[R] xyplot key

[Andrewjohnclose]

Hi,

I'm having trouble matching the symbols/color of the key to match those
specifiec in the plot.

Here is the code I used:


xyplot(GCR+GCT ~ FRAC, data=RWF, type=c(g,p),cex=1.2,pch=c(22,21),
xlab=expression(italic(f)),ylab=expression(italic(S)),
key=list(points=list(pch=c(22,21),cex=1.2),
text=list(c(Targeted Deletion,Random Deletion

I'm, sorry if this is an apparently easy/obvious mistake on my part.

With thanks

Andrew

http://www.nabble.com/file/p25681535/RWF.csv RWF.csv 
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[R] Minimum and blanks

[Chris Li]

Hi all,

I want to calculate the minimum of a column which contains blanks.

R returns  as the minimum, which is not I want.

Is there a way to overcome it?

Thanks in advance.
Chris
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[R] Confidence intervals PLS prediction

[lievelaurens]

I have switched from The Unscrambler to R for pls regression analysis and
have been able to calculate scores, coefficients, RMSEP from a large number
of PLS1 and PLS2 models. The ultimate goal is to use these models for
predicting unknown samples, which again is straight-forward with the
built-in predict() function. However, I’m struggling with prediction
uncertainty (i.e. confidence intervals) on predicted values (as an estimate
on the reliability of the predicted values). 

Has anyone looked into and/or developed an algorithm or function that
calculates the prediction uncertainty? In order to report on the accuracy
and reliability of the predicted values, we need to report on the yDeviation
(as in
http://www.camo.com/TheUnscrambler/Appendices/The%20Unscrambler%20Method%20References.pdf
on page 31). I have extensively read and searched the available literature
on plsr, mvr, predict, etc. as well as the Nabble forums but I couldn't find
any reference to this kind of uncertainty values.

I am considering writing my own function for this, but if this has already
been addressed, it would be most helpful and would save me a lot of time.

Thanks,

Lieve Laurens, PhD
National Renewable Energy Laboratory
Golden, CO 80401
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Re: [R] Calling R functions into C# or C++

[fayssal]

Hi,

It is possible to call R functions from .NET by using a .NET wrapper over
the R (D)Com server.  http://www.nabble.com/file/p25682136/RFromCsharp.zip
Attached  is a sample C# project that shows how to call R from C#. 

Best Regards,
Fayssal El Moufatich

http://www.nabble.com/file/p25682136/RFromCsharp.zip RFromCsharp.zip 
 

Shubha Vishwanath Karanth wrote:
 
 Hi R,
 
  
 
 I have a request...
 
  
 
 Can I call R functions/routines from C# or C++? If so, how do I do this?
 Do I need to have some knowledge on DLL to do this?
 
  
 
  
 
 Thanks a lot for your help,
 
 Shubha
 
 Shubha Karanth | Amba Research
 
 Ph +91 80 3980 8031 | Mob +91 94 4886 4510 
 
 Bangalore * Colombo * London * New York * San José * Singapore *
 www.ambaresearch.com
 
  
 
 This e-mail may contain confidential and/or privileged i...{{dropped:13}}
 
 
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[R] re ading and analyzing a word document

[PDXRugger]

file=(LUSDR/letter.doc)
Howdy Y'all, 


So i am looking to read a word document in the following formats(.doc) or
any type of accessible word processor software (e.g. text .txt, notepad,
etc).  Had the ability to search certain words, for instance banana,
peacock,Weapons Mass Destruction.  Then i could summarize and view
the results.  i looked and the only thing i could find was the below where i
want to analyze letter.doc and look for the words mentioned in quotes
above.  Its aparently wrong but im wondering if this is even possible. 
Please advise.  Thanks 

In Solidarity
JR

catbanana, peacock,Weapons Mass Destruction
file=(letter.doc),sep=\n)
readLines(file, n=-1)
unlink(letter.doc) # tidy up
## difference in blocking
cat(123\nabc, file = test1)
readLines(test1) # line with a warning
a=con - file(test1, r, blocking = FALSE)
readLines(con) # empty
cat( def\n, file = test1, append = TRUE)
readLines(con) # gets both
close(con)
unlink(test1) # tidy up

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[R] Input format for kcca in kernlab

[Guru Ananda]

Hi,

I'm trying to use kcca function from the kernlab package, and it requires 2
input datasets, both of which need to be matrices containing data index by
row.
I have two data frame objects which I converted to matrices using
data.frame(x). Their dimensions are 2264*10 and 2264*4. I then tried running
kcca on the two data matrices, only to get this error: Error in kcca(xm, ym)
: Number of colums in x, y matrixes is not equall
Does anyone know why I'm encountering this error? 
Also, just to make the number of columns equal, I transposed my two data
matrices, and reran kcca, on which I got a different error message: Error in
VK[(n + 1):(2 * n), ] - Ky : number of items to replace is not a multiple
of replacement length

I'm not sure how to proceed further. Any help would be greatly appreciated.

Thanks,
Guru.
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Re: [R] re ading and analyzing a word document

[PDXRugger]

Considering your instructions:

#Define words to find
to.find - c( 'the', 'is', 'are' ,'dr') 
#Read in the file... 
file.text - readLines( 'data/letter.txt' ) 
#Count number of occurnces of deined word in text
line.matches - unlist( lapply( to.find, grep, x = unlist(file.text[2]) ) ) 

Result:
 line.matches 
[1] 1 1 1

This is not right of course as there are actually four words and secondly
becasue the searched words appear multiple times.  

I think the problem is that the file.text is coming in so that file.text[2]
-\tHello sir, I write to you seeking your guidance organizing some data. 
I have a . So its reading the document its just putting them into this
type of format.  Im stuck, i tried doing it by saving the doc to a csv and
searching strings, tried using a match process.   It would also be useful to
simply get a run down similar to a summary expressing the most common words. 
Ideas? 



cls59 wrote:
 
 
 PDXRugger wrote:
 
 Howdy Y'all, 
 
 So i am looking to read a word document in the following formats(.doc) or
 any type of accessible word processor software (e.g. text .txt, notepad,
 etc).  Had the ability to search certain words, for instance banana,
 peacock,Weapons Mass Destruction.  Then i could summarize and
 view the results.  i looked and the only thing i could find was the below
 where i want to analyze letter.doc and look for the words mentioned in
 quotes above.  Its aparently wrong but im wondering if this is even
 possible.  Please advise.  Thanks 
 
 In Solidarity
 JR
 
 
 Well... you could make a vector of the words you want to find:
 
 to.find - c( 'banana', 'peacock', 'Weapons' )
 
 Read in the file...
 
 file.text - readLines( 'myFile.txt' )
 
 And recursively apply the grep command in order to determine which lines
 contain matches for your words:
 
 line.matches - unlist( lapply( to.find, grep, x = file.text ) )
 
 It may do what you want for plain text files, as for Microsoft Word
 files... well...
 
 Sometimes there is a price to pay for using a closed proprietary binary
 document format.
 
 Good luck!
 
 -Charlie
 

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[R] aproximate a titration kurve to the measure data.

[awayguy]

Halo

i'm studying chemistry, today we made an experiment and i have to draw a
titration kurve for my mess data. we can do it on a mm paper, or we can also
use a programe. people from chemistry recomend R
last year i studied civil eng. and we used Matlab, as I see, R ist very
similar to it, but its got other comands.
But i think R would be a good help for some exercises.

so my main question is: i have some measurement data from my titration, and
I want aproximate a kurve to this data. is it possible to do it with R?

a titration kurve looks like this:

http://www.nabble.com/file/p25685986/acetic-acid-titration-curve.png 

hope you can help me, and yes when its possible, if you know something like
a tutorial then i would be glad if you could post it.

with regards
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Re: [R] Minimum and blanks

[Peter Ehlers]

Chris,

What is your definition of the minimum of a *character* vector?

 -Peter Ehlers

Chris Li wrote:

Hi all,

I want to calculate the minimum of a column which contains blanks.

R returns  as the minimum, which is not I want.

Is there a way to overcome it?

Thanks in advance.
Chris


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Re: [R] Overview of error and warning messages for teaching + examples

[Tal Galili]

It would best be there - I agree.

But since I had no experience with the site - I didn't know the rules of
use for it.

Thanks for clarifying.
Tal


--


My contact information:
Tal Galili
E-mail: tal.gal...@gmail.com
Phone number: 972-52-7275845
FaceBook: Tal Galili
My Blogs:
http://www.talgalili.com (Web and general, Hebrew)
http://www.biostatistics.co.il (Statistics, Hebrew)
http://www.r-statistics.com/ (Statistics,R, English)




On Thu, Oct 1, 2009 at 4:14 AM, Ben Bolker bol...@ufl.edu wrote:

 Tal Galili tal.galili at gmail.com writes:

 
  Hi Joris,
 
  Good luck with your work.
 
  I know how to set up a wiki. But I wouldn't do it for just 1 page. And
 also,
  if you have little experience with it - I am not sure you would find it
 easy
  to jump into it.
  I'll have a look around to see what other collaborative tools there are
 out
  there.
 

   Remind me why this shouldn't just be done on the official R
 wiki, wiki.r-project.org ??

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Re: [R] Overview of error and warning messages for teaching + examples

[joris meys]

Hi Ben,

other members of the list also pointed me to this possibility. I'll
certainly add the manual.
Kind regards
Joris

On Thu, Oct 1, 2009 at 4:14 AM, Ben Bolker bol...@ufl.edu wrote:
 Tal Galili tal.galili at gmail.com writes:


 Hi Joris,

 Good luck with your work.

 I know how to set up a wiki. But I wouldn't do it for just 1 page. And also,
 if you have little experience with it - I am not sure you would find it easy
 to jump into it.
 I'll have a look around to see what other collaborative tools there are out
 there.


  Remind me why this shouldn't just be done on the official R
 wiki, wiki.r-project.org ??

 __
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[R] creating R roll in Centos OS

[Sukhbir Rattan]

Hi

I have Centos Operating System.

I m installing R on it. For this I have to create roll of R.

So, how to create the roll of R, regarding this what to be downloaded and
from where?

Plz help.

By
Sukhbir Singh Rattan.

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Re: [R] Minimum and blanks

[joris meys]

The minimum of a character vector is returned according to the unicode
or ascii code values, but I guess that's not what Chris is looking
for.

Chris, please always try to provide a minimal working example of code
to see what is wrong.

Something goes wrong with the input in your example. As Peter
rightfully pointed out, your vector is considered a character vector.
So you need to :

1) replace  with NA
  e.g. x -  ifelse(x=='',NA,x)
Better to do something like that when reading in the code.

2) use the argument na.rm : min (x, na.rm=T)

kind regards
Joris

On Thu, Oct 1, 2009 at 8:36 AM, Peter Ehlers ehl...@ucalgary.ca wrote:
 Chris,

 What is your definition of the minimum of a *character* vector?

  -Peter Ehlers

 Chris Li wrote:

 Hi all,

 I want to calculate the minimum of a column which contains blanks.

 R returns  as the minimum, which is not I want.

 Is there a way to overcome it?

 Thanks in advance.
 Chris

 __
 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
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Re: [R] Missing functions

[Paul Hiemstra]

Kenny Shen wrote:

Hi all,

I'm new to R and have been working hard to get familiarized with it. A
problem I'm facing now is that having installed some packages (psych, doBy),
I can't seem to access the functions even through there was no error
messages when I load them using library(). I get an error telling me the
function doesn't exist. But when I ran e.g. library(help = psych), the
function I want was missing.

I did find that when I load other packages, there will be some
initialisation messages, but loading psych and doBy just brings up the
prompt again with no output.

Any help is greatly appreciated.

Thanks,
Kenny

  

Hi,

Try psych:::theFunctionIWant, does this find the function?

cheers,
Paul

--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] Missing functions

[Kenny Shen]

hi paul,

i tried loading the package psych again and:

 library(psych)
Warning messages:
1: Display list redraw incomplete
2: Display list redraw incomplete
3: Display list redraw incomplete

typing library(psych) after that just brings me to an empty 

then with psych:::function,

Error: package 'psych' does not have a name space

is there a way to perhaps clean up and reinstall the packages?

thanks,
kenny

On Thu, Oct 1, 2009 at 3:54 PM, Paul Hiemstra p.hiems...@geo.uu.nl wrote:

 Kenny Shen wrote:

 Hi all,

 I'm new to R and have been working hard to get familiarized with it. A
 problem I'm facing now is that having installed some packages (psych,
 doBy),
 I can't seem to access the functions even through there was no error
 messages when I load them using library(). I get an error telling me the
 function doesn't exist. But when I ran e.g. library(help = psych), the
 function I want was missing.

 I did find that when I load other packages, there will be some
 initialisation messages, but loading psych and doBy just brings up the
 prompt again with no output.

 Any help is greatly appreciated.

 Thanks,
 Kenny



 Hi,

 Try psych:::theFunctionIWant, does this find the function?

 cheers,
 Paul

 --
 Drs. Paul Hiemstra
 Department of Physical Geography
 Faculty of Geosciences
 University of Utrecht
 Heidelberglaan 2
 P.O. Box 80.115
 3508 TC Utrecht
 Phone:  +3130 274 3113 Mon-Tue
 Phone:  +3130 253 5773 Wed-Fri
 http://intamap.geo.uu.nl/~paul http://intamap.geo.uu.nl/%7Epaul




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A mental model is good. I change mine all the time.

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Re: [R] Missing functions

[joris meys]

Hi Kenny,

what version of R are you using?

