[R] loading error of the Rcmdr library on Debian Sid [SOLVED]
Hello, hopefully someone will remember my previous problem to load the Rcmdr library from within GNU R resulting in an error message: libnvidia-tls.so.1: cannot handle TLS data. Some suggestions have been raised by Christian Schulz and others that unfortunately didn't work around this error. Nevertheless I felt very grateful for your suggestions! This morning I investigated this problem a bit more in depth. It turned out that a buggy NVidia driver (libnvidia-tls.so) is loaded by defualt provoking the reported problem. After renaming /usrlib/tls/ too /usr/lib/tls_old (can also be entirely removed!) the problem vanished inmediately and R Commander works smoothly out of the box! Just thought this might be of interest in case of someone else is affected by this NVidia related problem! regards Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] What is nu-regression for svm?
Does anyone knows what is the nu-regression option for the type parameter in svm (from package e1071)? I cannot find any explanation on that and I have a reasonable understanding on svm fundamentals. Thanks Joao Moreira __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] help with numerical solution for two simultaneous nonlinearequations in 2 variables
Hi, Suppose you have p equations in p unknowns: F1(x1,x2,...,xp) =0 . . . Fp(x1,x2,...,xp) = 0 You can solve the equivalent minimization problem: G(x1,x2,...,xp) = F1^2 + ... + Fp^2 = 0 So, you can use optim with G as your objective function. Hope this is helpful, Ravi. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Joshi, Yogesh Sent: Thursday, September 16, 2004 10:54 PM To: [EMAIL PROTECTED] Subject: [R] help with numerical solution for two simultaneous nonlinearequations in 2 variables Hi, I am relatively new to R and am trying to solve two simultaneous nonlinear equations in two variables numerically, and was wondering if anyone knew if any of the packages could do that. An alternative is writing my own code using Newton-Raphson; I did that but was not able to get good convergence. Any ideas please? Thanks Yogesh [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] pairs plot and legend
I would like to add a legend to a pairs plot. Is there a simple way to do this? Just doing legend(.) doesn't seem to get it. Thanks, Sean __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Proposal for New R List: Criticism? Comments?
Hi John et al.
I'm coming late to this thread (because of vacation),
JohnF == John Fox [EMAIL PROTECTED]
on Fri, 10 Sep 2004 10:56:51 -0400 writes:
JohnF Dear Brian et al.,
JohnF Jonathan's search site is excellent -- I use it
JohnF frequently -- and for some reason new users seem
JohnF unaware of help.search(), which, despite the fact
JohnF that it searches only in installed packages, I also
JohnF find very useful.
yes and yes.
JohnF A couple of comments, however: First, if help pages
JohnF from all packages were available at a central
JohnF location -- e.g., at CRAN -- help.search() could have
JohnF an option to search that location. Second, I still
JohnF feel that it would be useful to provide some other
JohnF way of searching the space of all available
JohnF functions. One idea, which I mentioned in an earlier
JohnF message on this thread, would be a keyword system
JohnF (again, different from the current set of standard
JohnF keywords).
\concept{} was introduced for this
JohnF The keywords could be accessed by help.search()
and this happens (by default) for \concept{} entries
JohnF and also compiled into an index.
this doesn't happen yet.
The ``real problem'' of course is that package authors need to
write all these \concept{} entries before such an index can
really become useful.
Martin Maechler
-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
Sent: Friday, September 10, 2004 5:26 AM
To: Jonathan Baron
Cc: Adaikalavan Ramasamy; John Fox; R-help; 'Berton Gunter'
Subject: Re: [R] Proposal for New R List: Criticism? Comments?
On Fri, 10 Sep 2004, Jonathan Baron wrote:
On 09/10/04 03:54, Adaikalavan Ramasamy wrote:
There is another issue to be considered. Currently you
need to have
the relevant packages installed before help.search() bring
it up. My
work around this is to install all available packages just in case
the function I need is nestled in some non-standard
packages. I also
update them rather frequently.
I do this too, at my search site (where
frequently=monthly) and you
can search functions only, and use Boolean search expressions and
phrases.
But right now the entire set of packages takes about 885
meg (if I'm
reading du correctly), which is less than my very modest
collection of
digital photos, and a tiny fraction of a 3-year-old standard hard
disk. In other words, it is no big deal to install all the
packages
if you have your own computer.
I am seeing about 520Mb for all base + CRAN packages under
1.9.1, and it will be rather less under 2.0.0 as more parts
are stored compressed.
BioC is a lot larger.
It is however, a BIG deal to install *all* the packages and
am I currently 10 short since they depend on other software
that I do not have a licence for or will not compile (and
there are three others I cannot reinstall using current gcc).
