Re: [R] problems installing package XML to a computer without an internet connection

2009-01-11 Thread Prof Brian Ripley

On Sun, 11 Jan 2009, Bob Green wrote:


Hello,

I am hoping for some advice regarding how I can install the XML package which 
I require to run package tm.


Normally I would use the install package option, however, I have to install 
the packages to a laptop running XP.


Windows, I presume.


The laptop does not have an internet connection.

Firstly I tried the file -   XML_1.99-0.tar.gz . Below is the error I 
received


What does 'try' mean?  That would work if you used Rcmd INSTALL on it, 
or install.packages(type="source").



Error in gzfile(file, "r") : cannot open the connection
In addition: Warning messages:
1: In zip.unpack(pkg, tmpDir) : error 1 in extracting from zip file
2: In gzfile(file, "r") :
 cannot open compressed file 'XML_1.99-0.tar.gz/DESCRIPTION', probable 
reason 'No such file or directory'


Then I tried XML 1.96-0.zip (from 
http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.7/). Below is the


Why from 2.7?  What version is your R?


error I received


So that worked: it is 'proxy' you are missing.  From the DESCRIPTION 
file


package: tm
Title: Text Mining Package
Version: 0.3-3
Date: 2008-12-20
Author: Ingo Feinerer, with contributions from Christian Buchta, Kurt 
Hornik, David Meyer, and Fridolin Wild

Maintainer: Ingo Feinerer 
Depends: R (>= 2.7.0), filehash, Matrix, methods, Snowball, XML
Imports: proxy
Suggests: Rgraphviz, Rmpi, Rstem (>= 0.3-1), snow

still you may need packages filehash, Matrix, methods, Snowball and 
proxy.


I suggest getting those from bin/windows/contrib/2.7/ on CRAN, and 
installing from the 'Local zip file' menu optipn.



Loading required package: XML
Error in loadNamespace(i, c(lib.loc, .libPaths())) :
 there is no package called 'proxy'
Error: package/namespace load failed for 'tm'

Any suggestions are appreciated,


Read the posting guide, remember to tell us what we asked for 'at a 
minumum' and what you actually did.



Bob

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

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Re: [R] Convert date/time string to date

2009-01-11 Thread Prof Brian Ripley

On Sun, 11 Jan 2009, Heston Capital wrote:


I am new to R and am trying to import a text file that contains
date/time and various fields.  I want to sort this matrix by date and
also perform calculations on the date field (difference between two
dates etc).

The format of the string looks as follows:

x<-c("25/2/2003 0:00:00")

I tried:

as.Date(x,format='%d/%m/%y')
[1] "2020-02-25"

Obviously I am doing something wrong here.  I would like to remove the


You have a 4-figure date, so need %Y not %y.  See ?strptime.


hh:mm:ss from the end of the string if possible.

Thanks for your help, I have been searching for hours and not getting anywhere.

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Brian D. Ripley,  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
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Re: [R] ftp connections for uploading files

2009-01-11 Thread Prof Brian Ripley

On Fri, 9 Jan 2009, Duncan Temple Lang wrote:



Hi Thomas

Rather than getting into the details of libcurl options
which are quite general and very flexible, I thought
it was easier to write an explicit ftpUpload() function
that takes care of the details.

You need a new version of the package (as it contains the function and
a small change to the C code), but I don't have the time to build the Windows 
version for the next few days.


One is on CRANextras now.



The function can be used as

 ftpUpload("path/to/file", "ftp://server/path/to/target/file";,
userpwd = "login:password")

and you can deal with contents in memory too rather than from a file.


HTH,
  D.

Thomas Loridan wrote:

Thanks a lot Duncan

Sorry to insist with my questions but I am very lost with these Rcurl
commands...
could you point out the few ones I need to set up an ftp connection
and just upload a file ?

Greatly appreciated

Thomas

2009/1/8 Duncan Temple Lang :


Prof Brian Ripley wrote:

Try system() with curl or a decent ftp client (I don't see that package
RCurl covers this, but it might despite its description only mentioning
HTTP).

It does support FTP, and all of the protocols that are supported in
the installed libcurl, so it depends the configuration options for libcurl
itself.

The protocols it handles can be found via the curlVersion() function, e.g.


curlVersion()

$age
[1] 3

$version
[1] "7.16.3"

$vesion_num
[1] 462851

$host
[1] "powerpc-apple-darwin9.0"

$features
   ipv6  ssl libz ntlm gssnegotiate largefile
  148   16   32   512

$ssl_version
[1] " OpenSSL/0.9.7l"

$ssl_version_num
[1] 0

$libz_version
[1] "1.2.3"

$protocols
[1] "tftp"   "ftp""telnet" "dict"   "ldap"   "http"   "file"   "https"
[9] "ftps"

$ares
[1] ""

$ares_num
[1] 0

$libidn
[1] ""



sessionInfo()
R version 2.9.0 Under development (unstable) (2008-09-27 r46576)
i386-apple-darwin9.5.0

locale:
C

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

other attached packages:
[1] ROOXML_0.1-0Rcompression_0.4-0  RGoogleDocs_0.2-0
[4] SVGAnnotation_0.1-0 lattice_0.17-15 RCurl_0.92-0
[7] XML_1.99-0  RTools_0.1-0bitops_1.0-4

loaded via a namespace (and not attached):
[1] grid_2.9.0




 From 'man curl'

  curl offers a busload of useful tricks like proxy support, user authen-
  tication,  ftp upload, HTTP post, SSL connections, cookies, file trans-
  fer resume and more. As you will see below, the amount of features will
  make your head spin!

Ftp protocols (and there are more than one) are fiendishly complicated,
especially if proxies are involved.

BTW, this is yet another case where knowing your OS would have helped 
give

a more precise answer. See the posting guide.

On Thu, 8 Jan 2009, Thomas Loridan wrote:


Hi all,

I would like to upload some plots I create wth R via ftp or something
similar but I don t really understand which command/syntax I should
use:
should I go for  make.socket + write.socket or try and create
environment variables like frp_proxy_user and then ftp my files? how?

many thanks for your help

Thomas

--
Thomas Loridan
King's College email: thomas.lori...@kcl.ac.uk
webpage:http://geography.kcl.ac.uk/micromet/tloridan/index.htm

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Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
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Oxford OX1 3TG, UKFax:  +44 1865 272595

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Re: [R] Extracting File Basename without Extension

2009-01-11 Thread Wacek Kusnierczyk
Gabor Grothendieck wrote:
> On Fri, Jan 9, 2009 at 4:20 PM, Wacek Kusnierczyk
>
>   
>> right;  there's a straightforward fix to my solution that accounts for
>> cases such as '.bashrc':
>>
>> names = c("foo.bar", ".zee")
>> sub("(.+)[.][^.]+$", "\\1", names)
>>
>> you could also use a lookbehind if possible (not in r, afaik).
>>
>> 
>
> or:
>
>   
>> sub(".*[.]", ".", names)
>> 
> [1] ".bar" ".zee"
>   

it was "foo" that was desired...

vQ

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Re: [R] Extracting File Basename without Extension

2009-01-11 Thread Wacek Kusnierczyk
Gabor Grothendieck wrote:
> On Fri, Jan 9, 2009 at 4:28 PM, Wacek Kusnierczyk
>  wrote:
>   
>> Rau, Roland wrote:
>> 
>>> P.S. Any suggestions how to become more proficient with regular
>>> expressions? The O'Reilly book ("Mastering...")? Whenever I tried
>>> anything more complicated than basic usage (things like ^ $ * . ) in R,
>>> I was way faster to write a new function (like above) instead of finding
>>> a regex solution.
>>>
>>>   
>> the book you mention is good.
>> you may also consider http://www.regular-expressions.info/
>>
>> regexes are usually well explained with lots of examples in perl books.
>>
>> 
>>> By the way: it might be still possible to *write* regular expressions,
>>> but what about code re-use? Are there people who can easily *read*
>>> complicated regular expressions?
>>>
>>>   
>> in some cases it is possible to write regular expressions in a way that
>> facilitates reading them by a human.  in perl, for example, you can use
>> so-called readable regexes:
>>
>> /
>>   (.+)# match and remember at least one arbitrary character
>>   [.] # match a dot
>>   [^.]+ # match at least one non-dot character
>>   $  # end of string anchor
>> /x;
>>
>> you can also use within regex comments:
>>
>> /(.+)(?# one or more chars)[.](?# a dot)[^.]+(?# one or more
>> non-dots)$(?# end of string)/
>>
>>
>> nothing of the sorts in r, however.
>> 
>
> Supports that if you begin the regular expression with (?x) and
> use perl = TRUE.  See ?regexp
>   

cool, i see ?xism is supported.  so the above can be written in r as:

names = c("foo.bar", ".zee")
sub("(?x) # alloow embedded comemnts
 (.+) # match and remember at least one arbitrary character
[.] # match a dot
[^.]+ # match at least one non-dot character
$ # end of string anchor",
"\\1", names, perl=TRUE)

is this what you wanted, roland?

vQ

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[R] PAW Update: Predictive analytics workshops and more case studies

2009-01-11 Thread EliseJ

Hi everyone,

Predictive Analytics World's program for Feb 18-19 in San Francisco
(www.predictiveanalyticsworld.com) has grown a bit since my post several
weeks ago, and is looking better than ever.  The conference covers today's
commercial deployment of predictive analytics, across industries and across
software vendors. In a nutshell, PAW is a warehouse of case studies.

In breaking news, the Netflix Prize leader slated to speak at PAW has now
won the Netflix Progress Prize (see
www.predictiveanalyticsworld.com/agenda.php#advancedapproaches)

We have two predictive analytics workshops that serve as a third-day option
on Feb 20 to complement the core conference program:

"The Best and the Worst of Predictive Analytics: Predictive Modeling Methods
and Common Data Mining Mistakes"
Instructor: John F. Elder, Ph.D., CEO and Founder, Elder Research, Inc.
www.predictiveanalyticsworld.com/predictive_modeling_methods.php

"Taking Action with Analytics: The Decision-Centric Enterprise - Putting
Predictive Analytics to Work Improving Every Business Decision"
Instructor: James Taylor, Co-Founder, Smart (enough) Systems
www.predictiveanalyticsworld.com/decision_centric_enterprise.php

And the list of case studies has expanded - we now have case studies from
all of: 3M, Acxiom, Affiliated Computer Services, Charles Schwab, Click
Forensics, Google, Linden Lab (Second Life), The National Rifle Association,
Pinnacol Assurance, Reed Elsevier, San Diego Supercomputer Center, Sun,
Telenor, Wells Fargo Credit Card Services, Wells Fargo Internet Services
Group -- plus special examples from Anheuser-Busch, Disney, Hewlett-Packard,
HSBC, IRS, Pfizer, Social Security Administration and WestWind Foundation.

For more info about the program, see:
www.predictiveanalyticsworld.com

Be sure to register by January 18th for the Early Bird rate - save $200 at:
www.predictiveanalyticsworld.com/register.php

If you'd like our informative event updates, sign up at:
www.predictiveanalyticsworld.com/notifications.php

For a summary of business applications of predictive analytics - and a named
case study for each - see the article, "Predictive Analytics Delivers Value
Across Business Applications" at
www.predictiveanalyticsworld.com/businessapplications.php

What is predictive analytics? See the Predictive Analytics Guide:
www.predictiveanalyticsworld.com/predictive_analytics.php

Take the Predictive Analytics World survey (on applications)  
As predictive analytics quickly expands across verticals and applications,
we need your help to understand what the evolving landscape looks like.
Please take a few minutes, answer a handful of questions, and help us keep
you informed:
https://www.surveymonkey.com/s.aspx?sm=8dHx_2bFz7yxw3FPKlbi3OVg_3d_3d

Available for immediate download: Free Industry Survey (on tools)
Download the Rexer Analytics 2008 Data Miner Survey report, covering the
most popular software tools, which verticals have embraced modeling and
more, at:
http://www.predictiveanalyticsworld.com/survey-signup.php

And finally, let us know if you have any questions.

Best,
Elise Johnson
Predictive Analytics World

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Re: [R] Arguments for Rcmd BATCH

2009-01-11 Thread Andrew Hicks
Professor Ripley,

Thank you very much.

I have used Rscript and it runs fine now.

Your help is very much appreciated.

Best wishes,

Andrew hicks

-Original Message-
From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk] 
Sent: 11 January 2009 01:23
To: Andrew Hicks
Cc: r-help@r-project.org
Subject: RE: [R] Arguments for Rcmd BATCH

I suggested you use Rscript, please do.

R CMD BATCH is the Unix-alike notation.  Rcmd BATCH is the recommended 
way on Windows, but R CMD BATCH is also accepted.

There is nothing to reproduce here, so here is a simple example.

tystie% cat foo.R
args <- commandArgs(TRUE)
print(args)

tystie% Rscript foo.R parms=1:33
[1] "parms=1:33"

You can redirect the output as you wish.

On Sun, 11 Jan 2009, Andrew Hicks wrote:

> Dear Professor Ripley,
>
> Firstly, thank you very much for your advice. I was not aware my R was so
> old. Sorry I must have missed the instruction on reading the posting
> guidelines.
>
> I have updated it and it now runs again. This is a big step forward.
However
> it is not running properly (or I am doing something wrong).
>
> There are still two problems may I ask for your help with please?
>
> 1. When I call the script it fails with the following message in the
output
> file:
>
>> ##First read in the arguments listed at the command line
>> args <- commandArgs(TRUE)
> Error in commandArgs(TRUE) : unused argument(s) (TRUE)
> Execution halted
>
> 2. The diagnostic details (that should be going to test01b.ROUT are now
> going to strange places, overwriting the test01b.R file if I do not
include
> the < and > redirectors.
>
> I am now using the following syntax, from the manual:
>
> Rcmd BATCH --no-save --no-restore --args parms=c(1,2,3) < test01b.R >
> test01b.ROUT

That's nothing like what is documented.