To clean up, try remove.packages
(http://stat.ethz.ch/R-manual/R-patched/library/utils/html/remove.packages.html)

On Thu, Oct 1, 2009 at 10:43 AM, Kenny Shen little...@gmail.com wrote:
 hi joris,

 i installed them using install.packages('psych') from within R

 i tried loading and this is what i got:

 library(psych)
 Warning messages:
 1: Display list redraw incomplete
 2: Display list redraw incomplete
 3: Display list redraw incomplete

 and also:

 psych:::describe(lvs_m1)
 Error: package 'psych' does not have a name space

 is there a way to clean up and reinstall the packages?

 thanks,
 Kenny

 On Thu, Oct 1, 2009 at 4:02 PM, joris meys jorism...@gmail.com wrote:

 Hi,

 It installed perfectly for me, both packages. the command library
 (help = psych) works too. What did you do exactly to install it? If
 you look in the list of loaded packages in the console, are they shown
 there?

 kind regards
 Joris

 On Thu, Oct 1, 2009 at 7:44 AM, Kenny Shen little...@gmail.com wrote:
  Hi all,
 
  I'm new to R and have been working hard to get familiarized with it. A
  problem I'm facing now is that having installed some packages (psych,
  doBy),
  I can't seem to access the functions even through there was no error
  messages when I load them using library(). I get an error telling me the
  function doesn't exist. But when I ran e.g. library(help = psych), the
  function I want was missing.
 
  I did find that when I load other packages, there will be some
  initialisation messages, but loading psych and doBy just brings up the
  prompt again with no output.
 
  Any help is greatly appreciated.
 
  Thanks,
  Kenny
 
  --
  -
  A mental model is good. I change mine all the time.
 
         [[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.
 



 --
 -
 A mental model is good. I change mine all the time.


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Re: [R] Missing functions

[Kenny Shen]

hi joris,

I'm using:

R version 2.8.1 (2008-12-22)

I'll give the remove a try and then do another install. hope that'll resolve
the issue.

thanks for your advice!


kenny

On Thu, Oct 1, 2009 at 4:51 PM, joris meys jorism...@gmail.com wrote:

 Hi Kenny,

 what version of R are you using?

 To clean up, try remove.packages
 (
 http://stat.ethz.ch/R-manual/R-patched/library/utils/html/remove.packages.html
 )

 On Thu, Oct 1, 2009 at 10:43 AM, Kenny Shen little...@gmail.com wrote:
  hi joris,
 
  i installed them using install.packages('psych') from within R
 
  i tried loading and this is what i got:
 
  library(psych)
  Warning messages:
  1: Display list redraw incomplete
  2: Display list redraw incomplete
  3: Display list redraw incomplete
 
  and also:
 
  psych:::describe(lvs_m1)
  Error: package 'psych' does not have a name space
 
  is there a way to clean up and reinstall the packages?
 
  thanks,
  Kenny
 
  On Thu, Oct 1, 2009 at 4:02 PM, joris meys jorism...@gmail.com wrote:
 
  Hi,
 
  It installed perfectly for me, both packages. the command library
  (help = psych) works too. What did you do exactly to install it? If
  you look in the list of loaded packages in the console, are they shown
  there?
 
  kind regards
  Joris
 
  On Thu, Oct 1, 2009 at 7:44 AM, Kenny Shen little...@gmail.com wrote:
   Hi all,
  
   I'm new to R and have been working hard to get familiarized with it. A
   problem I'm facing now is that having installed some packages (psych,
   doBy),
   I can't seem to access the functions even through there was no error
   messages when I load them using library(). I get an error telling me
 the
   function doesn't exist. But when I ran e.g. library(help = psych), the
   function I want was missing.
  
   I did find that when I load other packages, there will be some
   initialisation messages, but loading psych and doBy just brings up the
   prompt again with no output.
  
   Any help is greatly appreciated.
  
   Thanks,
   Kenny
  
   --
   -
   A mental model is good. I change mine all the time.
  
  [[alternative HTML version deleted]]
  
   __
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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.
  
 
 
 
  --
  -
  A mental model is good. I change mine all the time.
 




-- 
-
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Re: [R] Missing functions

[Kenny Shen]

Hi joris,

following your  link to the uninstall, then reinstall packages did the
trick.

thanks!

kenny

On Thu, Oct 1, 2009 at 4:55 PM, Kenny Shen little...@gmail.com wrote:

 hi joris,

 I'm using:

 R version 2.8.1 (2008-12-22)

 I'll give the remove a try and then do another install. hope that'll
 resolve the issue.

 thanks for your advice!


 kenny


 On Thu, Oct 1, 2009 at 4:51 PM, joris meys jorism...@gmail.com wrote:

 Hi Kenny,

 what version of R are you using?

 To clean up, try remove.packages
 (
 http://stat.ethz.ch/R-manual/R-patched/library/utils/html/remove.packages.html
 )

 On Thu, Oct 1, 2009 at 10:43 AM, Kenny Shen little...@gmail.com wrote:
  hi joris,
 
  i installed them using install.packages('psych') from within R
 
  i tried loading and this is what i got:
 
  library(psych)
  Warning messages:
  1: Display list redraw incomplete
  2: Display list redraw incomplete
  3: Display list redraw incomplete
 
  and also:
 
  psych:::describe(lvs_m1)
  Error: package 'psych' does not have a name space
 
  is there a way to clean up and reinstall the packages?
 
  thanks,
  Kenny
 
  On Thu, Oct 1, 2009 at 4:02 PM, joris meys jorism...@gmail.com wrote:
 
  Hi,
 
  It installed perfectly for me, both packages. the command library
  (help = psych) works too. What did you do exactly to install it? If
  you look in the list of loaded packages in the console, are they shown
  there?
 
  kind regards
  Joris
 
  On Thu, Oct 1, 2009 at 7:44 AM, Kenny Shen little...@gmail.com
 wrote:
   Hi all,
  
   I'm new to R and have been working hard to get familiarized with it.
 A
   problem I'm facing now is that having installed some packages (psych,
   doBy),
   I can't seem to access the functions even through there was no error
   messages when I load them using library(). I get an error telling me
 the
   function doesn't exist. But when I ran e.g. library(help = psych),
 the
   function I want was missing.
  
   I did find that when I load other packages, there will be some
   initialisation messages, but loading psych and doBy just brings up
 the
   prompt again with no output.
  
   Any help is greatly appreciated.
  
   Thanks,
   Kenny
  
   --
   -
   A mental model is good. I change mine all the time.
  
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   __
   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.
  
 
 
 
  --
  -
  A mental model is good. I change mine all the time.
 




 --
 -
 A mental model is good. I change mine all the time.




-- 
-
A mental model is good. I change mine all the time.

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Re: [R] Missing functions

[Paul Hiemstra]

Hi,

Look at remove.packages().

Paul

Kenny Shen wrote:

hi paul,

i tried loading the package psych again and:

 library(psych)
Warning messages:
1: Display list redraw incomplete
2: Display list redraw incomplete
3: Display list redraw incomplete

typing library(psych) after that just brings me to an empty 

then with psych:::function,

Error: package 'psych' does not have a name space

is there a way to perhaps clean up and reinstall the packages?

thanks,
kenny

On Thu, Oct 1, 2009 at 3:54 PM, Paul Hiemstra p.hiems...@geo.uu.nl 
mailto:p.hiems...@geo.uu.nl wrote:


Kenny Shen wrote:

Hi all,

I'm new to R and have been working hard to get familiarized
with it. A
problem I'm facing now is that having installed some packages
(psych, doBy),
I can't seem to access the functions even through there was no
error
messages when I load them using library(). I get an error
telling me the
function doesn't exist. But when I ran e.g. library(help =
psych), the
function I want was missing.

I did find that when I load other packages, there will be some
initialisation messages, but loading psych and doBy just
brings up the
prompt again with no output.

Any help is greatly appreciated.

Thanks,
Kenny

 


Hi,

Try psych:::theFunctionIWant, does this find the function?

cheers,
Paul

-- 
Drs. Paul Hiemstra

Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul http://intamap.geo.uu.nl/%7Epaul




--
-
A mental model is good. I change mine all the time.



--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

__
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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] Missing functions

[Kenny Shen]

Yes Paul,

that resolved the issue for me.

Thanks again!

On Thu, Oct 1, 2009 at 5:19 PM, Paul Hiemstra p.hiems...@geo.uu.nl wrote:

 Hi,

 Look at remove.packages().

 Paul

 Kenny Shen wrote:

 hi paul,

 i tried loading the package psych again and:

  library(psych)
 Warning messages:
 1: Display list redraw incomplete
 2: Display list redraw incomplete
 3: Display list redraw incomplete

 typing library(psych) after that just brings me to an empty 

 then with psych:::function,

 Error: package 'psych' does not have a name space

 is there a way to perhaps clean up and reinstall the packages?

 thanks,
 kenny

 On Thu, Oct 1, 2009 at 3:54 PM, Paul Hiemstra p.hiems...@geo.uu.nlmailto:
 p.hiems...@geo.uu.nl wrote:

Kenny Shen wrote:

Hi all,

I'm new to R and have been working hard to get familiarized
with it. A
problem I'm facing now is that having installed some packages
(psych, doBy),
I can't seem to access the functions even through there was no
error
messages when I load them using library(). I get an error
telling me the
function doesn't exist. But when I ran e.g. library(help =
psych), the
function I want was missing.

I did find that when I load other packages, there will be some
initialisation messages, but loading psych and doBy just
brings up the
prompt again with no output.

Any help is greatly appreciated.

Thanks,
Kenny


Hi,

Try psych:::theFunctionIWant, does this find the function?

cheers,
Paul

--Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul http://intamap.geo.uu.nl/%7Epaul 
 http://intamap.geo.uu.nl/%7Epaul




 --
 -
 A mental model is good. I change mine all the time.



 --
 Drs. Paul Hiemstra
 Department of Physical Geography
 Faculty of Geosciences
 University of Utrecht
 Heidelberglaan 2
 P.O. Box 80.115
 3508 TC Utrecht
 Phone:  +3130 274 3113 Mon-Tue
 Phone:  +3130 253 5773 Wed-Fri
 http://intamap.geo.uu.nl/~paul http://intamap.geo.uu.nl/%7Epaul




-- 
-
A mental model is good. I change mine all the time.

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

Re: [R] aproximate a titration kurve to the measure data.

[bartjoosen]

Hi,

This should be possible, even with automatic EP detection.
Can you give use some example titration data, or the used matlab code?

If you want some introduction papers to R, take a look at the documents at
CRAN (CRAN  other)

Bart



awayguy wrote:
 
 Halo
 
 i'm studying chemistry, today we made an experiment and i have to draw a
 titration kurve for my mess data. we can do it on a mm paper, or we can
 also use a programe. people from chemistry recomend R
 last year i studied civil eng. and we used Matlab, as I see, R ist very
 similar to it, but its got other comands.
 But i think R would be a good help for some exercises.
 
 so my main question is: i have some measurement data from my titration,
 and I want aproximate a kurve to this data. is it possible to do it with
 R?
 
 a titration kurve looks like this:
 
  http://www.nabble.com/file/p25685986/acetic-acid-titration-curve.png 
 
 hope you can help me, and yes when its possible, if you know something
 like a tutorial then i would be glad if you could post it.
 
 with regards
 

-- 
View this message in context: 
http://www.nabble.com/aproximate-a-titration-kurve-to-the-measure-data.-tp25685986p25695773.html
Sent from the R help mailing list archive at Nabble.com.

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

[R] pass ... to multiple sub-functions

[baptiste auguie]

Dear list,

I know I have seen this discussed before but I haven't been successful
in searching for ellipsis, dots, ... in the archives. I would
like to filter ... arguments according to their name, and dispatch
them to two sub-functions, say fun1 and fun2. I looked at lm() but it
seemed more complicated than I need as it modifies the calling
function among other things. What is the best approach for this? My
current version presented below seems very awkward.

Best regards,

baptiste

sessionInfo()
R version 2.9.2 (2009-08-24)
i386-apple-darwin8.11.1

fun1 - function(col, row){
  print(col)
  print(row)
}

fun2 - function(x){
  print(x)
}

foo - function(..., lty=1){

  dots - list(...)

  cl - match.call()

  col - eval.parent(cl$col)
  row - eval.parent(cl$row)

  params.fun1 -  c(col, row)

  removed - na.omit(match(names(cl), params.fun1))
  # index whichever arguments were passed to fun1

  fun1(col, row)

  fun2(dots[seq_along(dots)[-removed]])

}

foo()
foo(col=1)
foo(col=1, row=1, g=2, test = abc)

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Re: [R] How to use Subpopulation data?

[KABELI MEFANE]

Dear Helpers
 
I have a sample frame and i have sampled from it using three methods and now i 
want to calculate the statistics but i only get the population parameters.
 
H - matrix(rnorm(100, mean=5, sd=5000))
sampleframe=data.frame(type=c(rep(H,100)),value=c(H))
sampleframe
 
str=strata(sampleframe,c(type),size=c(20,), method=srswor)
sample.strat-getdata(sampleframe,str)
sample.strat
length(H)
i get: 
 
length(H)
[1] 100

Desire to get:
length(H)
[1] 20
 
Best Regards


 
 


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

Re: [R] aproximate a titration kurve to the measure data.

[Bernardo Rangel Tura]

On Wed, 2009-09-30 at 10:55 -0700, awayguy wrote:
 Halo
 
 i'm studying chemistry, today we made an experiment and i have to draw a
 titration kurve for my mess data. we can do it on a mm paper, or we can also
 use a programe. people from chemistry recomend R
 last year i studied civil eng. and we used Matlab, as I see, R ist very
 similar to it, but its got other comands.
 But i think R would be a good help for some exercises.
 
 so my main question is: i have some measurement data from my titration, and
 I want aproximate a kurve to this data. is it possible to do it with R?
 
 a titration kurve looks like this:
 
 http://www.nabble.com/file/p25685986/acetic-acid-titration-curve.png 
 
 hope you can help me, and yes when its possible, if you know something like
 a tutorial then i would be glad if you could post it.
 
 with regards

Hi,

I think do you need use drc package:

drc: Analysis of dose-response curves
Analysis of one or multiple curves with focus on concentration-response,
dose-response and time-response curves used, for example in biology,
environmental sciences, medicine, pharmacology, toxicology.

