and had them all running in parallel for
 the afternoon - no
 installation issues as I was able to run it off the
 network drive (windows
 as it happens).  If I was licence restricted this
 would not have been
 possible.
 
 Similarly I can do analyses at home on any machine
 or even if I'm visiting
 somewhere else!
 
 Regards
 Sean

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Re: [R] Pros and Cons of R

2008-05-23 Thread Spencer Graves



GREGOR Brian J wrote:

Monica, here are some other Pros to consider about R:
  

snip
2) R facilitates documentation and replication. 

snip

 When I finally made the effort to learn how to make R packages, I 
experienced a substantial increase in my productivity.  Before I start 
coding a new functions, I now write a help page including test cases in 
the examples.  Each function is part of a package.  After the code is 
complete, I check (and build and install) the package.  If a 
change to function A breaks something in functionB, this usually 
exposes it fairly quickly.  On average, I get working code much faster 
than I did previously.  Moreover, when I'm done, I have (almost for 
free) a package that is reasonably well documented that I can easily 
share with others. 

 This may not belong in a discussion to a group of people who may 
not develop new statistical procedures, but I believe it can help almost 
anyone who develops a procedure that will likely be used more than once 
or twice. 

 Spencer 


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[R] Seeking help with trellis: log scales on xyplot

2008-05-23 Thread hobie perry


Good afternoon.

The basic plot function can automatically generate log scales as follows:

 plot(calcium ~ soil_ph, log=y)

Here is my basic model in xyplot...

 xyplot(calcium+magnesium ~ soil_ph|depth*region)

I would like the calcium and magnesium values to be reported on a log scale.
I have tried manipulating scales and yscale.components to no effect. 

Many thanks for your kind assistance,
Hobie Perry
US Forest Service
St. Paul, MN
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Re: [R] Percentages for categorical data by group

2008-05-23 Thread Michael Conklin


 prop.table(table(factor(x,levels=1:5)))


Michael Conklin

Chief Methodologist - Advanced Analytics

 

MarketTools, Inc.

6465 Wayzata Blvd. Suite 170

Minneapolis, MN 55426 

Tel: 952.417.4719 | Mobile:612.201.8978

[EMAIL PROTECTED]

 

MarketTools(r)http://www.markettools.com

 

This e-mail and any attachments may contain privileged, confidential or
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that any review, copying, or distribution of this e-mail or any
attachment is strictly prohibited. If you have received this e-mail in
error, please return it to the sender immediately, and permanently
delete the original and any copies from your system. Thank you for your
cooperation.

 


-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Economics Guy
Sent: Friday, May 23, 2008 1:36 PM
To: [EMAIL PROTECTED]
Subject: Re: [R] Percentages for categorical data by group

I appreciate all the help.  The trouble is that in my real data set each
group does not always have an observation that choose each response.
This
results in some of the rows returned from prop.table() to be shorter
than
others so I get:

Warning message:
In function (..., deparse.level = 1)  :
  number of columns of result is not a multiple of vector length (arg 8)

Is there a way to tell rbind() or do.call() to treat missing values as
zero
or make prop.table() include the zero proportions?



On Fri, May 23, 2008 at 1:59 PM, Phil Spector
[EMAIL PROTECTED]
wrote:

 EG -
Thanks for the reproducible example!

When I run your code, and check the class of the result from
tapply(), I
 see that it is an
 array, and using dim(), I see it's an array
 of length 500.  How big is each element?

  table(sapply(res,length))


  5
 500

 So each piece is the same length.  That means we could
 make a 500x5 matrix as follows:

 do.call(rbind,res)
   - Phil Spector
 Statistical Computing Facility
 Department of Statistics
 UC Berkeley
 [EMAIL PROTECTED]








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[R] Installing R on Linux is easy. (was Re: Pros and Cons of R)