On AMD64 and Solaris there are several others, and something
like 20 do not install on Windows. (I could use
--install-fake as the CRAN checks do, but I have the almost
complete set installed to test R changes, not test packages.)
So I do see some merit in having a full-text search for R
help available at some URL, as Jonathan has kindly provided.
--
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] pairs plot and legend
Sean Davis wrote: I would like to add a legend to a pairs plot. Is there a simple way to do this? Just doing legend(.) doesn't seem to get it. For sure you have specified wrong x,y values. See par(usr) for the range or try it interactively using: legend(locator(1), ..) Uwe Ligges Thanks, Sean __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] help with numerical solution for two simultaneous nonlinearequations in 2 variables
Thank you - optim has solved my problem. Best regards, Yogesh -Original Message- Hi, Suppose you have p equations in p unknowns: F1(x1,x2,...,xp) =0 . . . Fp(x1,x2,...,xp) = 0 You can solve the equivalent minimization problem: G(x1,x2,...,xp) = F1^2 + ... + Fp^2 = 0 So, you can use optim with G as your objective function. Hope this is helpful, Ravi. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Joshi, Yogesh Sent: Thursday, September 16, 2004 10:54 PM To: [EMAIL PROTECTED] Subject: [R] help with numerical solution for two simultaneous nonlinearequations in 2 variables Hi, I am relatively new to R and am trying to solve two simultaneous nonlinear equations in two variables numerically, and was wondering if anyone knew if any of the packages could do that. An alternative is writing my own code using Newton-Raphson; I did that but was not able to get good convergence. Any ideas please? Thanks Yogesh [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] library functions looks up wrong directory
Hello, I just encountered this error from within R: -- library() Warning message: library '/usr/local/lib/R/site-library' contains no package in: library() --- which is basically correct since all the looked up packages are in /usr/lib/R/site-library, not in /usr/local Now I am looking for a possibility to adjust my config too /usr/lib/R/site-library. Is there a special config file to do this in R ? platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major1 minor9.1 year 2004 month06 day 21 language R __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] controlling printing precision in paste()
Rene, Look at ?format. Sean On Sep 17, 2004, at 9:21 AM, RenE J.V. Bertin wrote: Hello, I can't seem to find the way to modify the precision with which paste() prints its floating point numbers, more precisely the number of decimal digits printed. This is apparently not controlled by options( digits= ), and there is no appropriate argument to paste() itself. Is this possible, and if so, how? Does one have to use round() for all individual arguments, or is there a more global approach? Thanks, RenE Bertin __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] loading error of the Rcmdr library on Debian Sid [SOLVED]
That sounds like the result of having a too-old nvidia-common and
booting between 2.4 and 2.6 kernels.
I believe that nvidia until 2.6 likes the TLS libs, under 2.4 doesn't.
Thomas Schönhoff [EMAIL PROTECTED] writes:
Hello,
hopefully someone will remember my previous problem to load the Rcmdr
library from within GNU R resulting in an error message:
libnvidia-tls.so.1: cannot handle TLS data.
Some suggestions have been raised by Christian Schulz and others that
unfortunately didn't work around this error.
Nevertheless I felt very grateful for your suggestions!
This morning I investigated this problem a bit more in depth. It
turned out that a buggy NVidia driver (libnvidia-tls.so) is loaded by
defualt provoking the reported problem.
After renaming /usrlib/tls/ too /usr/lib/tls_old (can also be entirely
removed!) the problem vanished inmediately and R Commander works
smoothly out of the box!
Just thought this might be of interest in case of someone else is
affected by this NVidia related problem!
regards
Thomas
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--
Anthony Rossini Research Associate Professor
[EMAIL PROTECTED]http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email
CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}
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Re: [R] controlling printing precision in paste()
Hi RenE,
you could easily modify the paste function to get what you want,
i.e.,
paste. - function (..., digits=16, sep= , collapse=NULL) {
args - list(...)
if (length(args) == 0)
if (length(collapse) == 0)
character(0)
else
else{
for(i in seq(along=args))
if(is.numeric(args[[i]])) args[[i]] -
as.character(round(args[[i]], digits)) else args[[i]] -
as.character(args[[i]])
.Internal(paste(args, sep, collapse))
}
}
x - rnorm(3)
x
paste.(x1=, x[1], , x2=, x[2], , x3=, x[3], sep=,
collapse=,)
paste.(x1=, x[1], , x2=, x[2], , x3=, x[3], digits=3, sep=,
collapse=,)
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: +32/16/396887
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm
- Original Message -
From: RenE J.V. Bertin [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Friday, September 17, 2004 3:21 PM
Subject: [R] controlling printing precision in paste()
Hello,
I can't seem to find the way to modify the precision with which
paste() prints its floating point numbers, more precisely the number
of decimal digits printed. This is apparently not controlled by
options( digits= ), and there is no appropriate argument to paste()
itself.