-- 
Bernardo Rangel Tura, M.D,MPH,Ph.D
National Institute of Cardiology
Brazil

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Re: [R] How to use Subpopulation data?

[Bernardo Rangel Tura]

On Thu, 2009-10-01 at 10:06 +, KABELI MEFANE wrote:
 Dear Helpers
 
 I have a sample frame and i have sampled from it using three methods and now 
 i want to calculate the statistics but i only get the population parameters.
 
 H - matrix(rnorm(100, mean=5, sd=5000))
 sampleframe=data.frame(type=c(rep(H,100)),value=c(H))
 sampleframe
 
 str=strata(sampleframe,c(type),size=c(20,), method=srswor)

Try using

str=strata(sampleframe,c(type),size=20, method=srswor)

or better

str - strata(sampleframe,c(type),size=20, method=srswor)

-- 
Bernardo Rangel Tura, M.D,MPH,Ph.D
National Institute of Cardiology
Brazil

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

Re: [R] Compress (gzip) a pdf device - [ ] Message is from an unknown sender

[Daniele Amberti]

By now It seems nobody have idea.

zz - gzfile(C:/gzpdftest.gz, wb)
pdf(file = zz)
plot(USArrests)
dev.off()
close(zz)

produce a file named 3 without any extension in my working directory.

Also I don't have any news on how to gzip the pdf afterward (without using an 
external executable).

Daniele


From: Rainer M Krug [mailto:r.m.k...@gmail.com]
Sent: 30 September 2009 10:26
To: Daniele Amberti
Cc: r-help@r-project.org
Subject: Re: [R] Compress (gzip) a pdf device - [ ] Message is from an unknown 
sender


2009/9/30 Daniele Amberti 
daniele.ambe...@ors.itmailto:daniele.ambe...@ors.it
I have not found an easy way to compress a file on filesystem.
Especially I'd like to compress a pdf from pdf() function/device. Is it 
possible to compress It on the flight?
I'd like to do something like:
pdf(gzipconnection())
dev.off()

I guess this boils down to a question I asked some time ago concerning getting 
the filename of a pdf() device, as I wanted to create a compressed pdf from the 
uncompressed pdf created by R (not zipping the pdf).
It does not seem to be possible, at least I did not get any response which I 
could use to implement my idea (create my dev.off(), which calls dev.off() and 
afterwards compresses the pdf by using the file name).

If you find a solution, please let me know.

Cheers,

Rainer
If It is not possible, how can I create a gzip with the pdf?

Thanks
Daniele A.








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Re: [R] How to use Subpopulation data?

[KABELI MEFANE]

Thanks
 
i know, i was just simplying since i have a bigger set,
 
But the problem is not that.The problem is i have a sampled data and i need to 
use the results but when i only get the population results. How do i get the 
legnths,summary,etc of my sampled data not the population? 

--- On Thu, 1/10/09, Bernardo Rangel Tura t...@centroin.com.br wrote:


From: Bernardo Rangel Tura t...@centroin.com.br
Subject: Re: [R] How to use Subpopulation data?
To: KABELI MEFANE kabelimef...@yahoo.co.uk
Cc: R-help@r-project.org
Date: Thursday, 1 October, 2009, 11:24 AM


On Thu, 2009-10-01 at 10:06 +, KABELI MEFANE wrote:
 Dear Helpers
 
 I have a sample frame and i have sampled from it using three methods and now 
 i want to calculate the statistics but i only get the population parameters.
 
 H - matrix(rnorm(100, mean=5, sd=5000))
 sampleframe=data.frame(type=c(rep(H,100)),value=c(H))
 sampleframe
 
 str=strata(sampleframe,c(type),size=c(20,), method=srswor)

Try using

str=strata(sampleframe,c(type),size=20, method=srswor)

or better

str - strata(sampleframe,c(type),size=20, method=srswor)

-- 
Bernardo Rangel Tura, M.D,MPH,Ph.D
National Institute of Cardiology
Brazil




  
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[R] set package: more information about syntax

[Jarek Jasiewicz]

Dear All!

I have a few question about proper syntax for fuzzy rules in sets 
package (there is only little help about it):


1) how to use negation (NOT) operator there is only OR (||) in example 
it is NOT, !!, !. I also assume that AND is 

2) where it can be set. For example:

area %is NOT% large
area %is% NOT large
area %is% !large
etc...

3) how brackets works (as in typical logical operation, are allowed - 
some expert system do not allow use brackets)

Is proper following syntax?

(slope %is% flat  elevation %is% is high) || area %is% large, form 
%is% plateau


Where I can find more information about syntax rules used in that 
(fantastic!) package, except in Generalised and Customisable Sets in R 
where is nothing about rules. Maybe rules comes from other, more general 
rule syntax, if yes,I would be grateful for the source


thanks and greetings
Jarek

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[R] question

[hassan paylakhi]

hi
I am going to crazy.I want to use beadarray package in R, but I cant.
 when I want install it, I encounter to this message Loading required
package: hwriter
Loading required package: sma
Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc
= lib.loc) :
  'sma' is not a valid installed package
I cant find sma and hwriter packages, it seems that they are not anymore.
could you help me plz?

thanks in advance
Paylakhi

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[R] Nested Anova and type II sum of square

[Olga Ivanikova]

Dear R-users,
I’d like to make a nested anova on my data, and since I’m discovering both 
R and statistic, I’d like to be sure that I’m not doing something stupid.
Here is my data: I’ve measured some variable responses (Y, for example leaf 
size) for different plants grown on three differing conditions (A, B and C). 
These plants come from two different species (sp1 and sp2) and within each 
species, two to three varieties were tested (var1 and var2 within sp1 and var3 
to var5 within sp2). Finally I’ve got of course three replicates for each 
condition*plant combinations and I’ve got another factor (month) that 
corresponds to the “block” effect. Thus, my data looks like that:
 
month-c(jun,aug,nov,mar,sep,dec,mar,apr,jul,feb,apr,aug,feb,jun,jul,mar,sep,dec,mar,aug,oct,may,aug,dec,feb,may,nov,feb,apr,oct,may,jul,oct,feb,jun,aug,mar,jun,sep,mar,jun,jul,may,sep,nov)
condition-c(rep(A,15),rep(B,15),rep(C,15))
species-c(rep(sp1,6),rep(sp2,9),rep(sp1,6),rep(sp2,9),rep(sp1,6),rep(sp2,9))
variety-c(rep(var1,3),rep(var2,3),rep(var3,3),rep(var4,3),rep(var5,3),rep(var1,3),rep(var2,3),rep(var3,3),rep(var4,3),rep(var5,3),rep(var1,3),rep(var2,3),rep(var3,3),rep(var4,3),rep(var5,3))
leafsize-c(12.952971,14.183247,14.894708,12.623053,11.053027,14.062297,5.974159,5.273493,7.450258,6.030390,6.412735,6.867507,6.227527,7.153695,6.414014,19.856307,21.966194,21.445263,18.100480,17.887656,17.90,11.355896,12.246672,11.462910,12.484537,11.742058,11.937823,16.838480,15.412491,17.789735,11.660008,12.355745,12.963518,10.629601,11.781656,10.693390,5.637602,6.181518,6.853488,8.136201,9.224135,8.309939,10.938328,11.070514,10.965592)
exple-data.frame(cbind(month,condition,species,variety,leafsize))
exple[,5]-leafsize
exple
 
I’d like to estimate the effects of these different factors (condition, 
species, variety within species, interaction between condition*species, 
interaction between condition*variety within species and finally month) on my 
variable response, that is to say :
Y=condition + species + variety(species) + condition*species + condition* 
variety(species) + month + residual
The anova I wrote is the following:
anova(lm(leafsize~condition*(species/variety)+month,data=exple))
I’ve noticed that, depending on the order of my factors in my formula, the 
anova result varies, for example:
anova(lm(leafsize~month+condition*(species/variety),data=exple))
gives slightly different results. If I understood well, this is because anova() 
calculate type 1 sum of square. Thus, I would like to calculate type II, and I 
tried Anova() within car package:
library(car)
Anova( lm(leafsize~month+condition*(species/variety),data=exple))
I get the following error :
“One or more terms aliased in model”.
While if I remove the nested factor, the anova with type II works, for example:
Anova( lm(leafsize~month+condition*variety,data=exple))
 
My questions are:
1-      Is my nested anova model pertinent (ie does it actually estimate 
the effect of the factors as I hope it does?)
2-      Why can’t I realize my nested anova with type II sum of square?
 
I apologize if my knowledge of statistics is so weak that I’ve make or ask 
something stupid…
Many thanks in advance for time and consideration.
Olga


  
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[R] debugging S4 methods

[sebastian mueller]

Hi all,

Does anyone know how to debug S4 methods? In my case I want to find an
error in the specc-function of the kernlab-package.
As this seems to be a S4-method the normal S3 debugging can't be
applied apparently (e.g. debug(s3function.someclass)).

So in my case

 debug(specc:kernlab)
seems only to debug the generic-function:

 specc:kernlab
function (x, ...)
standardGeneric(specc)
environment: 0x9088080

which doesn't help me. Does anyone know how to debug the real-code?

Thanks for your help!
Sebastian

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Re: [R] debugging S4 methods

[Duncan Murdoch]

On 01/10/2009 7:02 AM, sebastian mueller wrote:

Hi all,

Does anyone know how to debug S4 methods? In my case I want to find an
error in the specc-function of the kernlab-package.
As this seems to be a S4-method the normal S3 debugging can't be
applied apparently (e.g. debug(s3function.someclass)).

So in my case


debug(specc:kernlab)

seems only to debug the generic-function:


specc:kernlab

function (x, ...)
standardGeneric(specc)
environment: 0x9088080

which doesn't help me. Does anyone know how to debug the real-code?


You can insert a call to browser() if you want to modify the source.  If 
you'd rather not do that, you can use trace() to set a breakpoint in it.
The new setBreakpoint() function in R 2.10.0 will also work, if you 
install the package from source with the R_KEEP_PKG_SOURCE=yes 
environment variable set.  It allows you to set a breakpoint at a 
particular line number in the source code.


Duncan Murdoch

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Re: [R] Calculating estimates from a sample

[KABELI MEFANE]

Dear Helpers
 
I have a simulated sample frame and i have sampled from it using three methods 
and now i want to calculate the statistics but i only get the population 
parameters.For example i need to get the summary,length,std.error,etc. this is 
just a simplified example.
 
H - matrix(rnorm(100, mean=5, sd=5000))
sampleframe=data.frame(type=c(rep(H,100)),value=c(H))
sampleframe
 
str=strata(sampleframe,c(type),size=c(20,), method=srswor)
sample.strat-getdata(sampleframe,str)
sample.strat
length(H)
i get: 
 
length(H)
[1] 100

Desire to get:
length(H)
[1] 20
 
Best Regards



  
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Re: [R] How to use Subpopulation data?

[Peter Ehlers]

I assume that you are using package:sampling? (Perhaps it
wouldn't be too much trouble to include that information
with your query.)

Read ?strata and pay attention to the 'Value' section.
This will tell you that the function returns a variable

 ID_unit - the identifier of the selected units

Use this to process your samples; e.g.

 idx - str$ID_unit
 mysample - sampleframe[idx,]

etc.

ps
Another way to see what's in 'str' is to use the str() *function*.

 str(str)

And, as someone will surely mention, would you call your dog 'dog'?
I.e. bad choice of object name.

 -Peter Ehlers


KABELI MEFANE wrote:

Thanks
 
i know, i was just simplying since i have a bigger set,
 
But the problem is not that.The problem is i have a sampled data and i need to use the results but when i only get the population results. How do i get the legnths,summary,etc of my sampled data not the population? 


--- On Thu, 1/10/09, Bernardo Rangel Tura t...@centroin.com.br wrote:


From: Bernardo Rangel Tura t...@centroin.com.br
Subject: Re: [R] How to use Subpopulation data?
To: KABELI MEFANE kabelimef...@yahoo.co.uk
Cc: R-help@r-project.org
Date: Thursday, 1 October, 2009, 11:24 AM


On Thu, 2009-10-01 at 10:06 +, KABELI MEFANE wrote:

Dear Helpers

I have a sample frame and i have sampled from it using three methods and now i 
want to calculate the statistics but i only get the population parameters.

H - matrix(rnorm(100, mean=5, sd=5000))
sampleframe=data.frame(type=c(rep(H,100)),value=c(H))
sampleframe

str=strata(sampleframe,c(type),size=c(20,), method=srswor)


Try using

str=strata(sampleframe,c(type),size=20, method=srswor)

or better

str - strata(sampleframe,c(type),size=20, method=srswor)





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Re: [R] Condition to factor (easy to remember)

[Dieter Menne]

Douglas Bates-2 wrote:
 
 On Wed, Sep 30, 2009 at 2:42 PM, Douglas Bates ba...@stat.wisc.edu
 wrote:
 And besides, Frank Harrell will soon be weighing in to tell you why
 you shouldn't dichotomize in the first place.
 

Subjects in this study received a 20 ml infusion of Kirsch (40%, Swiss
Brand) at t=10 minutes, therefore the second interval should read Prost
instead of Post. Even Frank would admit this is a valid dichotomization.

Dieter



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[R] Huge matrix: allocation works but assignment fails

[Remi]

Hello everyone,

I am working with one big matrix:
w=matrix(0,18000,18000)

on a Linux computer with 16Go of RAM.