2008-05-23 Thread Patrick Connolly

On Thu, 22-May-2008 at 09:28PM +0200, Hans Ekbrand wrote:

| On Thu, May 22, 2008 at 02:07:01PM -0400, R P Herrold wrote:
|  On Thu, 22 May 2008, Monica Pisica wrote:
| 
| [...]
| 
|  When a new R version is in place you 
|  cannot up-grade your old R version, you have to do a new 
|  installation and re-load all the packages you used to have 
|  and delete / un-install the old version
|  
|  ummm -- this is of course a function of the package manager 
|  and operating system being used, and not of R intrinsicly; 
|  under an RPM package manager, this issue is not present
| 
| Neither under .deb based OS:es such as Ubuntu and Debian.

I don't see in this discussion a mention of how easy it is to install
R on Linux from source.  The instructions are very clear and simple.

With three simple steps, it's easy to install one version in the
background while you're still using the previous one.  With judicious
arrangement of libraries, it's unnecessary to reinstall the packages
every time you install a new version, and it's simple to have multiple
versions of R on the same computer.  I don't know how one would keep
two or more versions of Genstat (say) on the same computer.

If it is desired to update the packages, that's ridiculously simple
also. 


-- 
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
   ___Patrick Connolly   
 {~._.~} Great minds discuss ideas
 _( Y )_Middle minds discuss events 
(:_~*~_:)Small minds discuss people  
 (_)-(_)   . Anon
  
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

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[R] maximizing the gamma likelihood

2008-05-23 Thread markleeds

for learning purposes and also to help someone, i used roger peng's 
document to get the mle's of the gamma where the gamma is defined as


f(y_i) = (1/gammafunction(shape)) * (scale^shape) * (y_i^(shape-1)) * 
exp(-scale*y_i)


( i'm defining the scale as lambda rather than 1/lambda. various books 
define it differently  ).


i found the likelihood to be n*shape*log(scale)  + 
(shape-1)*sum(log(y_i) - scale*sum(y_i)
then i wrote below which is just roger peng's likelihood example but 
using the gamma instead of the normal.
I get estimates back but i separately found that the analytical mle of 
the scale is equal to 1/ analytical mle(shape).
and my estimates aren't consistent with that fact ? this leads me to 
assume that my estimates are not correct.


can anyone tell me what i'm doing wrong. maybe my starting values are 
too far off ? thanks.


make.negloglik - function(data, fixed=c(FALSE,FALSE)) {
  op - fixed
  function(p) {
op[!fixed] - p
shape - exp(op[1])
scale - exp(op[2])
a - length(data)*shape*log(scale)
b - (shape-1)*sum(log(data))
c - -1.0*scale*sum(data)
-(a + b + c)
   }
}

vsamples- c(14.7, 18.8, 14, 15.9, 9.7, 12.8)
nLL - make.negloglik(vsamples)
temp - optim(c(scale=1,shape=1), nLL, method=BFGS)[[par]]
estimates - log(temp)
print(estimates)

check - estimates[1]/mean(vsamples)
print(check)

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[R] exrpression(), double subscript

2008-05-23 Thread Afshartous, David

All,
 
The first use of expression produces a double subscript while the second does 
not.
I searched in ?plotmath and the archives and didn't find anything.  I'm sure 
I'm missing
something obvious but can't seem to find.  any suggestions much appreciated.
 
Cheers,
David
 
 
plot(1:10, 1:10)
text(par(usr)[1] - .5, 5, adj = 1, labels = expression(hat(b)[11]), xpd = 
TRUE)
text(par(usr)[1] - .5, 5, adj = 1, labels = expression(hat(b)[0i]), xpd = 
TRUE)
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[R] van der Corput sequences

2008-05-23 Thread Carlos Ungil

Alberto,

I think the functions below do what you want:

 vanDerCorput(12,6)
 [1] 0.1667 0. 0.5000 0.6667 0.8333 0.0278
 [7] 0.1944 0.3611 0.5278 0.6944 0.8611 0.0556