Is this possible, and if so, how? Does one have to use round() for
all individual arguments, or is there a more global approach?
Thanks,
RenE Bertin
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http://www.R-project.org/posting-guide.html
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Re: [R] library functions looks up wrong directory
Thomas Schönhoff wrote: Hello, I just encountered this error from within R: -- library() Warning message: library '/usr/local/lib/R/site-library' contains no package in: library() --- which is basically correct since all the looked up packages are in /usr/lib/R/site-library, not in /usr/local Now I am looking for a possibility to adjust my config too /usr/lib/R/site-library. Is there a special config file to do this in R ? See ?Startup Uwe Ligges platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major1 minor9.1 year 2004 month06 day 21 language R __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Rggobi function error
Hello,
I was working with Rggobi and was trying to use the function
setIdentifyHandler.ggobi(f).
The error I am getting is
Error in setIdentifyHandler.ggobi(f) : attempt to apply non-function
The function setIdentifyHandler.ggobi is
function (f, .gobi = getDefaultGGobi())
{
gobj = unclass(.gobi)$ref
gobj$AddCallback(identify-point, function(gg, sp, which,
d) f(which, d))
}
AddCallback function is not recognised as a function and so the error -
non-function.
Did I install Rggobi properly, or do I need any other add-on packages to
implement the handlers?
I am using R-1.9.1 and Rggobi-1.0-0 in unix .
Thank you
Aruna
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[R] How many records could I store in a dataframe?
Hi all, I have a dataframe with 2 variables and 6,000,000 records. It seems R will crash when the number of record is larger than 3,000,000. How many records could I store in a dataframe Rui __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How many records could I store in a dataframe?
[EMAIL PROTECTED] wrote: Hi all, I have a dataframe with 2 variables and 6,000,000 records. It seems R will crash when the number of record is larger than 3,000,000. How many records could I store in a dataframe Which version of R, which OS? I don't think that R crashes, but it produces an error message telling that the amount of free memory R has access to is not sufficient. If it really crashes, please specify a reproducible example. In theory, if you have access to enough memory, I think something like 2^32-1, AFAIR. Uwe Ligges Rui __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Proposal for New R List: Criticism? Comments?
Dear Martin,
Thanks for pointing this out -- I'm ashamed to say that I forgot about
\concept{} entries. As you say (aside from people stupidly forgetting that
they exist), the problem is to get people to use them. How about requiring
one or more concept entries for each help file?
Regards,
John
-Original Message-
From: Martin Maechler [mailto:[EMAIL PROTECTED]
Sent: Friday, September 17, 2004 7:57 AM
To: John Fox
Cc: 'R-help'
Subject: RE: [R] Proposal for New R List: Criticism? Comments?
Hi John et al.
I'm coming late to this thread (because of vacation),
JohnF == John Fox [EMAIL PROTECTED]
on Fri, 10 Sep 2004 10:56:51 -0400 writes:
JohnF Dear Brian et al.,
JohnF Jonathan's search site is excellent -- I use it
JohnF frequently -- and for some reason new users seem
JohnF unaware of help.search(), which, despite the fact
JohnF that it searches only in installed packages, I also
JohnF find very useful.
yes and yes.
JohnF A couple of comments, however: First, if help pages
JohnF from all packages were available at a central
JohnF location -- e.g., at CRAN -- help.search() could have
JohnF an option to search that location. Second, I still
JohnF feel that it would be useful to provide some other
JohnF way of searching the space of all available
JohnF functions. One idea, which I mentioned in an earlier
JohnF message on this thread, would be a keyword system
JohnF (again, different from the current set of standard
JohnF keywords).
\concept{} was introduced for this
JohnF The keywords could be accessed by help.search()
and this happens (by default) for \concept{} entries
JohnF and also compiled into an index.
this doesn't happen yet.
The ``real problem'' of course is that package authors need
to write all these \concept{} entries before such an index
can really become useful.
Martin Maechler
-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
Sent: Friday, September 10, 2004 5:26 AM
To: Jonathan Baron
Cc: Adaikalavan Ramasamy; John Fox; R-help; 'Berton Gunter'
Subject: Re: [R] Proposal for New R List: Criticism? Comments?
On Fri, 10 Sep 2004, Jonathan Baron wrote:
On 09/10/04 03:54, Adaikalavan Ramasamy wrote:
There is another issue to be considered. Currently you
need to have
the relevant packages installed before help.search() bring
it up. My
work around this is to install all available
packages just in case
the function I need is nestled in some non-standard
packages. I also
update them rather frequently.
I do this too, at my search site (where
frequently=monthly) and you
can search functions only, and use Boolean search
expressions and
phrases.
