Re: [R] Indexing, and using an empty string as a name

[Prof Brian Ripley]

On Tue, 6 Nov 2007, Charilaos Skiadas wrote:

> Hello all,
>
> I ran into the following, to me unexpected, behavior. I have (for
> reasons that don't necessarily pertain to the question at hand, hence
> I won't go into them) the need/desire to use an empty string for the
> name of a vector entry.

The 'R Languge Definition' says

   The string "" is treated specially: it indicates `no name' and matches
   no element (not even those without a name).

and from ?names

   The name \code{""} is special: it is used to indicate that there is no
   name associated with an element of a (atomic or generic) vector.
   Subscripting by \code{""} will match nothing (not even elements which
   have no name).

so it should perhaps have been expected.


> Perhaps I did not read ?"[" very carefully,
> but it seems to me that he following lines should return "1" at the end:
>
> x<-1:4
> names(x) <- c("","a","b","c")
> x[""]
>
>
> Instead, they return NA. Could anyone provide an explanation for this
> behavior?

You can do

> x[[""]]
[1] 1

(which is arguably a bug given the quotes above) or

x[match("", names(x))]


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

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[R] Indexing, and using an empty string as a name

[Charilaos Skiadas]

Hello all,

I ran into the following, to me unexpected, behavior. I have (for  
reasons that don't necessarily pertain to the question at hand, hence  
I won't go into them) the need/desire to use an empty string for the  
name of a vector entry. Perhaps I did not read ?"[" very carefully,  
but it seems to me that he following lines should return "1" at the end:

x<-1:4
names(x) <- c("","a","b","c")
x[""]


Instead, they return NA. Could anyone provide an explanation for this  
behavior?

Thanks,
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College

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Re: [R] Integrating a function

[David Winsemius]

Does this do any better, or perhaps offer other ideas? I could not 
understand what the "Hct" and step()'s were doing from the description 
of your desired result, so they were omitted from geq(). I also could 
not understand why you were rounding off the integrals or why there wee 
two integral terms. I think the problem may be (in part) that 
integrate() returns a list unless you specify the value column. When I 
tested your function or my earliest efforts at fixing it I continued to 
get a single value despite passing it a sequence or a matrix.

surviv<-function(x){k=.001;alpha=0.3;tau=70; 
exp(-k*x)/(1+exp(alpha*(x-tau)))}
geq<-function(n){ integrate(surviv, 0,n)$value }

Nmax=250
gxt<-matrix(nrow=Nmax)
gxt<-as.matrix(1:250)
# there may be better methods o making this matrix

geq.results<-geq.results<-apply(gxt,1,geq)
geq.results
plot(gxt, geq.results)

I suspect that I have not understood what you wanted from geq(.) since 
the plot looks rather "boring". I am guessing that Hct0 is a hematocrit 
value. And geq basically returns a value very close to its input up 
until tau and then stays at approximately tau for the rest of time.

-- 
David Winsemius, MD

Robert Kalicki wrote:
> Hello everybody!
>
> I have problems with integrating my function.
>
> My primary function is a “survival function” of the following type:
>
> surviv <- exp(-k*x)/(1+exp(alpha*(x-tau)))
>
> I would like to integrate this function over a defined range and obtain a
> vector with all the values from integrate(surviv, 0, x) for x <- 1:N. 
>
> I unfortunately obtain just a scalar value corresponding to the last
> integrated x.
>
> How do I have to proceed if I want to obtain a vector with all the results?
>
> I have tried to solve this problem by adding a “while loop”. It works but
> the expression becomes to complex if I want to perform further optimization.
>
> Have any one a solution for this problem?
>
> Thanks a lot in advance.
>
>  
>
> Example
>
> # General equation
>
> beta1 <- 0.001
> beta2 <- 0
> Hct0 <- 0.27
> tau <- 70
> k <- 0.001
> alpha <- 0.3
> T2 <-40
>
> step <- function(x){
>if(x>=0) step <- 1
>else step <- 0
>
> }
>Nmax <- 250
>n <- 1
>   while(n  surviv <- function(n){
> surviv <- exp(-k*n)/(1+exp(alpha*(n-tau)))
>  }
>  geq <- function(n){
> geq <-
> Hct0+beta1*as.integer(integrate(surviv,0,n)[1])+step(n-T2)*(beta2-beta1)*as.
> integer(integrate(surviv,0,n-T2)[1])
>  }
> plot(n, geq(n), type="p", pch=19, xlim=c(0,250),
> ylim=c(0.25,0.35), xlab="time in days", ylab="Hct")
>
> par(new=T)
> print(c(n, surviv(n), geq(n),
> as.integer(integrate(surviv,0,n)[1]))
>n <- n + 1
>}
>   
> Robert M. Kalicki, MD
>
> Department of Nephrology and Hypertension

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Re: [R] R GUI for Linux

[ecatchpole]

Maura,

The workaround from https://bugzilla.novell.com/show_bug.cgi?id=330991 
seems to fix this for most people (but not me): just add

export LIBXCB_ALLOW_SLOPPY_LOCK=1

to your ~/.profile file (or to /etc/profile to make it available for all users).

Ted.




Maura E Monville wrote on 11/03/2007 04:35 AM:
> Thank you .
> I followed all the path on my installation. I got the following:
> [EMAIL PROTECTED]:/usr/lib/jvm/java-1.6.0.u3-sun-1.6.0.u3/jre/lib/i386> ll
> total 636
> -rwxr-xr-x 1 root root  80594 2007-09-25 01:10 libjavaplugin_jni.so
> -rwxr-xr-x 1 root root 297535 2007-09-25 01:10 libjavaplugin_nscp_gcc29.so
> -rwxr-xr-x 1 root root 257071 2007-09-25 01:10 libjavaplugin_nscp.so
>
> I do not have "xawt/libmawt.so" as you can see from the above.
> I do not know what that is.
> I run Linux/SuSE 10.3
>
>
>
> On 10/31/07, ecatchpole <[EMAIL PROTECTED]> wrote:
>   
>> This is a known problem with Suse10.3 --- lots of things that use Java
>> (e.g., Matlab) produce the same error message.  I'm currently trying to
>> fix this upon my machine, but haven't succeeded yet.  Josh Triplett
>> (http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6532373) suggested
>> the following:
>>
>> ---begin---
>> I worked with jcristau and christoph4 via IRC on #debian-x, and we
>> managed to
>> track down the problem with broken locking in Sun Java 1.5 and 1.6.  It
>> only
>> occurs if Java finds the Xinerama extension, at which point it does
>> something
>> broken with locking and triggers the assertion.  If Java never finds the
>> Xinerama extension, it doesn't trigger the assertion for broken locking.
>>
>> The following workarounds address this problem:
>>
>> For sun-java5-bin:
>> sed -i 's/XINERAMA/FAKEEXTN/g'
>> /usr/lib/jvm/java-1.5.0-sun-1.5.0.11/jre/lib/i386/xawt/libmawt.so
>> ---end---
>>
>> You need to modify the path for your jre.  This seems to have helped
>> several people.  But it didn't work for me.
>>
>> A sure fix is going back to Suse10.2!  :(
>>
>> Ted.
>>
>> --
>> Dr E.A. Catchpole
>> Visiting Fellow
>> Univ of New South Wales at ADFA, Canberra, Australia
>> _ and University of Kent, Canterbury, England
>>'v'- 
>> www.pems.adfa.edu.au/~ecatchpole
>>   /   \   - fax: +61 2 6268 8786
>>m m- ph:  +61 2 6268 8895
>>
>>
>>
>>
>> Maura E Monville wrote on 11/01/2007 09:43 AM:
>> 
>>> I have downloaded and tried to install JGR - Java GUI for R - Version
>>>   
>> 1.5.
>> 
>>> I followed all the instructions (at least in my best resolution) and
>>> installed Java latest version.
>>> R installation complete fine.
>>> Has anyone succeded in installing JGR on SuSE 10.3 ?
>>> In the following I hade detailed the failed installation,
>>>
>>> As root /i did the following:
>>> linux-Mimin:/usr/local/bin # ./R
>>>
>>> R version 2.6.0 (2007-10-03)
>>> Copyright (C) 2007 The R Foundation for Statistical Computing
>>> ISBN 3-900051-07-0
>>>
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>> You are welcome to redistribute it under certain conditions.
>>> Type 'license()' or 'licence()' for distribution details.
>>>
>>>   Natural language support but running in an English locale
>>>
>>> R is a collaborative project with many contributors.
>>> Type 'contributors()' for more information and
>>> 'citation()' on how to cite R or R packages in publications.
>>>
>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>> 'help.start()' for an HTML browser interface to help.
>>> Type 'q()' to quit R.
>>>
>>>
>>>   
 install.packages ("JGR",dep=TRUE)

 
>>> --- Please select a CRAN mirror for use in this session ---
>>> CRAN mirror
>>>
>>>  1: Argentina   2: Australia (QLD)
>>>  3: Australia (VIC) 4: Austria
>>>  5: Belgium 6: Brazil (PR)
>>>  7: Brazil (MG) 8: Brazil (RJ)
>>>  9: Brazil (SP 1)  10: Brazil (SP 2)
>>> 11: Canada (BC)12: Canada (ON)
>>> 13: Chile (Santiago)   14: Croatia
>>> 15: Czech Republic 16: Denmark
>>> 17: France (Toulouse)  18: France (Lyon)
>>> 19: France (Paris) 20: Germany (Bamberg)
>>> 21: Germany (Mainz)22: Germany (Muenchen)
>>> 23: India (Kolkata)24: India
>>> 25: Ireland26: Italy (Ferrara)
>>> 27: Italy (Milano) 28: Italy (Padua)
>>> 29: Italy (Palermo)30: Japan (Aizu)
>>> 31: Japan (Tokyo)  32: Japan (Tsukuba)
>>> 33: Korea  34: Netherlands (Amsterdam 2)
>>> 35: Netherlands (Amsterdam)36: Netherlands (Utrecht)
>>> 37: Norway 38: Poland (Lublin)
>>> 39: Poland (Wroclaw)   40: Portugal
>>> 41: Slovenia (Ljubljana)   42: South Africa
>>> 43: Spain (Madrid) 44: Sweden
>>> 45: Switzerland (Zuerich)  46: Switzerland (Bern)
>>> 47: Taiwan (Taichung)  48: Taiwan (Taipeh)
>>> 49: UK (Bristol)   

[R] Help of sort()

[Henrique Dallazuanna]

Hi,

In the documentarion of sort() it reads (Arguments section):
"...: arguments to be passed to or from methods or (for the default
  methods and objects without a class) to 'sim.int'."

should it be 'sort.int' instead of 'sim.int'?

Thank's

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

[[alternative HTML version deleted]]

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Re: [R] Pass Array input to web service

[Duncan Temple Lang]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1



Rohan7 wrote:
> Hello everybody,
>I'm using SSOAP and RCurl to call webservice. I got success in calling
> webservice with string as
> an input. Now i want to pass array as an input(can be single or
> multidimensional). When i do that i get
> error.
>  unable to find an inherited method for function "toSOAP", for signature
> "data.frame", "textConnection", "NULL"
> 
>   When i remove argument part then it doesn't give any error.
> 
> here is the code
> 
> inputarray <- read.table("path/to/file")
> Server <- SOAPServer("http://192.168.100.1/abc.php";)
> result <-  .SOAP(Server, "FunctionName", .soapArgs=list('tempInput' =
> inputarray),action="/abc.php")
> 
> Any suggestions.:working:


Hi.

 I imagine that you are experimenting with both sides of the
client/server interface and so you control all things.
Typically the server is fixed and expects a particular data
type for a parameter in the SOAP call. Once we know this
type (typically from the WSDL for the server), then we can
figure out how to serialize the R object appropriately.
Without that, the two sides have no way to agree on
how to send and how to interpret the information.


But since you are in charge of both sides, then
you can  make up any convention and write the
method for toSOAP that generates the XML representation
of the R object. There are tools in the XML package to aid
generating XML from within R. You could use StatDataML
and the work is already done. You could also
serialize the R object using dump/dput/save etc.
in any format (ASCII or XDR) and then put that
as the content of the XML for that parameter.
It depends what you are going to do with the
result on the server side. R's XDR format would
not be good for a PHP server, but great for an R server.

So there are lots of ways to go about this and you
have to think through both sides or have one already
defined.

There are terminology ambiguities here also.
R's concept of an array and SOAP's are quite different.


