[R] Extracting R plots from MS Word
Hi, I am revising a paper that I am a co-author of. The figures are plots generated from R but at the moment I do not have the R code that generates them. As this is time critical I would like to slightly abuse the list by asking whether anyone knows how to extract from MS Word into a stand-alone graphics file a plot that was pasted into Word from R (probably as a Windows Metafile, but possibly as a bitmap). I would be very grateful for help with this. Regards, Murray Jorgensen __ R-help@stat.math.ethz.ch 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] Problem with package sem
Hi experts, I just started to learn R today, and tried to work with an add-on package sem. I have a version of 2.3.1 on MacOS X 10.4.6 with sem put under /Library/Frameworks/R.framework/Versions/2.3/Resources/library However when I typed library(sem) the following error showed up: Error in library(sem) : 'sem' is not a valid package -- installed 2.0.0? Why is this? Thank you, Gang Chen [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Address of FactoMineR package author
I've tried to contact the author of part of the FactoMineR package
which was given as: [EMAIL PROTECTED]
However, the cedilla is not liked by any mail system I have access to,
so that address is a non-starter. I tried using a simple letter 'c'
which didn't cause a syntax error, but achieved nothing else.
Could it just be that the address was correct and it's the season in
France for people to be away and so not answering email? Or is there
something I should know about such characters in email addresses?
TIA
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_Middle minds discuss events
(:_~*~_:)Small minds discuss people
(_)-(_) . Anon
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Re: [R] Problem with package sem
Gang Chen wrote: Hi experts, I just started to learn R today, and tried to work with an add-on package sem. I have a version of 2.3.1 on MacOS X 10.4.6 with sem put under /Library/Frameworks/R.framework/Versions/2.3/Resources/library However when I typed library(sem) the following error showed up: Error in library(sem) : 'sem' is not a valid package -- installed 2.0.0? Please read the R Installation and Administration manual on how to install packages (e.g. with R CMD INTALL in the OS' console or install.packages() in R) Uwe Ligges Why is this? Thank you, Gang Chen [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] R project question (SEM)
Patrick Bedard wrote: Hi there, I just saw your question on the help list and tough you could help me with some start-up info I just downloaded the R project software to try running SEM analysis and I also downloaded the SEM package. But it just sits there on the desktop and R does not know where it is...I can¹t figure out how to organize the files...When I type ?sem in R it says object sem not found...I can¹t seem to find help on the web on how to set-up the packages Same answer: There is the R Installation and Administration manual. Uwe Ligges Well, thanks in advance __ Patrick Bedard Ph.D. Dept. of Neuroscience Brown University [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] re-direct to more or less
Dear list, sometimes my function generates too much data and shows them on screen, i cannot view first several lines until program ends and I have to scroll my mouse up to get them. Is there any re-direction function in R to pipeline outputs to more or less type functions? Thanks mike [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Question on memory allocation loop
Hello All,
I am trying to work on writing the following piece of (pseudo)
code in an optimal fashion:
# Two data frames with some data
a = data.frame(somedata)
b = data.frame(somedata)
for(i in 1:nrow(dt) {
# Merge dates for a given date into a new data frame
c = merge(a[a$dt==dt[i],),b[b$dt == dt[i],], by=c(some column));
}
Now, my understanding is that the data frame c in the above code is
malloc'ed in every count of the loop. Is that assumption correct?
Is the following attempt a better way of doing things?
a = data.frame(somedata)
b = data.frame(somedata)
# Pre-allocate data frame c
c = data.frame(for some size);
for(i in 1:nrow(dt) {
# Merge dates for a given date into a new data frame
# and copy the result into c
copy(c, merge(a[a$dt==dt[i],),b[b$dt == dt[i],], by=c(some column));
}
Now the question is, How can I copy the merged data into my
pre-allocated data frame c ? I tried rbind/cbind but they are pretty
fuzzy about having the right names and dimension hence it fails.
Any help would be greatly appreciated!
Thanks.
Manoj
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Re: [R] Problem with package sem
Dear Gang Chen, I expect that either you didn't install the package properly (see ?install.packages) or installed a version of the package for an earlier version of R. I hope this helps, John On Wed, 28 Jun 2006 17:14:10 -0400 Gang Chen [EMAIL PROTECTED] wrote: Hi experts, I just started to learn R today, and tried to work with an add-on package sem. I have a version of 2.3.1 on MacOS X 10.4.6 with sem put under /Library/Frameworks/R.framework/Versions/2.3/Resources/library However when I typed library(sem) the following error showed up: Error in library(sem) : 'sem' is not a valid package -- installed 2.0.0? Why is this? Thank you, Gang Chen [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html John Fox Department of Sociology McMaster University Hamilton, Ontario, Canada http://socserv.mcmaster.ca/jfox/ __ R-help@stat.math.ethz.ch 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] Building R: use the current version! {was Running R}
I'm not really answering your question, but if you install from the sources -- always a useful experience in finding out if your computer is well equipped with software -- *PLEASE* use the latest aka current version of R. Currently, that's 2.3.1 and not 2.3.0. A very reasonable alternative is also to work with R-patched (i.e. 'R 2.3.1 patched' at the moment), since we (aim to) ensure that R-patched only contains simple well tested bug fixes in addition to the respective released version. (Contrary to R-devel which always contains the current R development version with all potential new features and which is hence also designated 'unstable'.) Martin Maechler, ETH Zurich (and R-core) Pramod == Pramod Anugu [EMAIL PROTECTED] on Wed, 28 Jun 2006 15:18:10 -0500 writes: Pramod [EMAIL PROTECTED] R-2.3.0]# ./configure . . Pramod 1. tar -zxvf R-2.3.0.tar.gz Pramod 2. changed the directory to the newly created directory R-2.3.0 . . __ R-help@stat.math.ethz.ch 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] re-direct to more or less
maybe ?sink() or ?capture.output() could be useful, in this case. 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: Mike Wolfgang [EMAIL PROTECTED] To: R-help list r-help@stat.math.ethz.ch Sent: Thursday, June 29, 2006 4:28 AM Subject: [R] re-direct to more or less Dear list, sometimes my function generates too much data and shows them on screen, i cannot view first several lines until program ends and I have to scroll my mouse up to get them. Is there any re-direction function in R to pipeline outputs to more or less type functions? Thanks mike [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@stat.math.ethz.ch 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] Help needed understanding eval,quote,expression
I am trying to build up a quoted or character expression representing a
component in a list in order to reference it indirectly.