But right now the entire set of packages takes about 885
meg (if I'm
reading du correctly), which is less than my very modest
collection of
digital photos, and a tiny fraction of a 3-year-old
standard hard
disk. In other words, it is no big deal to install all the
packages
if you have your own computer.
I am seeing about 520Mb for all base + CRAN packages under
1.9.1, and it will be rather less under 2.0.0 as more parts
are stored compressed.
BioC is a lot larger.
It is however, a BIG deal to install *all* the packages and
am I currently 10 short since they depend on other software
that I do not have a licence for or will not compile (and
there are three others I cannot reinstall using current gcc).
On AMD64 and Solaris there are several others, and something
like 20 do not install on Windows. (I could use
--install-fake as the CRAN checks do, but I have the almost
complete set installed to test R changes, not test packages.)
So I do see some merit in having a full-text search for R
help available at some URL, as Jonathan has kindly provided.
--
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] RSPerl Causes Segfaults with Perl 5.8.0 and R 1.9.1 on Redhat9
RSPerl causes random segfaults (it occassionally works) in Rf_isValidName () from /usr/lib/R/bin/libR.so when I call wilcox.test on some perl array references. This is with R built from the r-project source RPM modified to have the --enable-shared-R option and RSPerl built with the default options, except for having to set PERL_MODULES to not include modperl or Apache. any ideas? eric. -- http://ir.iit.edu/~ej __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] bagplot()
BDR == Prof Brian Ripley [EMAIL PROTECTED] on Mon, 13 Sep 2004 16:49:31 +0100 (BST) writes: BDR There is no bagplot function in S-PLUS. BDR There is one by Rousseeuw et al for S at BDR http://www.agoras.ua.ac.be/Locdept.htm BDR and a reply in the archives about the problems of porting at: BDR http://maths.newcastle.edu.au/~rking/R/help/03b/4916.html BDR My guess is that like several other cases, R porting BDR has exposed bugs in the original code. Indeed! as mentioned in the r-help message in the above link, Christian Keller had spent some time in porting it, and I had (spent more time!) in try to modularize (separate computation from plotting) and other enhancements. This lead to more extensive testing that AFAIR revealed quite problematic bugs (hidden in Fortran) that I never got around to diagnose or fix. E.g., x0 - c(1, 5, 6, 6, 6, 6, 6, 7, 7, 8, 11, 13) y0 - c(2, 3.5,4, 4.5, 4.5,5, 5, 5, 5, 5.5,5.5, 7) r - bagplot(x0,y0, ident=FALSE) ## gives ## [1] The coordinates of the Tukey median are ( 6.75 , 4.875 ). ## [1] The bag is only plotted when there are at least 15 observations. ## and a 'spider' (instead of a bag) since it there only 12 observations. ## This is as desired. but repeating the bagplot() call twice (hence, doing it three times) leads to a segmentation fault, both in S-plus 6.2 with the original code and in R (all versions) with my improved code. BDR On Mon, 13 Sep 2004, Matthew David Sylvester wrote: I saw a little discussion about this in the archives, but it was unclear to me whether someone had submitted a port to R of the Splus bagplot() function. If so, does anyone know where I could get it? Thanks. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] (no subject)
I have one problem with finding the appropriate functions in R that would perform this operation: We have X, the independent variable, and Y, the response variable, so that a regression line of these variables can be calculated. Using the Student t distribution, we need to find the 95% prediction interval of the mean of Y for the certain value of X. For example, R has the built-in data ( data(cars) ) for cars' speed as the independent variable and cars' stopping distance as the response variable. Find 95% prediction interval of mean stopping distance for cars speeding at 30. I have another question: is there a certain function in R that can calculate the probability p using the Student t distribution given the certain value, the sample mean, and the sample standard deviation, and df (i.e., the one that functions like pnorm(), but deals with Student t distribution.) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] (no subject)
Have you considered predict.lm, at least in R 1.9.1? (If I understand your question, it is answered in the examples to predict.lm.) hope this helps. p.s. I believe this is described in Venables and Ripley, Modern Applied Statistics with S, but I don't have this book at my fingertips. Also, have you read the posting guide! http://www.R-project.org/posting-guide.html;? Its suggestions might help you get quicker answers for yourself without waiting for this list to reply and might improve the quality of the replies to questions you submit. wrote: I have one problem with finding the appropriate functions in R that would perform this operation: We have X, the independent variable, and Y, the response variable, so that a regression line of these variables can be calculated. Using the Student t distribution, we need to find the 95% prediction interval of the mean of Y for the certain value of X. For example, R has the built-in data ( data(cars) ) for cars' speed as the independent variable and cars' stopping distance as the response variable. Find 95% prediction interval of mean stopping distance for cars speeding at 30. I have another question: is there a certain function in R that can calculate the probability p using the Student t distribution given the certain value, the sample mean, and the sample standard deviation, and df (i.e., the one that functions like pnorm(), but deals with Student t distribution.) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Spencer Graves, PhD, Senior Development Engineer O: (408)938-4420; mobile: (408)655-4567 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] lattice: bwplot and panel.lmline()
On Friday 17 September 2004 13:52, RenE J.V. Bertin wrote:
Hello again,
I am doing regressions (using panel.lmline() (and panel.abline(
rlm(...))) ) inside a panel method which I pass to bwplot().