> 
> Thanks and regards,
> Rohan7
> 
> 
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iD8DBQFHMP5w9p/Jzwa2QP4RAheFAJ9V+ZMwzcA8RbTYcuHMTRE/T6MQKQCfWUlE
dJQyK2byAWPA901TzZyYAT0=
=czhX
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Re: [R] Algorithms for coincidences

[Greg Snow]

A paper that may help you:

"Methods for Studying Coincidences", Persi Diaconis; Frederick
Mosteller.  Journal of the American Statistical Association, vol 84, no.
408 (Dec., 1989), 853-861.

And remember that the birthday problem assumes independence, but if you
have 2 students that studied together (legitimately) then we would not
expect their scores to be independent.

Hope this helps,

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
 
 

> -Original Message-
> From: [EMAIL PROTECTED] 
> [mailto:[EMAIL PROTECTED] On Behalf Of Doran, Harold
> Sent: Tuesday, November 06, 2007 12:10 PM
> To: r-help
> Subject: [R] Algorithms for coincidences
> 
> I'm looking at algorithms for determining coincidences. In 
> educational testing, it is interesting to look at cheating 
> via the birthday problem where I can assess the probability 
> of n students having the same test score in a class of size k.
> 
> I was writing my own code for the b-day problem until I ran into the
> qbirthday() function, which has solutions for the overflow 
> problems I kept running into. There is no "see also" part of 
> this man page which would reference me to other functions 
> which may prove useful for such problems. But, that doesn't 
> mean they don't exist. 
> 
> I am just not familiar enough with this branch of mathematics 
> to know exactly what else I might look for. Does anyone know 
> of any other R functions that may be useful for me to look at 
> in thinking about this kind of problem? 
> 
> Harold
> 
>   [[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.
> 

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Re: [R] R validation

[Marc Schwartz]

On Wed, 2007-11-07 at 09:28 +1300, David Scott wrote:
> In regard to validation of R, there are test directories with test 
> code. See for example:
> https://svn.r-project.org/R/trunk/tests/
> and
> https://svn.r-project.org/R/trunk/src/library/stats/tests/
> 
> David Scott

Those are a part of the tests that are run when using 'make check all'
after building R from source.

As Tony noted, they can be used (and I do) for the IQ (Installation
Qualification) part of the validation process. In my case, I have a
shell script that runs the full process (svn checkout, configure, make
and make check all). The script, using 'mutt', e-mails me the output of
make check all, which has been re-directed to a file, as an attachment,
along with the SVN-REVISION file. I keep that as part of my internal
documentation.

Again as Tony noted, the specifications for the remainder of the OQ/PQ
(Operational Qualification and Performance Qualification) and other
components as required, need to be defined by the organization that
intends to use R in this domain.

As indicated in the R-FDA document, these are areas where the FDA has
provided generally non-prescriptive guidance. As a result, it is up to
each organization to assess its own requirements and implement solutions
that it feels reasonably satisfies those requirements.
 
A starting point might be to review the process currently in place for
similar applications within the organization and assess how they either
do or do not translate for R. You then have the basis for a 'gap'
analysis and can move forward from there.

HTH,

Marc Schwartz

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Re: [R] xtable.by

[Ari Friedman]

Thanks to all who helped out with this question.  I have a version 
that's working reasonably well for me right now, and will post code if I 
manage a more generalizable version.

Best,
Ari

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Re: [R] Problem with a non-factor, non-numeric variable in a data.frame

[Matthew Keller]

Alexandre,

Try rereading FAX 7.10, it explains why as.numeric() won't do it:

"In any case, do not call as.numeric() or their likes directly for the
task at hand as as.numeric() or unclass() give the internal codes"

I.e., the INTERNAL CODE of the factor is what as.numeric() is working
on rather than the numeric representation that you see.



On 11/6/07, Alexandre Santos <[EMAIL PROTECTED]> wrote:
> I tested
>
> as.numeric(as.character(Ratio))
>
> and it works perfectly!
>
> I still don't get why as.numeric(Ratio) was not enough, but at least
> now I know how to deal with it.
>
> Thanks for the tip, and sorry for missing the R-FAQ issue 7.10.
>
> Cheers,
> Alexandre Santos
>
>
> 2007/11/6, John Kane <[EMAIL PROTECTED]>:
> > Have a look at the R-FAQ issue 7.10.   It's a standard
> > problem
> >
> > For more information about your variable try
> >
> > str(variable).
> >
> >
> > --- Alexandre Santos <[EMAIL PROTECTED]>
> > wrote:
> >
> > > Dear R list,
> > >
> > > I would like to perform an ANOVA in a set of
> > > measurements, but I have
> > > problems formatting the data.
> > >
> > > The data is a two dimensional array containing two
> > > columns:
> > > - "Stim" : the type of stimulation (string)
> > > - "Ratio" : a ratio of two numeric values
> > >
> > > Now, because some values are missing in the data
> > > (defaulting to zero),
> > > part of this array will be populated with NA ratios.
> > > Maybe this is
> > > important later.
> > >
> > > In order to make the ANOVA analysis, I need to turn
> > > my vector into a data.frame.
> > >
> > > I tried vector.table=as.data.frame(vector)
> > >
> > > But I realized that
> > > is.numeric(Ratio) gives FALSE
> > > is.factor(Ratio) gives TRUE
> > >
> > > After reading the documentation, I tried
> > >
> > > vector.table=as.data.frame(vector, stringsAsFactors
> > > = FALSE)
> > >
> > > This time
> > >
> > > is.numeric(Ratio) gives FALSE
> > > is.factor(Ratio) gives FALSE
> > >
> > > So I don't even know what is Ratio, but it's not yet
> > > numeric (is this
> > > due to the NA values?).
> > >
> > > How can I get R to understand that Ratio is numeric?
> > > Checking the
> > > documentation it seems you can do it with I(x), but
> > > the details are
> > > not explained. I also tried as.numeric(Ratio), and
> > > everything was
> > > turned into zeros.
> > >
> > > Any suggestions?
> > >
> > > Cheers,
> > >
> > > Alexandre Santos
> > >
> > > Neuro-MPI, Martinsread, Germany
> > >
> > > __
> > > 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.
> > >
> >
> >
> >
> >   
> > Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark your 
> > favourite sites. Download it now at
> > http://ca.toolbar.yahoo.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.
>


-- 
Matthew C Keller
Asst. Professor of Psychology
University of Colorado at Boulder
www.matthewckeller.com

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Re: [R] Is it possible to modify the position of the graphic window ?

[Rolf Turner]

On 7/11/2007, at 9:12 AM, Prof Brian Ripley wrote:

> 1) Did you merge the resources or restart X?  You need to in order  
> to get new resources to be recognized.
>
> xrdb -merge ~/.Xresources would be needed to merge resources into  
> the current X session.

No I didn't.  Didn't know or didn't remember about the merge  
business.  Dang!
That works.  But only for the auto-start device, not for x11().
>
> I don't know if MacOS X11 is standard enough to support this, but  
> it is a very long-standing basic part of X11.
>
> 2)
> options(device=function() x11(xpos=-1))
> plot(1:10)
>
> should work (does for me): it does not affect x11() in any way,  
> just the auto-start graphics device.

Right.  That works too.  Missed the distinction between x11() and  
the auto-start device.

Thanks very much.

cheers,

Rolf

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Re: [R] help needed: taking a function out of a package and it can not find some funtions

[Katharine Mullen]

OK, well, the way I suggested will allow you to modify the C code too --
but reading your question I realize you probably don't want to do this.
If you want to use the definitions of the C functions from stats, you can
skip 2. below and add another modification to the calls to .C in your
def. of bw.SJ; add the argument PACKAGE="stats".

On Tue, 6 Nov 2007, Katharine Mullen wrote:

> bw.SJ calls C code from the file
> /usr/local/bin/R-2.6.0/src/library/stats/src/bandwidths.c
> You have to make this code available.
>
> You can do the following:
> 1. copy bandwidths.c and the definition of bw.SJ (the latter renamed) to a
> directory
> 2. compile bandwidths.c into a shared library with the command
> R CMD SHLIB bandwidths.c (see the manual writing R extensions for details)
> 3. in your definition of bw.SJ, in the 3 places .C is
> called, remove "R_" from the first argument and quote it; e.g.,
> C(R_band_phi4_bin, ..." becomes "C("band_phi4_bin","
> 4. in R, load the shared library you built with the dyn.load function; now
> your definition of the (renamed) function bw.SJ can be modified as you
> like.
>
> On Tue, 6 Nov 2007, Jason Liao wrote:
>
> >
> >  I tried to modify the R function bw.SJ (from the stats package) for my
> > own use. But if I just get the source code and run directly (without any
> > modification), it can no longer find some key functions called within
> > it. I understand this has something to do with searching path which I do
> > not understand well. Can anyone tell me how to modify the source code of
> > an R function and still make it part of an existing package?
> >
> > Thanks.
> >
> >
> > Jason Liao, http://www.geocities.com/jg_liao
> > Associate Professor of Biostatistics
> > Drexel University School of Public Health
> > 245 N. 15th Street, Mail Stop 660
> > Philadelphia, PA 19102-1192
> > phone 215-762-3934
> >
> > __
> > 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] Problem with a non-factor, non-numeric variable in a data.frame

[Alexandre Santos]

I tested

as.numeric(as.character(Ratio))

and it works perfectly!

I still don't get why as.numeric(Ratio) was not enough, but at least
now I know how to deal with it.

Thanks for the tip, and sorry for missing the R-FAQ issue 7.10.

Cheers,
Alexandre Santos


2007/11/6, John Kane <[EMAIL PROTECTED]>:
> Have a look at the R-FAQ issue 7.10.   It's a standard
> problem
>
> For more information about your variable try
>
> str(variable).
>
>
> --- Alexandre Santos <[EMAIL PROTECTED]>
> wrote:
>
> > Dear R list,
> >
> > I would like to perform an ANOVA in a set of
> > measurements, but I have
> > problems formatting the data.
> >
> > The data is a two dimensional array containing two
> > columns:
> > - "Stim" : the type of stimulation (string)
> > - "Ratio" : a ratio of two numeric values
> >
> > Now, because some values are missing in the data
> > (defaulting to zero),
> > part of this array will be populated with NA ratios.
> > Maybe this is
> > important later.
> >
> > In order to make the ANOVA analysis, I need to turn
> > my vector into a data.frame.
> >
> > I tried vector.table=as.data.frame(vector)
> >
> > But I realized that
> > is.numeric(Ratio) gives FALSE
> > is.factor(Ratio) gives TRUE
> >
> > After reading the documentation, I tried
> >
> > vector.table=as.data.frame(vector, stringsAsFactors
> > = FALSE)
> >
> > This time
> >
> > is.numeric(Ratio) gives FALSE
> > is.factor(Ratio) gives FALSE
> >
> > So I don't even know what is Ratio, but it's not yet
> > numeric (is this
> > due to the NA values?).
> >
> > How can I get R to understand that Ratio is numeric?
> > Checking the
> > documentation it seems you can do it with I(x), but
> > the details are
> > not explained. I also tried as.numeric(Ratio), and
> > everything was
> > turned into zeros.
> >
> > Any suggestions?
> >
> > Cheers,
> >
> > Alexandre Santos
> >
> > Neuro-MPI, Martinsread, Germany
> >
> > __
> > 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.
> >
>
>
>
>   
> Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark your 
> favourite sites. Download it now at
> http://ca.toolbar.yahoo.com.
>

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Re: [R] help needed: taking a function out of a package and it can not find some funtions

[Jason Liao]

Simple solution provide by  Prof. Ripley is to modify the relevant code as 
follows (he posted in the R-development group):


  SDh <- function(x, h, n, d) .C(stats:::R_band_phi4_bin,
 as.integer(n),
 as.integer(length(x)), as.double(d), x, as.double(h),
 u = double(1))$u
 TDh <- function(x, h, n, d) .C(stats:::R_band_phi6_bin,
 as.integer(n),
 as.integer(length(x)), as.double(d), x, as.double(h),
 u = double(1))$u
 Z <- .C(stats:::R_band_den_bin, as.integer(n), as.integer(nb), d =
 double(1),
 x, cnt = integer(nb))

It works great with minimum extra effort. Thanks.

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Re: [R] R validation

[David Scott]

In regard to validation of R, there are test directories with test 
code. See for example:
https://svn.r-project.org/R/trunk/tests/
and
https://svn.r-project.org/R/trunk/src/library/stats/tests/

David Scott


_
David Scott Department of Statistics, Tamaki Campus
The University of Auckland, PB 92019
Auckland 1142,NEW ZEALAND
Phone: +64 9 373 7599 ext 86830 Fax: +64 9 373 7000
Email:  [EMAIL PROTECTED]

Graduate Officer, Department of Statistics
Director of Consulting, Department of Statistics

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Re: [R] help needed: taking a function out of a package and it can not find some funtions

[Katharine Mullen]

bw.SJ calls C code from the file
/usr/local/bin/R-2.6.0/src/library/stats/src/bandwidths.c
You have to make this code available.