> Currently it is writing the output to "parms=c(1,2,3).ROUT"
>
> This is attached but says "fatal error cannot open file "--args"
>
> The file test01b.ROUT is created but empty.
>
> I get the same results if I start it with R CMD BATCH ...
>
> Is the a difference between R CMD... and Rcmd... please? The manual is not
> very clear on this.
>
> I am sorry to impose on you but guess I am still doing something wrong. I
> have looked through the documentation but cannot find much on this or many
> examples.
>
> Many thanks,
>
> Andrew Hicks
>
>
> -Original Message-
> From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk]
> Sent: 10 January 2009 18:18
> To: Andrew Hicks
> Cc: r-help@r-project.org
> Subject: Re: [R] Arguments for Rcmd BATCH
>
> Your R is far too old, and in particular too old for the example you
> are trying.
>
> Please do you as asked in the posting guide to do before posting, and
> upgrade.  Then you will have Rscript, as described in the current 'An
> Introduction to R' manual for this purpose (with examples).
>
> On Sat, 10 Jan 2009, Andrew Hicks wrote:
>
>> Sorry to bother you and I hope this will be easy to solve.
>>
>>
>> I am trying to run R scripts in batch, called from another programme,
> under
>> Windows XP. I have R 2.4.1
>>
>>
>>
>> I need to be able to pass a list of numeric arguments to the script as
> well.
>>
>>
>>
>> The Rscript and its input data file are attached.
>>
>>
>>
>> I have been trying the syntax below but it doesn't work:
>>
>>
>>
>> Rcmd BATCH -no-save -no-restore -args parms=c(1,2,3) test01b.R
>>
>>
>>
>> (each of these BATCH options is preceded by 2 - characters, but my
Outlook
>> is munging them together here)
>>
>>
>>
>> The script then accesses (or tries to) the variables as parms[1],
> parms[2],
>> etc.
>>
>>
>>
>> I get the respose "unable to open input file" at the command line and no
>> other diagnostic output.
>>
>>
>>
>> I got this syntax from p85 of the R-Intro doc and from the website
>> http://quantitative-ecology.blogspot.com/search/label/scripts. I could
not
>> find any other illustrations or instructions of how to use args with
> BATCH.
>>
>>
>>
>> Without using any parameter args it otherwise runs fine.
>>
>>
>>
>> Please can you advise what am I doing wrong and how should this command
be
>> structured? Do I also need to change the way the script is accessing the
>> arguments?
>>
>>
>>
>> Many thanks,
>>
>>
>>
>> Andrew Hicks
>>
>>
>
> -- 
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel:  +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UKFax:  +44 1865 272595
>

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

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P

[R] PHP and R

2009-01-11 Thread Applejus

Hi,

I know that using PHP command exec(...) you can call a unix command that
would run an R script, but how does it work on Windows platform?

Basically, I have an R function which takes a file and two strings as
arguments and I need to call this function and pass to it the arguments
automatically from PHP (when the user hits a submit button on the webpage),
any ideas??

Thanks!
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Re: [R] PHP and R

2009-01-11 Thread Prof Brian Ripley

On Sun, 11 Jan 2009, Applejus wrote:


I know that using PHP command exec(...) you can call a unix command that
would run an R script, but how does it work on Windows platform?


Exactly the same way.


Basically, I have an R function which takes a file and two strings as
arguments and I need to call this function and pass to it the arguments
automatically from PHP (when the user hits a submit button on the webpage),
any ideas??


See Rscript[.exe], which I gave an example of only this morning.

It is documented in 'An Introduction to R', amongst other places.

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

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[R] upgrade R version

2009-01-11 Thread ms.com












dear all contributors
i am new R user
i want to upgrade my R version from 2.7.1 to 2.8.1
i tried myself, but i could not do it as R is different from other software
could anyone guide me please

warm regard
madan 
student 
University of Bergen


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[R] Strange behaviour of paste

2009-01-11 Thread Oliver Bandel
Hello,


here I have some code, which behaves quite strange, IMHO.
There is a "res.txt" which will be collected before printing it.

There is a paste-statement, which has a comment at the end of the line,
which is this one: "# !HERE!".

If you throw out the first hash-mark "#" on that line,
the printout behaves like if it is done for each of the
for-loop iterations. If the hash mark will not be thrown out,
it behaves, as I would expect: done *once*, after the loop is finished.

I'm using "R version 2.7.1 (2008-06-23)" on Debian.

Can you please show me, what is going wrong here?


The code is not much, but too long (too many lines and
lines too long) for pasting it here, so I have placed
it here:

  http://www.first.in-berlin.de/trybug.R

Can you show me, why the behaviour differs so much,
when just removing that "#" ?!

Ciao,
  Oliver

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[R] Error in dyn.load()

2009-01-11 Thread Hadassa Brunschwig
Hi everyone!
I am relatively new to writing R extensions and to C programming. I thus hope
that my question is not too basic. I am trying to load a shared object into R
via the command dyn.load("convertR.so") and I get the following error:

Error in dyn.load("convertR.so") :
 unable to load shared library
'/Users/hadassa2/Documents/HUJI/Thesis/Sagiv_Project/LDhat/convertR.so':
 dlopen(/Users/hadassa2/Documents/HUJI/Thesis/Sagiv_Project/LDhat/convertR.so,
6): Symbol not found: _cmatrix
 Referenced from:
/Users/hadassa2/Documents/HUJI/Thesis/Sagiv_Project/LDhat/convertR.so
 Expected in: dynamic lookup

where cmatrix is a function defined in tools.c . I am including
tools.h in convertR.c . Does this error mean that I need
to create a shared object tools.so as well?
Or in general: including other functions into a .so means they need to
be of the type .so as well?

Thanks a lot for any comments.

Hadassa



-- 
Hadassa Brunschwig
PhD Student
Department of Statistics
The Hebrew University of Jerusalem
http://www.stat.huji.ac.il

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Re: [R] upgrade R version

2009-01-11 Thread Prof Brian Ripley
Since you are probably a Windows user (from the advert), see the R for 
Windows FAQ, at


http://cran.r-project.org/bin/windows/base/rw-FAQ.html

or on the menus in your existing R installation.

On Sun, 11 Jan 2009, ms.com wrote:


dear all contributors
i am new R user
i want to upgrade my R version from 2.7.1 to 2.8.1
i tried myself, but i could not do it as R is different from other software


I expect you mean 'better than other software' since this is actually 
in the FAQ.



could anyone guide me please

warm regard
madan
student
University of Bergen


Windows Live?: Keep your life in sync. Check it out.
Windows Live? Hotmail?: Chat. Store. Share. Do more with mail.  See how it 
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--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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Re: [R] Strange behaviour of paste

2009-01-11 Thread Mike Lawrence
I suspect your example code is too long & complicated for anyone to bother
attempting to help you. Try simplifying it to just a few lines; I've found
that the simplification process itself often leads me to the solution to my
own problem.

On Sun, Jan 11, 2009 at 6:50 AM, Oliver Bandel wrote:

> Hello,
>
>
> here I have some code, which behaves quite strange, IMHO.
> There is a "res.txt" which will be collected before printing it.
>
> There is a paste-statement, which has a comment at the end of the line,
> which is this one: "# !HERE!".
>
> If you throw out the first hash-mark "#" on that line,
> the printout behaves like if it is done for each of the
> for-loop iterations. If the hash mark will not be thrown out,
> it behaves, as I would expect: done *once*, after the loop is finished.
>
> I'm using "R version 2.7.1 (2008-06-23)" on Debian.
>
> Can you please show me, what is going wrong here?
>
>
> The code is not much, but too long (too many lines and
> lines too long) for pasting it here, so I have placed
> it here:
>
>  http://www.first.in-berlin.de/trybug.R
>
> Can you show me, why the behaviour differs so much,
> when just removing that "#" ?!
>
> Ciao,
>  Oliver
>
> __
> 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.
>



-- 
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University
www.thatmike.com

Looking to arrange a meeting? Check my public calendar:
http://www.thatmike.com/mikes-public-calendar

~ Certainty is folly... I think. ~

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Re: [R] problems installing package XML to a computer without an internet connection

2009-01-11 Thread Bob Green

Brian,

Thank you for your reply and advice. I hope that I did not give the 
impression that your build was the cause of the difficulties I 
experienced. If so, I apologise for this.


Your email was helpful in alerting me to the need to install 'proxy' 
and I subsequently located the current version zip file at:

http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.8/

Once I copied this version of the XML file that you wrote, the 
installation worked without problem.


Thank you again,

regards

Bob


At 06:03 PM 11/01/2009, Prof Brian Ripley wrote:

On Sun, 11 Jan 2009, Bob Green wrote:


Hello,

I am hoping for some advice regarding how I can install the XML 
package which I require to run package tm.


Normally I would use the install package option, however, I have to 
install the packages to a laptop running XP.


Windows, I presume.


The laptop does not have an internet connection.

Firstly I tried the file -   XML_1.99-0.tar.gz . Below is the error 
I received


What does 'try' mean?  That would work if you used Rcmd INSTALL on 
it, or install.packages(type="source").



Error in gzfile(file, "r") : cannot open the connection
In addition: Warning messages:
1: In zip.unpack(pkg, tmpDir) : error 1 in extracting from zip file
2: In gzfile(file, "r") :
 cannot open compressed file 'XML_1.99-0.tar.gz/DESCRIPTION', 
probable reason 'No such file or directory'


Then I tried XML 1.96-0.zip (from 
http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.7/). Below is the


Why from 2.7?  What version is your R?


error I received


So that worked: it is 'proxy' you are missing.  From the DESCRIPTION file

package: tm
Title: Text Mining Package
Version: 0.3-3
Date: 2008-12-20
Author: Ingo Feinerer, with contributions from Christian Buchta, 
Kurt Hornik, David Meyer, and Fridolin Wild

Maintainer: Ingo Feinerer 
Depends: R (>= 2.7.0), filehash, Matrix, methods, Snowball, XML
Imports: proxy
Suggests: Rgraphviz, Rmpi, Rstem (>= 0.3-1), snow

still you may need packages filehash, Matrix, methods, Snowball and proxy.

I suggest getting those from bin/windows/contrib/2.7/ on CRAN, and 
installing from the 'Local zip file' menu optipn.



Loading required package: XML
Error in loadNamespace(i, c(lib.loc, .libPaths())) :
 there is no package called 'proxy'
Error: package/namespace load failed for 'tm'

Any suggestions are appreciated,


Read the posting guide, remember to tell us what we asked for 'at a 
minumum' and what you actually did.



Bob

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


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Re: [R] I'm looking for a book about spatial point patterns (Diggle, 2003)

2009-01-11 Thread Mike Lawrence
Amazon lists 2 used copies for sale:
http://www.amazon.com/Statistical-Analysis-Spatial-Point-Patterns/dp/0340740701


On Sun, Jan 11, 2009 at 12:04 AM, Unangu  wrote:
>
> To understand some functions about spatial point patterns in "spatstat" ,I
> should know some background about it, and the best way is to read the
> monograph, and  "Statistical Analysis of Spatial Point Patterns" (2nd edt.)
> is a better choise. But I can not find it anywhere I can. Who can help me?
> Thank you!
>
> -
> una...@gmail.com
> --
> View this message in context: 
> http://www.nabble.com/I%27m-looking-for-a-book-about-spatial-point-patterns-%28Diggle%2C2003%29-tp21395908p21395908.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> 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.
>



-- 
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University
www.thatmike.com

Looking to arrange a meeting? Check my public calendar:
http://www.thatmike.com/mikes-public-calendar

~ Certainty is folly... I think. ~

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Re: [R] How to get solution of following polynomial?

2009-01-11 Thread Paul Smith
On Sun, Jan 11, 2009 at 6:03 AM, RON70  wrote:
>
> Hi, I want find all roots for the following polynomial :
>
> a <- c(-0.07, 0.17); b <- c(1, -4); cc <- matrix(c(0.24, 0.00, -0.08,
> -0.31), 2); d <- matrix(c(0, 0, -0.13, -0.37), 2); e <- matrix(c(0.2, 0,
> -0.06, -0.34), 2)
> A1 <- diag(2) + a %*% t(b) + cc; A2 <- -cc + d; A3 <- -d + e; A4 <- -e
> fn <- function(z)
>   {
>y <- diag(2) - A1*z - A2*z^2 - A3*z^3 - A4*z^4
>return(det(y))
>   }; uniroot(fn, c(-10, 1))
>
> Using uniroot function, I got only one solution of that. Is there any
> function to get all four solutions? I looked at polyroot() function, but I
> do not think it will work for my problem, because, my coef. are matrix, nor
> number

Use curve to plot the curve of your function. Then, see where the
roots are, and use uniroot with a small interval around the roots to
determine their exact value.

Example:

f <- function(x) x^2-1
curve(f,-5,5)
uniroot(f,c(-2,-0.2))
uniroot(f,c(0.2,2))

Paul

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[R] Makevars

2009-01-11 Thread Hadassa Brunschwig
Hi

I have sent a previous email "Error in dyn.load()" for which, shame on
me, I later found a partial answer.
I have been trying to look into what I exactly need to include into
Makevars and where
it needs to be located and have not found a satisfying answer yet.
Maybe the following questions
are helpful for other people as well.

Again, I am trying to include a C function tools.c into a main.c file
which needs to be run via R.
I include the header file via #include tools.h .
What I understood is that I need another file which specifically links
the header file
with the tools.c files (or .o file?). My questions are thus:

1. Can I just create a file Makevars with the variable
PKG_LIBS=-L/directory_of_tools -l/tools?
2. Does this file need to be located in the same directory as main.c?
3. When I then run the command R CMD SHLIB it does not make use of
Makevars. So what do I need to add?
4. Does tools.c need to be a shared object as well?

Thanks a lot!

Hadassa
-- 
Hadassa Brunschwig
PhD Student
Department of Statistics
The Hebrew University of Jerusalem
http://www.stat.huji.ac.il

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Re: [R] Strange behaviour of paste

2009-01-11 Thread Oliver
Mike Lawrence  thatmike.com> writes:

> 
> I suspect your example code is too long & complicated for anyone to bother
> attempting to help you.
[...]


Because of that I marked the line, where the error occured,
I thought it was easy to find out for experienced users.

But I just found the problem.

It seems the behaviour is correct,
but very unusual.

R has some peculiarities that aren't intuitive,
if you are coming from other languages.

It's power is also it's unusual-ness.

The problem was, that sample_times was not the number of
samples, but an array containing 1:(number-1).