What I would like to do is create a boxplot of categorised data
(binned on the independent variable), and superpose a regression line
which is calculated using the non-categorised, raw data. I expect
that would give more accurate regression results even if a bwplot
panel used 'world' co-ordinates.
My initial idea was to do something like
bwplot( y~x|cond, panel=bwpanel )
Does
xyplot( y~x|cond, panel=bwpanel, horizontal = FALSE )
do any better?
instead of
bwplot( y~ Classify(x, binwidth=0.2) | cond, panel=bwpanel )
with Classify a function which bins x and returns the result in an
ordered factor,
and
bwpanel - function(x,y, ... )
{
if( is.factor(x) ){
panel.bwplot(x,y, ... )
nx-as.numeric(x)
}
else{
nx-x
x-Classify(nx, binwidth=0.2 )
panel.bwplot(x,y, ... )
}
# add a line showing the means:
panel.linejoin(x,y, fun=function(x) mean(x,na.rm=TRUE),
col=red, lwd=2, ...)
panel.lmline( nx, y, ... )
# snip
}
But that doesn't work: bwplot seems to do work on/with x outside of
the panel function which require x to be a factor.
Yes, it does. If x and y are both numeric, you should use xyplot. It's
perfectly fine to use panel.bwplot as a panel function with xyplot.
I then tried to copy the code from bwplot into a wrapper which would
do the formula parsing, and call bwplot with x replaced by the
properly categorised version, but got stuck along the way.
I have thus written another wrapper, in which I basically do what I
wanted to do in bwpanel, storing the 'raw' data AND the condition
array in an environment. I then retrieve these inside bwpanel, make
the proper selection using
bwpanel(x, y, ... )
{
# snip
xx- xx[ cond == levels(cond)[ list(...)$panel.counter ] ]
# snip
}
The 'right' way to do this would be
bwpanel - function(x, y, subscripts, ... )
{
# snip
xx- xx[subscripts]
# snip
}
(xx will thus have the current-panel-appropriate subset of the raw
independent data). Then I can do the regression with the raw
observations (y being 'raw'), but now I have to transform the
obtained coefficients so that they are plotted correctly in the
viewport being used (basically, the smallest factor is mapped to 1,
the next to 2, etc).
I have this working (see http://rjvbertin.free.fr/RegrInBWPlot.pdf; I
can send the code if somebody is interested), but I wonder if
1) something like this has not been foreseen already in lattice (in
particular, panel.abline will in general not give correct results
when called from a bwplot panel function!
Could you expand on that? Incorrect results in what sense? panel.abline
just draws straight lines, it doesn't work with the panel data directly
(so, for instance, whether or not x is a factor cannot affect it). For
variables that are factors, the scales are set up so that the levels
correspond to integers (in other words, as.numeric(x) should give the
correct coordinates). Given that, I'm not sure how panel.abline can
give incorrect results.
2) Am I doing the right thing to subset my raw independent value
array -- in particular, there is also a list(...)$panel.number, which
I have only seen having the same value as $panel.counter?
As mentioned above, you should probably be using subscripts.
panel.number and panel.counter are going to be the same unless you mess
with perm.cond and index.cond.
Deepayan
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[R] Using R to send to SOAP server?
I have an R process continuously monitoring a data stream. When the
data meet certain criteria, I need to send a message to a SOAP server.
Currently I'm doing this by making a system() call to execute a perl
script, passing the message as an argument to the perl script.
I'm wondering if it can be done directly by R, and if so, whether
there might be any performance benefit.
I've looked at RSOAP, and as far as I can tell, it's designed to work
only in the other direction, that is, a SOAP server passes client
commands to R, and returns the R results to the client. If I'm wrong
about that, I'd appreciate being told so.
Thanks for any suggestions.