You can do the following:
1. copy bandwidths.c and the definition of bw.SJ (the latter renamed) to a
directory
2. compile bandwidths.c into a shared library with the command
R CMD SHLIB bandwidths.c (see the manual writing R extensions for details)
3. in your definition of bw.SJ, in the 3 places .C is
called, remove "R_" from the first argument and quote it; e.g.,
C(R_band_phi4_bin, ..." becomes "C("band_phi4_bin","
4. in R, load the shared library you built with the dyn.load function; now
your definition of the (renamed) function bw.SJ can be modified as you
like.

On Tue, 6 Nov 2007, Jason Liao wrote:

>
>  I tried to modify the R function bw.SJ (from the stats package) for my
> own use. But if I just get the source code and run directly (without any
> modification), it can no longer find some key functions called within
> it. I understand this has something to do with searching path which I do
> not understand well. Can anyone tell me how to modify the source code of
> an R function and still make it part of an existing package?
>
> Thanks.
>
>
> Jason Liao, http://www.geocities.com/jg_liao
> Associate Professor of Biostatistics
> Drexel University School of Public Health
> 245 N. 15th Street, Mail Stop 660
> Philadelphia, PA 19102-1192
> phone 215-762-3934
>
> __
> 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] Is it possible to modify the position of the graphic window ?

[Prof Brian Ripley]

1) Did you merge the resources or restart X?  You need to in order to get 
new resources to be recognized.

xrdb -merge ~/.Xresources would be needed to merge resources into the 
current X session.

I don't know if MacOS X11 is standard enough to support this, but it is a 
very long-standing basic part of X11.

2)
options(device=function() x11(xpos=-1))
plot(1:10)

should work (does for me): it does not affect x11() in any way, just the 
auto-start graphics device.

On Wed, 7 Nov 2007, Rolf Turner wrote:

>
> On 7/11/2007, at 6:39 AM, Prof Brian Ripley wrote:
>
>> Better to use resources.  But you can use (in .Rprofile)
>>
>> options(device=function() x11(xpos=-1))
>>
>> The resources version would be to put in ~/.Xresources something like
>>
>> R_x11*geometry: 700x700-0+0
>
>   Neither of these options appears to have any effect under Mac OSX.
>   I run R from the command line from a terminal window (not from the GUI)
>   and I have X11 installed so that in R
>
>   > x11()
>
>   does indeed put up a graphics window.  But it always puts it (the
> initial
>   window) in exactly the same place, irrespective of my having put the
>   specified line in ~/.Xresources before starting R, or having issued the
>   specified options() command immediately after having started R (before
>   issuing the x11() command).
>
>   It's no big deal --- I'm reasonably happy with the default position
> of the
>   window.  I just hate it when a computer refuses to follow
> instructions, with
>   no explanation. :-(
>
>   cheers,
>
>   Rolf Turner
>
> P. S.:
>
> > sessionInfo()
> R version 2.6.0 (2007-10-03)
> i386-apple-darwin8.10.1
>
> locale:
> C
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
> other attached packages:
> [1] misc_0.0-2
>
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-15
>
>
> ##
> Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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

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Re: [R] Problem with a non-factor, non-numeric variable in a data.frame

[John Kane]

Have a look at the R-FAQ issue 7.10.   It's a standard
problem

For more information about your variable try

str(variable).


--- Alexandre Santos <[EMAIL PROTECTED]>
wrote:

> Dear R list,
> 
> I would like to perform an ANOVA in a set of
> measurements, but I have
> problems formatting the data.
> 
> The data is a two dimensional array containing two
> columns:
> - "Stim" : the type of stimulation (string)
> - "Ratio" : a ratio of two numeric values
> 
> Now, because some values are missing in the data
> (defaulting to zero),
> part of this array will be populated with NA ratios.
> Maybe this is
> important later.
> 
> In order to make the ANOVA analysis, I need to turn
> my vector into a data.frame.
> 
> I tried vector.table=as.data.frame(vector)
> 
> But I realized that
> is.numeric(Ratio) gives FALSE
> is.factor(Ratio) gives TRUE
> 
> After reading the documentation, I tried
> 
> vector.table=as.data.frame(vector, stringsAsFactors
> = FALSE)
> 
> This time
> 
> is.numeric(Ratio) gives FALSE
> is.factor(Ratio) gives FALSE
> 
> So I don't even know what is Ratio, but it's not yet
> numeric (is this
> due to the NA values?).
> 
> How can I get R to understand that Ratio is numeric?
> Checking the
> documentation it seems you can do it with I(x), but
> the details are
> not explained. I also tried as.numeric(Ratio), and
> everything was
> turned into zeros.
> 
> Any suggestions?
> 
> Cheers,
> 
> Alexandre Santos
> 
> Neuro-MPI, Martinsread, Germany
> 
> __
> 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] translating R code to C code

[Rolf Turner]

On 7/11/2007, at 6:24 AM, Dieter Menne wrote:

> you have little chance to get a C program to work
> without some experience.

A fortune???

cheers,

Rolf Turner

##
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Re: [R] Is it possible to modify the position of the graphic window ?

[Rolf Turner]

On 7/11/2007, at 6:39 AM, Prof Brian Ripley wrote:

> Better to use resources.  But you can use (in .Rprofile)
>
> options(device=function() x11(xpos=-1))
>
> The resources version would be to put in ~/.Xresources something like
>
> R_x11*geometry: 700x700-0+0

Neither of these options appears to have any effect under Mac OSX.
I run R from the command line from a terminal window (not from the GUI)
and I have X11 installed so that in R

> x11()

does indeed put up a graphics window.  But it always puts it (the  
initial
window) in exactly the same place, irrespective of my having put the
specified line in ~/.Xresources before starting R, or having issued the
specified options() command immediately after having started R (before
issuing the x11() command).

It's no big deal --- I'm reasonably happy with the default position  
of the
window.  I just hate it when a computer refuses to follow  
instructions, with
no explanation. :-(

cheers,

Rolf Turner

P. S.:

 > sessionInfo()
R version 2.6.0 (2007-10-03)
i386-apple-darwin8.10.1

locale:
C

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

other attached packages:
[1] misc_0.0-2

loaded via a namespace (and not attached):
[1] rcompgen_0.1-15


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[R] color2D.matplot

[wragbag]

I am a true R novice aonly using it for this function ;)

I am trying to use color2D.matplot to form a image of my data using the
following conditions

color2D.matplot(fi1, c(dr), c(dg), c(db), nslices=7, ylab='Species',
xlab="gene", show.legend=TRUE) where fi1 is my matrix.

I have a matrix with 36 columns and 130 rows. most entries are 1 or 0 and I
am trying to get this function to plot these as either 0 = white or 1 =
black. This is fine but one column contains entries between 0 and 7. I would
entries between 2 and 7 to be different colors (as this is what I am trying
to show although I also need to see the black and white areas) using the
following:

> dr = c(1,0,1,0,0)
> dg = c(1,0,0,1,0)
> db = c(1,0,0,0,1)

I can get some color to work but I cannot get them all as if I but in a c()
range equalling 0-7 (i.e. one color for each number I get the following. I
cannot figure out from the documentation why it will not let me do what I
want :(

Error in rescale(x[segindex], redrange[c(seg, seg + 1)]) : 
  rescale: can't rescale a constant vector!

help please someone...
-- 
View this message in context: 
http://www.nabble.com/color2D.matplot-tf4760527.html#a13614400
Sent from the R help mailing list archive at Nabble.com.

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Re: [R] How to know created time of object in R?

[Patrick Connolly]

On Tue, 06-Nov-2007 at 08:17AM -0200, Alberto Monteiro wrote:

|> 
|> Prof Brian Ripley wrote:
|> >
|> >> I would like to know the created time and date of specific object.
|> >> Is there any function for it?
|> > 
|> > There isn't even the concept.  Most objects in R are a collection of 
|> > SEXPRECs created at different times.  Suppose you create a data 
|> > frame out of existing columns, and then later change the names? What 
|> > does 'created' mean for the data frame?
|> > 
|> > In any case, none of the possibly relevant date-times is stored.
|> > 
|> I imagine that it could be possible to create a class that
|> would store the "creation time" of its objects... but I have
|> no idea how to do it (I think I could do it in C++, but I am
|> illiterate in R++ oops S4 classes).

I never use the comment for anything else, so it's simple enough to
store that information there.  In my case, I'm only interested in the
date which is interesting information when revisiting a project months
or years later.  As Brian indicated, it's not entirely predictable,
but it's good enough for my purposes.  I'm mostly interested in
various versions of functions or lists that they create.


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

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[R] Algorithms for coincidences

[Doran, Harold]

I'm looking at algorithms for determining coincidences. In educational
testing, it is interesting to look at cheating via the birthday problem
where I can assess the probability of n students having the same test
score in a class of size k.

I was writing my own code for the b-day problem until I ran into the
qbirthday() function, which has solutions for the overflow problems I
kept running into. There is no "see also" part of this man page which
would reference me to other functions which may prove useful for such
problems. But, that doesn't mean they don't exist. 

I am just not familiar enough with this branch of mathematics to know
exactly what else I might look for. Does anyone know of any other R
functions that may be useful for me to look at in thinking about this
kind of problem? 

Harold

[[alternative HTML version deleted]]

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[R] help needed: taking a function out of a package and it can not find some funtions

[Jason Liao]

 I tried to modify the R function bw.SJ (from the stats package) for my own 
use. But if I just get the source code and run directly (without any 
modification), it can no longer find some key functions called within it. I 
understand this has something to do with searching path which I do not 
understand well. Can anyone tell me how to modify the source code of an R 
function and still make it part of an existing package?

Thanks.


Jason Liao, http://www.geocities.com/jg_liao
Associate Professor of Biostatistics
Drexel University School of Public Health
245 N. 15th Street, Mail Stop 660
Philadelphia, PA 19102-1192
phone 215-762-3934

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Re: [R] question about running out of memory on R -- memory.limit change in R 2.6.0?

[Earl F. Glynn]

"jim holtman" <[EMAIL PROTECTED]> wrote in message 
news:[EMAIL PROTECTED]
> --max-mem-size=N
> (Windows only) Specify a limit for the amount of memory to be used
> both for R objects and working areas. This is set by default to the
> smaller of 1.5Gb24 and the amount of physical RAM in the machine, and
> must be between 32Mb and 3Gb.

Something seems to have changed in R 2.6.0 -- the limit is no longer 3 GB.

On a PC with 3.5 GB with R 2.5.1 using default command line:

Default

> memory.limit()

[1] 1610612736



With --max-mem-size=3000M on the command line:



> memory.limit()

[1] 3145728000






Let's see what happens with R 2.6.0 on the same 3.5 GB PC (Windows XP):



Default command line:


> memory.limit()

[1] 1535.875



Note:  The format of the return value is now in MB instead of bytes.



With --max-mem-size=3000M on the command line:



Error message:  WARNING: --max-mem-size=3000M: too large and taken as 2047M



> memory.limit()

[1] 2047.875



This value is less than the value shown in R 2.5.1 (after converting both to 
the same basis).



But was this change a "fix" to report that a Windows process only has a 2 GB 
address space?  That is, the value returned by R 2.5.1 of 3145728000 wasn't 
strictly correct?



efg



Earl F. Glynn

Scientific Programmer

Stowers Institute

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Re: [R] Is it possible to modify the position of the graphic window ?

[Peter Dalgaard]

8rino-Luca Pantani wrote:
> I see.
> Thanks for your highly appreciated help, Prof. Ripley.
>
>
> I've been reading the x11 help file, only after people from this list 
> told me that it is the default in Linux
>
> Please consider that I recently (and definitely) moved to linux from 
> Windows, and I still need to re-learn a lot of things.
>
> I did'nt know that with "options" was possible to change the x11 windows.
> I typed the following, and it worked
> options(device= x11(xpos =500))
> moving the window on the left
> Now, if I'm allowed to push your patience a little further, how can I 
> make this change permanent ?
>   

Umm, I think that one only seemingly "works". It does the same as plain 
x11(xpos=500) followed by options(device=NULL) (try removing the window 
and then plot(0)).

More likely, you want
  options(device = function() x11(xpos=500) )
which you can handle using the techniques described under ?Startup (i.e. 
stick it in a .Rprofile file, for instance).