And paste did not just add it, it makes something like
an expand.grid-like way of blowing up the data.
It seems that does also contained the arguments, that followed
the sample_times-array, not only those before, but that I have
to explore in more detail.

Yes, R is so powerful, but some behaviour is really strange
because of that.


But I can admit, that it was my limited knowldege on paste()
that brought me to the conclusion that there might be a bug.

It seems with R one has to rethink a lot of assumed behaviour
one knows from other languages. So, reading the manual more
then one time might be necessary... ;-)

BTW: Is there a way to make pdf's out of the help-pages for
a function?

I know there is a big pdf-file as reference.

But the begin of the description of the functions do not fit
to one page.

I would like to have each function beginning on a seperate page.

How to achieve this? Do you know this?
(Maybe I should start a new thread with that topic...?!)

Ciao,
   Oliver

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[R] calibrate function

2009-01-11 Thread Elsa et Stéphane BOUEE
Hi all,

I have a question on the package « survey”

 

I have some difficulties to use the function ‘calibrate’. Although it works
well with one single factor variable, I cannot use it for 2 and get the
message

“Erreur dans regcalibrate.survey.design2(design, formula, population,
aggregate.stage = aggregate.stage,  :   Population and sample totals are not
the same length.”

 

Here is the format I use as a data.frame:

 

ecodiaMG[1:10, 71:73]

   age_cl1 sexe1 region1

1MG_54  MG_H   MG_NE

2MG_54  MG_H   MG_NE

3MG_54  MG_H   MG_NE

4MG_54  MG_H   MG_NE

5MG_54  MG_H   MG_NE

6MG_54  MG_H   MG_NE

7MG_54  MG_H   MG_NE

8MG_54  MG_H   MG_NE

9MG_54  MG_H   MG_NE

10   MG_54  MG_H   MG_NE

…

My program is:

 

grap<-svydesign(id=~1, data=ecodiaMG)

regMG <-c(region1MG_NE =852, region1MG_NO=662, region1MG_P=636,
region1MG_SE=961, region1MG_SO=545)

sexMG <-c(sexe1MG_F =976, sexe1MG_H=2680)

ageMG <-c(age_cl1MG_40 =380, age_cl1MG_4054=2099, age_cl1MG_54=1177)

grap2<- calibrate(grap, formula= ~ age_cl1-1, c(ageMG))

grap3<- calibrate(grap2, formula= ~ sexe1-1, c(sexMG))

grap4<- calibrate(grap3, formula= ~region1-1, c(regMG))

 

I can calibrate the variables one by one, which is wrong, so I would like to
do it all in once:

grap2<- calibrate(grap, formula= ~ age_cl1+ sexe1+ regMG -1, c(ageMG, sexMG,
regMG ))

 

This line does not work, but I cannot find the correct  one

 

Thank you for your help

 

Stéphane


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Re: [R] How to get solution of following polynomial?

2009-01-11 Thread Erich Neuwirth
In theory,
you could define the following 2 functions

powermat <- function(myvec) {
  powervec <- function(x,maxpower)
sapply(0:maxpower,function(n)x^n)
  sapply(myvec,function(x)powervec(x,length(myvec)-1))
}

polycoeffs <- function(fn,order,support=0:order)
  solve(t(powermat(support)),sapply(support,Vectorize(fn)))

and then use polycoeffs(fn,4)
with your function fn to extract the coefficients of the polynomial.
polycoeffs takes a function and the order of a polynomial
as its input and computes the coefficients of the polynomial
or the given order with the same values as the function
at the points 0:order.
If the function is a polynomial of the given order, it gives you
exactly the coefficients you need.
You may use another set of support points (points where the function is
evaluated) as an optional argument.
Still, this method is not extremely reliable. If the support points are
not chosen well, you might get rather unreliable results.

A safer way would be to use a computer algebra system to extract the
coefficients of your polynomial. You could use Ryacas to do this from R.
But you still would have to grasp the syntax of yacas.







Paul Smith wrote:
> On Sun, Jan 11, 2009 at 6:03 AM, RON70  wrote:
>> Hi, I want find all roots for the following polynomial :
>>
>> a <- c(-0.07, 0.17); b <- c(1, -4); cc <- matrix(c(0.24, 0.00, -0.08,
>> -0.31), 2); d <- matrix(c(0, 0, -0.13, -0.37), 2); e <- matrix(c(0.2, 0,
>> -0.06, -0.34), 2)
>> A1 <- diag(2) + a %*% t(b) + cc; A2 <- -cc + d; A3 <- -d + e; A4 <- -e
>> fn <- function(z)
>>   {
>>y <- diag(2) - A1*z - A2*z^2 - A3*z^3 - A4*z^4
>>return(det(y))
>>   }; uniroot(fn, c(-10, 1))
>>
>> Using uniroot function, I got only one solution of that. Is there any
>> function to get all four solutions? I looked at polyroot() function, but I
>> do not think it will work for my problem, because, my coef. are matrix, nor
>> number
> 
> Use curve to plot the curve of your function. Then, see where the
> roots are, and use uniroot with a small interval around the roots to
> determine their exact value.
> 
> Example:
> 
> f <- function(x) x^2-1
> curve(f,-5,5)
> uniroot(f,c(-2,-0.2))
> uniroot(f,c(0.2,2))
> 
> Paul
> 
> __
> 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.
> 
> 
> 
> 
> 
> No virus found in this incoming message.
> Checked by AVG - http://www.avg.com 
> Version: 8.0.176 / Virus Database: 270.10.5/1886 - Release Date: 1/10/2009 
> 6:01 PM
> 

-- 
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Faculty of Computer Science
Computer Supported Didactics Working Group
Visit our SunSITE at http://sunsite.univie.ac.at
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Re: [R] Convert date/time string to date

2009-01-11 Thread Gabor Grothendieck
If the file represents a time series then you might want to look
at the zoo package.  See read.zoo, in particular and
?strptime and R News 4/1 for the % codes and other
date/time info.  Also ?lag.zoo

On Sun, Jan 11, 2009 at 12:22 AM, Heston Capital
 wrote:
> I am new to R and am trying to import a text file that contains
> date/time and various fields.  I want to sort this matrix by date and
> also perform calculations on the date field (difference between two
> dates etc).
>
> The format of the string looks as follows:
>
> x<-c("25/2/2003 0:00:00")
>
> I tried:
>
> as.Date(x,format='%d/%m/%y')
> [1] "2020-02-25"
>
> Obviously I am doing something wrong here.  I would like to remove the
> hh:mm:ss from the end of the string if possible.
>
> Thanks for your help, I have been searching for hours and not getting 
> anywhere.
>
> __
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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[R] Reference-pages: each function beginning on seperate page?

2009-01-11 Thread Oliver
Hello,


is the reference manual also available with each explained
function beginning on a seperate page?

Or can this somehow be done easily?

I prefer reading documentation on paper, but printing makes more
sense, when each function can be printed seperated
(like in man-pages).

Any idea, how to achieve this?

TIA,
 Oliver

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[R] Problem using odfWeave

2009-01-11 Thread Mark Heckmann
Hi everybody,

I don't get odfWeave to run properly. My odt file is as a simple as:


Some text.

<>= 
print(1:10)
@
---

The output I get ist the following:

---

> odfWeave("roffice.odt", "rofficeOUT.odt")
  Copying  roffice.odt 
  Setting wd to  D:\DOKUME~1\Peter\LOKALE~1\Temp\RtmpNcNDxY/odfWeave11041520167 
  Unzipping ODF file using unzip -o "roffice.odt" 
Archive:  roffice.odt
 extracting: mimetype
   creating: Configurations2/statusbar/
  inflating: Configurations2/accelerator/current.xml  
   creating: Configurations2/floater/
   creating: Configurations2/popupmenu/
   creating: Configurations2/progressbar/
   creating: Configurations2/menubar/
   creating: Configurations2/toolbar/
   creating: Configurations2/images/Bitmaps/
  inflating: content.xml 
  inflating: styles.xml  
 extracting: meta.xml
  inflating: Thumbnails/thumbnail.png  
  inflating: settings.xml
  inflating: META-INF/manifest.xml   

  Removing  roffice.odt 
  Creating a Pictures directory

  Pre-processing the contents
  Sweaving  content.Rnw 

  Writing to file content_1.xml
  Processing code chunks ...
1 : term verbatim

  'content_1.xml' has been Sweaved

  Removing content.xml

  Post-processing the contents
Premature end of data in tag office:text line 2
Premature end of data in tag office:body line 2
Premature end of data in tag office:document-content line 2
Error: 1: Premature end of data in tag office:text line 2
2: Premature end of data in tag office:body line 2
3: Premature end of data in tag office:document-content line 2
In addition: Warning message:
closing unused connection 5 (content.xml) 

---

No rofficeOUT.odt is rendered. What can I do about it?

TIA, Mark
-- 
Mark Heckmann (Dipl. Wirt.-Ing.)
phone +49 (0) 421/1614618

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[R] Boxplot from matrices

2009-01-11 Thread johnhj

Hii,

I will create boxplots from matrices. I have the following data sets:
5.0  1.78  2.99  2.019 0
10.0  1.79  3.00  1.744 0
15.0  1.78  2.98  1.936 0
20.0  1.78  2.99  1.975 0
25.0  1.73  2.91  3.591 0
30.0  1.79  3.00  1.966 0
35.0  1.79  3.00  2.451 0
40.0  1.79  3.00  1.853 0
45.0  1.79  3.00  2.077 0
50.0  1.79  3.00  1.943 0
55.0  1.79  3.00  2.608 0
60.0  1.79  3.00  1.790 0
65.0  1.79  3.00  1.893 0
70.0  1.79  3.00  2.079 0
75.0  1.77  2.97  2.200 0
80.0  1.79  3.01  1.868 0
85.0  1.78  2.99  2.179 0
90.0  1.70  2.85  2.305 0
95.0  1.71  2.87  1.854 0
100.0  1.79  3.00  2.362 0
105.0  1.79  3.00  3.634 0
110.0  1.79  3.00  1.578 0
115.0  1.79  3.00  1.835 0
120.0  1.79  3.00  2.359 0
125.0  1.79  3.00  2.542 0
130.0  1.76  2.95  2.620 0
135.0  1.79  3.00  4.181 0
140.0  1.79  3.00  1.375 0
145.0  1.79  3.00  2.872 0
150.0  1.79  3.00  3.002 0
155.0  1.79  3.00  3.712 0
160.0  1.79  3.01  3.175 0
165.0  1.79  3.00  2.821 0
170.0  1.79  3.00  3.320 0.078
175.0  1.79  3.00  2.076 0
180.0  1.77  2.97  2.186 0
185.0  1.78  2.99  4.652 0
190.0  1.79  3.01  2.051 0
195.0  1.79  3.00  1.922 0
200.0  1.79  3.00  1.945 0

The first thing I do is, to run the command
y<-matrix(c(test$V3),ncol=8)
to divide the third column in 8 matrices to create 8 boxplots.
The I run the command
w<-summary(y) 
to get the values min, max, mean, median, 1.Quan, 3.Quan

My problem is, I cann't run the plot command to create the 8 boxplots in a
graph...
The command 
plot(y)
gives me an error..

Can anybody help me to create the boxplot from matrices in a graph ?

greetings,
j

-- 
View this message in context: 
http://www.nabble.com/Boxplot-from-matrices-tp21399085p21399085.html
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[R] Sweave removes \end{table}

2009-01-11 Thread Keith Jones

Hi,

I have found that when I run my .rnw file through Sweave it removes 
the \end{table} LaTeX command after the table that was not generated 
using R.:


excerpt from my .rnw file
...
6.000 -- 6.003 &  3 &0.6 \\
\hline
8.500 -- 8.505 &  4 &0.8 \\
\hline
Grand Total &493 &\\
\hline
\end{tabular}
\label{tbl:sbbs}

\end{table}
\section{Recommendations}

excerpt from the .tex file generated by Sweave
...
6.000 -- 6.003 &  3 &0.6 \\
\hline
8.500 -- 8.505 &  4 &0.8 \\
\hline
Grand Total &493 &\\
\hline
\end{tabular}
\label{tbl:sbbs}

\section{Recommendations}

If I put two \end{table} commands in the table only one is removed by Sweave.

Has anyone else seen this?

Thanks,

Keith Jones, Ph.D.
VTS Pumps

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Re: [R] Boxplot from matrices

2009-01-11 Thread Carlos J. Gil Bellosta
Hello,

The following code may help you:

> my.matrix <- matrix( rnorm(16), ncol = 4 )
> boxplot( my.matrix ~ col(  my.matrix ) )

Best regards,

Carlos J. Gil Bellosta
http://www.datanalytics.com



On Sun, 2009-01-11 at 05:23 -0800, johnhj wrote:
> Hii,
> 
> I will create boxplots from matrices. I have the following data sets:
> 5.0  1.78  2.99  2.019 0
> 10.0  1.79  3.00  1.744 0
> 15.0  1.78  2.98  1.936 0
> 20.0  1.78  2.99  1.975 0
> 25.0  1.73  2.91  3.591 0
> 30.0  1.79  3.00  1.966 0
> 35.0  1.79  3.00  2.451 0
> 40.0  1.79  3.00  1.853 0
> 45.0  1.79  3.00  2.077 0
> 50.0  1.79  3.00  1.943 0
> 55.0  1.79  3.00  2.608 0
> 60.0  1.79  3.00  1.790 0
> 65.0  1.79  3.00  1.893 0
> 70.0  1.79  3.00  2.079 0
> 75.0  1.77  2.97  2.200 0
> 80.0  1.79  3.01  1.868 0
> 85.0  1.78  2.99  2.179 0
> 90.0  1.70  2.85  2.305 0
> 95.0  1.71  2.87  1.854 0
> 100.0  1.79  3.00  2.362 0
> 105.0  1.79  3.00  3.634 0
> 110.0  1.79  3.00  1.578 0
> 115.0  1.79  3.00  1.835 0
> 120.0  1.79  3.00  2.359 0
> 125.0  1.79  3.00  2.542 0
> 130.0  1.76  2.95  2.620 0
> 135.0  1.79  3.00  4.181 0
> 140.0  1.79  3.00  1.375 0
> 145.0  1.79  3.00  2.872 0
> 150.0  1.79  3.00  3.002 0
> 155.0  1.79  3.00  3.712 0
> 160.0  1.79  3.01  3.175 0
> 165.0  1.79  3.00  2.821 0
> 170.0  1.79  3.00  3.320 0.078
> 175.0  1.79  3.00  2.076 0
> 180.0  1.77  2.97  2.186 0
> 185.0  1.78  2.99  4.652 0
> 190.0  1.79  3.01  2.051 0
> 195.0  1.79  3.00  1.922 0
> 200.0  1.79  3.00  1.945 0
> 
> The first thing I do is, to run the command
> y<-matrix(c(test$V3),ncol=8)
> to divide the third column in 8 matrices to create 8 boxplots.
> The I run the command
> w<-summary(y) 
> to get the values min, max, mean, median, 1.Quan, 3.Quan
> 
> My problem is, I cann't run the plot command to create the 8 boxplots in a
> graph...
> The command 
> plot(y)
> gives me an error..
> 
> Can anybody help me to create the boxplot from matrices in a graph ?
> 
> greetings,
> j
>

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[R] Converting Numerical Matrix to List of Strings

2009-01-11 Thread Gundala Viswanath
Hi all,

Given a matrix:

> mat

[,1] [,2] [,3]
[1,]000
[2,]333
[3,]111
[4,]211


How can I convert it to a list of strings:

> desired_output
[1] "aaa" "ttt" "ccc" "gcc"


In principle:

1. Number of Column in matrix = length of string (= 3)
2. Number of Row in matrix = length of vector ( = 4).
3. Character "a" encode as "0",
  "c" -> "1",
  "g" -> "2",
  "t" -> "3"


Length of strings are assumed to be uniform within the vector,
and it can be greater than 3 (up to 40 characters).