-Don
Here are the essential parts of the perl script.
use SOAP::Lite;
## assumes one arg
$msg = $ARGV[0];
if ($msg) {
print [gm-nsps.pl] sending to NSPS\n;
$soap = SOAP::Lite
- uri('http://chous-devpc.eedad.llnl.gov:9000/axis/services')
-
proxy('http://chous-devpc.eedad.llnl.gov:9000/axis/services/NspsIncidentService')
- notifyIncidents( $msg );
}
Version information:
version
_
platform powerpc-apple-darwin6.8.5
arch powerpc
os darwin6.8.5
system powerpc, darwin6.8.5
status
major1
minor9.1
year 2004
month06
day 21
language R
--
--
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
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RE: [R] lattice: bwplot and panel.lmline()
I think that for this kind of purpose, it would be more intuitive if bwplot would accept numerical x data, together with a 'binning' argument (like histogram's nint). RenE I strongly disagree. That's what cut() and R's functional programming style is for. The number of arguments should be (usually) minimized in favor of expecting users to use the features that R already provides. I think Deepayan (and Bill Cleveland, his forbearer with trellis plots in S-Plus) has done a fine job of doing this. -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA The business of the statistician is to catalyze the scientific learning process. - George E. P. Box __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Confused about specifying plot colors as RGB values
Based on reading 'rgb' documentation, I would have thought the following would have produced identical results. Can someone explain how to make this happen? I need to be able to specify an array of rgb values for the 'col' parameter. colnames.col - c(black, red, blue, green) colnames.rgb - apply(as.matrix(colnames.col), 1, col2rgb) dimnames(colnames.rgb)[[2]] - colnames.col baseline - 1:32 offset2 - 2*baseline offset3 - 3*baseline offset4 - 4*baseline offsets - cbind(offset2, offset3, offset4) # Produces expected result X11() matplot(baseline, col = colnames.col[1], type = l) matlines(offsets, col = colnames.col[-1]) # Displays a ??yellow?? line X11() matplot(baseline, col = as.matrix(colnames.rgb[,1]), type = l) matlines(offsets, col = colnames.rgb[,-1]) -- SIGSIG -- signature too long (core dumped) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Using R to send to SOAP server?
On Fri, 17 Sep 2004, Don MacQueen wrote: I have an R process continuously monitoring a data stream. When the data meet certain criteria, I need to send a message to a SOAP server. Currently I'm doing this by making a system() call to execute a perl script, passing the message as an argument to the perl script. I'm wondering if it can be done directly by R, and if so, whether there might be any performance benefit. I've looked at RSOAP, and as far as I can tell, it's designed to work only in the other direction, that is, a SOAP server passes client commands to R, and returns the R results to the client. If I'm wrong about that, I'd appreciate being told so. SSOAP allows R to invoke SOAP methods provided by a SOAP server. -- SIGSIG -- signature too long (core dumped) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Ploting Mean and SE on regression lines
Dear all, I wanted to plot the mean and standard error on the regression equation (instead of individual data points) in the following code, but I could not find the right code in the help files. Could someone please show how to do this. Thank you very much. temp - c(16,16,16,16,16, 20,20,20,20,20, 24,24,24,24,24, 28,28,28,28,28, 32,32,32,32,32) dev1hr - c(36.2, 34, 32.2, 36.4, 36, 23.8, 24.4, 24, 23, 23.25, 17.5, 18.37, 20.25, 21, 19.47, 14.37, 15, 13.42, 12, 13.2, 8, 8, 7.15, 7, 8.25) predict(lm(dev1hr ~ temp+I(temp^2)+I(temp^3))) new - data.frame(temp = seq(16, 32, 0.5)) predict(lm(dev1hr ~ temp+I(temp^2)), new, se.fit = TRUE) pred.w.plim - predict(lm(dev1hr ~ temp+I(temp^2)+I(temp^3)), new, interval=prediction) pred.w.clim - predict(lm(dev1hr ~ temp+I(temp^2)+I(temp^3)), new, interval=confidence) plot.new() plot.window(xlim=range(temp),ylim = range(pred.w.plim[,-1])) axis(1,at=seq(16,32,by=4),tck=.03,font.axis=6,labels=FALSE) axis(2,at=seq(5,40,by=8),tck=.03,las=1,font.axis=6) title (ylab=Development time (Days),cex.lab=1.5,font.lab=6) matpoints(new$temp,cbind(pred.w.clim, pred.w.plim[,-1]), lty=c(1,3,3,4,4), type=l, col = black, lwd = 1.5) points(temp, pch=o, dev1hr) mtext(A:1 h,line=-3,cex=.8,font=6,adj=.9) box(bty=L) Sivakumar Mohandass, Department of Entomology, Kansas State University [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Removing constants from a data frame
Suppose I have
x-data.frame(v1=1:4, v2=c(2,4,NA,7), v3=rep(1,4),
v4=LETTERS[1:4],v5=rep('Z',4))
or a much larger frame, and I wish to test for and remove the constant
numeric columns.
I made:
is.constant-function(x){identical(min(x),max(x))}
and
apply(x,2,is.constant) # Works for numerics
x[,-which(apply(x,2,is.constant))]
I'd really like to be able to delete the constant columns without losing
my non-numerics. Ignoring the character columns would be OK.