(xpos=-1 might be better if you switch between different-sized screens, 
though)
> Thanks again
> Ottorino Pantani
>
> Prof Brian Ripley ha scritto:
>   
>> On Linux the default graphics device is X11(), and not so on Windows.
>>
>> ?X11 tells you no less than *two* ways to do this: I do wonder why you 
>> don't just read the help file?
>>
>> ?options (see 'device') tells you how to set up a default device which 
>> you could use to change default arguments, but using the X11 geometry 
>> resources is the canonical way to do this.
>>
>> On Tue, 6 Nov 2007, 8rino-Luca Pantani wrote:
>>
>> 
>>> There's a Renviron file under /etc/R, but there are no lines with
>>> "position (x, y)".
>>>
>>> Henrique Dallazuanna ha scritto:
>>>   
 In the Windows the file Rconsole contains the position(x,y) of the 
 graphics.
 I don't know if file have the same name in Ubuntu.

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


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

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Re: [R] Why can repeated measures anova with within & between subjects design not be done if group sizes are unbalanced?

[Dieter Menne]

Charles C. Berry  tajo.ucsd.edu> writes:

> As the posting guide suggests, you could perform a search using
> 
> > RSiteSearch("repeated measures", restric="functions")
> 
> say.
> 
> That generates an inventory of functions that pertain to repeated 
> measures designs.

The problem I noted in practice with researcher is that  nlme is not among those
associated with "repeated measurements", with the exception of the citation of 

Davidian, M. and Giltinan, D.M. (1995) "Nonlinear Mixed Effects Models for
Repeated Measurement Data", Chapman and Hall.

somewhere in the nlme documentation. And as far as I remember, the word
"repeated measurements" cannot be found in text of Pinheiro & Bates; which
otherwise is the most worn-out book on my shelf.

I may be slightly off with both statements, but the association (mixed model)
<=> (repeated measurements) is not at all obvious. 

For the record: forget repeated measurements. It definitively pays to be fluent
in mixed models. Once you have your data in the "long" form, most work is done.
And if lme tells you it cannot solve your problem, it has damned good reasons
for it.

Dieter

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Re: [R] Is it possible to modify the position of the graphic window ?

[Prof Brian Ripley]

On Tue, 6 Nov 2007, 8rino-Luca Pantani wrote:

> I see.
> Thanks for your highly appreciated help, Prof. Ripley.
>
>
> I've been reading the x11 help file, only after people from this list told me 
> that it is the default in Linux
>
> Please consider that I recently (and definitely) moved to linux from Windows, 
> and I still need to re-learn a lot of things.
>
> I did'nt know that with "options" was possible to change the x11 windows.
> I typed the following, and it worked
> options(device= x11(xpos =500))
> moving the window on the left
> Now, if I'm allowed to push your patience a little further, how can I make 
> this change permanent ?

Better to use resources.  But you can use (in .Rprofile)

options(device=function() x11(xpos=-1))

The resources version would be to put in ~/.Xresources something like

R_x11*geometry: 700x700-0+0


> Thanks again
> Ottorino Pantani
>
> Prof Brian Ripley ha scritto:
>> On Linux the default graphics device is X11(), and not so on Windows.
>> 
>> ?X11 tells you no less than *two* ways to do this: I do wonder why you 
>> don't just read the help file?
>> 
>> ?options (see 'device') tells you how to set up a default device which you 
>> could use to change default arguments, but using the X11 geometry resources 
>> is the canonical way to do this.
>> 
>> On Tue, 6 Nov 2007, 8rino-Luca Pantani wrote:
>> 
>>> There's a Renviron file under /etc/R, but there are no lines with
>>> "position (x, y)".
>>> 
>>> Henrique Dallazuanna ha scritto:
 In the Windows the file Rconsole contains the position(x,y) of the 
 graphics.
 I don't know if file have the same name in Ubuntu.
 
>>> 
>>> __
>>> R-help@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide 
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>> 
>> 
>
>

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

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Re: [R] R validation

[Terry Therneau]

 For the survival package, you might want to reference appendix E of Therneau 
and Grambsh, Modeling Survival Data, Springer-Verlag, 2000.  This contains a 
set 
of small example data sets for which results have been worked out in closed 
form.  S-plus and R pass all the tests: they are a portion of the test suite of 
the package.  (SAS does not pass, BTW.  It doesn't compute dfbeta residuals for 
a Cox model quite right under the Efron approximation.  The error is small and 
almost certainly unimportant in practical data, but I like to keep it in hand 
as 
a counterexample to believers of SAS infallability).
 
Terry Therneau

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Re: [R] translating R code to C code

[Dieter Menne]

Pedro Mardones  gmail.com> writes:

> 
> I would like to try to implement a big series of nested loops in a C
> code and then call it from R; however I'm not familiar with C
> programming. Does anyone know about some sort of reference I can use
> that help me to translate my code to C? (I'm thinking on something
> like to Octave to R reference posted in CRAN)
> thanks

No. R and C are not comparable, so there is not "reference". R, Octave and
Matlab have more similarities. Best is to ask someone who knows C, and explain
him/her what has to be done; you have little chance to get a C program to work
without some experience.

Dieter

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Re: [R] Is it possible to modify the position of the graphic window ?

[8rino-Luca Pantani]

I see.
Thanks for your highly appreciated help, Prof. Ripley.


I've been reading the x11 help file, only after people from this list 
told me that it is the default in Linux

Please consider that I recently (and definitely) moved to linux from 
Windows, and I still need to re-learn a lot of things.

I did'nt know that with "options" was possible to change the x11 windows.
I typed the following, and it worked
options(device= x11(xpos =500))
moving the window on the left
Now, if I'm allowed to push your patience a little further, how can I 
make this change permanent ?

Thanks again
Ottorino Pantani

Prof Brian Ripley ha scritto:
> On Linux the default graphics device is X11(), and not so on Windows.
>
> ?X11 tells you no less than *two* ways to do this: I do wonder why you 
> don't just read the help file?
>
> ?options (see 'device') tells you how to set up a default device which 
> you could use to change default arguments, but using the X11 geometry 
> resources is the canonical way to do this.
>
> On Tue, 6 Nov 2007, 8rino-Luca Pantani wrote:
>
>> There's a Renviron file under /etc/R, but there are no lines with
>> "position (x, y)".
>>
>> Henrique Dallazuanna ha scritto:
>>> In the Windows the file Rconsole contains the position(x,y) of the 
>>> graphics.
>>> I don't know if file have the same name in Ubuntu.
>>>
>>
>> __
>> 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.
>>
>

-- 
Ottorino-Luca Pantani, Università di Firenze
Dip. Scienza del Suolo e Nutrizione della Pianta
P.zle Cascine 28 50144 Firenze Italia
Tel 39 055 3288 202 (348 lab) Fax 39 055 333 273 
[EMAIL PROTECTED]  http://www4.unifi.it/dssnp/

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Re: [R] C++ and R interface

[Deepankar Basu]

Thanks for the help.

On Tue, 2007-11-06 at 14:48 -0200, Alberto Monteiro wrote:
> Deepankar Basu wrote:
> > 
> > I am trying to do an ML estimation in R. My likelihood function has
> > several nested loops and so it takes a lot of time (days when I use the
> > genetic algorithm for optimization) for the optimization to finish.
> > Unable to avoid loops, I am thinking of writing the likelihood function
> > in C++ and calling it from within R when using *optim()*. I found 
> > that one can call C functions (once they have been compiled) from 
> > within R with
> > 
> > > dyn.load("file.so")
> > 
> > and
> > 
> > > .C("function", ...)
> > 
> > Can the same be done for C++ code?
> > 
> If it can be done in C, it probably (P > 99%) can be done in C++, 
> because C++ can call C functions. Just write the C++ code as:
> 
> extern "C" int myfunction(int x1, int x2)
> {
>   // write C++ code here
>   return rval;
> }
> 
> Alberto Monteiro
>

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Re: [R] How to know created time of object in R?

[Duncan Temple Lang]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1


Of course, Brian is correct that the problem requires a great
deal more specificity.  However, one could imagine that it would
be useful to tag objects created by top-level expressions
with the time they were created in much the same way that the
file system provides a modification time.

It is easy enough to add the time as an attribute of an object,
but I imagine you are asking how to automate this.
To this end, you could do something with the addTaskCallback() function
which allows you to specify a function that is invoked
at the completion of each top-level evaluation.  You could
get store some useful time information with the object
or perhaps go further and work with the expressions
to determine dependencies and capture the dependencies in
a series of computations.

 D.

Dong-hyun Oh wrote:
> Dear UseRs,
> 
> I would like to know the created time and date of specific object.
> Is there any function for it?
> 
> Thank you in advance.
> 
> 
> Sincerely,
> 
> __
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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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[R] Problem with a non-factor, non-numeric variable in a data.frame

[Alexandre Santos]

Dear R list,

I would like to perform an ANOVA in a set of measurements, but I have
problems formatting the data.

The data is a two dimensional array containing two columns:
- "Stim" : the type of stimulation (string)
- "Ratio" : a ratio of two numeric values

Now, because some values are missing in the data (defaulting to zero),
part of this array will be populated with NA ratios. Maybe this is
important later.

In order to make the ANOVA analysis, I need to turn my vector into a data.frame.

I tried vector.table=as.data.frame(vector)

But I realized that
is.numeric(Ratio) gives FALSE
is.factor(Ratio) gives TRUE

After reading the documentation, I tried

vector.table=as.data.frame(vector, stringsAsFactors = FALSE)

This time

is.numeric(Ratio) gives FALSE
is.factor(Ratio) gives FALSE

So I don't even know what is Ratio, but it's not yet numeric (is this
due to the NA values?).

How can I get R to understand that Ratio is numeric? Checking the
documentation it seems you can do it with I(x), but the details are
not explained. I also tried as.numeric(Ratio), and everything was
turned into zeros.

Any suggestions?

Cheers,

Alexandre Santos

Neuro-MPI, Martinsread, Germany

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Re: [R] C++ and R interface

[Alberto Monteiro]

Deepankar Basu wrote:
> 
> I am trying to do an ML estimation in R. My likelihood function has
> several nested loops and so it takes a lot of time (days when I use the
> genetic algorithm for optimization) for the optimization to finish.
> Unable to avoid loops, I am thinking of writing the likelihood function
> in C++ and calling it from within R when using *optim()*. I found 
> that one can call C functions (once they have been compiled) from 
> within R with
> 
> > dyn.load("file.so")
> 
> and
> 
> > .C("function", ...)
> 
> Can the same be done for C++ code?
> 
If it can be done in C, it probably (P > 99%) can be done in C++, 
because C++ can call C functions. Just write the C++ code as:

extern "C" int myfunction(int x1, int x2)
{
  // write C++ code here
  return rval;
}

Alberto Monteiro

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Re: [R] Produce a multiple formats graphic

[Gabor Grothendieck]

You didn't mention your platform but if its windows then try this:

plot(1:10)
for(p in c("ps", "pdf", "jpg")) savePlot("myplot", type=p)

and if not look up ?dev.copy and RSiteSearch("dev.copy")


On Nov 6, 2007 9:18 AM, Cuvelier Etienne <[EMAIL PROTECTED]> wrote:
> Is it possible to produce the same graphic in different formats
> in one shot?
> Now if I want to produce the same graphic in pdf, ps and jpeg
> I run the producing code, but I change the graphic device, and
> I choose successively :
> pdf(...)
> ps(...)
> jpeg(...)
>
> So in this case I run the same code 3 times, or I have
> to choose a format and use converters...
>
> Is it possible to produce the 3 graphics in once ?
>
>
> Thank you very much
>
> --
> ===
> Cuvelier Etienne
> Assistant
> FUNDP - Institut d'Informatique
> rue Grandgagnage, 21   B-5000 Namur (Belgique)
> tel: 32.81.72.49.93fax: 32.81.72.49.67
> ===
> Top 10 reasons to become a Statistician
>
>  1. Deviation is considered normal
>  2. We feel complete and sufficient
>  3. We are 'mean' lovers
>  4. Statisticians do it discretely and
> continuously
>  5. We are right 95% of the time
>  6. We can legally comment on someone's
> posterior distribution
>  7. We may not be normal, but we are
> transformable
>  8. We never have to say we are certain
>  9. We are honestly significantly different
>  10. No one wants our jobs
>
> __
> 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] C++ and R interface

[Prof Brian Ripley]

On Tue, 6 Nov 2007, Deepankar Basu wrote:

> Hi All,
>
> I am trying to do an ML estimation in R. My likelihood function has
> several nested loops and so it takes a lot of time (days when I use the
> genetic algorithm for optimization) for the optimization to finish.
> Unable to avoid loops, I am thinking of writing the likelihood function
> in C++ and calling it from within R when using *optim()*. I found that
> one can call C functions (once they have been compiled) from within R
> with
>
>> dyn.load("file.so")
>
> and
>
>> .C("function", ...)
>
> Can the same be done for C++ code?