- Gundala Viswanath
Jakarta - Indonesia

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Re: [R] Makevars

2009-01-11 Thread Dirk Eddelbuettel

Hadassa,

On 11 January 2009 at 15:29, Hadassa Brunschwig wrote:
| Again, I am trying to include a C function tools.c into a main.c file
| which needs to be run via R.
| I include the header file via #include tools.h .
| What I understood is that I need another file which specifically links
| the header file
| with the tools.c files (or .o file?). My questions are thus:
| 
| 1. Can I just create a file Makevars with the variable
| PKG_LIBS=-L/directory_of_tools -l/tools?

Yes...

| 2. Does this file need to be located in the same directory as main.c?

Yes...

| 3. When I then run the command R CMD SHLIB it does not make use of
| Makevars. So what do I need to add?

... but Makevars is for R package building. See the 'R Extensions' manual for
documentation, and literally hundreds of packages on CRAN for live examples
to look at _in source_ on how to link C code to R code.

| 4. Does tools.c need to be a shared object as well?

tools.c is source code, tools.o would be object code. If you want to
dynamically load it, then it needs to be a shared object too.

Worked examples are also in my 'introduction to high-performance computing
with R' slides from August and December.  It covers added compiled code to R
on a few slides with worked examples using the inline and Rcpp packages.

Dirk


-- 
Three out of two people have difficulties with fractions.

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Re: [R] I'm looking for a book about spatial point patterns (Diggle, 2003)

2009-01-11 Thread Unangu

Thank you very much!

Mike Lawrence-7 wrote:
> 
> Amazon lists 2 used copies for sale:
> http://www.amazon.com/Statistical-Analysis-Spatial-Point-Patterns/dp/0340740701
> 
> 
> On Sun, Jan 11, 2009 at 12:04 AM, Unangu  wrote:
>>
>> To understand some functions about spatial point patterns in "spatstat"
>> ,I
>> should know some background about it, and the best way is to read the
>> monograph, and  "Statistical Analysis of Spatial Point Patterns" (2nd
>> edt.)
>> is a better choise. But I can not find it anywhere I can. Who can help
>> me?
>> Thank you!
>>
>> -
>> una...@gmail.com
>> --
>> View this message in context:
>> http://www.nabble.com/I%27m-looking-for-a-book-about-spatial-point-patterns-%28Diggle%2C2003%29-tp21395908p21395908.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
>> __
>> 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.
>>
> 
> 
> 
> -- 
> Mike Lawrence
> Graduate Student
> Department of Psychology
> Dalhousie University
> www.thatmike.com
> 
> Looking to arrange a meeting? Check my public calendar:
> http://www.thatmike.com/mikes-public-calendar
> 
> ~ Certainty is folly... I think. ~
> 
> __
> 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.
> 
> 


-
una...@gmail.com
-- 
View this message in context: 
http://www.nabble.com/I%27m-looking-for-a-book-about-spatial-point-patterns-%28Diggle%2C2003%29-tp21395908p21400640.html
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Re: [R] Reference-pages: each function beginning on seperate page?

2009-01-11 Thread Duncan Murdoch

On 11/01/2009 10:06 AM, Oliver wrote:

Hello,


is the reference manual also available with each explained
function beginning on a seperate page?

Or can this somehow be done easily?

I prefer reading documentation on paper, but printing makes more
sense, when each function can be printed seperated
(like in man-pages).

Any idea, how to achieve this?


It doesn't offer that, but it sounds like it would be an easy 
modification, if you know where to do it.  The reference manual is built 
by commands listed in the RHOME/doc/manual/Makefile.win file on Windows, 
and the Makefile on other platforms.  The sort of change you want could 
likely be made to the RHOME/tools/pkg2tex.pl Perl script, but do note 
that the documentation production tools are being overhauled for R 2.9.0 
(due in March or April), and I expect this will be an easier change 
after that's done than before.


Duncan Murdoch

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[R] help me

2009-01-11 Thread jolka sukyte
Hello,

Can You help me? How to save this functions in cd:

install.packages("Ryacas", dep = TRUE)
library(Ryacas)
yacasInstall()
yacas("Integrate(z,1,2-x-y)1")
yacas("Integrate(y,0,1-x)2 - x - y - 1")
yacas("Integrate(x,0,1)(1 - x)^2 - (1 - x)^2/2")

Thanks You,
Sincerely, Jolka

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Re: [R] Problem using odfWeave

2009-01-11 Thread Max Kuhn
You need to cat the results using odfCAt, otherwise you are just  
writing the output with no XML around it.


Max



On Jan 11, 2009, at 8:42 AM, "Mark Heckmann"   
wrote:



Hi everybody,

I don't get odfWeave to run properly. My odt file is as a simple as:


Some text.

<>=
print(1:10)
@
---

The output I get ist the following:

---


odfWeave("roffice.odt", "rofficeOUT.odt")

 Copying  roffice.odt
 Setting wd to  D:\DOKUME~1\Peter\LOKALE~1\Temp\RtmpNcNDxY/ 
odfWeave11041520167

 Unzipping ODF file using unzip -o "roffice.odt"
Archive:  roffice.odt
extracting: mimetype
  creating: Configurations2/statusbar/
 inflating: Configurations2/accelerator/current.xml
  creating: Configurations2/floater/
  creating: Configurations2/popupmenu/
  creating: Configurations2/progressbar/
  creating: Configurations2/menubar/
  creating: Configurations2/toolbar/
  creating: Configurations2/images/Bitmaps/
 inflating: content.xml
 inflating: styles.xml
extracting: meta.xml
 inflating: Thumbnails/thumbnail.png
 inflating: settings.xml
 inflating: META-INF/manifest.xml

 Removing  roffice.odt
 Creating a Pictures directory

 Pre-processing the contents
 Sweaving  content.Rnw

 Writing to file content_1.xml
 Processing code chunks ...
   1 : term verbatim

 'content_1.xml' has been Sweaved

 Removing content.xml

 Post-processing the contents
Premature end of data in tag office:text line 2
Premature end of data in tag office:body line 2
Premature end of data in tag office:document-content line 2
Error: 1: Premature end of data in tag office:text line 2
2: Premature end of data in tag office:body line 2
3: Premature end of data in tag office:document-content line 2
In addition: Warning message:
closing unused connection 5 (content.xml)

---

No rofficeOUT.odt is rendered. What can I do about it?

TIA, Mark
--
Mark Heckmann (Dipl. Wirt.-Ing.)
phone +49 (0) 421/1614618

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Re: [R] Converting Numerical Matrix to List of Strings

2009-01-11 Thread jim holtman
try this:

> mapping <- c('0'='a', '1'='c', '2'='g', '3'='t')
> x <- matrix(sample(0:3, 30, TRUE), ncol=3)
> x
  [,1] [,2] [,3]
 [1,]311
 [2,]132
 [3,]111
 [4,]111
 [5,]213
 [6,]130
 [7,]132
 [8,]310
 [9,]030
[10,]330
> apply(x, 1, function(z){
+ paste(mapping[as.character(z)], collapse='')
+ })
 [1] "tcc" "ctg" "ccc" "ccc" "gct" "cta" "ctg" "tca" "ata" "tta"
>
>


On Sun, Jan 11, 2009 at 10:38 AM, Gundala Viswanath  wrote:
> Hi all,
>
> Given a matrix:
>
>> mat
>
>[,1] [,2] [,3]
> [1,]000
> [2,]333
> [3,]111
> [4,]211
>
>
> How can I convert it to a list of strings:
>
>> desired_output
> [1] "aaa" "ttt" "ccc" "gcc"
>
>
> In principle:
>
> 1. Number of Column in matrix = length of string (= 3)
> 2. Number of Row in matrix = length of vector ( = 4).
> 3. Character "a" encode as "0",
>  "c" -> "1",
>  "g" -> "2",
>  "t" -> "3"
>
>
> Length of strings are assumed to be uniform within the vector,
> and it can be greater than 3 (up to 40 characters).
>
>
> - Gundala Viswanath
> Jakarta - Indonesia
>
> __
> 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.
>



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

What is the problem that you are trying to solve?

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Re: [R] Converting Numerical Matrix to List of Strings

2009-01-11 Thread Dimitris Rizopoulos

one way is the following:

mat <- matrix(sample(0:3, 12, TRUE), 4, 3)
strg <- c("a", "c", "g", "t")

out <- strg[mat + 1]
dim(out) <- dim(mat)
apply(out, 1, paste, collapse = "")


I hope it helps.

Best,
Dimitris


Gundala Viswanath wrote:

Hi all,

Given a matrix:


mat


[,1] [,2] [,3]
[1,]000
[2,]333
[3,]111
[4,]211


How can I convert it to a list of strings:


desired_output

[1] "aaa" "ttt" "ccc" "gcc"


In principle:

1. Number of Column in matrix = length of string (= 3)
2. Number of Row in matrix = length of vector ( = 4).
3. Character "a" encode as "0",
  "c" -> "1",
  "g" -> "2",
  "t" -> "3"


Length of strings are assumed to be uniform within the vector,
and it can be greater than 3 (up to 40 characters).


- Gundala Viswanath
Jakarta - Indonesia

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--
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus Medical Center

Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014

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Re: [R] Converting Numerical Matrix to List of Strings

2009-01-11 Thread Douglas Bates
On Sun, Jan 11, 2009 at 9:38 AM, Gundala Viswanath  wrote:
> Hi all,
>
> Given a matrix:
>
>> mat
>
>[,1] [,2] [,3]
> [1,]000
> [2,]333
> [3,]111
> [4,]211

> How can I convert it to a list of strings:

>> desired_output
> [1] "aaa" "ttt" "ccc" "gcc"

Are you looking for a general solution or do you want something
specific for these 64 potential codon-like patterns?  If you just want
the patterns corresponding to all possible triplets of A, C, G, T then

colSums(4^(0:2) * t(mat)) + 1

gives you a set of indices between 1 and 64.  Then you need to create
the 64 possible patterns.  Here is one way

> bases <- factor(c("A","C","G","T"))
> head(patterns <- do.call(paste, expand.grid(bases, bases, bases)))
[1] "A A A" "C A A" "G A A" "T A A" "A C A" "C C A"
> (mat <- matrix(c(0,3,1,2,0,3,1,1,0,3,1,1), ncol = 3))
 [,1] [,2] [,3]
[1,]000
[2,]333
[3,]111
[4,]211
> colSums(4^(0:2) * t(mat)) + 1
[1]  1 64 22 23
> patterns[colSums(4^(0:2) * t(mat)) + 1]
[1] "A A A" "T T T" "C C C" "G C C"

We will leave the elimination of the blanks in the patterns as an
exercise for the reader.

>
> In principle:
>
> 1. Number of Column in matrix = length of string (= 3)
> 2. Number of Row in matrix = length of vector ( = 4).
> 3. Character "a" encode as "0",
>  "c" -> "1",
>  "g" -> "2",
>  "t" -> "3"
>
>
> Length of strings are assumed to be uniform within the vector,
> and it can be greater than 3 (up to 40 characters).
>
>
> - Gundala Viswanath
> Jakarta - Indonesia
>
> __
> 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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Re: [R] help me

2009-01-11 Thread Gabor Grothendieck
Do you mean how to create an R function, CD, that
represents the resulting function of x?   If that's it
then try this:

> CD <- function(x) {}
> body(CD) <- yacas("Integrate(y,0,1-x)2 - x - y - 1")[[1]]
> CD
function (x)
(1 - x)^2 - (1 - x)^2/2

See ?bodyAsExpression for more info.  Also try:
demo("Ryacas-Function")


On Sun, Jan 11, 2009 at 11:13 AM, jolka sukyte  wrote:
> Hello,
>
> Can You help me? How to save this functions in cd:
>
> install.packages("Ryacas", dep = TRUE)
> library(Ryacas)
> yacasInstall()
> yacas("Integrate(z,1,2-x-y)1")
> yacas("Integrate(y,0,1-x)2 - x - y - 1")
> yacas("Integrate(x,0,1)(1 - x)^2 - (1 - x)^2/2")
>
> Thanks You,
> Sincerely, Jolka
>
> __
> 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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Re: [R] upgrade R version

2009-01-11 Thread Dieter Menne
ms.com  hotmail.com> writes:

> i want to upgrade my R version from 2.7.1 to 2.8.1


Gabor's 

http://code.google.com/p/batchfiles/

can help you getting the libraries right after an upgrade.