Any suggestions?
Dave
--
Dave Forrest
[EMAIL PROTECTED](804)684-7900w
[EMAIL PROTECTED] (804)642-0662h
http://maplepark.com/~drf5n/
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[R] Help w/ custom pkg: ERROR: installing package indices failed
I'm using R 1.9.1 on Linux and am having trouble installing a package
that I've written. Would very much appreciate a hint as to where to
look to find my mistake.
I can build the package, but when I try to install it, I get an error like:
Error in FUN(X[[as.integer(1)]], ...) : subscript out of bounds
Execution halted
ERROR: installing package indices failed
After some trial and error, I find that there is one troublesome Rd
file. If I remove it, I can build and install the package. But I can't
figure out what's wrong with the Rd file! E.g., in ESS it previews just
fine and appears to get built in the transcript below.
Below is a transcript of building and installing...
Building:
$ ls capsim
DESCRIPTION R man
$ R CMD build capsim
* checking for file 'capsim/DESCRIPTION' ... OK
* preparing 'capsim':
* removing junk files
* building 'capsim_1.0.tar.gz'
Installing:
$ R CMD INSTALL capsim_1.0.tar.gz
* Installing *source* package 'capsim' ...
** R
** help
Building/Updating help pages for package 'capsim'
Formats: text html latex example
collect texthtmllatex
collectRunDatatexthtmllatex
combineAges texthtmllatex
combineAges.singletexthtmllatex
combineAges3 texthtmllatex
combineIncidenceData texthtmllatex
combineMortalityData texthtmllatex
getAgeAdjustmentCountstexthtmllatex
getAllStageIncidence texthtmllatex
getMortByStagetexthtmllatex
getRunResults texthtmllatex
getSeerStageInflateMatrix texthtmllatex
inflateSeerData texthtmllatex
loadIncidenceData texthtmllatex
loadMortalityData texthtmllatex
loadRRSurvDatatexthtmllatex
loadSeerData texthtmllatex
Error in FUN(X[[as.integer(1)]], ...) : subscript out of bounds
Execution halted
ERROR: installing package indices failed
** Removing '/home/sfalcon/util/lib/R/capsim'
Here's the troublesome Rd file:
\name{combineAges3}
\title{Age adjust data and combine SEER, SEERInflated and model data
frames.}
\description{
Use \code{getAgeAdjustmentCounts} to get standard population counts and
combine age categories using appropriate weights.
}
\usage{
combineAges3(seer, seerInflated, model, col.names)
}
\arguments{
\item{seer}{A data frame containing SEER data. Must contain columns
``year'' and ``age''.}
\item{seerInflated}{A data frame containing inflated SEER data. Must
contain columns ``year'' and ``age''.}
\item{model}{A data frame containing model data. Must contain
columns ``year'' and ``age''. }
\item{col.names}{ Column name of the column in both data frames that
should be adjusted.
For example, ``incidence'' or ``mortality''. }
}
\details{
Hmm, not yet.
}
\value{
A data frame with columns: year, age, and source, \code{col.names}. The
source column is a factor with levels ``model'', ``seer'', and
``seerInflated'' indicating the source of the data.
}
\references{No ref}
\author{Seth Falcon}
\note{No Notes}
\keyword{manip}
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Re: [R] Help w/ custom pkg: ERROR: installing package indices failed
Turns out adding an \alias{} line to the problem Rd file fixed the
issue. I'm somewhat surprised that a missing \alias line leads to error
in FUN(X[[as.interger(1)]], ...) message. Perhaps there was something
else going on (my Rd file is admittedly a bit sloppy)...
+ seth
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[R] ANOVA help
Hi, I have a question about applying ANOVA model on a specific experiment. I have cell samples from 3 subjects. Now I take some cells from them and treat them with two agents at two levels each. The data look like this. 3 samples of control cell 3 cell samples of level 1 of treatment 1 3 cell samples of level 2 of treatment 1 3 cell samples of level 1 of treatment 2 3 cell samples of level 2 of treatment 2 Can I analyze the data with two-way ANOVA? Thanks for the response. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Removing constants from a data frame
David Forrest wrote:
Suppose I have
x-data.frame(v1=1:4, v2=c(2,4,NA,7), v3=rep(1,4),
v4=LETTERS[1:4],v5=rep('Z',4))
or a much larger frame, and I wish to test for and remove the constant
numeric columns.
I made:
is.constant-function(x){identical(min(x),max(x))}
and
apply(x,2,is.constant) # Works for numerics
x[,-which(apply(x,2,is.constant))]
I'd really like to be able to delete the constant columns without losing
my non-numerics. Ignoring the character columns would be OK.