Yes, and the manual about C ('Writing R Extensions') discusses C++ as well.

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

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Re: [R] C++ and R interface

[Ingmar Visser]

Yes, this can be done and the call is the same, however the C++ needs to
be indicated as , see details in the writing R extensions  
manual.
hth, Ingmar

On 6 Nov 2007, at 17:05, Deepankar Basu wrote:

> Hi All,
>
> I am trying to do an ML estimation in R. My likelihood function has
> several nested loops and so it takes a lot of time (days when I use  
> the
> genetic algorithm for optimization) for the optimization to finish.
> Unable to avoid loops, I am thinking of writing the likelihood  
> function
> in C++ and calling it from within R when using *optim()*. I found that
> one can call C functions (once they have been compiled) from within R
> with
>
>> dyn.load("file.so")
>
> and
>
>> .C("function", ...)
>
> Can the same be done for C++ code?
>
>
> Deepankar
>
> __
> 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.

Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
The Netherlands
t: +31-20-5256723



[[alternative HTML version deleted]]

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Re: [R] Kolmogorov-Smirnoff test

[Ted Harding]

On 06-Nov-07 15:53:53, Oarabile Molaodi wrote:
> I am trying to determine whether two samples are identical or not.
> I'm aware that somebody can use the Kolmogorov-Smirnoff test to
> compare empirical distributions, but since my samples have ties
> I'm not sure if I'm getting the right p-values for the comparison.
> Can the Kolmogorov-Smirnoff test be adjusted for the case when ties
> exists and are there any functions that already exists in R
> (Kolmogorov-Smirnoff test )performing  that can be used in the case
> of the existance of ties?
> 
> Thank you in advance for your help.
> 
> Oarabile

Tests like the Kolmogorov-Smirnov whose theoretical null
distribution assume continuous random variables (hence
wothout ties) do not have definite null distributions
when ties are possible. Whatever null distribution the
test may have when ties are present (e.g. due to data
being recorded to a relatively coarse precision) will
depend on the pattern of ties.

However, it is possible to investigate the effect of
ties on the P-value by randomly breaking ties.

For instance, suppose your data are recorded to a precision
of 0.1, and you have two such samples X and Y, then let

X.rand <- X + 0.0001*runif(length(X)
Y.rand <- Y + 0.0001*runif(length(Y)

and then do a K-S test on X.rand vs Y.rand.

You will get a P-value. Repeat this many time. You will get
a distribution of P-values. You can extract any relevant
property of this distrobution of P-values, for instance
its mean, it's 95th percentile (so you can be 96% confident
that the tie-broken P-value is less than this value).
and so on.

Hoping this helps,
Ted.


E-Mail: (Ted Harding) <[EMAIL PROTECTED]>
Fax-to-email: +44 (0)870 094 0861
Date: 06-Nov-07   Time: 16:23:34
-- XFMail --

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Re: [R] Is it possible to modify the position of the graphic window ?

[Prof Brian Ripley]

On Linux the default graphics device is X11(), and not so on Windows.

?X11 tells you no less than *two* ways to do this: I do wonder why you 
don't just read the help file?

?options (see 'device') tells you how to set up a default device which you 
could use to change default arguments, but using the X11 geometry 
resources is the canonical way to do this.

On Tue, 6 Nov 2007, 8rino-Luca Pantani wrote:

> There's a Renviron file under /etc/R, but there are no lines with
> "position (x, y)".
>
> Henrique Dallazuanna ha scritto:
>> In the Windows the file Rconsole contains the position(x,y) of the graphics.
>> I don't know if file have the same name in Ubuntu.
>>
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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

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[R] translating R code to C code

[Pedro Mardones]

I would like to try to implement a big series of nested loops in a C
code and then call it from R; however I'm not familiar with C
programming. Does anyone know about some sort of reference I can use
that help me to translate my code to C? (I'm thinking on something
like to Octave to R reference posted in CRAN)
thanks
PM

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[R] Fwd: Produce a multiple formats graphic

[Mark Wardle]

-- Forwarded message --
From: Mark Wardle <[EMAIL PROTECTED]>
Date: 6 Nov 2007 16:01
Subject: Re: [R] Produce a multiple formats graphic
To: Cuvelier Etienne <[EMAIL PROTECTED]>


You have several options:

1. Write a function that creates your plot, and call that function
repeatedly manually.
2. Write a wrapper function that takes the name of a function, and an
output filename, and calls that function repeatedly after creating
different graphics devices.
3. Create as PDF, and use something else (like ImageMagick) to convert
to different formats.

I tend to do option 3 as it is the most flexible.

Best wishes,

Mark

On 06/11/2007, Cuvelier Etienne <[EMAIL PROTECTED]> wrote:
> Is it possible to produce the same graphic in different formats
> in one shot?
> Now if I want to produce the same graphic in pdf, ps and jpeg
> I run the producing code, but I change the graphic device, and
> I choose successively :
> pdf(...)
> ps(...)
> jpeg(...)
>
> So in this case I run the same code 3 times, or I have
> to choose a format and use converters...
>
> Is it possible to produce the 3 graphics in once ?
>
>
> Thank you very much
>
> --
> ===
> Cuvelier Etienne
> Assistant
> FUNDP - Institut d'Informatique
> rue Grandgagnage, 21   B-5000 Namur (Belgique)
> tel: 32.81.72.49.93fax: 32.81.72.49.67
> ===
> Top 10 reasons to become a Statistician
>
>   1. Deviation is considered normal
>   2. We feel complete and sufficient
>   3. We are 'mean' lovers
>   4. Statisticians do it discretely and
>  continuously
>   5. We are right 95% of the time
>   6. We can legally comment on someone's
>  posterior distribution
>   7. We may not be normal, but we are
>  transformable
>   8. We never have to say we are certain
>   9. We are honestly significantly different
>  10. No one wants our jobs
>
> __
> 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.
>
>
> __
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email
> __
>


--
Dr. Mark Wardle
Specialist registrar, Neurology
Cardiff, UK


-- 
Dr. Mark Wardle
Specialist registrar, Neurology
Cardiff, UK

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

[R] Kolmogorov-Smirnoff test

[Oarabile Molaodi]

I am trying to determine whether two samples are identical or not. I'm 
aware that somebody can use the Kolmogorov-Smirnoff test to compare 
empirical distributions, but since my samples have ties I'm not sure if 
I'm getting the right p-values for the comparison. Can the 
Kolmogorov-Smirnoff test be adjusted for the case when ties exists and 
are there any functions that already exists in R ( Kolmogorov-Smirnoff 
test )performing  that can be used in the case of the existance of ties?

Thank you in advance for your help.

Oarabile

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[R] seasonal time serie with missing values

[Joao Santos]

Hello All,

I trying to find some way to fill in missing values in a seasonal time
series. All the function that I find until now, don't have any reference to
seasonal data and the output is very different of what I looking for.
I also searched the forum but this problem don't have many information or
people asking.

Could someone indicate some links or packages related to this question?


Thanks in advance,

João Santos  

 
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[R] C++ and R interface

[Deepankar Basu]

Hi All,

I am trying to do an ML estimation in R. My likelihood function has
several nested loops and so it takes a lot of time (days when I use the
genetic algorithm for optimization) for the optimization to finish.
Unable to avoid loops, I am thinking of writing the likelihood function
in C++ and calling it from within R when using *optim()*. I found that
one can call C functions (once they have been compiled) from within R
with 

> dyn.load("file.so")

and

> .C("function", ...)

Can the same be done for C++ code?


Deepankar

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Re: [R] Produce a multiple formats graphic

[Uwe Ligges]

Cuvelier Etienne wrote:
> Is it possible to produce the same graphic in different formats
> in one shot?
> Now if I want to produce the same graphic in pdf, ps and jpeg
> I run the producing code, but I change the graphic device, and
> I choose successively :
> pdf(...)
> ps(...)
> jpeg(...)
> 
> So in this case I run the same code 3 times, 

Yes, or write a small piece of code that does it for you.

Uwe Ligges


 > or I have
> to choose a format and use converters...
> 
> Is it possible to produce the 3 graphics in once ?
 >
> 
> Thank you very much
>

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Re: [R] Statistics for the Grouped data

[John Kane]

Hi Shubha,  

Have a look at the Hmisc package and try ?wtd.mean  as
the help command. This may be what you need.  Also you
might want to look at ?summerize in the Hmisc package.


--- Shubha Vishwanath Karanth
<[EMAIL PROTECTED]> wrote:

> Hi R,
> 
>  
> 
> I have the data,
> 
>  
> 
> Value
> 
> 0
> 
> 1
> 
> 2
> 
> 3
> 
> 4
> 
> 5
> 
> 6
> 
> Frequency:
> 
> 258
> 
> 125
> 
> 106
> 
> 94
> 
> 85
> 
> 12
> 
> 5
> 
>  
> 
> Say:
> 
> Value=c(0,1,2,3,4,5,6)
> 
> Frequency=c(258,125,106,94,85,12,5)
> 
>  
> 
>  
> 
> In R, how can I find the mean, variance, skewness
> and kurtosis for this
> grouped data? Is there a direct way of handling this
> type of grouped
> data, instead of writing the code for calculating
> these statistics?
> 
>  
> 
> Thanks for your help,
> 
> Shubha
> 
> 
>   [[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.
>

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] Produce a multiple formats graphic

[Cuvelier Etienne]

Is it possible to produce the same graphic in different formats
in one shot?
Now if I want to produce the same graphic in pdf, ps and jpeg
I run the producing code, but I change the graphic device, and
I choose successively :
pdf(...)
ps(...)
jpeg(...)

So in this case I run the same code 3 times, or I have
to choose a format and use converters...

Is it possible to produce the 3 graphics in once ?


Thank you very much

-- 
===
Cuvelier Etienne
Assistant
FUNDP - Institut d'Informatique
rue Grandgagnage, 21   B-5000 Namur (Belgique)
tel: 32.81.72.49.93fax: 32.81.72.49.67
===
Top 10 reasons to become a Statistician 
 
  1. Deviation is considered normal 
  2. We feel complete and sufficient 
  3. We are 'mean' lovers 
  4. Statisticians do it discretely and 
 continuously 
  5. We are right 95% of the time 
  6. We can legally comment on someone's 
 posterior distribution 
  7. We may not be normal, but we are 
 transformable 
  8. We never have to say we are certain 
  9. We are honestly significantly different 
 10. No one wants our jobs

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[R] Non-parametric tolerance limits

[Svempa]

Does anyone know if there exists a package for non-parametric tolerance
limits in R? Or any other way to do it?
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Re: [R] Is it possible to modify the position of the graphic window ?

[Henrique Dallazuanna]

The lines are:

## Initial position of the graphics window
## (pixels, <0 values from opposite edge)
xgraphics = 200
ygraphics = 10


On 06/11/2007, 8rino-Luca Pantani <[EMAIL PROTECTED]> wrote:
>
> There's a Renviron file under /etc/R, but there are no lines with
> "position (x, y)".
>
> Henrique Dallazuanna ha scritto:
> > In the Windows the file Rconsole contains the position(x,y) of the
> graphics.
> > I don't know if file have the same name in Ubuntu.
> >
>
> __
> 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.
>



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

[[alternative HTML version deleted]]

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[R] pipe scan timeout

[yoooooo]

Hi all, 

 Usually when I do a command in shell and have the output read from R, I
like to do this:

 pp <- pipe(cmd)
 sol <- scan(pp, what="character", sep="\n")

 I prefer this one over read.table since read.table somewhere has a gc
call and it's slow. 

 However, sometimes the cmd takes a while to run and somehow scan/pipe
waits for like 5 seconds and return 0 results (even though the shell command
returns something if i were to put it in shell after 2 min). So i THINK
there's some timeout kicking around somewhere. Do you guys know what the
options would be or if this is a timeout issue at all or if there's a better
way to do this? 

 I tried options('timeout') and I have it set to 60 seconds.. so i don't
think it's that options.. 

Thanks!
-yo


 
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[R] Statistics for the Grouped data

[Shubha Vishwanath Karanth]

Hi R,

 

I have the data,

 

Value

0

1

2

3

4

5

6

Frequency:

258

125

106

94

85

12

5

 

Say:

Value=c(0,1,2,3,4,5,6)

Frequency=c(258,125,106,94,85,12,5)

 

 

In R, how can I find the mean, variance, skewness and kurtosis for this
grouped data? Is there a direct way of handling this type of grouped
data, instead of writing the code for calculating these statistics?