Dieter

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Re: [R] R in the NY Times

2009-01-11 Thread Marc Schwartz
on 01/10/2009 01:50 PM Kingsford Jones wrote:
> The reactions to the NYT article have certainly made for some
> interesting reading.
> 
> Here are some of the links:
> 
> http://overdetermined.net/site/content/new-york-times-article-r
> 
> http://jackman.stanford.edu/blog/?p=1053
> 
> http://ggorjan.blogspot.com/2009/01/new-york-times-on-r.html
> 
> several posts on Andrew Gelman's blog:
> http://www.stat.columbia.edu/~gelman/blog/
> 
> http://www.reddit.com/r/programming/comments/7nwgq/the_new_york_times_notices_the_r_programming/
> 
> comments here: http://bits.blogs.nytimes.com/2009/01/08/r-you-ready-for-r/
> 
> 
> It's too bad that SAS has reacted to the negative reactions to their
> NYT quote with more FUD.  The quote that Tony posted is just a
> thinly-veiled jab at R (veiled by a disingenuous "we value open
> source" veneer).  Perhaps SAS is shooting themselves in the foot with
> their reactions; aren't they making it harder if they should ever
> decide the best thing to do is to embrace R and the philosophies
> behind it?  Four years ago, Marc Schwartz posted interesting comments
> realted to this:
> 
> http://tolstoy.newcastle.edu.au/R/help/04/12/9497.html


Thanks for pointing this out Kingsford. The books referenced there are
excellent for providing an understanding of the dynamics that have been
the subject of many of these threads here since the NYT article was
published.

There is a natural tension between leading edge adopters, the "main
stream" and the laggards. Moore's "Crossing the Chasm" provides good
insights into this tension and the acceptance of new products and
technology.

Grove's "Only the Paranoid Survive" shows how individual companies and
even entire industries (think banking and autos today) can suddenly face
an unexpected risk to their survival when they fail to comprehend
marketplace dynamics and take appropriate action.

Microsoft's mis-steps vis-a-vis Vista opened the door for Apple and
Linux to increase their respective marketshare and for open source more
generally (eg. Firefox).

BTW, readers might find this commentary of interest:

Commentary: Create a tech-friendly U.S. government
By Jimmy Wales and Andrea Weckerle

http://www.cnn.com/2009/TECH/01/07/wales.obama.cto/index.html


> On another note, I wonder why in the various conversations there seems
> to be pervasive views that a) the FDA won't accept work done in R, and
> b) SAS is the only way to effectively handle data?


I strongly believe that the comments regarding R and the FDA are overly
negative and pessimistic.

The hurdles to the use of R for clinical trials are shrinking. There has
been substantive activity over the past several years, both internally
at the FDA and within the R community to increase R's acceptance in this
domain.

At the Joint Statistical Meetings in 2006, Sue Bell from the FDA spoke
during a session with a presentation entitled Times 'R' A Changing: FDA
Perspectives on Use of "Open Source". A copy of this presentation is
available here:

  http://www.fda.gov/cder/Offices/Biostatistics/Bell.pdf

In 2007, during an FDA committee meeting reviewing the safety profile of
Avandia (Rosiglitazone), the internal FDA meta-analysis performed by Joy
Mele, the FDA statistician, was done using R. A copy of this
presentation is available here:
  http://www.fda.gov/ohrms/dockets/ac/07/slides/2007-4308s1-05-fda-mele.ppt

Given the high profile nature of drug safety issues today, that R was
used for this analysis by the FDA itself speaks volumes.

Also in 2007, at the annual R user meeting at Iowa State University, I
had the pleasure and privilege of Chairing a session on the use of R for
clinical trials. The speakers included Frank Harrell (well known to R
users here), Tony Rossini and David James (Novartis Pharmaceuticals) and
Mat Soukup (FDA statistician). Copies of our presentations are available
here, a little more than half way down the page:

  http://user2007.org/program/

At that meeting, we also introduced a document that has been updated
since then and approved formally by the R Foundation for Statistical
Computing. The document provides guidance for the use of R in the
regulated clinical trials domain, addresses R's compliance with the
relevant regulations (eg. 21 CFR 11) as well as describing the
development, testing and quality processes in place for R, also known as
the Software Development Life Cycle.

That document is available here:

  http://www.r-project.org/doc/R-FDA.pdf

I have heard directly from colleagues in industry that this document has
provided significant value in their internal discussions regarding
implementing the use of R within their respective environments and
assuaging many fears regarding R's use.

Additionally, presentations regarding the use of open source software
and R specifically for clinical trials have been made at DIA and other
industry meetings. This fall, there is a session on the use of R
scheduled for the FDA's Industry Statistics Workshop in Washington,

Re: [R] I'm looking for a book about spatial point patterns (Diggle, 2003)

2009-01-11 Thread Kingsford Jones
Unangu,

If you haven't seen the 200pg workshop notes that Adrian Baddeley has
made available from his spatstat webpage, I highly recommend them:

http://www.csiro.au/files/files/pn0y.pdf


hth,
Kingsford Jones

On Sat, Jan 10, 2009 at 9:04 PM, Unangu  wrote:
>
> To understand some functions about spatial point patterns in "spatstat" ,I
> should know some background about it, and the best way is to read the
> monograph, and  "Statistical Analysis of Spatial Point Patterns" (2nd edt.)
> is a better choise. But I can not find it anywhere I can. Who can help me?
> Thank you!
>
> -
> una...@gmail.com
> --
> View this message in context: 
> http://www.nabble.com/I%27m-looking-for-a-book-about-spatial-point-patterns-%28Diggle%2C2003%29-tp21395908p21395908.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> 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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Re: [R] I'm looking for a book about spatial point patterns (Diggle, 2003)

2009-01-11 Thread milton ruser
Hi Unangu
I also put my two cents on the Kingsford´s suggestion.
The "BOOK" the Adrian turned available are very very well informative!
I enjoyed so much!

Best wishes

miltinho,

brazil

On Sun, Jan 11, 2009 at 3:48 PM, Kingsford Jones
wrote:

> Unangu,
>
> If you haven't seen the 200pg workshop notes that Adrian Baddeley has
> made available from his spatstat webpage, I highly recommend them:
>
> http://www.csiro.au/files/files/pn0y.pdf
>
>
> hth,
> Kingsford Jones
>
> On Sat, Jan 10, 2009 at 9:04 PM, Unangu  wrote:
> >
> > To understand some functions about spatial point patterns in "spatstat"
> ,I
> > should know some background about it, and the best way is to read the
> > monograph, and  "Statistical Analysis of Spatial Point Patterns" (2nd
> edt.)
> > is a better choise. But I can not find it anywhere I can. Who can help
> me?
> > Thank you!
> >
> > -
> > una...@gmail.com
> > --
> > View this message in context:
> http://www.nabble.com/I%27m-looking-for-a-book-about-spatial-point-patterns-%28Diggle%2C2003%29-tp21395908p21395908.html
> > Sent from the R help mailing list archive at Nabble.com.
> >
> > __
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

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


[R] R, clinical trials and the FDA

2009-01-11 Thread Kingsford Jones
I hope that Marc doesn't mind, but I felt that part of his recent post
was important enough to deserve it's own subject line rather then
being lost in a 60-msg-long thread...



On Sun, Jan 11, 2009 at 10:08 AM, Marc Schwartz
 wrote:

...

I strongly believe that the comments regarding R and the FDA are overly
negative and pessimistic.

The hurdles to the use of R for clinical trials are shrinking. There has
been substantive activity over the past several years, both internally
at the FDA and within the R community to increase R's acceptance in this
domain.

At the Joint Statistical Meetings in 2006, Sue Bell from the FDA spoke
during a session with a presentation entitled Times 'R' A Changing: FDA
Perspectives on Use of "Open Source". A copy of this presentation is
available here:

 http://www.fda.gov/cder/Offices/Biostatistics/Bell.pdf

In 2007, during an FDA committee meeting reviewing the safety profile of
Avandia (Rosiglitazone), the internal FDA meta-analysis performed by Joy
Mele, the FDA statistician, was done using R. A copy of this
presentation is available here:
 http://www.fda.gov/ohrms/dockets/ac/07/slides/2007-4308s1-05-fda-mele.ppt

Given the high profile nature of drug safety issues today, that R was
used for this analysis by the FDA itself speaks volumes.

Also in 2007, at the annual R user meeting at Iowa State University, I
had the pleasure and privilege of Chairing a session on the use of R for
clinical trials. The speakers included Frank Harrell (well known to R
users here), Tony Rossini and David James (Novartis Pharmaceuticals) and
Mat Soukup (FDA statistician). Copies of our presentations are available
here, a little more than half way down the page:

 http://user2007.org/program/

At that meeting, we also introduced a document that has been updated
since then and approved formally by the R Foundation for Statistical
Computing. The document provides guidance for the use of R in the
regulated clinical trials domain, addresses R's compliance with the
relevant regulations (eg. 21 CFR 11) as well as describing the
development, testing and quality processes in place for R, also known as
the Software Development Life Cycle.

That document is available here:

 http://www.r-project.org/doc/R-FDA.pdf

I have heard directly from colleagues in industry that this document has
provided significant value in their internal discussions regarding
implementing the use of R within their respective environments and
assuaging many fears regarding R's use.

Additionally, presentations regarding the use of open source software
and R specifically for clinical trials have been made at DIA and other
industry meetings. This fall, there is a session on the use of R
scheduled for the FDA's Industry Statistics Workshop in Washington, D.C.

For those unfamiliar, I would also point out the membership and
financial donors to the R Foundation for Statistical Computing and take
note of the plethora of large pharma companies and clinical research
institutions:

 http://www.r-project.org/foundation/memberlist.html

The use of R within this domain is increasing and will only continue to
progress as R's value becomes increasingly clear to even risk averse
industry decision makers.


Regards,

Marc Schwartz

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Re: [R] R, clinical trials and the FDA

2009-01-11 Thread Marc Schwartz
I don't mind at all.

Very kind of you Kingsford.

Thanks,

Marc

on 01/11/2009 01:05 PM Kingsford Jones wrote:
> I hope that Marc doesn't mind, but I felt that part of his recent post
> was important enough to deserve it's own subject line rather then
> being lost in a 60-msg-long thread...
> 
> 
> 
> On Sun, Jan 11, 2009 at 10:08 AM, Marc Schwartz
>  wrote:
> 
> ...
> 
> I strongly believe that the comments regarding R and the FDA are overly
> negative and pessimistic.
> 
> The hurdles to the use of R for clinical trials are shrinking. There has
> been substantive activity over the past several years, both internally
> at the FDA and within the R community to increase R's acceptance in this
> domain.
> 
> At the Joint Statistical Meetings in 2006, Sue Bell from the FDA spoke
> during a session with a presentation entitled Times 'R' A Changing: FDA
> Perspectives on Use of "Open Source". A copy of this presentation is
> available here:
> 
>  http://www.fda.gov/cder/Offices/Biostatistics/Bell.pdf
> 
> In 2007, during an FDA committee meeting reviewing the safety profile of
> Avandia (Rosiglitazone), the internal FDA meta-analysis performed by Joy
> Mele, the FDA statistician, was done using R. A copy of this
> presentation is available here:
>  http://www.fda.gov/ohrms/dockets/ac/07/slides/2007-4308s1-05-fda-mele.ppt
> 
> Given the high profile nature of drug safety issues today, that R was
> used for this analysis by the FDA itself speaks volumes.
> 
> Also in 2007, at the annual R user meeting at Iowa State University, I
> had the pleasure and privilege of Chairing a session on the use of R for
> clinical trials. The speakers included Frank Harrell (well known to R
> users here), Tony Rossini and David James (Novartis Pharmaceuticals) and
> Mat Soukup (FDA statistician). Copies of our presentations are available
> here, a little more than half way down the page:
> 
>  http://user2007.org/program/
> 
> At that meeting, we also introduced a document that has been updated
> since then and approved formally by the R Foundation for Statistical
> Computing. The document provides guidance for the use of R in the
> regulated clinical trials domain, addresses R's compliance with the
> relevant regulations (eg. 21 CFR 11) as well as describing the
> development, testing and quality processes in place for R, also known as
> the Software Development Life Cycle.
> 
> That document is available here:
> 
>  http://www.r-project.org/doc/R-FDA.pdf
> 
> I have heard directly from colleagues in industry that this document has
> provided significant value in their internal discussions regarding
> implementing the use of R within their respective environments and
> assuaging many fears regarding R's use.
> 
> Additionally, presentations regarding the use of open source software
> and R specifically for clinical trials have been made at DIA and other
> industry meetings. This fall, there is a session on the use of R
> scheduled for the FDA's Industry Statistics Workshop in Washington, D.C.
> 
> For those unfamiliar, I would also point out the membership and
> financial donors to the R Foundation for Statistical Computing and take
> note of the plethora of large pharma companies and clinical research
> institutions:
> 
>  http://www.r-project.org/foundation/memberlist.html
> 
> The use of R within this domain is increasing and will only continue to
> progress as R's value becomes increasingly clear to even risk averse
> industry decision makers.
> 
> 
> Regards,
> 
> Marc Schwartz
>

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Re: [R] How to get solution of following polynomial?

2009-01-11 Thread Ravi Varadhan
Hi,

You can use the "polynomial" package to solve your problem.

The key step is to find the exact polynomial representation of fn().  Noting 
that it is a 8-th degree polynomial, we can get its exact form using the 
poly.calc() function.  Once we have that, it is a simple matter of finding the 
roots using the solve() function.

require(polynomial)

a <- c(-0.07, 0.17)
b <- c(1, -4)
cc <- matrix(c(0.24, 0.00, -0.08, -0.31), 2)
d <- matrix(c(0, 0, -0.13, -0.37), 2)
e <- matrix(c(0.2, 0, -0.06, -0.34), 2)
A1 <- diag(2) + a %*% t(b) + cc
A2 <- -cc + d
A3 <- -d + e
A4 <- -e

# I am vectorizing your function
fn <- function(z)
   {
sapply(z, function(z) {
y <- diag(2) - A1*z - A2*z^2 - A3*z^3 - A4*z^4
det(y)
})
   }


x <- seq(-5, 5, length=9) # note we need 9 points to exactly determine a 8-th 
degree polynomial
y <- fn(x)

p <- poly.calc(x, y)  # uses Lagrange interpolation to determine polynomial form
p
> 1 - 1.18*x + 0.2777*x^2 - 0.2941*x^3 - 0.1004*x^4 + 0.3664*x^5 - 0.0636*x^6 + 
> 0.062*x^7 - 0.068*x^8 

# plot showing that p is the exact polynomial representation of fn(z)
pfunc <- as.function(p)
x1 <-seq(-5, 5, length=100)
plot(x1, fn(x1),type="l")
lines(x1, pfunc(x1), col=2, lty=2)   

solve(p)  # gives you the roots (some are, of course, complex)


Hope this helps,
Ravi.





Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University

Ph. (410) 502-2619
email: rvarad...@jhmi.edu


- Original Message -
From: RON70 
Date: Sunday, January 11, 2009 1:05 am
Subject: [R]  How to get solution of following polynomial?
To: r-help@r-project.org


>  Hi, I want find all roots for the following polynomial :
>  
>  a <- c(-0.07, 0.17); b <- c(1, -4); cc <- matrix(c(0.24, 0.00, -0.08,
>  -0.31), 2); d <- matrix(c(0, 0, -0.13, -0.37), 2); e <- matrix(c(0.2, 
> 0,
>  -0.06, -0.34), 2)
>  A1 <- diag(2) + a %*% t(b) + cc; A2 <- -cc + d; A3 <- -d + e; A4 <- -e
>  fn <- function(z)
> {
>  y <- diag(2) - A1*z - A2*z^2 - A3*z^3 - A4*z^4
>  return(det(y))
> }; uniroot(fn, c(-10, 1))
>  
>  Using uniroot function, I got only one solution of that. Is there any
>  function to get all four solutions? I looked at polyroot() function, 
> but I
>  do not think it will work for my problem, because, my coef. are 
> matrix, nor
>  number
>  
>  Thanks
> 
>  
>  
>  -- 
>  View this message in context: 
>  Sent from the R help mailing list archive at Nabble.com.
>  
>  __
>  R-help@r-project.org mailing list
>  
>  PLEASE do read the posting guide 
>  and provide commented, minimal, self-contained, reproducible code.

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[R] summary with variance / sd

2009-01-11 Thread Jörg Groß

Hi,

I have a data frame and would like to have summary statistics for  
grouped data.


With summary() I get the central tendencies for the overall data.


How can I get descriptive statistics with variances and standard  
deviations?



for example my data.frame:

group   x   y
exp 2   4
exp 3   5
exp 2   4
control 1   2
control 2   3
control 1   2


now I want tables with summary statistics (variances included) for  
each group.


Is there an easy way to get this?

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Re: [R] summary with variance / sd

2009-01-11 Thread Stephan Kolassa

Hi Jörg,

?by

here probably something like

by(data=mydata,INDICES=mydata$group, FUN=sd, ...)

HTH,
Stephan


Jörg Groß schrieb:

Hi,

I have a data frame and would like to have summary statistics for 
grouped data.


With summary() I get the central tendencies for the overall data.


How can I get descriptive statistics with variances and standard 
deviations?



for example my data.frame:

groupxy
exp24
exp35
exp24
control12
control23
control12


now I want tables with summary statistics (variances included) for each 
group.


Is there an easy way to get this?

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

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



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[R] boxplots: yaxp does not work

2009-01-11 Thread Jörg Groß

Hi,

I'd like to change the y-tickmarks of a boxplot.
But it doesn't work with yaxp (like I would do it in a plot-function).

Can someone help me out?

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Re: [R] summary with variance / sd

2009-01-11 Thread Søren Højsgaard
You can use summaryBy() in the doBy package:
 
summaryBy(y+x~group, data=mydata, FUN=c(mean,sd))
 
Søren



Fra: r-help-boun...@r-project.org på vegne af Jörg Groß
Sendt: sø 11-01-2009 22:38
Til: r-help@r-project.org
Emne: [R] summary with variance / sd



Hi,

I have a data frame and would like to have summary statistics for 
grouped data.

With summary() I get the central tendencies for the overall data.


How can I get descriptive statistics with variances and standard 
deviations?


for example my data.frame:

group   x   y
exp 2   4
exp 3   5
exp 2   4
control 1   2
control 2   3
control 1   2


now I want tables with summary statistics (variances included) for 
each group.

Is there an easy way to get this?

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

__
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Re: [R] summary with variance / sd

2009-01-11 Thread David Winsemius


On Jan 11, 2009, at 4:38 PM, Jörg Groß wrote:


Hi,

I have a data frame and would like to have summary statistics for  
grouped data.


With summary() I get the central tendencies for the overall data.


How can I get descriptive statistics with variances and standard  
deviations?


In the future, you really should do your own searching before posting  
this sort of basic question.



help.search("standard deviation")  produced reference to a function  
with the obvious name "sd"
Using the same strategy for variance produces a longer list but "var"  
is among them.



for example my data.frame:

group   x   y
exp 2   4
exp 3   5
exp 2   4
control 1   2
control 2   3
control 1   2


#Create dataframe ( and please note that you are asked to offer  
examples in a form that does not require responders to create the  
objects for you):

 df1 <- read.table(stdin(), header=TRUE)

#Paste in the data:
0: groupxy
1: exp24
2: exp35
3: exp24
4: control12
5: control23
6: control12
# empty line stops input.

by(data=df1, df1$group, summary)
by(data=df1, df1$group, sd)
by(data=df1, df1$group, var)

Or use negative indexing to exclude the first column,  and add  
some annotation to do it in one step


by(data=df1[-1], df1$group, function(x){ list(summary(x), "Group S.D.s  
are ...", sd(x), "Group Variances are ...", var(x) )} )



You could also look at how the pro's do constructed summary()  by  
reviewing the code of:


base:::summary.default
base:::summary.data.frame

--
David Winsemius






now I want tables with summary statistics (variances included) for  
each group.


Is there an easy way to get this?

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


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Re: [R] Boxplot from matrices

2009-01-11 Thread johnhj

Thank you very much for you help...




Carlos J. Gil Bellosta wrote:
> 
> Hello,
> 
> The following code may help you:
> 
>> my.matrix <- matrix( rnorm(16), ncol = 4 )
>> boxplot( my.matrix ~ col(  my.matrix ) )
> 
> Best regards,
> 
> Carlos J. Gil Bellosta
> http://www.datanalytics.com
> 
> 
> 
> On Sun, 2009-01-11 at 05:23 -0800, johnhj wrote:
>> Hii,
>> 
>> I will create boxplots from matrices. I have the following data sets:
>> 5.0  1.78  2.99  2.019 0
>> 10.0  1.79  3.00  1.744 0
>> 15.0  1.78  2.98  1.936 0
>> 20.0  1.78  2.99  1.975 0
>> 25.0  1.73  2.91  3.591 0
>> 30.0  1.79  3.00  1.966 0
>> 35.0  1.79  3.00  2.451 0
>> 40.0  1.79  3.00  1.853 0
>> 45.0  1.79  3.00  2.077 0
>> 50.0  1.79  3.00  1.943 0
>> 55.0  1.79  3.00  2.608 0
>> 60.0  1.79  3.00  1.790 0
>> 65.0  1.79  3.00  1.893 0
>> 70.0  1.79  3.00  2.079 0
>> 75.0  1.77  2.97  2.200 0
>> 80.0  1.79  3.01  1.868 0
>> 85.0  1.78  2.99  2.179 0
>> 90.0  1.70  2.85  2.305 0
>> 95.0  1.71  2.87  1.854 0
>> 100.0  1.79  3.00  2.362 0
>> 105.0  1.79  3.00  3.634 0
>> 110.0  1.79  3.00  1.578 0
>> 115.0  1.79  3.00  1.835 0
>> 120.0  1.79  3.00  2.359 0
>> 125.0  1.79  3.00  2.542 0
>> 130.0  1.76  2.95  2.620 0
>> 135.0  1.79  3.00  4.181 0
>> 140.0  1.79  3.00  1.375 0
>> 145.0  1.79  3.00  2.872 0
>> 150.0  1.79  3.00  3.002 0
>> 155.0  1.79  3.00  3.712 0
>> 160.0  1.79  3.01  3.175 0
>> 165.0  1.79  3.00  2.821 0
>> 170.0  1.79  3.00  3.320 0.078
>> 175.0  1.79  3.00  2.076 0
>> 180.0  1.77  2.97  2.186 0
>> 185.0  1.78  2.99  4.652 0
>> 190.0  1.79  3.01  2.051 0
>> 195.0  1.79  3.00  1.922 0
>> 200.0  1.79  3.00  1.945 0
>> 
>> The first thing I do is, to run the command
>> y<-matrix(c(test$V3),ncol=8)
>> to divide the third column in 8 matrices to create 8 boxplots.
>> The I run the command
>> w<-summary(y) 
>> to get the values min, max, mean, median, 1.Quan, 3.Quan
>> 
>> My problem is, I cann't run the plot command to create the 8 boxplots in
>> a
>> graph...
>> The command 
>> plot(y)
>> gives me an error..
>> 
>> Can anybody help me to create the boxplot from matrices in a graph ?
>> 
>> greetings,
>> j
>>
> 
> __
> R-help@r-project.org mailing list
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> 

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[R] connecting boxplots

2009-01-11 Thread johnhj

Hii,

I created some boxplots with this commands:

x <-read.table(file="test.txt") 
x$group <- rep(1:8, each=5)
boxplot(V3~gruppe, data=x) 

Now, I will connect the boxplots to each other to the min, max and median
values. 
Can anybody help me how to do it ?

greetings,
J
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Re: [R] How to get solution of following polynomial?

2009-01-11 Thread RON70

Hi Ravi, Thanks for this reply. However I could not understand meaning of
"vectorizing the function". Can you please be little bit elaborate on that?
Secondly the package "polynomial" is not available in CRAN it seems. What is
the alternate package?

Thanks,


Ravi Varadhan wrote:
> 
> Hi,
> 
> You can use the "polynomial" package to solve your problem.
> 
> The key step is to find the exact polynomial representation of fn(). 
> Noting that it is a 8-th degree polynomial, we can get its exact form
> using the poly.calc() function.  Once we have that, it is a simple matter
> of finding the roots using the solve() function.
> 
> require(polynomial)
> 
> a <- c(-0.07, 0.17)
> b <- c(1, -4)
> cc <- matrix(c(0.24, 0.00, -0.08, -0.31), 2)
> d <- matrix(c(0, 0, -0.13, -0.37), 2)
> e <- matrix(c(0.2, 0, -0.06, -0.34), 2)
> A1 <- diag(2) + a %*% t(b) + cc
> A2 <- -cc + d
> A3 <- -d + e
> A4 <- -e
> 
> # I am vectorizing your function
> fn <- function(z)
>{
> sapply(z, function(z) {
>   y <- diag(2) - A1*z - A2*z^2 - A3*z^3 - A4*z^4
>   det(y)
>   })
>}
> 
> 
> x <- seq(-5, 5, length=9) # note we need 9 points to exactly determine a
> 8-th degree polynomial
> y <- fn(x)
> 
> p <- poly.calc(x, y)  # uses Lagrange interpolation to determine
> polynomial form
> p
>> 1 - 1.18*x + 0.2777*x^2 - 0.2941*x^3 - 0.1004*x^4 + 0.3664*x^5 -
>> 0.0636*x^6 + 0.062*x^7 - 0.068*x^8 
> 
> # plot showing that p is the exact polynomial representation of fn(z)
> pfunc <- as.function(p)
> x1 <-seq(-5, 5, length=100)
> plot(x1, fn(x1),type="l")
> lines(x1, pfunc(x1), col=2, lty=2)   
> 
> solve(p)  # gives you the roots (some are, of course, complex)
> 
> 
> Hope this helps,
> Ravi.
> 
> 
> 
> 
> 
> Ravi Varadhan, Ph.D.
> Assistant Professor,
> Division of Geriatric Medicine and Gerontology
> School of Medicine
> Johns Hopkins University
> 
> Ph. (410) 502-2619
> email: rvarad...@jhmi.edu
> 
> 
> - Original Message -
> From: RON70 
> Date: Sunday, January 11, 2009 1:05 am
> Subject: [R]  How to get solution of following polynomial?
> To: r-help@r-project.org
> 
> 
>>  Hi, I want find all roots for the following polynomial :
>>  
>>  a <- c(-0.07, 0.17); b <- c(1, -4); cc <- matrix(c(0.24, 0.00, -0.08,
>>  -0.31), 2); d <- matrix(c(0, 0, -0.13, -0.37), 2); e <- matrix(c(0.2, 
>> 0,
>>  -0.06, -0.34), 2)
>>  A1 <- diag(2) + a %*% t(b) + cc; A2 <- -cc + d; A3 <- -d + e; A4 <- -e
>>  fn <- function(z)
>> {
>>  y <- diag(2) - A1*z - A2*z^2 - A3*z^3 - A4*z^4
>>  return(det(y))
>> }; uniroot(fn, c(-10, 1))
>>  
>>  Using uniroot function, I got only one solution of that. Is there any
>>  function to get all four solutions? I looked at polyroot() function, 
>> but I
>>  do not think it will work for my problem, because, my coef. are 
>> matrix, nor
>>  number
>>  
>>  Thanks
>> 
>>  
>>  
>>  -- 
>>  View this message in context: 
>>  Sent from the R help mailing list archive at Nabble.com.
>>  
>>  __
>>  R-help@r-project.org mailing list
>>  
>>  PLEASE do read the posting guide 
>>  and provide commented, minimal, self-contained, reproducible code.
> 
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> 

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Re: [R] boxplots: yaxp does not work

2009-01-11 Thread jim holtman
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

I have no idea of what you would like to do with the tick marks.  I
assume you can always use 'axis' to label your axis:

boxplot(len ~ dose, data = ToothGrowth,
boxwex = 0.25, at = 1:3 + 0.2, yaxt='n',
subset = supp == "OJ", col = "orange")
axis(2, at=7:31, labels=rep("",25))   # put tick mark every number

axis(2, at=seq(7,31,5))  # put labels on some



On Sun, Jan 11, 2009 at 5:38 PM, Jörg Groß  wrote:
> Hi,
>
> I'd like to change the y-tickmarks of a boxplot.
> But it doesn't work with yaxp (like I would do it in a plot-function).
>
> Can someone help me out?
>
> __
> 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.
>



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

What is the problem that you are trying to solve?