Regards,

Carlos

number2digits=function(n,base){
  #first digit in output is the least significant
  digit=n%%base
  if (nbase)
digit
  else
c(digit,number2digits((n-digit)/base,base))
}

digits2number=function(digits,base){
  #first digit in input should be the most significant
  result=0
  for (digit in digits)
result=(base*result)+digit
  result
}

vanDerCorput=function(n,base=2){
  #generate n first digits of the van der Corput sequence
  output=NA*1:n
  for(i in 1:n){
digits=number2digits(i,base)
output[i]=digits2number(digits,base)/base^length(digits)
  }
  output
}

-
In package fOptions, there are functions that generate
Halton sequences.

The van der Corput sequence for base 2 is a particular case
of the Halton sequence generated by:

n - 8 # anything here...
x - runif.halton(n, 1)

In fact, x - runif.halton(n, dim) will generate the van der Corput
sequences for the base b as the i-th prime number in x[,i].

(in other words, if I want the van der Corput sequence for
base b = 5, I do x - runif.halton(n, 3) and take x[,3]).

However, it's possible to have van der Corput sequences for
non-prime basis, like (for b = 10):

0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.01, 0.11, 0.21, 0.31, 0.41,
0.51, 0.61, 0.71, 0.81, 0.91, 0.02, 0.12, 0.22, 0.32,


Is there any R function that generates those sequences?

Alberto Monteiro

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[R] dividing the data

2008-05-23 Thread kayj


hello,

I have data of individuals; with their age and other infromation. Each row
corresponds to a single individual. I would like to divide the data and
store them into two files. one file with people less than 50 years of age
and the other with people more than 50 years of age. I am new into R and I
appreciate if someone can help.

thanks
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[R] SVD on a matix

2008-05-23 Thread kayj


Hi All,

I performed an svd on a matrix X and saved the first three column of the
left singular matrix U. ( I assume that they correspond to the projection of
the matrix on the first three  eigen vectors that corresponds to the first
three largest eigenvalues). I would like to know how much variance is
explained by the first eigenvectors? how can I find that.

Thanks for your help
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Re: [R] dividing the data

2008-05-23 Thread Marianne Promberger

On 05/23/08 14:34, kayj wrote:
 
 hello,
 
 I have data of individuals; with their age and other infromation. Each row
 corresponds to a single individual. I would like to divide the data and
 store them into two files. one file with people less than 50 years of age
 and the other with people more than 50 years of age. 

Assuming you have your data in a dataframe  x with one column called
age (get the data into R e.g. with read.csv)

young - x[x$age  50,]

write.table(young,file=young.txt)

etc.

m.



-- 
Marianne Promberger
Graduate student in Psychology
http://www.psych.upenn.edu/~mpromber

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[R] Shared Library Error

2008-05-23 Thread what's in the name?

Can anyone help me resolve this? A part of the R function looks like this:

   print(is.loaded('merge_xtabs_patterns_file'))
   print(is.loaded('merge_xtabs_patterns_file_'))

.Fortran('merge_xtabs_patterns_file_',ydim[1],ydim[2],x=as.integer(as.matrix(y)),na=as.integer(c),

maxD=as.integer(maxD),lrowmem=length(rowmem),rowmem=as.integer(rowmem),

sequential=as.integer(Sequential),nclust=as.integer(nclust))




The corresponding output:

[1] FALSE
[1] TRUE
Error in .Fortran(merge_xtabs_patterns_file_, ydim[1], ydim[2], x =
as.integer(as.matrix(y)),  :
  Fortran symbol name merge_xtabs_patterns_file_ not in load table





Why is it that I get a TRUE for is.loaded with the same symbol, but when
using that under .Fortran I get the above error?