I can actually create the matrix, and even access elements:
w[10,10]
0

but if I try to change one element, it fails:
w[10,10]=1
Erreur : impossible d'allouer un vecteur de taille 2531250 Ko
(Failed to allocate a vector of size...)

What can I do? And, maybe even more important, how can one explains such 
a behavior?


Thank you for any help/advice

Rémi Proville.

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[R] GAM question

[Daniel Rabczenko]

Hello evyrone,
I would be grateful if you could help me in (I hope) simple problem.
I fit a gam model (from mgcv package) with several smooth functions .
I don't know how to extract values of just one smooth function. Can you 
please help me in this?

Kind regards,
Daniel Rabczenko

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Re: [R] creating R roll in Centos OS

[Marc Schwartz]

On Oct 1, 2009, at 2:44 AM, Sukhbir Rattan wrote:


Hi

I have Centos Operating System.

I m installing R on it. For this I have to create roll of R.

So, how to create the roll of R, regarding this what to be  
downloaded and

from where?

Plz help.

By
Sukhbir Singh Rattan.



If by roll, you are referring to an RPM, they are available via the  
EPEL, which is a repository that provides RPMs for RHEL and CentOS.  
More information is here:


  https://fedoraproject.org/wiki/EPEL

There are instructions for configuring your system to use the EPEL  
(via 'yum') and how to download and install RPMs from it.


Once you get the EPEL configured on your system, you can install R by  
using:


  sudo yum install R


HTH,

Marc Schwartz

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Re: [R] re ading and analyzing a word document

[David Winsemius]

On Oct 1, 2009, at 12:18 AM, cls59 wrote


PDXRugger wrote:


Considering your instructions:

#Define words to find
to.find - c( 'the', 'is', 'are' ,'dr')
#Read in the file...
file.text - readLines( 'data/letter.txt' )
#Count number of occurnces of deined word in text
line.matches - unlist( lapply( to.find, grep, x =  
unlist(file.text[2]) )

)

Result:

line.matches

[1] 1 1 1

This is not right of course as there are actually four words and  
secondly

becasue the searched words appear multiple times.




The example I gave was only meant to identify those lines on which  
matches
occurred. Using x = unlist(file.text[2]) only feeds one line of the  
file
into the matching routine so the result indicates that all the  
matches were

on line 1-- the only line present for searching.

If you want to count the individual occurrences of the words on each  
line,

you may need to look at using a function such as gregexpr. grep only
indicates if a match or matches is present in a line of text--  
gregexpr

indicates at which positions those matches occur in the line.

However, you may be getting to the point with this where R is no  
longer an
appropriate tool for this job. R is amazingly flexible it is  
possible that
it can give you what you want. However, R was not designed to  
perform text
processing-- Perl comes to mind as being a language that was  
explicitly

designed to perform these sorts of operations.


Perhaps you should use the R-search facilities for such questions:

http://finzi.psych.upenn.edu/R/library/tau/html/00Index.html
http://finzi.psych.upenn.edu/views/NaturalLanguageProcessing.html
http://www.jstatsoft.org/v25/i05/

R may not have been designed for text processing, but it is rather  
amazing how much has been done.





--

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] question

[David Winsemius]

On Oct 1, 2009, at 4:33 AM, hassan paylakhi wrote:


hi
I am going to crazy.I want to use beadarray package in R, but I cant.
when I want install it, I encounter to this message Loading required
package: hwriter
Loading required package: sma
Error in library(pkg, character.only = TRUE, logical.return = TRUE,  
lib.loc

= lib.loc) :
 'sma' is not a valid installed package
I cant find sma and hwriter packages, it seems that they are not  
anymore.

could you help me plz?


Binary versions of sma and hwriter can be found on your CRAN repository.

How they get installed may depend to some extent on which repository  
you use and your OS (which you have not offered).


?install.packages

--

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] re ad.delim skips first column (why?)

[HBaize]

I can't determine what is going on in you example, but my approach would be
to read the text file into a text editor that will display hidden characters
(tab, etc.) so you can see the pattern. It could be that there is an extra
tab in some locations. You could then use the editor's replace function to
remove the control characters that are causing the problem. 


Giovanni Dall'Olio wrote:
 
 Hi people,
 I have a text file like this one posted:
 
 
 When I use read.delim (or any read function) on it, R skips the first
 column, and I don' understand why.
 
 
 

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Re: [R] How to use Subpopulation data?

[KABELI MEFANE]

Thanks 
 
i was not aware of str, i have a very large code since i am new to r.
I forgot to mention that the package is sampling. Actually i have this 
simulated code:
 
n - c(100,400,1000,1500,2000)
x - c(2,3,3,3,5)
y - c(7,7,9,10,10)
s - function(mn, mx, n) {sample(mn:mx, n, replace=TRUE)}
rating=unlist(mapply(s, x, y, n))

Hypermarket - matrix(rnorm(100, mean=5, sd=5000))
Supermarket - matrix(rnorm(400, mean=34000, sd=3000))
Minimarket  - matrix(rnorm(1000, mean=1,sd=2000))
Cornershop  - matrix(rnorm(1500, mean=2500, sd=500))
Spazashop   - matrix(rnorm(2000, mean=1000, sd=250))
dat=data.frame(type=c(rep(Hypermarket,100), rep(Supermarket,400),
rep(Minimarket,1000),rep(Cornershop,1500), rep(Spazashop,2000)),
value=c(Hypermarket, Supermarket, Minimarket, Cornershop,Spazashop))
 
##sample frame
sampleframe=data.frame(type=c(rep(Hypermarket,100), rep(Supermarket,400),
rep(Minimarket,1000),rep(Cornershop,1500), rep(Spazashop,2000)),
value=c(Hypermarket, Supermarket, Minimarket, Cornershop,Spazashop),
ratings =cbind(rating))
 
## package sampling
 
stra=strata(sampleframe,c(type,value,rating),size=c(20,80,200,300,400),
method=srswor)
sample.strat-getdata(sampleframe,stra)

sample.strat

now i want to find different estimates from sample.strat
 
Help appreciated.





  
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[R] Help for 3D Plotting Data on 'Irregular' Grid

[Lorenzo Isella]

Dear All,
Here is what I am trying to achieve: I would like to plot some data in 3D.
Usually, one has a matrix of the kind

y_1(x_1) , y_1(x_2).y_1(x_i)
y_2(x_1) , y_2(x_2).y_2(x_i)
...
y_n(x_1) , y_n(x_2)..y_n(x_i)


where e.g. y_2(x_1) is the value of y at time 2 at point x_1 (see that 
the grid in x is the same for the y values at all times).
Instead, in my case, the quantity y is observed at each time on a 
different grid in x; in other words not only do I have a different 
number of observations (y values) at each time, but I also have 
observations taken on a a different x grid each time.
As a matter of fact, it is as if I had a set of independent 
observations, for each of which I can create effortlessly a 2D plot, 
that I want to stitch together into a 3D plot.
I have no idea of how to achieve that. Examples I have found with 
lattice or scatterplot3D all assume a regular grid like the one I 
described above.

Any help is really appreciated.
Many thanks

Lorenzo

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[R] Treating variables as symbols

[ZeMajik]

Hey,
I'm trying to find how to perform operations with a variable treated as a
symbol.
For, an extremely simple, example I want to integrate a*x with respect to x
and I want to find the indefinite integral of this, (a*x^2/2), or the
definite integral with some interval for x.

Another example of such a use would be to create a function
y-function(x) {a*x}
and by typig y(2) I would get the result 2*a

Is there a way to treat variables as merely symbols?
Any help much appreciated

-M

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Re: [R] Treating variables as symbols

[Jorge Ivan Velez]

Hi Zemajik,
Try this:

 y - function(a) paste(a, '*x', sep=)
 y(2)
[1] 2*x

Also, take a look at the Ryacas package.

HTH,
Jorge


On Thu, Oct 1, 2009 at 9:46 AM, ZeMajik  wrote:

 Hey,
 I'm trying to find how to perform operations with a variable treated as a
 symbol.
 For, an extremely simple, example I want to integrate a*x with respect to x
 and I want to find the indefinite integral of this, (a*x^2/2), or the
 definite integral with some interval for x.

 Another example of such a use would be to create a function
 y-function(x) {a*x}
 and by typig y(2) I would get the result 2*a

 Is there a way to treat variables as merely symbols?
 Any help much appreciated

 -M

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Re: [R] pass ... to multiple sub-functions

[Peter Ruckdeschel]

Dear Baptiste,

 I know I have seen this discussed before but I haven't been successful
 in searching for ellipsis, dots, ... in the archives. I would
 like to filter ... arguments according to their name, and dispatch
 them to two sub-functions, say fun1 and fun2. I looked at lm() but it
 seemed more complicated than I need as it modifies the calling
 function among other things. What is the best approach for this? My
 current version presented below seems very awkward.
 
 Best regards,
 
 baptiste
 
 sessionInfo()
 R version 2.9.2 (2009-08-24)
 i386-apple-darwin8.11.1
 
 fun1 - function(col, row){
   print(col)
   print(row)
 }
 
 fun2 - function(x){
   print(x)
 }
 
 foo - function(..., lty=1){
 
   dots - list(...)
 
   cl - match.call()
 
   col - eval.parent(cl$col)
   row - eval.parent(cl$row)
 
   params.fun1 -  c(col, row)
 
   removed - na.omit(match(names(cl), params.fun1))
   # index whichever arguments were passed to fun1
 
   fun1(col, row)
 
   fun2(dots[seq_along(dots)[-removed]])

Instead of passing all remaining arguments stacked into
one list (= 1 argument x to function fun2) you might want
to be able to retain them as distinct arguments;

so you might want to replace fun2 by

  fun2.a - function(...) print(list(...))

and the call to fun2 in foo by

  do.call(fun2.a, dots.remaining)

where, sticking to your code, you could obtain
dots.remaining as

   removed - na.omit(match(names(cl), params.fun1))
   dots.remaining - dots[seq_along(dots)[-removed]]

or by

   removed - c(lty,params.fun1)
   ## I assume you do not want to pass on argument lty...
   dots.remaining - cl[-1] ### remove the function name
   dots.remaining - dots.remaining[! names(dots.remaining)
 %in% removed]

Best, Peter

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Re: [R] Treating variables as symbols

[Henrique Dallazuanna]

Try this:

y - function(a)
substitute(a * x, list(a = a))

On Thu, Oct 1, 2009 at 10:46 AM, ZeMajik zema...@gmail.com wrote:
 Hey,
 I'm trying to find how to perform operations with a variable treated as a
 symbol.
 For, an extremely simple, example I want to integrate a*x with respect to x
 and I want to find the indefinite integral of this, (a*x^2/2), or the
 definite integral with some interval for x.

 Another example of such a use would be to create a function
 y-function(x) {a*x}
 and by typig y(2) I would get the result 2*a

 Is there a way to treat variables as merely symbols?
 Any help much appreciated

 -M

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-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O

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Re: [R] set package: more information about syntax

[Jarek Jasiewicz]

Dear All!

I have a few question about proper syntax for fuzzy rules in sets 
package (there is only little help about it):


1) how to use negation (NOT) operator there is only OR (||) in example 
it is NOT, !!, !. I also assume that AND is 

2) where it can be set. For example:

area %is NOT% large
area %is% NOT large
area %is% !large
etc...

3) how brackets works (as in typical logical operation, are allowed - 
some expert system do not allow use brackets)

Is proper following syntax?

(slope %is% flat  elevation %is% is high) || area %is% large, form 
%is% plateau


Where I can find more information about syntax rules used in that 
(fantastic!) package, except in Generalised and Customisable Sets in 
R where is nothing about rules. Maybe rules comes from other, more 
general rule syntax, if yes,I would be grateful for the source


thanks and greetings
Jarek

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I add this question because I cannot form any proper rule when I use ! 
(negation) or I use more complex rules rules with brackets I always receive:


Error in gset_charfun(x) : Argument 'x' must be a generalized set.

in fact function fuzzy_inferance works only if I use maximum two 
arguments rules without brackets.


Jarek

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[R] typo in install manual

[Daniel Dekic]

http://cran.r-project.org/doc/manuals/R-admin.pdf
page 8 and page 13

testInstallPackages(recommended)
- testInstalledPackages(recommended)

same problem in .html


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CTM Clinical Trials Management GmbH
Mariahilferstraße 47/III/3/5
1060 Vienna, Austria

Phone: +43 (0) 1 / 585 80 63
Fax:   +43 (0) 1 / 585 79 67
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[R] (no subject)

[Jens Oehlschlägel]

Hi,
Does anyone know where the following package is available: 

Holleczek B, Gondos A, Brenner H.
PeriodR - an R package to calculate long term survival estimates using period 
analysis.
Methods of Information in Medicine 2009; 48: 123-128.

Thanks
Jens Oehlschlägel
-- 
GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT!

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[R] Getting formatted character from call

[Iago Mosqueira]

Hi,

I need to get a character vector from an object of class call. But
using as.character() returns something based on the internal structure
of the object, and not, as I would like, some akin to the output of
show() on a call object.

Any idea on how to obtain the same output returned by show?

Thanks,


Iago Mosqueira

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Re: [R] question

[Martin Morgan]

hassan paylakhi wrote:
 hi
 I am going to crazy.I want to use beadarray package in R, but I cant.
  when I want install it, I encounter to this message Loading required
 package: hwriter
 Loading required package: sma
 Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc
 = lib.loc) :
   'sma' is not a valid installed package
 I cant find sma and hwriter packages, it seems that they are not anymore.
 could you help me plz?