Any suggestions?
Dave
what about defing is.constant as
is.constant - function(x) {
if (is.numeric(x)) identical(min(x), max(x)) else
FALSE }
Kjetil halvorsen
--
Kjetil Halvorsen.
Peace is the most effective weapon of mass construction.
-- Mahdi Elmandjra
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Re: [R] lattice: bwplot and panel.lmline()
On Friday 17 September 2004 15:04, RenE J.V. Bertin wrote: [...] Yes, somebody else pointed that out too. I had seen the argument, but not seen that it would carry the subscripts to the values being plotted in a given panel. Now it is obvious, of course ;) BTW: the xyplot manpage is not very explicit as to what arguments are common to all functions described: are they all? Yes, pretty much, unless explicitly mentioned otherwise (e.g. for 'box.ratio'). For functions not documented along with xyplot (like cloud, splom, etc), their own help pages will sometimes override the descriptions in ?xyplot. 8-) 1) something like this has not been foreseen already in lattice (in 8-) particular, panel.abline will in general not give correct results 8-) when called from a bwplot panel function! 8-) 8-) Could you expand on that? Incorrect results in what sense? panel.abline 8-) just draws straight lines, it doesn't work with the panel data directly 8-) (so, for instance, whether or not x is a factor cannot affect it). For 8-) variables that are factors, the scales are set up so that the levels 8-) correspond to integers (in other words, as.numeric(x) should give the 8-) correct coordinates). Given that, I'm not sure how panel.abline can 8-) give incorrect results. My in general above was a little bold. Incorrect results occur when your factors are in fact numerical categories, as in my case, where I 'bin' a [0:1] continuous variable into 0.2 wide bins. So I have factors 0, 0.2, ..., 1 . If I plot the full range, my category 0 will be mapped onto your plotting co-ordinate 1, and my 1 onto your 6. If I then plot e.g. a unity line with panel.abline( 0, 1, ...), the drawn line does not correspond to the labels on the axes. Is it clear like that? In other words: the co-ordinates I need are as.numeric(as.character(x)), as my lines are expressed in terms of the numbers shown along both axes, and not in a frame where the leftmost point has X==1 and the rightmost X==levels(x) Right, so the problem is not with panel.abline, which is doing what it's supposed to do, but with bwplot forcing one of its arguments from numeric - factor - numeric (actually numeric - shingle - numeric), in the process changing the numeric values. In this light, I'm not sure how panel.bwplot() is going to work when called through xyplot with numerical data: one would have to call it with factor(x)?. I think that for this kind of purpose, it would be more intuitive if bwplot would accept numerical x data, together with a 'binning' argument (like histogram's nint). I see your point, but I don't think it makes sense to have bwplot accept numeric data. bwplot (as well as dotplot, stripplot and barchart) is designed to have a factor (or shingle) as one of it's variables, and in fact that's the main thing that makes it different from xyplot. If you really want both variables to be numeric, you should use xyplot. Unfortunately, as you point out, panel.bwplot doesn't work correctly with xyplot; e.g., the following doesn't work: xyplot(sample(0:5/5, 100, T) ~ rnorm(100), panel = panel.bwplot) This should definitely be fixed, and in fact it is fixed in the pre-release version of 2.0.0, where panel.bwplot draws a boxplot for each unique value of y (or x if horizontal = F). The only thing is that the thickness of the `box'-es are calculated assuming a distance of 1 between consecutive positions, so that has to be explicitly controlled, as in xyplot(sample(0:5/5, 100, T) ~ rnorm(100), panel = panel.bwplot, box.ratio = 0.1) Deepayan __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Pharmacokinetics using R
Hi, I just wonder if R is still used for PK analysis. However, I have to use R for some purposes anyways. Here is a really strange problem I am running into and I hope to get some assistance from the group. The following code works fine in S-Plus (Population estimates and MAP estimates look reasonable ). cs.fit-nlme ( CONC~phenoModel(CID,TIME, DOSE, lCl, lV), fixed = lCl+lV ~1, random = pdDiag(lCl+lV ~1), data = cs1grp, start = c(-5, 0), na.action=na.include, naPattern = ~ !is.na(CONC) ) But if I run the same problem in R, I get the following error: Error in chol((value + t(value))/2) : the leading minor of order 1 is not positive definite These are simulated data with a total of 100 subjects studied at one dose level and rich sampling scheme. (I can send the dataset, if required. I had some unsuccessful attempts to send by default). If it was a problem with parameterization of the model , I don't understand how come sparse sampling in generic Phenobarb data does not have a problem in R or S. BTW, the exact same code for Phenobarb runs in R and S-Plus w/o any modification needed. Thank you in anticipation. Pravin Pravin Jadhav [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