I also tried replacing the third line with the following (removing the last
underscore from the symbol name):

.Fortran('merge_xtabs_patterns_file',ydim[1],ydim[2],x=as.integer(as.matrix(y)),na=as.integer(c),

maxD=as.integer(maxD),lrowmem=length(rowmem),rowmem=as.integer(rowmem),

sequential=as.integer(Sequential),nclust=as.integer(nclust))


The corresponding error:

Error in .Fortran(merge_xtabs_patterns_file, ydim[1], ydim[2], x =
as.integer(as.matrix(y)),  :
  Fortran symbol name merge_xtabs_patterns_file not in load table



Can anyone help?

Thanks,
A

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Re: [R] Seeking help with trellis: log scales on xyplot

2008-05-23 Thread Deepayan Sarkar

On 5/23/08, hobie perry [EMAIL PROTECTED] wrote:

  Good afternoon.

  The basic plot function can automatically generate log scales as follows:

  plot(calcium ~ soil_ph, log=y)

  Here is my basic model in xyplot...

  xyplot(calcium+magnesium ~ soil_ph|depth*region)

  I would like the calcium and magnesium values to be reported on a log scale.
  I have tried manipulating scales and yscale.components to no effect.

Try something like

xyplot(calcium+magnesium ~ soil_ph|depth*region,
   scales = list(y = list(log = 2)))

-Deepayan

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Re: [R] exrpression(), double subscript

2008-05-23 Thread Bert Gunter

Not sure what you mean by double subscript. 11 is the number eleven and
that is what is shown, as expected.

0i is the complex number 0+0i (type it at your console), and that is what is
shown.

Does that solve the mystery? Maybe try it with 11i as the subscript to help
you see it.

-- Bert Gunter
Genentech

-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Afshartous, David
Sent: Friday, May 23, 2008 2:43 PM
To: r-help@r-project.org
Subject: [R] exrpression(), double subscript

All,
 
The first use of expression produces a double subscript while the second
does not.
I searched in ?plotmath and the archives and didn't find anything.  I'm sure
I'm missing
something obvious but can't seem to find.  any suggestions much appreciated.
 
Cheers,
David
 
 
plot(1:10, 1:10)
text(par(usr)[1] - .5, 5, adj = 1, labels = expression(hat(b)[11]), xpd =
TRUE)
text(par(usr)[1] - .5, 5, adj = 1, labels = expression(hat(b)[0i]), xpd =
TRUE)

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[R] Spatial Overlay - SQL - Geoprocessing

2008-05-23 Thread Paulo Cardoso

Can we by any change perform in R something similar geoprocessing or, more
advanced, Spatial SQL over vectorial data?

Paulo


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Re: [R] How to pass variable of for loop on read table text

2008-05-23 Thread Charilaos Skiadas


?paste

paste('text',y,'.txt', sep=)

and you likely need data[[y]] instead of data$y.

On May 23, 2008, at 9:05 PM, Jason Lee wrote:


Hi,

I have a couple of text and would like to automate of reading these  
multiple

files using
(namely; text1.txt, text2.txt)

for(y in 3:10){
data$y-read.table('text$y.txt')}

But it seems not allow. Any idea?


Thanks.

[[alternative HTML version deleted]]



Haris Skiadas
Department of Mathematics and Computer Science
Hanover College

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Re: [R] How to pass variable of for loop on read table text

2008-05-23 Thread markleeds

maybe this should also be a FAQ because i've seen it a lot since I've 
been on this list ?


assign each data.frame to a component of a list, rather than to a 
component of a dataframe. you also need paste to get the number.


listDFs-list()

for ( y in 3:10 ) {
 listDFs[[y]]-read.table(paste(text1,y,sep=),header=TRUE if there 
are headings, whateverelse)

}

listDFs[[1]] will then contain the first data frame, listDFs[[2]] the 
second etc.





On Fri, May 23, 2008 at  9:05 PM, Jason Lee wrote:


Hi,

I have a couple of text and would like to automate of reading these 
multiple

files using
(namely; text1.txt, text2.txt)

for(y in 3:10){
data$y-read.table('text$y.txt')}

But it seems not allow. Any idea?