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[R] Orthogonal Complement

2009-01-11 Thread megh

Is there any R function which calculate the Orthogonal Complement of a mxn
matrix (with full column rank)?

Thanks in advance
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Re: [R] Orthogonal Complement

2009-01-11 Thread Richard M. Heiberger
Yes, download the HH package from CRAN and then see
?HH::orthog.complete
for the function description and several examples.

Rich

-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of megh
Sent: Sunday, January 11, 2009 19:29
To: r-help@r-project.org
Subject: [R] Orthogonal Complement


Is there any R function which calculate the Orthogonal Complement of a mxn
matrix (with full column rank)?

Thanks in advance
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[R] R "Threatens" SAS According to The NYT

2009-01-11 Thread Farrel Buchinsky
The article was dugg on Digg.
http://digg.com/software/Data_Analysts_Captivated_by_R_s_Power_3

If you Digg, why not digg this.

Farrel Buchinsky

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[R] writing an own function - is.factor

2009-01-11 Thread Jörg Groß

Hi,

I try to write an own function in R.
I want a summary table with descriptive statistics.


For example, I have this data.frame:


 d <- data.frame(c(rep("m",5), rep("f",5)), c(1:10))
 names(d) <- c("x", "y")
 d
 x  y
1   m  1
2   m  2
3   m  3
4   m  4
5   m  5
6   f  6
7   f  7
8   f  8
9   f  9
10  f 10


now I want to get the mean and sd, as long as the column is not of  
type factor.

So the function should skip the first column.


But how can I check this, if I don't know the column name?

Because

is.factor(d[1])
produces "FALSE".

Only
is.factor(d$x)
gives the correct result.


But how can I check the column if I don't know the column name?


I tried s.th. like this;

is.factor(d$names(d[1]))


but that kind of structure is not possible.



Can someone help me with that problem?

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[R] Spitting a df Column Name

2009-01-11 Thread jimdare

Hi,

If I have the following column names: 

names(data)
[1] "count.run"   "count.walk"   "count.drive"

How do I split these so i get

names(datanamessplit)
[1] "run"   "walk"   "drive"

Thanks for your help,
Jim
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[R] fitting curve to data

2009-01-11 Thread Nathan S. Watson-Haigh
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

I have the following data:

> y
 [1] 0.000 0.004 0.008 0.016 0.024 0.032 0.044 0.064 0.072 0.088 0.108 0.140
[13] 0.156 0.180 0.208 0.236 0.264 0.296 0.320 0.360 0.408 0.444 0.472 0.524
[25] 0.576
> x
 [1]  100  200  300  400  500  600  700  800  900 1000 1100 1200 1300 1400 1500
[16] 1600 1700 1800 1900 2000 2100 2200 2300 2400 2500

I'd like to plot the points and calculate a curved line of best fit. I know I 
need to use nls(), but
I'm unsure how to beginany pointers?

Cheers,
Nathan


- --
- 
Dr. Nathan S. Watson-Haigh
OCE Post Doctoral Fellow
CSIRO Livestock Industries
Queensland Bioscience Precinct
St Lucia, QLD 4067
Australia

Tel: +61 (0)7 3214 2922
Fax: +61 (0)7 3214 2900
Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html
- 

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iEYEARECAAYFAklqqJsACgkQ9gTv6QYzVL4gCgCgy4qShoFX/9QWgKsBqHPhLCDS
r+AAnRD3kbkImG3rVaBN6d4BP2cUmqYZ
=yVLj
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Re: [R] Spitting a df Column Name

2009-01-11 Thread Simon Blomberg
names(datanamessplit) <- gsub("count.", "", names(data))


On Sun, 2009-01-11 at 18:13 -0800, jimdare wrote:
> Hi,
> 
> If I have the following column names: 
> 
> names(data)
> [1] "count.run"   "count.walk"   "count.drive"
> 
> How do I split these so i get
> 
> names(datanamessplit)
> [1] "run"   "walk"   "drive"
> 
> Thanks for your help,
> Jim
-- 
Simon Blomberg, BSc (Hons), PhD, MAppStat. 
Lecturer and Consultant Statistician 
Faculty of Biological and Chemical Sciences 
The University of Queensland 
St. Lucia Queensland 4072 
Australia
Room 320 Goddard Building (8)
T: +61 7 3365 2506
http://www.uq.edu.au/~uqsblomb
email: S.Blomberg1_at_uq.edu.au

Policies:
1.  I will NOT analyse your data for you.
2.  Your deadline is your problem.

The combination of some data and an aching desire for 
an answer does not ensure that a reasonable answer can 
be extracted from a given body of data. - John Tukey.

__
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Re: [R] writing an own function - is.factor

2009-01-11 Thread jim holtman
try this:

> d <- data.frame(c(rep("m",5), rep("f",5)), c(1:10))
>  names(d) <- c("x", "y")
>  d
   x  y
1  m  1
2  m  2
3  m  3
4  m  4
5  m  5
6  f  6
7  f  7
8  f  8
9  f  9
10 f 10
> lapply(d, function(x) if (is.numeric(x)) c(mean=mean(x), sd=sd(x)))
$x
NULL

$y
mean   sd
5.50 3.027650

>


On Sun, Jan 11, 2009 at 9:04 PM, Jörg Groß  wrote:
> Hi,
>
> I try to write an own function in R.
> I want a summary table with descriptive statistics.
>
>
> For example, I have this data.frame:
>
>
>  d <- data.frame(c(rep("m",5), rep("f",5)), c(1:10))
>  names(d) <- c("x", "y")
>  d
> x  y
> 1   m  1
> 2   m  2
> 3   m  3
> 4   m  4
> 5   m  5
> 6   f  6
> 7   f  7
> 8   f  8
> 9   f  9
> 10  f 10
>
>
> now I want to get the mean and sd, as long as the column is not of type
> factor.
> So the function should skip the first column.
>
>
> But how can I check this, if I don't know the column name?
>
> Because
>
> is.factor(d[1])
> produces "FALSE".
>
> Only
> is.factor(d$x)
> gives the correct result.
>
>
> But how can I check the column if I don't know the column name?
>
>
> I tried s.th. like this;
>
> is.factor(d$names(d[1]))
>
>
> but that kind of structure is not possible.
>
>
>
> Can someone help me with that problem?
>
> __
> 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.
>



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

What is the problem that you are trying to solve?

__
R-help@r-project.org mailing list
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Re: [R] fitting curve to data

2009-01-11 Thread Simon Blomberg
First, try plot(x,y)


If you want to use nls, you have to specify a nonlinear function to fit
to your data. See ?nls.

If you are really stuck on how to fit regression models, you should
consult a statistician (CSIRO has a lot of expertise).

Simon.

On Mon, 2009-01-12 at 12:19 +1000, Nathan S. Watson-Haigh wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> I have the following data:
> 
> > y
>  [1] 0.000 0.004 0.008 0.016 0.024 0.032 0.044 0.064 0.072 0.088 0.108 0.140
> [13] 0.156 0.180 0.208 0.236 0.264 0.296 0.320 0.360 0.408 0.444 0.472 0.524
> [25] 0.576
> > x
>  [1]  100  200  300  400  500  600  700  800  900 1000 1100 1200 1300 1400 
> 1500
> [16] 1600 1700 1800 1900 2000 2100 2200 2300 2400 2500
> 
> I'd like to plot the points and calculate a curved line of best fit. I know I 
> need to use nls(), but
> I'm unsure how to beginany pointers?
> 
> Cheers,
> Nathan
> 
> 
> - --
> - 
> Dr. Nathan S. Watson-Haigh
> OCE Post Doctoral Fellow
> CSIRO Livestock Industries
> Queensland Bioscience Precinct
> St Lucia, QLD 4067
> Australia
> 
> Tel: +61 (0)7 3214 2922
> Fax: +61 (0)7 3214 2900
> Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html
> - 
> 
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.9 (MingW32)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
> 
> iEYEARECAAYFAklqqJsACgkQ9gTv6QYzVL4gCgCgy4qShoFX/9QWgKsBqHPhLCDS
> r+AAnRD3kbkImG3rVaBN6d4BP2cUmqYZ
> =yVLj
> -END PGP SIGNATURE-
> 
> __
> 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.
-- 
Simon Blomberg, BSc (Hons), PhD, MAppStat. 
Lecturer and Consultant Statistician 
Faculty of Biological and Chemical Sciences 
The University of Queensland 
St. Lucia Queensland 4072 
Australia
Room 320 Goddard Building (8)
T: +61 7 3365 2506
http://www.uq.edu.au/~uqsblomb
email: S.Blomberg1_at_uq.edu.au

Policies:
1.  I will NOT analyse your data for you.
2.  Your deadline is your problem.

The combination of some data and an aching desire for 
an answer does not ensure that a reasonable answer can 
be extracted from a given body of data. - John Tukey.

__
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
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Re: [R] fitting curve to data

2009-01-11 Thread Gabor Grothendieck
As x goes from 200 to 400, y goes from ,004 to .016 so y is
quadrupling while x doubles -- quadratic growth.Fitting
to a quadratic and plotting shows this to be the case.  Note
that for y to be quadratic in x it must be linear in the coefficients
of x so we can just use lm and don't need nls:

plot(y ~ x)
y.lm <- lm(y ~ poly(x, 2))
lines(x, fitted(y.lm))
y.lm

On Sun, Jan 11, 2009 at 9:19 PM, Nathan S. Watson-Haigh
 wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> I have the following data:
>
>> y
>  [1] 0.000 0.004 0.008 0.016 0.024 0.032 0.044 0.064 0.072 0.088 0.108 0.140
> [13] 0.156 0.180 0.208 0.236 0.264 0.296 0.320 0.360 0.408 0.444 0.472 0.524
> [25] 0.576
>> x
>  [1]  100  200  300  400  500  600  700  800  900 1000 1100 1200 1300 1400 
> 1500
> [16] 1600 1700 1800 1900 2000 2100 2200 2300 2400 2500
>
> I'd like to plot the points and calculate a curved line of best fit. I know I 
> need to use nls(), but
> I'm unsure how to beginany pointers?
>
> Cheers,
> Nathan
>
>
> - --
> - 
> Dr. Nathan S. Watson-Haigh
> OCE Post Doctoral Fellow
> CSIRO Livestock Industries
> Queensland Bioscience Precinct
> St Lucia, QLD 4067
> Australia
>
> Tel: +61 (0)7 3214 2922
> Fax: +61 (0)7 3214 2900
> Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html
> - 
>
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> Version: GnuPG v1.4.9 (MingW32)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iEYEARECAAYFAklqqJsACgkQ9gTv6QYzVL4gCgCgy4qShoFX/9QWgKsBqHPhLCDS
> r+AAnRD3kbkImG3rVaBN6d4BP2cUmqYZ
> =yVLj
> -END PGP SIGNATURE-
>
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> 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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Re: [R] fitting curve to data

2009-01-11 Thread S Ellison
Just 'cos it's bent doesn't mean you need nls.

With your data, lm fits (suspicously!) well...

y<-c(0.000,0.004,0.008,0.016,0.024,0.032,0.044,0.064,0.072,0.088,0.108,0.140
,0.156,0.180,0.208,0.236,0.264,0.296,0.320,0.360,0.408,0.444,0.472,0.524
,0.576)
x<-c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500
,1600,1700,1800,1900,2000,2100,2200,2300,2400,2500)
plot(x,y)
lines(x, predict(lm(y~I(x^2


>>> "Nathan S. Watson-Haigh"  01/12/09
2:19 AM >>>
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

I have the following data:

> y
 [1] 0.000 0.004 0.008 0.016 0.024 0.032 0.044 0.064 0.072 0.088 0.108
0.140
[13] 0.156 0.180 0.208 0.236 0.264 0.296 0.320 0.360 0.408 0.444 0.472
0.524
[25] 0.576
> x
 [1]  100  200  300  400  500  600  700  800  900 1000 1100 1200 1300
1400 1500
[16] 1600 1700 1800 1900 2000 2100 2200 2300 2400 2500

I'd like to plot the points and calculate a curved line of best fit. I
know I need to use nls(), but
I'm unsure how to beginany pointers?

Cheers,
Nathan


- --
- 
Dr. Nathan S. Watson-Haigh
OCE Post Doctoral Fellow
CSIRO Livestock Industries
Queensland Bioscience Precinct
St Lucia, QLD 4067
Australia

Tel: +61 (0)7 3214 2922
Fax: +61 (0)7 3214 2900
Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html
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Re: [R] writing an own function - is.factor

2009-01-11 Thread Stavros Macrakis
On Sun, Jan 11, 2009 at 9:04 PM, Jörg Groß  wrote:

> ...now I want to get the mean and sd, as long as the column is not of type
> factor.
> ...But how can I check this, if I don't know the column name?
>
...
> is.factor(d[1])
> produces "FALSE".
>

Try is.factor(d[[1]]).  Remember that in R, x[...] selects a *subsequence*,
not an *element*.  Only x[[...]] selects an element. What makes this
confusing to learn is that for vectors, a subsequence of length 1 is treated
the same as an element.  But for lists, they are not the same thing.

You can iterate over the columns in various ways, e.g.

for (i in 1:length(d)) ... d[[i]] ...
for (i in names(d)) ... d[[i]] ...


>
> Only
> is.factor(d$x)
> gives the correct result.
>

Remember that

   d$x == d[["x"]]

Hope this helps,

  -s

[[alternative HTML version deleted]]

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Re: [R] connecting boxplots

2009-01-11 Thread johnhj

In other words: I will connect the median, min and the max area of the
boxplot with a line.
The function lines() could help me, but I don't know which parameters the
lines() function should have. 