 

Thanks for your help,

Shubha


[[alternative HTML version deleted]]

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Re: [R] wilcox test on two data frames

[Thomas Lumley]

On Tue, 6 Nov 2007, Diogo Alagador wrote:

> Hi all,
>
> Basically I have 2 data frames with equal dimension and I want to apply 
> the wilcox.test to compare columns in the same position (i.e. 1st of 
> df.A with 1st of df.B, 2nd of df.A with 2nd of df.B,...). Anyone give me 
> an hint on this, as I think it is nicer to avoid loops, specially for 
> huge dataframes (3 x 200)

Avoiding loops is unlikely to help with speed. It is more likely to be 
useful to avoid large dataframes (using lists or matrices) but you may 
need the dataframe structure for something else.

If you really want to avoid loops because it is nicer you could use 
mapply():
   mapply(wilcox.test, df.A, df.B)
but this might be slower than a loop.

-thomas

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Re: [R] Is it possible to modify the position of the graphic window ?

[8rino-Luca Pantani]

There's a Renviron file under /etc/R, but there are no lines with 
"position (x, y)".

Henrique Dallazuanna ha scritto:
> In the Windows the file Rconsole contains the position(x,y) of the graphics.
> I don't know if file have the same name in Ubuntu.
>

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Re: [R] wilcox test on two data frames

[Dimitris Rizopoulos]

I don't think that the loop-part puts a great penalty in this case; 
however, it'd be better to convert the data.frames to matrices, since 
matrix indexing is faster, e.g.,

# I presume that you only want to keep the p-values
mat.A <- data.matrix(df.A)
mat.B <- data.matrix(df.B)
pvalues <- numeric(200)
for (i in 1:200) {
pvalues[i] <- wilcox.test(x = mat.A[, i], y = mat.B[, i])$p.value
}


I hope it helps.

Best,
Dimitris


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

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
 http://www.student.kuleuven.be/~m0390867/dimitris.htm


- Original Message - 
From: "Diogo Alagador" <[EMAIL PROTECTED]>
To: 
Sent: Tuesday, November 06, 2007 12:30 PM
Subject: [R] wilcox test on two data frames


Hi all,

Basically I have 2 data frames with equal dimension and I want to 
apply the wilcox.test to compare columns in the same position (i.e. 
1st of df.A with 1st of df.B, 2nd of df.A with 2nd of df.B,...).
Anyone give me an hint on this, as I think it is nicer to avoid loops, 
specially for huge dataframes (3 x 200)

Thanks in advance,

Diogo André Alagador
Portugal

[[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.
> 


Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

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Re: [R] library(tcltk) fails

[Sven Garbade]

On Tue, 2007-11-06 at 08:03 -0600, Dirk Eddelbuettel wrote: 
> On Tue, Nov 06, 2007 at 01:08:40PM +0100, Sven Garbade wrote:
> > Dear list,
> > 
> > I cannot load the tcltk library:
> > 
> > > library(tcltk)
> > Loading Tcl/Tk interface ... Error in fun(...) : 
> >   Can't find a usable tk.tcl in the following directories: 
> > /usr/share/tcltk/tcl8.4/tk8.4 ./lib/tk8.4 /usr/local/lib/tcltk/tk8.4 
> > /usr/local/share/tcltk/tk8.4 /usr/lib/tcltk/tk8.4 /usr/share/tcltk/tk8.4 
> > ./library ./tk8.4.16/library
> > 
> > 
> > 
> > This probably means that tk wasn't installed properly.
> > 
> > Error : .onLoad failed in 'loadNamespace' for 'tcltk'
> > Error: package/namespace load failed for 'tcltk'
> > 
> > Cannot remember that I uninstalled anything related to Tcl/Tk, and I can
> > start Tcl/TK application I wrote. Some system information:
> > 
> > > Sys.info()
> > sysnamerelease 
> >"Linux"   "2.6.22" 
> >version   nodename 
> > "#2 Mon Oct 22 09:58:25 CEST 2007" "meta" 
> >machine  login 
> > "i686"  "unknown" 
> >   user 
> >  "sfg" 
> > 
> > on Debian testing, Tcl/Tk:
> > 
> > $ ldconfig -p | grep libtk
> > libtk8.5.so.0 (libc6) => /usr/lib/libtk8.5.so.0
> > libtk8.4.so.0 (libc6) => /usr/lib/libtk8.4.so.0
> > libtk8.4.so (libc6) => /usr/lib/libtk8.4.so
> > 
> > $ ldconfig -p | grep libtcl
> > libtcl8.5.so.0 (libc6) => /usr/lib/libtcl8.5.so.0
> > libtcl8.4.so.0 (libc6) => /usr/lib/libtcl8.4.so.0
> > libtcl8.4.so (libc6) => /usr/lib/libtcl8.4.so
> > 
> > Anything wrong with my Tcl/Tk installation?
> 
> You didn't tell us your operating system -- but a few days ago on the
> r-sig-debian list we looked at the same issue and found that the tk8.4
> package from Debian unstable fixes this.

Operating system is Debian lenny/sid:
$ uname -a
Linux meta 2.6.22 #2 Mon Oct 22 09:58:25 CEST 2007 i686 GNU/Linux

I now "fixed" this with a symbolic link from /usr/local/lib/tcltk/ (were
R (?) looks for the Tcl/TK libs) to /usr/lib/ were the Tcl/Tk libs are.
I wait until tk8.4 package from Debian unstable is in testing, because
sometimes unstable is really unstable...

Thanks, Sven

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Re: [R] library(tcltk) fails

[Dirk Eddelbuettel]

On Tue, Nov 06, 2007 at 01:08:40PM +0100, Sven Garbade wrote:
> Dear list,
> 
> I cannot load the tcltk library:
> 
> > library(tcltk)
> Loading Tcl/Tk interface ... Error in fun(...) : 
>   Can't find a usable tk.tcl in the following directories: 
> /usr/share/tcltk/tcl8.4/tk8.4 ./lib/tk8.4 /usr/local/lib/tcltk/tk8.4 
> /usr/local/share/tcltk/tk8.4 /usr/lib/tcltk/tk8.4 /usr/share/tcltk/tk8.4 
> ./library ./tk8.4.16/library
> 
> 
> 
> This probably means that tk wasn't installed properly.
> 
> Error : .onLoad failed in 'loadNamespace' for 'tcltk'
> Error: package/namespace load failed for 'tcltk'
> 
> Cannot remember that I uninstalled anything related to Tcl/Tk, and I can
> start Tcl/TK application I wrote. Some system information:
> 
> > Sys.info()
> sysnamerelease 
>"Linux"   "2.6.22" 
>version   nodename 
> "#2 Mon Oct 22 09:58:25 CEST 2007" "meta" 
>machine  login 
> "i686"  "unknown" 
>   user 
>  "sfg" 
> 
> on Debian testing, Tcl/Tk:
> 
> $ ldconfig -p | grep libtk
>   libtk8.5.so.0 (libc6) => /usr/lib/libtk8.5.so.0
> libtk8.4.so.0 (libc6) => /usr/lib/libtk8.4.so.0
> libtk8.4.so (libc6) => /usr/lib/libtk8.4.so
> 
> $ ldconfig -p | grep libtcl
> libtcl8.5.so.0 (libc6) => /usr/lib/libtcl8.5.so.0
> libtcl8.4.so.0 (libc6) => /usr/lib/libtcl8.4.so.0
> libtcl8.4.so (libc6) => /usr/lib/libtcl8.4.so
> 
> Anything wrong with my Tcl/Tk installation?

You didn't tell us your operating system -- but a few days ago on the
r-sig-debian list we looked at the same issue and found that the tk8.4
package from Debian unstable fixes this.

Hth, Dirk

> 
> Thanks, Sven
> 
> __
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-- 
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[R] wilcox test on two data frames

[Diogo Alagador]

Hi all,
 
Basically I have 2 data frames with equal dimension and I want to apply the 
wilcox.test to compare columns in the same position (i.e. 1st of df.A with 1st 
of df.B, 2nd of df.A with 2nd of df.B,...).
Anyone give me an hint on this, as I think it is nicer to avoid loops, 
specially for huge dataframes (3 x 200) 
 
Thanks in advance,
 
Diogo André Alagador
Portugal

[[alternative HTML version deleted]]

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[R] Integrating a function

[Robert Kalicki]

Hello everybody!

I have problems with integrating my function.

My primary function is a “survival function” of the following type:

surviv <- exp(-k*x)/(1+exp(alpha*(x-tau)))

I would like to integrate this function over a defined range and obtain a
vector with all the values from integrate(surviv, 0, x) for x <- 1:N. 

I unfortunately obtain just a scalar value corresponding to the last
integrated x.

How do I have to proceed if I want to obtain a vector with all the results?

I have tried to solve this problem by adding a “while loop”. It works but
the expression becomes to complex if I want to perform further optimization.

Have any one a solution for this problem?

Thanks a lot in advance.

 

Example

# General equation

beta1 <- 0.001

beta2 <- 0

Hct0 <- 0.27

tau <- 70

k <- 0.001

alpha <- 0.3

T2 <-40

 

step <- function(x){

   if(x>=0) step <- 1

   else step <- 0

}

 

   Nmax <- 250

   n <- 1

  while(n__
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[R] Combining Density plots

[Monica Pisica]

 
Hi,
 
you may want to look at Macdonald P (2006) Mixdist package for R
www.math.mcmaster.ca/peter/mix/mix.html
 
It also has an anova test for your model so you would know if your "possible 
sub-populations" are statistically significant of not. I don't know why 
actually this package is not posted on CRAN, though!
 
I hope this helps,
 
Monica
 
 
-
Message: 50Date: Tue, 6 Nov 2007 11:40:07 +1300From: "Gareth Campbell" <[EMAIL 
PROTECTED]>Subject: [R] Combining Density plotsTo: "R Help" 
Message-ID:<[EMAIL PROTECTED]>Content-Type: text/plain 
Hello, What I am trying to do is: Generate a density plot of a population of 
data. This data has a bimodaldistribution so I've isolated a couple of possible 
sub-populations and Iwant to overlay these two density plots over the first to 
see whether theyare contributing to the bimodal population. I can do this fine 
with plot(density(...)) and lines(density(...)) . Butthe resulting plots seem 
to NOT share the same scale or something. I've hada read up on bandwidth and 
fiddled with this but I can't quite get them howthey should look. Needless to 
say that the sub-populations are smaller (n)than the overall population. Does 
anyone know how to scale the populations so they all plot on the samescale with 
the density function? Tha!
 nks very much -- Gareth CampbellPhD CandidateThe University of Auckland P +649 
815 3670M +6421 256 3511E [EMAIL PROTECTED]@gmail.com
_

Get it now.

6971033
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[R] Solution: ploting a comparison of two scores, including the labels in the plot

[Hans Ekbrand]

Thanks to Greg Snow and John Kane I now have a working function that
does what I wanted, that is compares two scores in a plot.

Here is the function:

## compare.ratings: plots two lists corresponding to two different
## ratings. For each element, a line connects the position of that
## element in the two lists.

compare.ratings <- function(data.frame=df, vector1=rating1, vector2=rating2, 
vector3=labels) {
  treshold <- 0.1

  data.frame <- data.frame[sort.list(data.frame[[vector2]]),]

  for(i in 2:length(data.frame[,vector2])) {
 data.frame[i,vector2] <- data.frame[i,vector2] + (treshold * (i-1))
   }

  data.frame <- data.frame[sort.list(data.frame[[vector1]]),]
  
  for(i in 1:length(data.frame[,vector1])) {
data.frame[i,vector1] <- data.frame[i,vector1] + (treshold * (i-1))
  }

  tmp <- c(rbind( data.frame[[vector1]], data.frame[[vector2]], NA ))
  tmp2 <- rep( c(1,2,NA), nrow(data.frame) )
 
  plot(tmp2, tmp, type='b', xlim=c(0,3), xlab='', ylab='', lwd=0.5)
  text(0.9, data.frame[[vector1]], data.frame[[vector3]], adj=1, cex=0.75)
  text(2.1, data.frame[[vector2]], data.frame[[vector3]], adj=0, cex=0.75)

}

-- 
Hans Ekbrand (http://sociologi.cjb.net) <[EMAIL PROTECTED]>
A. Because it breaks the logical sequence of discussion
Q. Why is top posting bad?


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Re: [R] Produce graph that looks nice on screen and on paper

[Deepayan Sarkar]

On 11/6/07, Van Campenhout Bjorn <[EMAIL PROTECTED]> wrote:
> Hi all,
>
> I made a dotplot() with lattice, which comes out nice on the graphics
> device.  I can save this as a eps using postscript() and include this in
> a word document.  This prints nice, but does not look good on screen.
> If I produce a pdf, it is nice on screen, but not on paper.  How can I
> save a graph that looks nice on paper and on screen?