Thanks.

[[alternative HTML version deleted]]

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Re: [R] Colspan rowspan

2008-05-23 Thread Gabor Grothendieck

latex in Hmisc can do that with the n.cgroup= and n.rgroup= args
although if your tables are getting very complicated you might
be best off just generating the latex yourself since then you
get all the flexibility of latex.

On Fri, May 23, 2008 at 1:26 PM, Arshavir [EMAIL PROTECTED] wrote:
 Hi,

 What's the best way to build tables with multiple sets of column/row
 headings, each spanning 1 or more cols/rows, similar to the colspan/rowspan
 options in HTML.

 I am using Sweave but couldn't find an option to do this in xtable. I can
 obviously build it by hand, just wanted to make sure there wasn't an easier
 way.

 Thanks.

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[R] Importing data in text file into R

2008-05-23 Thread amarjit singh sethi

Dear all,
I am quite new to R; facing certain problems:
Say, I have a text file( named as try):
YearC1  C2  C3  C4  C5  C6
Y1  3.5 13.89.5 6.8 0.4 24.2
Y2  3.8 13.99.9 7.6 0.7 12.8
Y3  4.5 14.514.29.2 0.6 14.5
Y4  5.9 16.224.612.70.2 24.3
Y5  7.2 20.440.618.20.8 28.2
Y6  5.9 18.637.414.50.3 36.9
Y7  8.0 16.188.624.10.1 34.6
Y8  13.621.156.319.00.7 33.3

I wish to import the file into R and make certain
computations, like intercorrelation matrix. I tried
the following syntax:

# Inputting the data file (saved in text format)
df=trial.txt
idt=read.table(df,header=T, sep=\t)
idt
# To generate intercorrelatio matrix
r = cor(idt)
r=round(r, 4)
r

The seems to have been read, but further computations
not made, with the following output:

 # Inputting the data file (saved in text format)
 df=trial.txt
 idt=read.table(df,header=T, sep=\t)
 idt
  Year   C1   C2   C3   C4  C5   C6
1   Y1  3.5 13.8  9.5  6.8 0.4 24.2
2   Y2  3.8 13.9  9.9  7.6 0.7 12.8
3   Y3  4.5 14.5 14.2  9.2 0.6 14.5
4   Y4  5.9 16.2 24.6 12.7 0.2 24.3
5   Y5  7.2 20.4 40.6 18.2 0.8 28.2
6   Y6  5.9 18.6 37.4 14.5 0.3 36.9
7   Y7  8.0 16.1 88.6 24.1 0.1 34.6
8   Y8 13.6 21.1 56.3 19.0 0.7 33.3
 # To generate intercorrelatio matrix
 r = cor(idt)
Error in cor(idt) : missing observations in cov/cor
In addition: Warning message:
In cor(idt) : NAs introduced by coercion
 r=round(r, 4)
Error: object r not found
 r
Error: object r not found

Kindly advise me as to how to get rid of the error
message.

AJSS

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Re: [R] Importing data in text file into R

2008-05-23 Thread John Fox


Dear AJSS,

The problem is that the way you've read the data, the first column of  
the data frame is a factor, not a numerical variable, and thus is not  
suitable for computing correlations.


You could use the command cor(idt[,-1]) to compute correlations on all  
but the first column, but your intention was probably to use the first  
column of the input file for row names, not as a variable. One way to  
do this is simply to omit the variable name Year in the first row of  
the input data file.