Hi Hassan --

The sma author no longer wishes to maintain this package, and beadarray
depends on sma. The workaround is to manually install sma from its
archive: download

  http://cran.fhcrc.org/src/contrib/Archive/sma/sma_0.5.15.tar.gz

and install.packages(sma_0.5.15.tar.gz, repos=NULL).

beadarray is a Bioconductor packages, so please follow up on the
Bioconductor mailing list

  http://bioconductor.org/docs/mailList.html

Martin

 
 thanks in advance
 Paylakhi
 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
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[R] The problem of readLines

[Tammy Ma]

Dear R-users,


I use readLines to read data, but when processing the large data set, there 
are few files which can not be readed in:

48: In readLines(name_c[i]) ... :
  incomplete final line found on 'C:/Documents and Settings/lma/My 
Documents/habitdata/244052900243997/calllog/calllog_log-20050505T121611.txt'
...



Whats the problem about this?

Regards,
Tammy


  
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[R] Maintaining sort order when transpose

[Dry, Jonathan R]

Hi all - I have a data frame and have sorted it by a particular column, with 
rownames set to a different variable.  I wish to transpose this data frame, 
naming columns by the rowname variable but maintaining the sorted order through 
to the order of columns in my transposed table, however use of  t(DF) results 
in a transposed table where the columns are ordered alphabetically by the 
original rownames.  Any ideas how I can get around this?

--
AstraZeneca UK Limited is a company incorporated in Engl...{{dropped:21}}

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[R] Color of graph

[Ashta]

I am trying to plot a line graph for 3 or more regression lines

abline(m1)
abline(m2)
abline(m3)

Can I change the color of each line? if so how?

Thanks in advance
Ashta

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Re: [R] Evaluating expresssions as parameter values

[Erich Neuwirth]

Let us walk through my problem step by step:

1.
print(xyplot(yield ~ variety | site,groups=year,data=barley))
2.
print(xyplot(as.formula(yield ~ variety |  
site),groups=year,data=barley))


The above two statements work, the next one does not work

3.
print(xyplot(as.formula(yield ~ variety | site),groups=parse 
(text=year),data=barley))


But the following one works

4.
arglist-list(as.formula(yield ~ variety | site),groups=parse 
(text=year),data=barley)

print(do.call(xyplot,arglist))


why does 3 not work and 4 work?
Is there a way of coercing the string year into something which can  
directly be used in

3 as the argument used with groups= ???


The next one

print(xyplot(as.formula(yield ~ variety | site),groups=eval(parse 
(text=year)),data=barley))


also works, but in this case the groups expression is evaluated before  
xyplot is applied,

and I think this is bad style (at least, if not worse).


On Sep 30, 2009, at 1:20 PM, Deepayan Sarkar wrote:


xyplot(Sepal.Length ~ Petal.Length, iris, groups = ~Species)


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Re: [R] The problem of readLines

[Henrique Dallazuanna]

From the help page for readLines:

 If the final line is incomplete (no final EOL marker) the
 behaviour depends on whether the connection is blocking or not.
 For a non-blocking text-mode connection the incomplete line is
 pushed back, silently.  For all other connections the line will be
 accepted, with a warning. 

You can disable the warning with;

readLines('your_file', warn = FALSE)

On Thu, Oct 1, 2009 at 9:39 AM, Tammy Ma metal_lical...@live.com wrote:

 Dear R-users,


 I use readLines to read data, but when processing the large data set, there 
 are few files which can not be readed in:

 48: In readLines(name_c[i]) ... :
  incomplete final line found on 'C:/Documents and Settings/lma/My 
 Documents/habitdata/244052900243997/calllog/calllog_log-20050505T121611.txt'
 ...



 Whats the problem about this?

 Regards,
 Tammy



 _
 More than messages–check out the rest of the Windows Live™.
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-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O

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Re: [R] (no subject)

[Jorge Ivan Velez]

Hi Jens,
Take a look at http://www.krebsregister.saarland.de/improve/periodR_en.html

HTH,
Jorge


2009/10/1 Jens Oehlschlägel 

 Hi,
 Does anyone know where the following package is available:

 Holleczek B, Gondos A, Brenner H.
 PeriodR - an R package to calculate long term survival estimates using
 period analysis.
 Methods of Information in Medicine 2009; 48: 123-128.

 Thanks
 Jens Oehlschlägel
 --
 GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT!

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Re: [R] Getting formatted character from call

[Gabor Grothendieck]

Please read the last line to every message to r-help.  There is no
reproducible code in your post.

Anyways, it works for me:

 class(call(round, 1.5))
[1] call

 as.character(call(round, 1.5))
[1] round 1.5

 format(call(round, 1.5))
[1] round(1.5)


On Thu, Oct 1, 2009 at 7:58 AM, Iago Mosqueira iago.mosque...@gmail.com wrote:
 Hi,

 I need to get a character vector from an object of class call. But
 using as.character() returns something based on the internal structure
 of the object, and not, as I would like, some akin to the output of
 show() on a call object.

 Any idea on how to obtain the same output returned by show?

 Thanks,


 Iago Mosqueira

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Re: [R] (no subject)

[Andris Jankevics]

Actually that is stated in paper abstract:

http://www.krebsregister.saarland.de/improve/periodR_en.html

Andris

2009/10/1 Jens Oehlschlägel oehl_l...@gmx.de:
 Hi,
 Does anyone know where the following package is available:

 Holleczek B, Gondos A, Brenner H.
 PeriodR - an R package to calculate long term survival estimates using period 
 analysis.
 Methods of Information in Medicine 2009; 48: 123-128.

 Thanks
 Jens Oehlschlägel
 --
 GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT!

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 https://stat.ethz.ch/mailman/listinfo/r-help
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Re: [R] Color of graph

[Henrique Dallazuanna]

Try this:

abline(m1, col = 'blue')
abline(m1, col = 'red')
abline(m1, col = 'green')

On Thu, Oct 1, 2009 at 10:57 AM, Ashta sewa...@gmail.com wrote:
 I am trying to plot a line graph for 3 or more regression lines

 abline(m1)
 abline(m2)
 abline(m3)

 Can I change the color of each line? if so how?

 Thanks in advance
 Ashta

        [[alternative HTML version deleted]]

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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.




-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O

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Re: [R] Color of graph

[smu]

abline(m1, col=red)

regards,
 Stefan

On Thu, Oct 01, 2009 at 09:57:11AM -0400, Ashta wrote:
 I am trying to plot a line graph for 3 or more regression lines
 
 abline(m1)
 abline(m2)
 abline(m3)
 
 Can I change the color of each line? if so how?
 
 Thanks in advance
 Ashta
 
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Re: [R] Color of graph

[Charlie Sharpsteen]

On Thu, Oct 1, 2009 at 6:57 AM, Ashta sewa...@gmail.com wrote:

 I am trying to plot a line graph for 3 or more regression lines

 abline(m1)
 abline(m2)
 abline(m3)

 Can I change the color of each line? if so how?

 Thanks in advance
 Ashta


Try passing the 'col' parameter to abline:

abline( m1, col = 'red' )
ablime( m1, col = 'blue' )
abline( m1, col = 'purple' )

See ?par for other plot parameters like col that can be set this way. ?rgb
gives an example of setting color by RGB value. Other specifications such as
HSV are possible. The colors() function will show a list of all built colors
that may be specified using a string such as 'red' . ?rainbow will show
information concerning built in functions for generating color palettes. The
RColorBrewer package also contains some great palettes.

Also, a help search such as:

??'colors'

Will turn up all kinds of other functions that may deal with setting or
creating colors.

Hope this helps!

-Charlie

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Re: [R] Color of graph

[Jorge Ivan Velez]

Hi Ashta,
See the ... in ?abline.

HTH,
Jorge


On Thu, Oct 1, 2009 at 9:57 AM, Ashta  wrote:

 I am trying to plot a line graph for 3 or more regression lines

 abline(m1)
 abline(m2)
 abline(m3)

 Can I change the color of each line? if so how?

 Thanks in advance
 Ashta

[[alternative HTML version deleted]]

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 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
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Re: [R] re ading and analyzing a word document

[spencerg]

library(sos)
tm - findFn('text mining')
tm


 This produced 15 matches, which you could also find using 
RSiteSearch('text mining', 'function').  The difference is that 
findFn{sos} displays the results in a table sorted to place the package 
with the most matches first.  In this case, there is actually a Text 
Mining Package called tm.  summary(tm) says these 15 matches are in 
11 packages.  The first of the 11 is FactoMineR. 



 Hope this helps. 
 Spencer Graves



David Winsemius wrote:


On Oct 1, 2009, at 12:18 AM, cls59 wrote


PDXRugger wrote:


Considering your instructions:

#Define words to find
to.find - c( 'the', 'is', 'are' ,'dr')
#Read in the file...
file.text - readLines( 'data/letter.txt' )
#Count number of occurnces of deined word in text
line.matches - unlist( lapply( to.find, grep, x = 
unlist(file.text[2]) )

)

Result:

line.matches

[1] 1 1 1

This is not right of course as there are actually four words and 
secondly

becasue the searched words appear multiple times.




The example I gave was only meant to identify those lines on which 
matches

occurred. Using x = unlist(file.text[2]) only feeds one line of the file
into the matching routine so the result indicates that all the 
matches were

on line 1-- the only line present for searching.

If you want to count the individual occurrences of the words on each 
line,

you may need to look at using a function such as gregexpr. grep only
indicates if a match or matches is present in a line of text-- gregexpr
indicates at which positions those matches occur in the line.

However, you may be getting to the point with this where R is no 
longer an
appropriate tool for this job. R is amazingly flexible it is possible 
that
it can give you what you want. However, R was not designed to perform 
text

processing-- Perl comes to mind as being a language that was explicitly
designed to perform these sorts of operations.


Perhaps you should use the R-search facilities for such questions:

http://finzi.psych.upenn.edu/R/library/tau/html/00Index.html
http://finzi.psych.upenn.edu/views/NaturalLanguageProcessing.html
http://www.jstatsoft.org/v25/i05/

R may not have been designed for text processing, but it is rather 
amazing how much has been done.







--
Spencer Graves, PE, PhD
President and Chief Operating Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph:  408-655-4567

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[R] package:snow, timeOut for makeSOCKcluster()

[Markus Loecher]

Dear snow users,
is there any way to specify a max time after which makeSOCKcluster() stops
trying to create socket connections and gives up/returns ?
In my current setup (MAC OSX 10.5.8, R version 2.9) I have to force quit R
if the host specified in makeSOCKcluster() either does not exist or does not
respond.
On Linux, I can at least manually interrupt the function via Ctrl-C

Any help would be greatly appreciated,

Thanks,

Markus

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Re: [R] GAM question

[joris meys]

Hi Daniel,

I presume you mean coefficients by values. Try ?gamObject and read the
info in the help file. A GAM object (returned by the function gam() )
contains an element coefficients that is easily accessible. That one
contains all estimated coefficients, including those for the smooth
functions.

On Thu, Oct 1, 2009 at 1:49 PM, Daniel Rabczenko dan...@medstat.waw.pl wrote:
 Hello evyrone,
 I would be grateful if you could help me in (I hope) simple problem.
 I fit a gam model (from mgcv package) with several smooth functions .
 I don't know how to extract values of just one smooth function. Can you
 please help me in this?
 Kind regards,
 Daniel Rabczenko

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Re: [R] typo in install manual

[Duncan Murdoch]

On 10/1/2009 5:37 AM, Daniel Dekic wrote:

http://cran.r-project.org/doc/manuals/R-admin.pdf
page 8 and page 13

testInstallPackages(recommended)
- testInstalledPackages(recommended)



Thanks, will fix.


Duncan Murdoch

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[R] cdplot????

[kayj]

I am having difficulties interpreting a cdplot, I have a binary variable y
that I want to cdplot against a continuous variable x,below is the R command

 cdplot(y~x, data=mydata)

you get a plot with a dark shaded area and a light shaded area. what do
these areas mean? and how to interpret the plot?

you help is greatly appreciated


-- 
View this message in context: 
http://www.nabble.com/cdplot-tp25696905p25696905.html
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Re: [R] Maintaining sort order when transpose

[Kevin Wright]

An example would be helpful, but if I understand correctly, can't you do
something like

TDF=t(DF)
TDF=TDF[,rownames(DF)]

Kevin Wright


On Thu, Oct 1, 2009 at 9:04 AM, Dry, Jonathan R 
jonathan@astrazeneca.com wrote:

 Hi all - I have a data frame and have sorted it by a particular column,
 with rownames set to a different variable.  I wish to transpose this data
 frame, naming columns by the rowname variable but maintaining the sorted
 order through to the order of columns in my transposed table, however use of
  t(DF) results in a transposed table where the columns are ordered
 alphabetically by the original rownames.  Any ideas how I can get around
 this?

 --
 AstraZeneca UK Limited is a company incorporated in Engl...{{dropped:21}}

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Re: [R] Debug

[Tammy Ma]

From: metal_lical...@live.com
To: r-help@r-project.org
Subject: Debug
Date: Thu, 1 Oct 2009 15:21:42 +0300








Hi, R-Users,'
I have written a programe to process the bunch of files in one folder.
 But there is a error came out;
How can I know which file returns error when being processed?
I have tested the first 1-10th files, no any problem. But the problems is I 
have more than 500 files. How can I know which file has the problem?

Thanks 
Tammy
  
Invite your mail contacts to join your friends list with Windows Live Spaces. 
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Re: [R] Treating variables as symbols

[ZeMajik]

Thanks guys, Ryacas is pretty much what I'm looking for!However, I can't
seem to get it to work properly.