Although you haven't said so, I presume your 'paper' output is
produced by a black and white printer?

You have to define a "theme" (a collection of graphical parameters)
that is "nice" for both screen and paper. Once you come up with such a
collection of parameters, ?trellis.par.set should tell you how to set
them globally. If you want someone else to come up with such a list,
you are probably out of luck (but see ?col.whitebg for a not-very-good
approach).

-Deepayan

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Re: [R] Is it possible to modify the position of the graphic window ?

[Henrique Dallazuanna]

In the Windows the file Rconsole contains the position(x,y) of the graphics.
I don't know if file have the same name in Ubuntu.


On 06/11/2007, 8rino-Luca Pantani <[EMAIL PROTECTED]> wrote:
>
> Dear R users,
> is there a way to tell R where to draw the windows where the plots are
> drawn ?
>
> I always get that window on the right of my screen, where it interferes
> with my Xemacs + ESS window where I'm writing lines.
>
> Of course I can move it manually, but I would like to have it
> permanently on the right, rather than on the left.
>
> Thanks for any advice
>
> Ottorino
>
>
> Ubuntu 7.10
> Xemacs 21.4 patch 20
> ESS version 5.3.4
> R version 2.5.1 (2007-06-27)
>
> __
> 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.
>



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

[[alternative HTML version deleted]]

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[R] Produce graph that looks nice on screen and on paper

[Van Campenhout Bjorn]

Hi all,

I made a dotplot() with lattice, which comes out nice on the graphics
device.  I can save this as a eps using postscript() and include this in
a word document.  This prints nice, but does not look good on screen.
If I produce a pdf, it is nice on screen, but not on paper.  How can I
save a graph that looks nice on paper and on screen?

Bjorn

Bjorn Van Campenhout
Institute of Development Policy and Management (IDPM)
University of Antwerp
Lange Sint Annastraat 7 (S119)
2000 Antwerp - Belgium

++32 3 275 59 35
www.ua.ac.be/bjorn.vancampenhout

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Re: [R] Help translating S-Plus command

[Bernat Claramunt Lopez]

Thank you very much.
Worked perfectly !!

El dl 05 de 11 del 2007 a les 22:17 +, en/na Prof Brian Ripley va
escriure:
> It would help if we knew what that command was supposed to do.  My guess 
> is that you want the Tr$size with the smallest value of Tr$dev, in which 
> case
> 
> Tr$size[which.min(Tr$dev)]
> 
> would seem to do it.  However, there are details like what is to happen if 
> there are ties for the smallest value.
> 
> (There are simpler ways in S-PLUS to sort one variable by the values of 
> another, for example Tr$size[sort.list(Tr$dev)] which works the same way 
> as in R.)
> 
> On Mon, 5 Nov 2007, [EMAIL PROTECTED] wrote:
> 
> > Dear all
> > I have a small routine in S-Plus that I would like to use in R.  There are 
> > some small changes I've been able to adapt, but I don't know how to 
> > translate the line starting with "g1<-sort.col" and the one "Size<- 
> > c(Size...")  (I also add some lines before)
> > (...)
> > Size<-NULL
> > g<-cbind(Tr$dev,Tr$size)
> > (...)
> > g<-data.frame(g)
> >
> > # these next two lines are the ones I need help for
> >
> > g1 <- sort.col(target=g, columns.to.sort="@ALL", columns.to 
> > sort.by=list("g.1"), ascending=T)
> > Size<-c(Size,g1[1,2])
> >
> > Thanks in advance
> > Bernat
> >
> >
> > [[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.
> >
>

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[R] Is it possible to modify the position of the graphic window ?

[8rino-Luca Pantani]

Dear R users,
is there a way to tell R where to draw the windows where the plots are 
drawn ?

I always get that window on the right of my screen, where it interferes 
with my Xemacs + ESS window where I'm writing lines.

Of course I can move it manually, but I would like to have it 
permanently on the right, rather than on the left.

Thanks for any advice

Ottorino


Ubuntu 7.10
Xemacs 21.4 patch 20
ESS version 5.3.4
R version 2.5.1 (2007-06-27)

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[R] library(tcltk) fails

[Sven Garbade]

Dear list,

I cannot load the tcltk library:

> library(tcltk)
Loading Tcl/Tk interface ... Error in fun(...) : 
  Can't find a usable tk.tcl in the following directories: 
/usr/share/tcltk/tcl8.4/tk8.4 ./lib/tk8.4 /usr/local/lib/tcltk/tk8.4 
/usr/local/share/tcltk/tk8.4 /usr/lib/tcltk/tk8.4 /usr/share/tcltk/tk8.4 
./library ./tk8.4.16/library



This probably means that tk wasn't installed properly.

Error : .onLoad failed in 'loadNamespace' for 'tcltk'
Error: package/namespace load failed for 'tcltk'

Cannot remember that I uninstalled anything related to Tcl/Tk, and I can
start Tcl/TK application I wrote. Some system information:

> Sys.info()
sysnamerelease 
   "Linux"   "2.6.22" 
   version   nodename 
"#2 Mon Oct 22 09:58:25 CEST 2007" "meta" 
   machine  login 
"i686"  "unknown" 
  user 
 "sfg" 

on Debian testing, Tcl/Tk:

$ ldconfig -p | grep libtk
libtk8.5.so.0 (libc6) => /usr/lib/libtk8.5.so.0
libtk8.4.so.0 (libc6) => /usr/lib/libtk8.4.so.0
libtk8.4.so (libc6) => /usr/lib/libtk8.4.so

$ ldconfig -p | grep libtcl
libtcl8.5.so.0 (libc6) => /usr/lib/libtcl8.5.so.0
libtcl8.4.so.0 (libc6) => /usr/lib/libtcl8.4.so.0
libtcl8.4.so (libc6) => /usr/lib/libtcl8.4.so

Anything wrong with my Tcl/Tk installation?

Thanks, Sven

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Re: [R] Running R2WinBUGS on Linux using Wine

[Uwe Ligges]

Quin Wills wrote:
> Hello all
> 
> (1) My departmental IT guru has installed the latest Wine (0.9.48) on a 
> well maintained Fedora 7 server, so that I can run WinBUGS from R via 
> R2WinBUGS (this seems like the only real option for running BUGS from R 
> on a Linux platform?)
> (2) WinBUGS seems to run okay, except for the following output errors:
> === === ===
> fixme:keyboard:RegisterHotKey (0x10024,13,0x0002,3): stub
> fixme:ole:GetHGlobalFromILockBytes cbSize is 13824
> err:ole:CoGetClassObject class {0003000a---c000-0046} 
> not registered
> err:ole:CoGetClassObject class {0003000a---c000-0046} 
> not registered
> err:ole:CoGetClassObject no class object 
> {0003000a---c000-0046} could be created for context 0x3
> === === ===
> 
> (3) I found a previous posting suggesting that this is a Wine related 
> issue, which doesn't seem too major, and is likely to be fixed (pasted 
> below).  As I'm not too technical, I am naturally concerned that this 
> problem might be doing horrible things with my analysis, which I haven't 
> spotted yet. This mailing is just a sanity check with any of you gurus 
> out there - for words of wisdom, advice, and perhaps what to watch out for.

No words of wisdom, my statement is the same as before, this is some 
wine (running WinBUGS) related problem. You posted to an R mailing list, 
but not to a wine mailing list.

Best,
Uwe





> Thanks,
> Quin
> 
> 
> === === ===
> From: Uwe Ligges  >
>  
> 
> Date: Thu, 26 Jul 2007 18:54:54 +0200
> 
> meyerjp_at_jmu.edu wrote:
>  > I am trying to run WinBUGS 1.4 from the Ubuntu 6.10 Linux 
> distribution. I am using the R2WinBUGS packages with the source file 
> listed below. WinBUGS appears to run properly, but I get the following 
> message after WinBUGS starts in WINE. Does anyone know what may be 
> causing this error and what the correction may be? 
> 
> /> /
> /> Thanks /
> /> /
> */> ERROR MESSAGE: /
> */> /
> /> fixme:ole:GetHGlobalFromILockBytes cbSize is 13824 /
> /> err:ole:CoGetClassObject class {0003000a---c000-0046} 
> not registered /
> /> err:ole:CoGetClassObject class {0003000a---c000-0046} 
> not registered /
> /> err:ole:CoGetClassObject no class object 
> {0003000a---c000-0046} could be created for context 0x3 /
> /> fixme:keyboard:RegisterHotKey (0x10032,13,0x0002,3): stub /
> /> fixme:ntdll:RtlNtStatusToDosErrorNoTeb no mapping for 800a /
> /> err:ole:local_server_thread Failure during ConnectNamedPipe 317 /
> 
> This is wine, not R2WinBUGS nor WinBUGS nor R, I fear, and the "fixme:" 
> sounds promising that things go away in a more recent version of wine...
> 
> Uwe Ligges
> === === ===
> 
> __
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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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[R] Running R2WinBUGS on Linux using Wine

[Quin Wills]

Hello all

(1) My departmental IT guru has installed the latest Wine (0.9.48) on a 
well maintained Fedora 7 server, so that I can run WinBUGS from R via 
R2WinBUGS (this seems like the only real option for running BUGS from R 
on a Linux platform?)

(2) WinBUGS seems to run okay, except for the following output errors:
=== === ===
fixme:keyboard:RegisterHotKey (0x10024,13,0x0002,3): stub
fixme:ole:GetHGlobalFromILockBytes cbSize is 13824
err:ole:CoGetClassObject class {0003000a---c000-0046} 
not registered
err:ole:CoGetClassObject class {0003000a---c000-0046} 
not registered
err:ole:CoGetClassObject no class object 
{0003000a---c000-0046} could be created for context 0x3
=== === ===

(3) I found a previous posting suggesting that this is a Wine related 
issue, which doesn't seem too major, and is likely to be fixed (pasted 
below).  As I'm not too technical, I am naturally concerned that this 
problem might be doing horrible things with my analysis, which I haven't 
spotted yet. This mailing is just a sanity check with any of you gurus 
out there - for words of wisdom, advice, and perhaps what to watch out for.

Thanks,
Quin


=== === ===
From: Uwe Ligges mailto:ligges_at_statistik.uni-dortmund.de?Subject=Re:%20%5BR%5D%20error%20in%20using%20R2WinBUGS%20on%20Ubuntu%206.10%20Linux>>
 

Date: Thu, 26 Jul 2007 18:54:54 +0200

meyerjp_at_jmu.edu wrote:
 > I am trying to run WinBUGS 1.4 from the Ubuntu 6.10 Linux 
distribution. I am using the R2WinBUGS packages with the source file 
listed below. WinBUGS appears to run properly, but I get the following 
message after WinBUGS starts in WINE. Does anyone know what may be 
causing this error and what the correction may be? 

/> /
/> Thanks /
/> /
*/> ERROR MESSAGE: /
*/> /
/> fixme:ole:GetHGlobalFromILockBytes cbSize is 13824 /
/> err:ole:CoGetClassObject class {0003000a---c000-0046} 
not registered /
/> err:ole:CoGetClassObject class {0003000a---c000-0046} 
not registered /
/> err:ole:CoGetClassObject no class object 
{0003000a---c000-0046} could be created for context 0x3 /
/> fixme:keyboard:RegisterHotKey (0x10032,13,0x0002,3): stub /
/> fixme:ntdll:RtlNtStatusToDosErrorNoTeb no mapping for 800a /
/> err:ole:local_server_thread Failure during ConnectNamedPipe 317 /

This is wine, not R2WinBUGS nor WinBUGS nor R, I fear, and the "fixme:" 
sounds promising that things go away in a more recent version of wine...

Uwe Ligges
=== === ===

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Re: [R] How to know created time of object in R?

[Prof Brian Ripley]

On Tue, 6 Nov 2007, Alberto Monteiro wrote:

>
> Prof Brian Ripley wrote:
>>
>>> I would like to know the created time and date of specific object.
>>> Is there any function for it?
>>
>> There isn't even the concept.  Most objects in R are a collection of
>> SEXPRECs created at different times.  Suppose you create a data
>> frame out of existing columns, and then later change the names? What
>> does 'created' mean for the data frame?
>>
>> In any case, none of the possibly relevant date-times is stored.
>>
> I imagine that it could be possible to create a class that
> would store the "creation time" of its objects... but I have
> no idea how to do it (I think I could do it in C++, but I am
> illiterate in R++ oops S4 classes).