I hope this helps,
 John

On 23-May-08, at 11:40 PM, amarjit singh sethi wrote:


Dear all,
I am quite new to R; facing certain problems:
Say, I have a text file( named as try):
YearC1  C2  C3  C4  C5  C6
Y1  3.5 13.89.5 6.8 0.4 24.2
Y2  3.8 13.99.9 7.6 0.7 12.8
Y3  4.5 14.514.29.2 0.6 14.5
Y4  5.9 16.224.612.70.2 24.3
Y5  7.2 20.440.618.20.8 28.2
Y6  5.9 18.637.414.50.3 36.9
Y7  8.0 16.188.624.10.1 34.6
Y8  13.621.156.319.00.7 33.3

I wish to import the file into R and make certain
computations, like intercorrelation matrix. I tried
the following syntax:

# Inputting the data file (saved in text format)
df=trial.txt
idt=read.table(df,header=T, sep=\t)
idt
# To generate intercorrelatio matrix
r = cor(idt)
r=round(r, 4)
r

The seems to have been read, but further computations
not made, with the following output:


# Inputting the data file (saved in text format)
df=trial.txt
idt=read.table(df,header=T, sep=\t)
idt

 Year   C1   C2   C3   C4  C5   C6
1   Y1  3.5 13.8  9.5  6.8 0.4 24.2
2   Y2  3.8 13.9  9.9  7.6 0.7 12.8
3   Y3  4.5 14.5 14.2  9.2 0.6 14.5
4   Y4  5.9 16.2 24.6 12.7 0.2 24.3
5   Y5  7.2 20.4 40.6 18.2 0.8 28.2
6   Y6  5.9 18.6 37.4 14.5 0.3 36.9
7   Y7  8.0 16.1 88.6 24.1 0.1 34.6
8   Y8 13.6 21.1 56.3 19.0 0.7 33.3

# To generate intercorrelatio matrix
r = cor(idt)

Error in cor(idt) : missing observations in cov/cor
In addition: Warning message:
In cor(idt) : NAs introduced by coercion

r=round(r, 4)

Error: object r not found

r

Error: object r not found

Kindly advise me as to how to get rid of the error
message.

AJSS

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


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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Importing data in text file into R

2008-05-23 Thread Patrick Connolly

On Fri, 23-May-2008 at 08:40PM -0700, amarjit singh sethi wrote:

| Dear all,
| I am quite new to R; facing certain problems:
| Say, I have a text file( named as try):


|  idt=read.table(df,header=T, sep=\t)
|  idt
|   Year   C1   C2   C3   C4  C5   C6
| 1   Y1  3.5 13.8  9.5  6.8 0.4 24.2
| 2   Y2  3.8 13.9  9.9  7.6 0.7 12.8
| 3   Y3  4.5 14.5 14.2  9.2 0.6 14.5
| 4   Y4  5.9 16.2 24.6 12.7 0.2 24.3
| 5   Y5  7.2 20.4 40.6 18.2 0.8 28.2
| 6   Y6  5.9 18.6 37.4 14.5 0.3 36.9
| 7   Y7  8.0 16.1 88.6 24.1 0.1 34.6
| 8   Y8 13.6 21.1 56.3 19.0 0.7 33.3
|  # To generate intercorrelatio matrix
|  r = cor(idt)
| Error in cor(idt) : missing observations in cov/cor
| In addition: Warning message:
| In cor(idt) : NAs introduced by coercion


The help file for cor says this about x and y:

   x: a numeric vector, matrix or data frame.

   y: 'NULL' (default) or a vector, matrix or data frame with
  compatible dimensions to 'x'.  The default is equivalent to
  'y = x' (but more efficient).

Your x isn't a numeric vector, matrix or data frame.

x[,-1] is, and that might give what you want, but read the rest of the
help file to determine if that's what you want it to do.  Having
rownames on your dataframe might help seeing what is happening.  The
easiest way I can see to get row names is in your read.table line.
Add row.names = 1.

HTH

-- 
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
   ___Patrick Connolly   
 {~._.~} Great minds discuss ideas
 _( Y )_Middle minds discuss events 
(:_~*~_:)Small minds discuss people  
 (_)-(_)   . Anon
  
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

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