For example:

 yacas(Integrate(x) x)
Error in parse(text = text, srcfile = NULL) :
  unexpected numeric constant in / (^ (x ,2 2

Same thing with expressions such as yacas(x*x)

However

 yacas(2*2)
expression(4)

So it seems there is a successful connection between yacas and R.
I didn't find any info on the problem by googling it unfortunately! Any
ideas what it might be?

Thanks again,
M

On Thu, Oct 1, 2009 at 3:50 PM, Jorge Ivan Velez
jorgeivanve...@gmail.comwrote:

 Hi Zemajik,
 Try this:

  y - function(a) paste(a, '*x', sep=)
  y(2)
 [1] 2*x

 Also, take a look at the Ryacas package.

 HTH,
 Jorge


 On Thu, Oct 1, 2009 at 9:46 AM, ZeMajik  wrote:

 Hey,
 I'm trying to find how to perform operations with a variable treated as a
 symbol.
 For, an extremely simple, example I want to integrate a*x with respect to
 x
 and I want to find the indefinite integral of this, (a*x^2/2), or the
 definite integral with some interval for x.

 Another example of such a use would be to create a function
 y-function(x) {a*x}
 and by typig y(2) I would get the result 2*a

 Is there a way to treat variables as merely symbols?
 Any help much appreciated

 -M

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Re: [R] Compress (gzip) a pdf device - [ ] Message is from an unknown sender

[Ista Zahn]

I guess I don't understand what your're trying to do. gzip-ing a file
from within R is easy enough:

pdf(file=CompressMe.pdf)
plot(rnorm(100))
dev.off()
system(gzip CompressMe.pdf)

I think you want something more complicated, but I'm not sure what.

-Ista

On Thu, Oct 1, 2009 at 6:41 AM, Daniele Amberti daniele.ambe...@ors.it wrote:
 By now It seems nobody have idea.

 zz - gzfile(C:/gzpdftest.gz, wb)
 pdf(file = zz)
 plot(USArrests)
 dev.off()
 close(zz)

 produce a file named 3 without any extension in my working directory.

 Also I don't have any news on how to gzip the pdf afterward (without using an 
 external executable).

 Daniele


 From: Rainer M Krug [mailto:r.m.k...@gmail.com]
 Sent: 30 September 2009 10:26
 To: Daniele Amberti
 Cc: r-help@r-project.org
 Subject: Re: [R] Compress (gzip) a pdf device - [ ] Message is from an 
 unknown sender


 2009/9/30 Daniele Amberti 
 daniele.ambe...@ors.itmailto:daniele.ambe...@ors.it
 I have not found an easy way to compress a file on filesystem.
 Especially I'd like to compress a pdf from pdf() function/device. Is it 
 possible to compress It on the flight?
 I'd like to do something like:
 pdf(gzipconnection())
 dev.off()

 I guess this boils down to a question I asked some time ago concerning 
 getting the filename of a pdf() device, as I wanted to create a compressed 
 pdf from the uncompressed pdf created by R (not zipping the pdf).
 It does not seem to be possible, at least I did not get any response which I 
 could use to implement my idea (create my dev.off(), which calls dev.off() 
 and afterwards compresses the pdf by using the file name).

 If you find a solution, please let me know.

 Cheers,

 Rainer
 If It is not possible, how can I create a gzip with the pdf?

 Thanks
 Daniele A.



 



 
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Re: [R] Treating variables as symbols

[Gabor Grothendieck]

Read the troubleshooting section on the home page: http://ryacas.googlecode.com
Note, in particular, that it currently only works with an older
version of the XML package.

 library(Ryacas)
 packageDescription(XML)$Version
[1] 1.96-0
 x - Sym(x)
 Integrate(x*x, x)
[1] Starting Yacas!
expression(x^3/3)


On Thu, Oct 1, 2009 at 11:08 AM, ZeMajik zema...@gmail.com wrote:
 Thanks guys, Ryacas is pretty much what I'm looking for!However, I can't
 seem to get it to work properly.

 For example:

 yacas(Integrate(x) x)
 Error in parse(text = text, srcfile = NULL) :
  unexpected numeric constant in / (^ (x ,2 2

 Same thing with expressions such as yacas(x*x)

 However

 yacas(2*2)
 expression(4)

 So it seems there is a successful connection between yacas and R.
 I didn't find any info on the problem by googling it unfortunately! Any
 ideas what it might be?

 Thanks again,
 M

 On Thu, Oct 1, 2009 at 3:50 PM, Jorge Ivan Velez
 jorgeivanve...@gmail.comwrote:

 Hi Zemajik,
 Try this:

  y - function(a) paste(a, '*x', sep=)
  y(2)
 [1] 2*x

 Also, take a look at the Ryacas package.

 HTH,
 Jorge


 On Thu, Oct 1, 2009 at 9:46 AM, ZeMajik  wrote:

 Hey,
 I'm trying to find how to perform operations with a variable treated as a
 symbol.
 For, an extremely simple, example I want to integrate a*x with respect to
 x
 and I want to find the indefinite integral of this, (a*x^2/2), or the
 definite integral with some interval for x.

 Another example of such a use would be to create a function
 y-function(x) {a*x}
 and by typig y(2) I would get the result 2*a

 Is there a way to treat variables as merely symbols?
 Any help much appreciated

 -M

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Re: [R] Debug

[Steve Lianoglou]

Hi Tammy,

On Oct 1, 2009, at 11:04 AM, Tammy Ma wrote:


Hi, R-Users,'
I have written a programe to process the bunch of files in one folder.
But there is a error came out;
How can I know which file returns error when being processed?
I have tested the first 1-10th files, no any problem. But the  
problems is I have more than 500 files. How can I know which file  
has the problem?


See ?tryCatch

Here's some (untested) code that should give you an idea of what to do:

which.files - dir(path=/directory/with/files, full.names=TRUE)
for (file.name in which.files) {
  result - tryCatch(process.file(file.name), error=function(err) err)
  if (inherits(result, 'error')) {
cat(File, file.name, is hosed\n)
  }
}

This assumes you have a function called 'process.file' that does what  
you want. If the function throws an error, it will be caught and  
stored in the result variable. In this case, the file.name will be  
written to your workspace.


Instead of just printing to your workspace, you could consider storing  
the bad file names in a list and post-process later.


Hope that helps,
-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
  |  Memorial Sloan-Kettering Cancer Center
  |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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Re: [R] Compress (gzip) a pdf device - [ ] Message is from an unknown sender

[Daniele Amberti]

system() invokes the OS command specified by command, in the example you gave 
it means that gzip is installed and (assuming Windows OS) it is in your search 
path.

I'd like to have a solution that do not use external programs.

Thanks
Daniele

-Original Message-
From: Ista Zahn [mailto:istaz...@gmail.com]
Sent: 01 October 2009 17:11
To: Daniele Amberti
Cc: r-help@r-project.org; Rainer M Krug
Subject: Re: [R] Compress (gzip) a pdf device - [ ] Message is from an unknown 
sender

I guess I don't understand what your're trying to do. gzip-ing a file
from within R is easy enough:

pdf(file=CompressMe.pdf)
plot(rnorm(100))
dev.off()
system(gzip CompressMe.pdf)

I think you want something more complicated, but I'm not sure what.

-Ista

On Thu, Oct 1, 2009 at 6:41 AM, Daniele Amberti daniele.ambe...@ors.it wrote:
 By now It seems nobody have idea.

 zz - gzfile(C:/gzpdftest.gz, wb)
 pdf(file = zz)
 plot(USArrests)
 dev.off()
 close(zz)

 produce a file named 3 without any extension in my working directory.

 Also I don't have any news on how to gzip the pdf afterward (without using an 
 external executable).

 Daniele


 From: Rainer M Krug [mailto:r.m.k...@gmail.com]
 Sent: 30 September 2009 10:26
 To: Daniele Amberti
 Cc: r-help@r-project.org
 Subject: Re: [R] Compress (gzip) a pdf device - [ ] Message is from an 
 unknown sender


 2009/9/30 Daniele Amberti 
 daniele.ambe...@ors.itmailto:daniele.ambe...@ors.it
 I have not found an easy way to compress a file on filesystem.
 Especially I'd like to compress a pdf from pdf() function/device. Is it 
 possible to compress It on the flight?
 I'd like to do something like:
 pdf(gzipconnection())
 dev.off()

 I guess this boils down to a question I asked some time ago concerning 
 getting the filename of a pdf() device, as I wanted to create a compressed 
 pdf from the uncompressed pdf created by R (not zipping the pdf).
 It does not seem to be possible, at least I did not get any response which I 
 could use to implement my idea (create my dev.off(), which calls dev.off() 
 and afterwards compresses the pdf by using the file name).

 If you find a solution, please let me know.

 Cheers,

 Rainer
 If It is not possible, how can I create a gzip with the pdf?

 Thanks
 Daniele A.



 



 
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http://yourpsyche.org

ORS Srl

Via Agostino Morando 1/3 12060 Roddi (Cn) - Italy
Tel. +39 0173 620211
Fax. +39 0173 620299 / +39 0173 433111
Web Site www.ors.it


Qualsiasi utilizzo non autorizzato del presente messaggio e dei suoi allegati è 
vietato e potrebbe costituire reato.
Se lei avesse ricevuto erroneamente questo messaggio, Le saremmo grati se 
provvedesse alla distruzione dello stesso
e degli eventuali allegati.
Opinioni, conclusioni o altre informazioni riportate nella e-mail, che non 
siano relative alle attività e/o
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Re: [R] Unable to install lme4

[jamesmcc]

I am baffled by this as well. I'm having the same issue. Using suse linux,
with 64 bit R2.8.1.

Thanks, 

james



Zege, Andrew wrote:
 
 I am unable to install package lme4, after several attempts to do so using
 various repository URLs.
 Just to make sure everything works fine with proxy, connection, etc, I
 installed ggplot2 and it worked fine.
 
 I am using command
 
 install.packages(lme4, lib=/myRlibs),
 
 optionally using contrib argument with different URLs.
 
 Error message the I get is
 
 Warning message;
 In install.packages(lme4, lib=/myRlibs)
  package 'lme4' is not available
 
 
 Some other details, not sure how relevant are:
 
 getOption(repos) returns http://lib.stat.cmu.edu/R/CRAN;
 
 I tried setting contrib to various other URL, such as 
 http://cran.mtu.edu/src/contrib; or Berkeley URL, but with no success.
 Actually, when I did available.packages() on this repos, I didn't see lme4
 in the package indices.
 My machine has x86_64bit RedHat Linux.
 
 Would appreciate any tips or directions,
 
 Thanks
 Andre
 
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Re: [R] cdplot????

[Achim Zeileis]

On Thu, 1 Oct 2009, kayj wrote:


I am having difficulties interpreting a cdplot, I have a binary variable y
that I want to cdplot against a continuous variable x,below is the R command

cdplot(y~x, data=mydata)

you get a plot with a dark shaded area and a light shaded area. what do
these areas mean? and how to interpret the plot?

you help is greatly appreciated


See ?cdplot. It's a display that graphs (an approximation of) P(y | x) 
against x. The areas above and below the line are simply shaded in 
different levels of gray.


To obtain P(y | x), the idea is to use

  f(y | x) = f(x | y) * f(x)/f(y)

where for f(x) and f(x | y) are obtained by (unconditional and 
conditional, respectively) kernel density smoothers from density().

f(y) is simply the unconditional proportion of the category y.

hth,
Z



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Re: [R] The problem of readLines

[Tammy Ma]

I have a more problem: Because there are few files which can't be read into R 
completely, so on the following subsequence programme, I use write.table, which 
creates the NA files for those incomplete files autimatically. 
I don't want those NA files. How can I do the following:
whenever readLines can't completely read one file, then autimatically remove it 
from my dataset?

Thanks.
Tammy





 From: www...@gmail.com
 Date: Thu, 1 Oct 2009 11:06:35 -0300
 Subject: Re: [R] The problem of readLines
 To: metal_lical...@live.com
 CC: r-help@r-project.org
 
 From the help page for readLines:
 
  If the final line is incomplete (no final EOL marker) the
  behaviour depends on whether the connection is blocking or not.
  For a non-blocking text-mode connection the incomplete line is
  pushed back, silently.  For all other connections the line will be
  accepted, with a warning. 
 
 You can disable the warning with;
 
 readLines('your_file', warn = FALSE)
 
 On Thu, Oct 1, 2009 at 9:39 AM, Tammy Ma metal_lical...@live.com wrote:
 
  Dear R-users,
 
 
  I use readLines to read data, but when processing the large data set, 
  there are few files which can not be readed in:
 
  48: In readLines(name_c[i]) ... :
   incomplete final line found on 'C:/Documents and Settings/lma/My 
  Documents/habitdata/244052900243997/calllog/calllog_log-20050505T121611.txt'
  ...
 
 
 
  Whats the problem about this?
 
  Regards,
  Tammy
 
 
 
  _
  More than messages–check out the rest of the Windows Live™.
  http://www.microsoft.com/windows/windowslive/
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 -- 
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 Curitiba-Paraná-Brasil
 25° 25' 40 S 49° 16' 22 O
  
_
Drag n’ drop—Get easy photo sharing with Windows Live™ Photos.

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[R] Can You Recommend Books for Linear Mixed Models in R

[Pat Schmitz]

All

I have been looking into the books on performing statistics in R, in
particular I am interested in General Linear Mixed Models, for Randomized
Complete Block Design Experiments

The list I have come away with so far is:

Mixed Effects Models in S and S-plus by Pinheiro (2002)
http://www.amazon.com/Mixed-Effects-Models-S-S-Plus/dp/0387989579/ref=wl_itt_dp_o?ie=UTF8coliid=I1WXOBRXMHD30Vcolid=38N475HUK5VPJ

Linear Models with R by Faraway (2004)
http://www.amazon.com/Linear-Models-Texts-Statistical-Science/dp/1584884258/ref=sr_1_1?ie=UTF8s=booksqid=1254412763sr=1-1

Extending the Linear Model with R by Faraway (2005)
http://www.amazon.com/Extending-Linear-Model-Generalized-Nonparametric/dp/158488424X/ref=pd_sim_b_7

Which of these would you as statisticians, researchers, scientists most
recommend?
Are there others in this realm of statistics that I have not discovered,
that might be more effective?