You could record the time at which you recorded the time by e.g.

attr(x, "creation time") <- Sys.time()

but this would be subject to all the ambiguities I mentioned.  For an S4 
class you could have a slot for time and assign it in the constructor, but 
it is commonplace to use new() to create a skeleton object and then fill 
it in.  You would then need to arrange for all the subset and 
subassignment methods to either preserve or update the time.

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

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[R] virus warning from escan to mail-sender!

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[R] Importing Data

[Yemi Oyeyemi]

Dear,
I am having problem importing data from other packages or spreadsheet 
to R. The data file contains characters and numerics variables.

[EMAIL PROTECTED] wrote:
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of R-help digest..."


Today's Topics:

1. Help in error of mixed models (Bernardo Rangel Tura)
2. Where to ask general stats questions? (francogrex)
3. Re: structure vs. matrix (Mark Difford)
4. Problems with garch() function tseries package R 2.6.0
(Jos? Augusto Morais de Andrade J?nior - JAMAJ)
5. Re: Where to ask general stats questions? (Patrick Drechsler)
6. help on error message!!! (david csongor)
7. Re: structure vs. matrix (Duncan Murdoch)
8. Re: structure vs. matrix (Duncan Murdoch)
9. Re: help on error message!!! (Duncan Murdoch)
10. Re: help on error message!!! (Bernardo Rangel Tura)
11. Re: Problems with garch() function tseries package R 2.6.0
(Prof Brian Ripley)
12. Re: structure vs. matrix (Prof Brian Ripley)
13. Why can repeated measures anova with within & between
subjects design not be done if group sizes are unbalanced? (Gilbert G)
14. Re: markov regime switching models (Liviu Andronic)
15. Re: Why can repeated measures anova with within & between
subjects design not be done if group sizes are unbalanced?
(Charles C. Berry)
16. Problem implementing adapt() (Sergey Goriatchev)
17. Problem implementing adapt() (Sergey Goriatchev)
18. Re: [Spam] Re: Problems with garch() function tseries package
R 2.6.0 (Jos? Augusto Morais de Andrade J?nior - JAMAJ)
19. Re: Problems with garch() function tseries package R 2.6.0
(Jos? Augusto Morais de Andrade J?nior - JAMAJ)
20. install problem 2.6 mac os x 10.5 (Oscar Moreno)
21. Re: R CMD SHLIB gives error: bad value (generic) for -mtune=
switch (McKay Curtis)
22. hierarchical mixed model (Irene Mantzouni)
23. Re: Problems with garch() function tseries package R 2.6.0
(Jos? Augusto Morais de Andrade J?nior - JAMAJ)
24. Re: Problems with garch() function tseries package R 2.6.0
(Jos? Augusto Morais de Andrade J?nior - JAMAJ)
25. Re: unable to install package ff (Matthew Keller)
26. Re: install problem 2.6 mac os x 10.5 (Matthew Keller)
27. Re: Help in error of mixed models (Andrew Robinson)
28. Re: install problem 2.6 mac os x 10.5 (Chung-hong Chan)
29. R package "segmented" (Maura E Monville)
30. Re: structure vs. matrix (Edna Bell)
31. Sending E-Mail from R (Josh Kalish)
32. Re: structure vs. matrix (Gabor Grothendieck)
33. Re: Sending E-Mail from R (Gabor Grothendieck)
34. Re: Sending E-Mail from R ( (Ted Harding))
35. Re: perl module for R (Lux Zhang)
36. Re: Sending E-Mail from R (Benilton Carvalho)
37. multidensional integration with adapt (Helene)
38. multidimensional integration with adapt (Helene)
39. R2HTML package and Open Office: text only pasted (Graham Smith)
40. How to reconstitute a Product-Outcome table? (francogrex)
41. Fw: Creating a barplot--advice needed (Thomas L Jones, PhD)
42. Help about exception handling in r-project. (ANUSHA AIYALU KANNAN)
43. Garch() function of tseries package doesnt work anymore
(Jos? Augusto Morais de Andrade J?nior - JAMAJ)
44. SuSE 10.3 R GUI up&running (Maura E Monville)
45. Installing R on Mac OS X Leopard (Mitch Ohriner)
46. Re: Installing R on Mac OS X Leopard (Chung-hong Chan)
47. Re: cumsum (ONKELINX, Thierry)
48. Re: How to reconstitute a Product-Outcome table?
(Gabor Grothendieck)
49. Re: Trellis dotplot label keys (Patrick Connolly)
50. Odp: Fw: Creating a barplot--advice needed (Petr PIKAL)
51. do.call without arguments? (Antje)
52. Re: do.call without arguments? (Peter Dalgaard)
53. Re: do.call without arguments? (Antje)


--

Message: 1
Date: Sun, 04 Nov 2007 09:18:09 -0200
From: Bernardo Rangel Tura 
Subject: [R] Help in error of mixed models
To: r-help 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="us-ascii"


Hi R-masters

I read the article: Bivariate analysis of sensitivity and specificity
produces informative summary measures in diagnostic reviews.

In this paper i proposed a bivariate mixed model and use SAS proc mixed
to adjust the estimates.


I thinks use R to make the same and try with this code:

base<-read.csv("base.csv")
adj<-.5
attach(base)

sens<-(VP+adj)/(VP+FN+2*adj)
log.S<-log(sens/(1-sens))
var.log.S<-1/(sens*(1-sens)*(VP+FN))
dis<-rep(1,length(log.S))
non.dis<-rep(0,length(log.S))
data.S<-data.frame(id,Modality,log.S,var.log.S,dis,non.dis)
names(data.S)<-c("id","Modality","logit","var.logit","dis","non.dis")

esp<-(VN+adj)/(VN+FP+2*adj)
log.E<-log((1-esp)/esp)
var.log.E<-1/(esp*(1-esp)*(VN+FP))
dis<-rep(0,length(log.E))
no

Re: [R] How to know created time of object in R?

[Alberto Monteiro]

Prof Brian Ripley wrote:
>
>> I would like to know the created time and date of specific object.
>> Is there any function for it?
> 
> There isn't even the concept.  Most objects in R are a collection of 
> SEXPRECs created at different times.  Suppose you create a data 
> frame out of existing columns, and then later change the names? What 
> does 'created' mean for the data frame?
> 
> In any case, none of the possibly relevant date-times is stored.
> 
I imagine that it could be possible to create a class that
would store the "creation time" of its objects... but I have
no idea how to do it (I think I could do it in C++, but I am
illiterate in R++ oops S4 classes).

Alberto Monteiro

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Re: [R] How to find the zero (only the real solution) with the package polynom ?

[Ptit_Bleu]

Hi again,

I found a solution (but maybe it is not the best one) : I converted the
poynom into a function.

pderiv<-as.function((deriv(polynomial(pfit$coefficients
uniroot(pderiv, c(0.8,0.2))[[1]]
[1] 0.4778413

Now I just have to find the corresponding "b" to this "a" but I think it
must be quite easy (am I right ?).

I don't delete my post as it maybe be helpful to someone else but if the
Administrator wants to delete it, it is ok to me.

See you,
Ptit Bleu.

---



Ptit_Bleu wrote:
> 
> Hello,
> 
> I have 3 columns : a, b and a*b
> I would like to find the pair (a,b) so that a*b is the minimum but not
> from the points I measured but from the fit of the curve (I have more
> points that the ones given below but I fit only on this part because I 
> know that the minimum a*b is in this interval).
> 
> I thought doing it this way :
> 
> - to fit a*b=f(a)
> abfit<-lm(ab ~ poly(a,8,raw=T))
> 
> - to use the package polynom to make the polynom 
> library(polynom)
> polynomial(abfit$coefficients)
> 0.03537506 - 0.8506516*x + 8.302545*x^2 - 44.80418*x^3 + 144.2161*x^4 -
> 283.2458*x^5 + 331.1776*x^6 - 210.5144*x^7 + 55.86646*x^8
> 
> - to derive the polynom
> deriv(polynomial(pfit$coefficients))
> -0.8506516 + 16.60509*x - 134.4125*x^2 + 576.8643*x^3 - 1416.229*x^4 +
> 1987.066*x^5 - 1473.601*x^6 + 446.9317*x^7
> 
> - to find the zero
> solve(deriv(polynomial(pfit$coefficients)))
> [1] 0.1749897+0.0568886i 0.1749897-0.0568886i 0.3742571-0.1235393i
> 0.3742571+0.1235393i 0.4778418+0.000i 0.8604070+0.1306799i
> 0.8604070-0.1306799i
> 
> And here is my little problem : I don't want the complex solutions, only
> the real one (0.4778418).
> 
> I also tried uniroot but I got an error message :
> uniroot(deriv(polynomial(pfit$coefficients)), c(0.8,0.2))
> Error in uniroot(deriv(polynomial(abfit$coefficients)), c(0.8, 0.2)) : 
> Impossible to find the function "f"
> 
> Is there a way to extract this real solution ?
> 
> I thank you in advance for your help,
> Have a nice day,
> Ptit Bleu. 
> 
> -
> Set of points
> aba*b
> 0.8   0.033320357 0.026656286
> 0.76  0.023930636 0.018187283
> 0.72  0.0153903   0.011081016
> 0.68  0.007844914 0.005334542
> 0.64  0.001598132 0.001022804
> 0.6   -0.00315939 -0.001895634
> 0.56  -0.006402796-0.003585566
> 0.52  -0.008379886-0.004357541
> 0.48  -0.009528793-0.004573821
> 0.44  -0.010198446-0.004487316
> 0.4   -0.010638282-0.004255313
> 0.36  -0.010937536-0.003937513
> 0.32  -0.011169004-0.003574081
> 0.28  -0.011343229-0.003176104
> 0.24  -0.0114878  -0.002757072
> 0.2   -0.011630636-0.002326127
> 0.16  -0.011724586-0.001875934
> 
> 

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Re: [R] xtable.by

[A Friedman]

A point of clarification: the measurements are continuous; the road surface
is discrete with four levels, and the road capacity is discrete with five
levels.  Each measured point has both a surface and capacity associated with
it.

Thanks,
Ari

  I have a series of measurements
>

[[alternative HTML version deleted]]

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[R] How to find the zero (only the real solution) with the package polynom ?

[Ptit_Bleu]

Hello,

I have 3 columns : a, b and a*b
I would like to find the pair (a,b) so that a*b is the minimum but not from
the points I measured but from the fit of the curve (I have more points that
the ones given below but I fit only on this part because I 
know that the minimum a*b is in this interval).

I thought doing it this way :

- to fit a*b=f(a)
abfit<-lm(ab ~ poly(a,8,raw=T))

- to use the package polynom to make the polynom 
library(polynom)
polynomial(abfit$coefficients)
0.03537506 - 0.8506516*x + 8.302545*x^2 - 44.80418*x^3 + 144.2161*x^4 -
283.2458*x^5 + 331.1776*x^6 - 210.5144*x^7 + 55.86646*x^8

- to derive the polynom
deriv(polynomial(pfit$coefficients))
-0.8506516 + 16.60509*x - 134.4125*x^2 + 576.8643*x^3 - 1416.229*x^4 +
1987.066*x^5 - 1473.601*x^6 + 446.9317*x^7

- to find the zero
solve(deriv(polynomial(pfit$coefficients)))
[1] 0.1749897+0.0568886i 0.1749897-0.0568886i 0.3742571-0.1235393i
0.3742571+0.1235393i 0.4778418+0.000i 0.8604070+0.1306799i
0.8604070-0.1306799i

And here is my little problem : I don't want the complex solutions, only the
real one (0.4778418).

I also tried uniroot but I got an error message :
uniroot(deriv(polynomial(pfit$coefficients)), c(0.8,0.2))
Error in uniroot(deriv(polynomial(abfit$coefficients)), c(0.8, 0.2)) : 
Impossible to find the function "f"

Is there a way to extract this real solution ?

I thank you in advance for your help,
Have a nice day,
Ptit Bleu. 

-
Set of points
aba*b
0.8 0.033320357 0.026656286
0.760.023930636 0.018187283
0.720.0153903   0.011081016
0.680.007844914 0.005334542
0.640.001598132 0.001022804
0.6 -0.00315939 -0.001895634
0.56-0.006402796-0.003585566
0.52-0.008379886-0.004357541
0.48-0.009528793-0.004573821
0.44-0.010198446-0.004487316
0.4 -0.010638282-0.004255313
0.36-0.010937536-0.003937513
0.32-0.011169004-0.003574081
0.28-0.011343229-0.003176104
0.24-0.0114878  -0.002757072
0.2 -0.011630636-0.002326127
0.16-0.011724586-0.001875934

-- 
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http://www.nabble.com/How-to-find-the-zero-%28only-the-real-solution%29-with-the-package-polynom---tf4756646.html#a13602364
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__
R-help@r-project.org mailing list
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