 
 




johnhj wrote:
> 
> Hii,
> 
> I created some boxplots with this commands:
> 
> x <-read.table(file="test.txt")   
> x$group <- rep(1:8, each=5)
> boxplot(V3~gruppe, data=x) 
> 
> Now, I will connect the boxplots to each other to the min, max and median
> values. 
> Can anybody help me how to do it ?
> 
> greetings,
> J
> 

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Re: [R] I'm looking for a book about spatial point patterns (Diggle, 2003)

2009-01-11 Thread Unangu

Hi,Jones,
Got it! And only pn0y is enough? 
Best wishes and Happy New Year!


Kingsford Jones wrote:
> 
> Unangu,
> 
> If you haven't seen the 200pg workshop notes that Adrian Baddeley has
> made available from his spatstat webpage, I highly recommend them:
> 
> http://www.csiro.au/files/files/pn0y.pdf
> 
> 
> hth,
> Kingsford Jones
> 
> On Sat, Jan 10, 2009 at 9:04 PM, Unangu  wrote:
>>
>> To understand some functions about spatial point patterns in "spatstat"
>> ,I
>> should know some background about it, and the best way is to read the
>> monograph, and  "Statistical Analysis of Spatial Point Patterns" (2nd
>> edt.)
>> is a better choise. But I can not find it anywhere I can. Who can help
>> me?
>> Thank you!
>>
>> -
>> una...@gmail.com
>> --
>> View this message in context:
>> http://www.nabble.com/I%27m-looking-for-a-book-about-spatial-point-patterns-%28Diggle%2C2003%29-tp21395908p21395908.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
> 
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> 


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Re: [R] fitting curve to data

2009-01-11 Thread Nathan S. Watson-Haigh
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

S Ellison wrote:
> Just 'cos it's bent doesn't mean you need nls.

Sorry, my bad! :o(


> With your data, lm fits (suspicously!) well...

Nothing suspiciousjust benchmarking some functions with different sized 
inputs!

Thanks for the help!
Nathan

> 
> y<-c(0.000,0.004,0.008,0.016,0.024,0.032,0.044,0.064,0.072,0.088,0.108,0.140
> ,0.156,0.180,0.208,0.236,0.264,0.296,0.320,0.360,0.408,0.444,0.472,0.524
> ,0.576)
> x<-c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500
> ,1600,1700,1800,1900,2000,2100,2200,2300,2400,2500)
> plot(x,y)
> lines(x, predict(lm(y~I(x^2
> 
> 
 "Nathan S. Watson-Haigh"  01/12/09
> 2:19 AM >>>
> I have the following data:
> 
>> y
>  [1] 0.000 0.004 0.008 0.016 0.024 0.032 0.044 0.064 0.072 0.088 0.108
> 0.140
> [13] 0.156 0.180 0.208 0.236 0.264 0.296 0.320 0.360 0.408 0.444 0.472
> 0.524
> [25] 0.576
>> x
>  [1]  100  200  300  400  500  600  700  800  900 1000 1100 1200 1300
> 1400 1500
> [16] 1600 1700 1800 1900 2000 2100 2200 2300 2400 2500
> 
> I'd like to plot the points and calculate a curved line of best fit. I
> know I need to use nls(), but
> I'm unsure how to beginany pointers?
> 
> Cheers,
> Nathan
> 
> 

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Queensland Bioscience Precinct
St Lucia, QLD 4067
Australia

Tel: +61 (0)7 3214 2922
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Re: [R] I'm looking for a book about spatial point patterns (Diggle, 2003)

2009-01-11 Thread Unangu

Hi miltinho,
The book "Analysing Spatial Point Pattern Data" is still coming soon. I
concerned it for a long time. Do you get it? Just like you said, I think it
will be very very well informative!
Thank you!
I have some 100m*100m plot data about almost one tree species, but I do not
know how to explain it well. Only the analysing result is not enough, the
ecological background is important.
Perhaps, I can image the process of the forest... ...
Seedlings, juniors, small trees, and big trees, then/with competition and
death.. with the patterns changing. Oh, complex problem. 


milton ruser wrote:
> 
> Hi Unangu
> I also put my two cents on the Kingsford´s suggestion.
> The "BOOK" the Adrian turned available are very very well informative!
> I enjoyed so much!
> 
> Best wishes
> 
> miltinho,
> 
> brazil
> 
> On Sun, Jan 11, 2009 at 3:48 PM, Kingsford Jones
> wrote:
> 
>> Unangu,
>>
>> If you haven't seen the 200pg workshop notes that Adrian Baddeley has
>> made available from his spatstat webpage, I highly recommend them:
>>
>> http://www.csiro.au/files/files/pn0y.pdf
>>
>>
>> hth,
>> Kingsford Jones
>>
>> On Sat, Jan 10, 2009 at 9:04 PM, Unangu  wrote:
>> >
>> > To understand some functions about spatial point patterns in "spatstat"
>> ,I
>> > should know some background about it, and the best way is to read the
>> > monograph, and  "Statistical Analysis of Spatial Point Patterns" (2nd
>> edt.)
>> > is a better choise. But I can not find it anywhere I can. Who can help
>> me?
>> > Thank you!
>> >
>> > -
>> > una...@gmail.com
>> > --
>> > View this message in context:
>> http://www.nabble.com/I%27m-looking-for-a-book-about-spatial-point-patterns-%28Diggle%2C2003%29-tp21395908p21395908.html
>> > Sent from the R help mailing list archive at Nabble.com.
>> >
>> > __
>> > R-help@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>> >
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
> 
>   [[alternative HTML version deleted]]
> 
> 
> __
> R-help@r-project.org mailing list
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> 
> 


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[R] merge table rows (\multirow)

2009-01-11 Thread Felipe Carrillo
Hi:
I need help merging rows.
I am trying to merge the 'Month' column using \multirow. For example for the 
column 'Week' I want July to be merged into one row(weeks 27,28,29,30) and so 
on for the following weeks.
Below, I am creating a PDF using Sweave, MikTex,R-2.8.1 and windows XP to show 
an example.


\documentclass[11pt]{article}
\usepackage{longtable,verbatim}
\title{How to implement multirow with Sweave}
\begin{document}
\maketitle
<>=
sampDat <- "Month, Week, Est.passage, Med.FL
July 27665   34
July 282,232   35
July 299,241   35
July 3028,464  35
Aug  3141,049  35
Aug 32 82,216  35
Aug 33 230,411  35
Aug 34 358,541  35
Sept 35747,839  35
Sept 36459,682  36
Sept 37609,567  36
Sept 38979,475  36
Sept 39837,189  36"
DF <- read.table(textConnection(sampDat), header = TRUE)
attach(DF)
@
\begin{verbatim}
Using Hmisc.
\end{verbatim}
<>=
library(Hmisc)
mytab <- data.frame(DF)
latex(DF,label="tab:hola",longtable=FALSE,caption='Sample table.')
@
\begin{verbatim}
Or with xtable
\end{verbatim}
<>=
library(xtable)
table2 <- data.frame(DF)
table2 <- xtable(DF,label='tab2',caption='table 2 with xtable',digits=0)
print(table2,floating=FALSE)
@
\end{document}

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

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Re: [R] Help needed for Loading "tm" package

2009-01-11 Thread Kum-Hoe Hwang
Thank Prof. Brian Ripley for your comments.

Based on Prof Brian Ripley's comments, I checked Java environments in
my PC. But I have not solved a "tm" package problem in Win R software.
I am not sure but my current conclusion is that the Win-based R binary
software has definitely a problem with Rweka package or subpackage.

Should I wait for another upgraded R binary version under the window
XP, "tm' package or Rweka ets?
Or I'd better migrate to non-window OS such as Linux, etc?

Kum Hwang, Ph.D.

On Sat, Jan 10, 2009 at 8:06 PM, Prof Brian Ripley
 wrote:
> On Sat, 10 Jan 2009, Kum-Hoe Hwang wrote:
>
>> Howdy Gurus again
>>
>> Thanks to  Tony.Breyal, I was able to writing the following script for
>> analyzing a text document.
>> But I got an error with "tm' package. I don't why I got the error from the
>> R
>> script below. I think I followed proccess of R tm manual.
>
> Please do read the messages you got.  I see
>
>> Error in .jinit(system.file("jar", c("weka.jar", "RWeka.jar"), package =
>> pkgname,  :
>>  Cannot create Java virtual machine (-1)
>
> so the problem is with your Java installation and RWeka, not 'tm'.
>
> First make sure you have a working installation of RWeka -- I suspect you do
> not even have Java installed, but it could be a version or path issue (but
> very unlikely to be an R issue).
>
>>
>> I use R v2.8.1. and tm_0.3-3.zip under Win XP.
>>
>> Thanks in advance,
>>
>> Kum Hwang
>>
>>> # setting directory
>>> my.path <-'C:\\_work\\Daddy"s\\myProjects\\2009
>>
>> defaultProject\\R\\textfile\\'
>>>
>>> # text miner pakacge
>>> library(tm)
>>
>> Loading required package: Snowball
>> Loading required package: RWeka
>> -
>> Error in .jinit(system.file("jar", c("weka.jar", "RWeka.jar"), package =
>> pkgname,  :
>>  Cannot create Java virtual machine (-1)
>> Error : .onLoad failed in 'loadNamespace' for 'RWeka'
>> Error: package 'RWeka' could not be loaded
>>>
>>> my.corpurs <-Corpus(DirSource(my.path), readerControl =
>>
>> list(reader=readPlain))
>> Error: could not find function "Corpus"
>>>
>>> my.tdm <- TermDocMatrix(my.corpus)
>>
>> Error: could not find function "TermDocMatrix"
>>>
>>> my.tdm[1,]
>>
>> Error: object "my.tdm" not found
>>
>>
>> --
>> Kum-Hoe Hwang, Ph.D.
>>
>> Phone : 82-31-250-3516
>> Email : phdhw...@gmail.com
>>
>>[[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> --
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel:  +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UKFax:  +44 1865 272595
>



-- 
Kum-Hoe Hwang, Ph.D.

Phone : 82-31-250-3516
Email : phdhw...@gmail.com

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Re: [R] [R} how to build TermDocMatrix in tm text mining package of R

2009-01-11 Thread Kum-Hoe Hwang
Thank your comments very much.

Thank to your help, I understood a flow for a text analysis.

However, I could not run the above R scripts because tm package does
not work in my PC that is a critical error.

Kum Hwang Ph.D.


On Sat, Jan 10, 2009 at 12:39 AM, Tony Breyal
 wrote:
> Hi there, I think something like the following is what you want:
>
> ### R start...
> # if you put your plain text files in a folder like this
> my.path <- 'C:\\Documents and Settings\\tony\\Desktop\\texts\\'
>
> # then you can construct a simple tdm like this
> library(tm)
> my.corpus <- Corpus(DirSource(my.path), readerControl = list
> (reader=readPlain))
> my.tdm <- TermDocMatrix(my.corpus)
>
> # this show show how words are distributed in the first text document
> my.tdm[1, ]
> ### R end.
>
> by the way, there are some nice examples of using the tm package in
> the last Rnews letter (Volume 8/2, October 2008), under the section
> 'An Introduction to Text Mining in R':
> http://cran.r-project.org/doc/Rnews/Rnews_2008-2.pdf
>
> Hope that helps a little bit,
> Tony Breyal
>
> On 9 Jan, 14:21, "Kum-Hoe Hwang"  wrote:
>> Howdy Gurus
>>
>> I 'd like to ask a question about how to build TermDocMatrix in tm text
>> mining package.
>>
>> It is not clear about importing a plain text file, and them converting that
>> text file into TermDocMatrix file, etc to me.
>> How can I build a TermDocMatrix of " a plain text document file for text
>> association?
>> Or are there any good manuals?
>>
>> Thank you in advance,
>>
>> --
>> Kum-Hoe Hwang, Ph.D.
>>
>> Phone : 82-31-250-3516
>> Email : phdhw...@gmail.com
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> r-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>



-- 
Kum-Hoe Hwang, Ph.D.

Phone : 82-31-250-3516
Email : phdhw...@gmail.com

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Re: [R] connecting boxplots

2009-01-11 Thread David Winsemius
You do not provide a workable example and it appears you may be  
conflating the German and English spellings of "group", but perhaps  
this code fragment using the first example in boxplots help menu will  
move you along. It results in drawing the connecting lines to the  
minimum value in each group.


> boxplot(count ~ spray, data = InsectSprays, col = "lightgray")   
#draws the plot

> str(boxplot(count ~ spray, data = InsectSprays, col = "lightgray")  )
List of 6
 $ stats: num [1:5, 1:6] 7 11 14 18.5 23 7 12 16.5 18 21 ...

# Notice that the "stats" element is a matrix that has the first row  
as the minimums, third as the medians, and maxs are fifth.


 $ n: num [1:6] 12 12 12 12 12 12
 $ conf : num [1:2, 1:6] 10.579 17.421 13.763 19.237 0.588 ...
 $ out  : num [1:2] 7 12
 $ group: num [1:2] 3 4
 $ names: chr [1:6] "A" "B" "C" "D" ...

> boxplot(count ~ spray, data = InsectSprays, col = "lightgray") 
$stats[c(1,5),]

 [,1] [,2] [,3] [,4] [,5] [,6]
[1,]770219  # minimums
[2,]   23   21466   26  # maximumns

> lines(boxplot(count ~ spray, data = InsectSprays, col = "lightgray") 
$stats[c(1),]  )  #adds the lines through minimums


--
David Winsemius

On Jan 11, 2009, at 8:00 PM, johnhj wrote:



In other words: I will connect the median, min and the max area of the
boxplot with a line.
The function lines() could help me, but I don't know which  
parameters the

lines() function should have.

johnhj wrote:


Hii,

I created some boxplots with this commands:

x <-read.table(file="test.txt")
x$group <- rep(1:8, each=5)
boxplot(V3~gruppe, data=x)

Now, I will connect the boxplots to each other to the min, max and  
median

values.
Can anybody help me how to do it ?

greetings,
J



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[R] How to reference previous row?

2009-01-11 Thread Heston Capital
I am trying to write some code where the factor references its
previous value, but can't find a solution searching through the
archive.

> X
  first second  
1 A  1
2 A  2
3 B  3
4 B  4
5 B  5
6 C  6
7 C  7

I need a third column, in pseudo code-
 If value of first=previous value of first:
third=previous value of third
 else third = second

So the third column would look like:
0
0
3
3
3
6
6


Thanks!

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