Thanks
Pat



-- 
Patrick Schmitz
Graduate Student
Plant Biology
1206 West Gregory Drive
RM 1500

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[R] Using optimize with array variables

[Vik]

Hello,

I am trying to figure out how to use optimize() with array variables
as inputs. I have a for loop in the function definition:

SS - function(int,slo,x,y){
for(i in 1:length(x)) ((int+slo*x[i])-y[i])^2-squares[i]
sum(squares)-sum_squares
output_txt = c (The sum of squares is, sum_squares)
print(output_txt, quote=FALSE)}

Even assuming I make x and y single-integer variables, for example:

optimize(SS, c(0,1), tol = 0.0001, x=1, y=1, slo=1)

I get the error:

Error in optimize(SS, c(0, 1), tol = 1e-04, x = 1, y = 1, slo = 1) :
  invalid function value in 'optimize'

Not sure what that means. This also happens when x and y are defined
as arrays. Does optimize require me to input values for all variables
that are not being optimized (i.e. for n-1 of the inputs)? Why am I
getting an error.

I am new to R and under pressure to get some calculations done for my
work. I'd appreciate an answer to the specific question - and I fully
understand that I need to read up on R basics in more depth, which I
am doing as best I can while trying to get this work done. Thanks!

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Re: [R] pass ... to multiple sub-functions

[baptiste auguie]

2009/10/1 Peter Ruckdeschel peter.ruckdesc...@web.de:


   removed - c(lty,params.fun1)
   ## I assume you do not want to pass on argument lty...
   dots.remaining - cl[-1] ### remove the function name
   dots.remaining - dots.remaining[! names(dots.remaining)
 %in% removed]

 Best, Peter



Thank you, that's very helpful.

I vaguely remember there was also a package to deal with this problem
(among other things). Have I dreamed that?

Best,

baptiste

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Re: [R] Help me replace a for loop with an apply function

[jim holtman]

Will this work:

 x - read.table(textConnection(   day user_id
+ 2008/11/012001
+ 2008/11/012002
+ 2008/11/012003
+ 2008/11/012004
+ 2008/11/012005
+ 2008/11/022001
+ 2008/11/022005
+ 2008/11/032001
+ 2008/11/032003
+ 2008/11/032004
+ 2008/11/032005
+ 2008/11/042001
+ 2008/11/042003
+ 2008/11/042004
+ 2008/11/042005), header=TRUE)
 closeAllConnections()
 # convert to Date
 x$day - as.Date(x$day, format=%Y/%m/%d)
 # split by user and then look for contiguous days
 contig - sapply(split(x$day, x$user_id), function(.days){
+ .diff - cumsum(c(TRUE, diff(.days) != 1))
+ max(table(.diff))
+ })
 contig
2001 2002 2003 2004 2005
   41224




On Thu, Oct 1, 2009 at 11:29 AM, gd047 gd...@mineknowledge.com wrote:

 ...if that is possible

 My task is to find the longest streak of continuous days a user participated
 in a game.

 Instead of writing an sql function, I chose to use the R's rle function, to
 get the longest streaks and then update my db table with the results.

 The (attached) dataframe is something like this:

    day         user_id
 2008/11/01    2001
 2008/11/01    2002
 2008/11/01    2003
 2008/11/01    2004
 2008/11/01    2005
 2008/11/02    2001
 2008/11/02    2005
 2008/11/03    2001
 2008/11/03    2003
 2008/11/03    2004
 2008/11/03    2005
 2008/11/04    2001
 2008/11/04    2003
 2008/11/04    2004
 2008/11/04    2005



 --- R code follows
 --


 # turn it to a contingency table
 my_table - table(user_id, day)

 # get the streaks
 rle_table - apply(my_table,1,rle)

 # verify the longest streak of 1s for user 2001
 # as.vector(tapply(rle_table$'2001'$lengths, rle_table$'2001'$values,
 max)[1])

 # loop to get the results
 # initiate results matrix
 res-matrix(nrow=dim(my_table)[1], ncol=2)

 for (i in 1:dim(my_table)[1]) {
 string - paste(as.vector(tapply(rle_table$', rownames(my_table)[i],
 '$lengths, rle_table$', rownames(my_table)[i], '$values, max)['1']),
 sep=)
 res[i,]-c(as.integer(rownames(my_table)[i]) , eval(parse(text=string)))
 }


 
 --- end of R code

 Unfortunately this for loop takes too long and I' wondering if there is a
 way to produce the res matrix using a function from the apply family.

 Thank you in advance
 --
 View this message in context: 
 http://www.nabble.com/Help-me-replace-a-for-loop-with-an-%22apply%22-function-tp25696937p25696937.html
 Sent from the R help mailing list archive at Nabble.com.

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+1 513 646 9390

What is the problem that you are trying to solve?

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[R] Normal distribution

[Noela Sánchez]

Hi,

I am dealing with how to check in R if some data that I have belongs to a
normal distribution or not. I am not interested in obtaining the
theoreticall frequencies. I am only interested in determing if (by means of
a test as Kolmogorov, or whatever), if my data are normal or not.

But I have tried with ks.test() and I have not got it.


-- 
Noela
Grupo de Recursos Marinos y Pesquerías
Universidad de A Coruña

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[R] .Rprofile file

[Data Analytics Corp.]

Hi,

I want to use the .RProfile to set defaults such as text editor.  Is 
this a file I need to create?  Also, where should I put it?  I tend to 
create .RData files for different projects, putting each in a different 
Windows (Vista) folder.  Is one .Rprofile file created  that any  
instance of R can access  (I would imagine so)?


Thanks,

Walt



--


Walter R. Paczkowski, Ph.D.
Data Analytics Corp.
44 Hamilton Lane
Plainsboro, NJ 08536

(V) 609-936-8999
(F) 609-936-3733
w...@dataanalyticscorp.com
www.dataanalyticscorp.com

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Re: [R] Huge matrix: allocation works but assignment fails

[Uwe Ligges]

Remi wrote:

Hello everyone,

I am working with one big matrix:
w=matrix(0,18000,18000)

on a Linux computer with 16Go of RAM.

I can actually create the matrix, and even access elements:
w[10,10]
0

but if I try to change one element, it fails:
w[10,10]=1


In this case your object is copied and you need two times the space for 
your object.


Best,
Uwe Ligges



Erreur : impossible d'allouer un vecteur de taille 2531250 Ko
(Failed to allocate a vector of size...)

What can I do? And, maybe even more important, how can one explains such 
a behavior?


Thank you for any help/advice

Rémi Proville.

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Re: [R] Normal distribution

[Richardson, Patrick]

?shapiro.test


-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of Noela Sánchez
Sent: Thursday, October 01, 2009 12:47 PM
To: r-help@r-project.org
Subject: [R] Normal distribution

Hi,

I am dealing with how to check in R if some data that I have belongs to a 
normal distribution or not. I am not interested in obtaining the theoreticall 
frequencies. I am only interested in determing if (by means of a test as 
Kolmogorov, or whatever), if my data are normal or not.

But I have tried with ks.test() and I have not got it.


--
Noela
Grupo de Recursos Marinos y Pesquerías
Universidad de A Coruña

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[R] Looking for a better way to document my packages

[Steve Lianoglou]

Hi all,

Trying to do what my subject says.

As I'm trying to be better about making packages out of my code, I'd  
like the packages themselves to be better, which means *.Rd- 
documenting my code. The thing is, from years of programming other  
languages prior to landing in the R pond, I've grown accustomed to  
documenting my functions inline. I'm not just used to it, but I like  
it more than having function documentation completely removed from my  
function, code.


So, for example

myNeatFunction - function(arg1, arg2, arg3=NULL, ...) {
  # One liner describing the neat thing this function does.
  #
  # More comments, probably very much what would be in the
  # \description section of the *Rd
  #
  # Parameters
  # --
  # arg1 : some comments
  # arg2 : some comments
  # ... This is essentially the same exact stuff that would
  # be in the \arguments{} section of the *.Rd
  #
  # Returns
  # ---
  # A description of what's returned, let's say this is
  # what you'd find in the \value{} section.
  #
  # Notes
  # -
  # Maybe something like the \details{} section, though this
  # might as well be up in the description section, too.
  # etc.
}

There's essentially a 1-to-1 mapping of the comments I write here and  
what I would write in an *.Rd file, but I'd rather have it written in  
my function definition than an external document.


Are there any tools that help facilitate this? Or are there better  
ways you folks have figured out to do something similar?


I don't need the function comment block to be exactly what I showed  
here, but it's just an example of how I'm currently writing my stuff.  
I'm thinking something like sphinx (http://sphinx.pocoo.org/) from the  
python world would be cool. Perhaps there's a way to make a plugin for  
that to parse R-code. That's more work than I want to bit off right  
now, but if there isn't something useful in R-land already, it might  
be a fun side project.


Just curious,
-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
  |  Memorial Sloan-Kettering Cancer Center
  |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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[R] Revolutions blog: September roundup

[David M Smith]

I write about R every weekday at the Revolutions blog:
http://blog.revolution-computing.com .

In case you missed them, here are some articles from last month of
particular interest to R users.

http://bit.ly/WYAnM shows how to create a URL for a Google Spreadsheet
so you can read the data directly from the cloud in R with read.csv.

http://bit.ly/FuUNw reported on Google's use of R to predict economic
statistics from search activity.

http://bit.ly/10UbHc showed how to use the New York Times' API to mine
articles for word frequency data.

http://bit.ly/VKqSh discussed the similarities between Grand Central
Dispatch for Snow Leopard and parallel processing with foreach.

http://bit.ly/lRbAX announced a new R user group in Madison, Wisconsin.

http://bit.ly/2Ms5nM noted the popular blog flowingdata.com uses R as
the tool of choice for graphics (with touchups by Illustrator).

http://bit.ly/BIU9V remarked on the Flash Mob which has populated
stackoverflow.com with useful answers for many R questions.

http://bit.ly/2cysLh reviews Jeroen Ooms' web-based financial plotting
tool built on R.

http://bit.ly/TcfD1 linked to a script in R for 7 common machine
learning techniques. (And

http://bit.ly/YInMs touched on the distinctions between machine
learning and statistics.)

http://bit.ly/XgBoR linked to an analysis done in R of the
demographics of readers of Hacker News.

http://bit.ly/Eec5z noted that TechCruch Trends is using R for its
analysis of startup activity.

http://bit.ly/akFNd gave tips for adding error bars to barplots with ggplot2.

http://bit.ly/xxBNm showed how to present hierarchical clustering
models as a circular cladogram.

http://bit.ly/iteac gave some tips for getting started with bootstrapping in R.

http://bit.ly/2no2C showed how R is used to analyze milk yields.

http://bit.ly/VC7LE linked to a comprehensive reference to R for Matlab users.

http://bit.ly/1CqP6n gave a practical demonstration of ggplot2's
grammar of graphics concept.

http://bit.ly/tP3Ci is a pictorial story of how one user converted a
workflow based on Perl, Stata and Matlab to one solely based on R.

http://bit.ly/OY2CR reviewed some of the airline performance posters
from this year's Data Expo at the JSM.

Other non-R-specific stories in the last month covered stochastic
psychics (http://bit.ly/BIU9V), identifying individuals in anonymous
data (http://bit.ly/ho0Df), an apology for Turing
(http://bit.ly/QqW29), the Mythbusters' statistical philosophy
(http://bit.ly/f8Nia), the Bulgarian lottery coincidence
(http://bit.ly/Y1gaU), keyboards for pirates (http://bit.ly/t1C7a),
the Netflix prize (http://bit.ly/eS1nb), and which line to choose at
the supermarket (http://bit.ly/nHJkQ).

(I've provided short URLs above because many mailers break the long
direct URLs.)

The R Community Calendar has also been updated at:
http://blog.revolution-computing.com/calendar.html

September was the highest-traffic month yet for the Revolutions blog.
The Bulgarian Lottery article was quoted in the Wall Street Journal,
and the machine learning post was very popular on Hacker News. As
always, thanks for the comments and please keep sending suggestions to
me at da...@revolution-computing.com .

Don't forget you can also follow the blog using an RSS reader like
Google Reader, or by following me on Twitter (I'm @revodavid).

Cheers to all,
# David Smith
--
David M Smith da...@revolution-computing.com
Director of Community, REvolution Computing www.revolution-computing.com
Tel: +1 (206) 577-4778 x3203 (San Francisco, USA)

Check out our upcoming events schedule at www.revolution-computing.com/events

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Re: [R] Huge matrix: allocation works but assignment fails

[Ben Bolker]

 Remi wrote:

 
  (Failed to allocate a vector of size...)
  What can I do? And, maybe even more important, how can one explains such 
  a behavior?

 If your matrices are not sparse, get more memory. If they are,

 help(sparseMatrix,package=Matrix) ?

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Re: [R] Using optimize with array variables

[Charles C. Berry]

On Thu, 1 Oct 2009, Vik wrote:


Hello,

I am trying to figure out how to use optimize() with array variables
as inputs. I have a for loop in the function definition:

SS - function(int,slo,x,y){
for(i in 1:length(x)) ((int+slo*x[i])-y[i])^2-squares[i]
sum(squares)-sum_squares
output_txt = c (The sum of squares is, sum_squares)
print(output_txt, quote=FALSE)}




Try running your code in a clean session. There is an error (and not the 
one you quote below).



After you get rid of that error, try

val - SS ( 0.1, 1, 1, 1 )

then

print( val )

The difficulty optimize is having should be apparent.

In spite of the pressure you are under, you will need to slow down, write 
readable code, and take the time to learn about writing functions in R 
before you can hope to get anywhere with a problem like this.


Read the posting guide. For a problem like this one, the 'Some' mentioned 
below includes many of the people on this list who can provide useful, 
knowledgeable answers:


Some consider it good manners to include a concise signature
specifying affiliation


HTH,

Chuck


p.s. do not use '-' or '-' until you really, really know what it does 
(which means you understand 'scoping')!



Even assuming I make x and y single-integer variables, for example:

optimize(SS, c(0,1), tol = 0.0001, x=1, y=1, slo=1)

I get the error:

Error in optimize(SS, c(0, 1), tol = 1e-04, x = 1, y = 1, slo = 1) :
 invalid function value in 'optimize'

Not sure what that means. This also happens when x and y are defined
as arrays. Does optimize require me to input values for all variables
that are not being optimized (i.e. for n-1 of the inputs)? Why am I
getting an error.

I am new to R and under pressure to get some calculations done for my
work. I'd appreciate an answer to the specific question - and I fully
understand that I need to read up on R basics in more depth, which I
am doing as best I can while trying to get this work done. Thanks!

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu   UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901

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Re: [R] Looking for a better way to document my packages

[baptiste auguie]

Hi,

I know of three options that resemble your query,

- the roxygen package

- a ruby script called weeder by Hadley Wikham

- the inlinedocs package on r-forge

I only ever used roxygen though, so i can't speak for the relative
merits of the others.

HTH,

baptiste


2009/10/1 Steve Lianoglou mailinglist.honey...@gmail.com:
 Hi all,

 Trying to do what my subject says.

 As I'm trying to be better about making packages out of my code, I'd like
 the packages themselves to be better, which means *.Rd-documenting my code.
 The thing is, from years of programming other languages prior to landing in
 the R pond, I've grown accustomed to documenting my functions inline. I'm
 not just used to it, but I like it more than having function documentation
 completely removed from my function, code.

 So, for example

 myNeatFunction - function(arg1, arg2, arg3=NULL, ...) {
  # One liner describing the neat thing this function does.
  #
  # More comments, probably very much what would be in the
  # \description section of the *Rd
  #
  # Parameters
  # --
  # arg1 : some comments
  # arg2 : some comments
  # ... This is essentially the same exact stuff that would
  # be in the \arguments{} section of the *.Rd
  #
  # Returns
  # ---
  # A description of what's returned, let's say this is
  # what you'd find in the \value{} section.
  #
  # Notes
  # -
  # Maybe something like the \details{} section, though this
  # might as well be up in the description section, too.
  # etc.
 }

 There's essentially a 1-to-1 mapping of the comments I write here and what I
 would write in an *.Rd file, but I'd rather have it written in my function
 definition than an external document.

 Are there any tools that help facilitate this? Or are there better ways you
 folks have figured out to do something similar?

 I don't need the function comment block to be exactly what I showed here,
 but it's just an example of how I'm currently writing my stuff. I'm thinking
 something like sphinx (http://sphinx.pocoo.org/) from the python world would
 be cool. Perhaps there's a way to make a plugin for that to parse R-code.
 That's more work than I want to bit off right now, but if there isn't
 something useful in R-land already, it might be a fun side project.

 Just curious,
 -steve

 --
 Steve Lianoglou
 Graduate Student: Computational Systems Biology
  |  Memorial Sloan-Kettering Cancer Center
  |  Weill Medical College of Cornell University
 Contact Info: http://cbio.mskcc.org/~lianos/contact

 __
 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.


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

Re: [R] Unable to install lme4

[jamesmcc]

This is the first time I've encountered R having difficulty with package and
R version compatibility. I cant believe no one has fixed generally so that
your version of R can get the latest package appropriate to that version.
How nice would that be? :)

Anyway, I figured it out for my version (2.8.1). I needed to install Matrix
package first, which was also outdated.

 R CMD INSTALL -l lib Matrix_0.999375-22.tar.gz
 R CMD INSTALL -l lib lme4_0.999375-28.tar.gz

it loads now within R. I haven used it much yet.



jamesmcc wrote:
 
 I am baffled by this as well. I'm having the same issue. Using suse linux,
 with 64 bit R2.8.1.
 
 Thanks, 
 
 james
 
 
 
 Zege, Andrew wrote:
 
 I am unable to install package lme4, after several attempts to do so
 using various repository URLs.
 Just to make sure everything works fine with proxy, connection, etc, I
 installed ggplot2 and it worked fine.
 
 I am using command
 
 install.packages(lme4, lib=/myRlibs),
 
 optionally using contrib argument with different URLs.
 
 Error message the I get is
 
 Warning message;
 In install.packages(lme4, lib=/myRlibs)
  package 'lme4' is not available
 
 
 Some other details, not sure how relevant are:
 
 getOption(repos) returns http://lib.stat.cmu.edu/R/CRAN;
 
 I tried setting contrib to various other URL, such as 
 http://cran.mtu.edu/src/contrib; or Berkeley URL, but with no success.
 Actually, when I did available.packages() on this repos, I didn't see
 lme4 in the package indices.
 My machine has x86_64bit RedHat Linux.
 
 Would appreciate any tips or directions,
 
 Thanks
 Andre
 
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View this message in context: 
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Re: [R] Normal distribution

[Steve Lianoglou]

Hi,

I think you can also use a qq-plot to do the same, no? You won't get a
statistic score + p.value, but perhaps you're more of a visual person?
:-)

-steve

On Thu, Oct 1, 2009 at 12:56 PM, Richardson, Patrick
patrick.richard...@vai.org wrote:
 ?shapiro.test


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
 Behalf Of Noela Sánchez
 Sent: Thursday, October 01, 2009 12:47 PM
 To: r-help@r-project.org
 Subject: [R] Normal distribution

 Hi,

 I am dealing with how to check in R if some data that I have belongs to a 
 normal distribution or not. I am not interested in obtaining the theoreticall 
 frequencies. I am only interested in determing if (by means of a test as 
 Kolmogorov, or whatever), if my data are normal or not.

 But I have tried with ks.test() and I have not got it.


 --
 Noela
 Grupo de Recursos Marinos y Pesquerías
 Universidad de A Coruña

[[alternative HTML version deleted]]

 This email message, including any attachments, is for th...{{dropped:6}}

 __
 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.




-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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Re: [R] Normal distribution

[Richardson, Patrick]

I don't disagree. And to that end one could probably look at the skewness and 
kurtosis values as well. A combination of several techniques would probably be 
a good idea.

Best regards,

Patrick

-Original Message-
From: Steve Lianoglou [mailto:mailinglist.honey...@gmail.com] 
Sent: Thursday, October 01, 2009 1:18 PM
To: Richardson, Patrick
Cc: Noela Sánchez; r-help@r-project.org
Subject: Re: [R] Normal distribution

Hi,

I think you can also use a qq-plot to do the same, no? You won't get a
statistic score + p.value, but perhaps you're more of a visual person?
:-)

-steve

On Thu, Oct 1, 2009 at 12:56 PM, Richardson, Patrick
patrick.richard...@vai.org wrote:
 ?shapiro.test


 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
 Behalf Of Noela Sánchez
 Sent: Thursday, October 01, 2009 12:47 PM
 To: r-help@r-project.org
 Subject: [R] Normal distribution

 Hi,

 I am dealing with how to check in R if some data that I have belongs to a 
 normal distribution or not. I am not interested in obtaining the theoreticall 
 frequencies. I am only interested in determing if (by means of a test as 
 Kolmogorov, or whatever), if my data are normal or not.

 But I have tried with ks.test() and I have not got it.


 --
 Noela
 Grupo de Recursos Marinos y Pesquerías
 Universidad de A Coruña

[[alternative HTML version deleted]]

 This email message, including any attachments, is for ...{{dropped:25}}

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

Re: [R] Looking for a better way to document my packages

[Steve Lianoglou]

Ah, great!

Thanks for the refs, I'll look into them.

-steve

On Thu, Oct 1, 2009 at 1:12 PM, baptiste auguie
baptiste.aug...@googlemail.com wrote:
 Hi,

 I know of three options that resemble your query,

 - the roxygen package

 - a ruby script called weeder by Hadley Wikham

 - the inlinedocs package on r-forge

 I only ever used roxygen though, so i can't speak for the relative
 merits of the others.

 HTH,

 baptiste


 2009/10/1 Steve Lianoglou mailinglist.honey...@gmail.com:
 Hi all,

 Trying to do what my subject says.

 As I'm trying to be better about making packages out of my code, I'd like
 the packages themselves to be better, which means *.Rd-documenting my code.
 The thing is, from years of programming other languages prior to landing in
 the R pond, I've grown accustomed to documenting my functions inline. I'm
 not just used to it, but I like it more than having function documentation
 completely removed from my function, code.

 So, for example

 myNeatFunction - function(arg1, arg2, arg3=NULL, ...) {
  # One liner describing the neat thing this function does.
  #
  # More comments, probably very much what would be in the
  # \description section of the *Rd
  #
  # Parameters
  # --
  # arg1 : some comments
  # arg2 : some comments
  # ... This is essentially the same exact stuff that would
  # be in the \arguments{} section of the *.Rd
  #
  # Returns
  # ---
  # A description of what's returned, let's say this is
  # what you'd find in the \value{} section.
  #
  # Notes
  # -
  # Maybe something like the \details{} section, though this
  # might as well be up in the description section, too.
  # etc.
 }

 There's essentially a 1-to-1 mapping of the comments I write here and what I
 would write in an *.Rd file, but I'd rather have it written in my function
 definition than an external document.

 Are there any tools that help facilitate this? Or are there better ways you
 folks have figured out to do something similar?

 I don't need the function comment block to be exactly what I showed here,
 but it's just an example of how I'm currently writing my stuff. I'm thinking
 something like sphinx (http://sphinx.pocoo.org/) from the python world would
 be cool. Perhaps there's a way to make a plugin for that to parse R-code.
 That's more work than I want to bit off right now, but if there isn't
 something useful in R-land already, it might be a fun side project.

 Just curious,
 -steve

 --
 Steve Lianoglou
 Graduate Student: Computational Systems Biology
  |  Memorial Sloan-Kettering Cancer Center
  |  Weill Medical College of Cornell University
 Contact Info: http://cbio.mskcc.org/~lianos/contact

 __
 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.





-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

__
R-help@r-project.org mailing list
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] launching two RGUI computations from two different Excel workbooks

[Erich Neuwirth]

Please send questions like this to the rcom mailing list.
You can subscribe at rcom.univie.ac.at.


On Sep 28, 2009, at 1:34 PM, sowh...@o2.pl wrote:


Hello,

I have the following problem:

I have excel workbooks connected with R through RExcel package. Data  
are being loaded from excel, then they are processed in R and then  
the results are being put in excel. Everything works fine, except  
the fact that I can't launch two or more excel workbooks (and two or  
more R servers in the background) at the same time.
I have to wait until one computation is finished and then launch  
another one. It would be much easier and quicker for me to launch  
two or more computations at the same time. Is this possible to  
launch two different R servers from Excel?


Regards,

Wojciech Turski

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Re: [R] Normal distribution

[Peter Ehlers]

Noela,

Package nortest has 5 tests of normality.

A word of caution: the wording of your question suggests that
you believe that, if the test you use does not reject the
normality hypothesis, you then have proof that your data come
from a Normal distribution. That's *NOT* true. Normality will
still be an *assumption*, albeit perhaps a reasonable one.
This is particularly important to realize if you have small
samples.

 -Peter Ehlers

Noela Sánchez wrote:

Hi,

I am dealing with how to check in R if some data that I have belongs to a
normal distribution or not. I am not interested in obtaining the
theoreticall frequencies. I am only interested in determing if (by means of
a test as Kolmogorov, or whatever), if my data are normal or not.

But I have tried with ks.test() and I have not got it.






__
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.


__
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.

Re: [R] Normal distribution

[Peter Ehlers]

Another interesting visual technique is given by the
qreference() function in pkg:DAAG. I've used this type
of display effectively with non-stats people as well
as in teaching intro courses in stats.
(I would randomize the location of the actual-data panel
and not use a different colour. The question then is,
can you discern the actual data from the simulated data?)

 -Peter Ehlers

Steve Lianoglou wrote:

Hi,

I think you can also use a qq-plot to do the same, no? You won't get a
statistic score + p.value, but perhaps you're more of a visual person?
:-)

-steve

On Thu, Oct 1, 2009 at 12:56 PM, Richardson, Patrick
patrick.richard...@vai.org wrote:

?shapiro.test


-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of Noela Sánchez
Sent: Thursday, October 01, 2009 12:47 PM
To: r-help@r-project.org
Subject: [R] Normal distribution

Hi,

I am dealing with how to check in R if some data that I have belongs to a 
normal distribution or not. I am not interested in obtaining the theoreticall 
frequencies. I am only interested in determing if (by means of a test as 
Kolmogorov, or whatever), if my data are normal or not.

But I have tried with ks.test() and I have not got it.


--
Noela
Grupo de Recursos Marinos y Pesquerías
Universidad de A Coruña

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[R] caret package for time series applications

[zubin]

Hello, I have some time series applications, where i have a large set of 
X variables (hundreds) and thousands of time data points (sampling every 
minute). 

I like to use the caret package to support the analysis, variable 
selection and model selection.  However, reading the documentation, it 
looks like caret uses resampling methods.  Not sure if these methods 
work with time series, as you need  a block bootstrap or such. 


My question:  Does the caret package support the usage of time series data?

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