For instance, I have a list that has data I want to pull, and another list
that has character vectors and/or lists of characters containing the names
of the components in the first list.
It seems that the way to do this is as evaluating expressions, but I seem
to be missing something. The concept should be similar to the snippet
below:
For instance:
$x = list(y=list(y1=hello,y2=world),z=list(z1=foo,z2=bar))
$y = quote(x$y$y1)
$eval(y)
[1] hello
but, I'm trying to accomplish this by building up y as a character and
then evaluating it, and having no success.
$y1=paste(x$y$,y1,sep=)
$y1
[1] x$y$y1
How can I evaluate y1 as I did with y previously? or can I?
Much Thanks !
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Re: [R] Question on memory allocation loop
On Thu, 29 Jun 2006, Manoj wrote:
Hello All,
I am trying to work on writing the following piece of (pseudo)
code in an optimal fashion:
# Two data frames with some data
a = data.frame(somedata)
b = data.frame(somedata)
for(i in 1:nrow(dt) {
# Merge dates for a given date into a new data frame
c = merge(a[a$dt==dt[i],),b[b$dt == dt[i],], by=c(some column));
}
Note that only the last iteration of that loop is actually needed.
What are you really trying to do, and why are you worrying about memory?
E.g. merge() in R-devel is a lot more efficient for some operations,
including perhaps your example.
Now, my understanding is that the data frame c in the above code is
malloc'ed in every count of the loop. Is that assumption correct?
No. Here 'c' is just a symbol, and assignment (please use - in public
code, it is easier to read) binds the symbol to the data frame returned by
merge(). So the allocation (not 'malloc' necessarily) is going on inside
merge(). Also, 'c' is a system object, so you are confusing people by
using its name for your own object.
When you assign to 'c' you change the binding to a different already
allocated object. Eventually garbage collection will recover (to R) the
memory allocated to objects which are no longer bound to symbols.
I am not aware of any account which describes in detail how R works at
this level, and end users do not need to know it. (It is also the case
that R maintains a number of illusions and internally may not do what it
appears to do.)
Is the following attempt a better way of doing things?
a = data.frame(somedata)
b = data.frame(somedata)
# Pre-allocate data frame c
c = data.frame(for some size);
for(i in 1:nrow(dt) {
# Merge dates for a given date into a new data frame
# and copy the result into c
copy(c, merge(a[a$dt==dt[i],),b[b$dt == dt[i],], by=c(some column));
}
Now the question is, How can I copy the merged data into my
pre-allocated data frame c ? I tried rbind/cbind but they are pretty
fuzzy about having the right names and dimension hence it fails.
Any help would be greatly appreciated!
Thanks.
Manoj
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Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] re-direct to more or less
Something like
less - function(a){
fn - paste(tempdir(),\\dataframe.txt,sep='',collapse='')
write.table(a, quote=F, file=fn)
system(paste(less ,fn))
}
could perhaps help you (assuming that you have less on your computer). I agree
that it would be very nice to have a built-in version...
Regards
Søren
-Oprindelig meddelelse-
Fra: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] På vegne af Mike Wolfgang
Sendt: 29. juni 2006 04:29
Til: R-help list
Emne: [R] re-direct to more or less
Dear list,
sometimes my function generates too much data and shows them
on screen, i cannot view first several lines until program
ends and I have to scroll my mouse up to get them. Is there
any re-direction function in R to pipeline outputs to more
or less type functions?
Thanks
mike
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
Aarti Dahiya wrote: I am getting this error:- Error: evaluation nested too deeply: infinite recursion / options(expressions=)? The reason is probbaly because I am calling methods within methods. Maybe at some point you get an infinite recursion because you forgot to unclass something? I read related posts. It said the solution is to set options(expressions = 1000). I wanted to know where in my code or system to set options(expressions = 1000)? Bewore you start the problematic code, but probably you really have infinite recursion Uwe Ligges Thanks. Aarti __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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 needed understanding eval,quote,expression
You are missing eval(parse(text=)). E.g.
x - list(y=list(y1=hello,y2=world),z=list(z1=foo,z2=bar))
(what do you mean by the $ at the start of these lines?)
eval(parse(text=x$y$y1))
[1] hello
However, bear in mind
fortune(parse)
If the answer is parse() you should usually rethink the question.
-- Thomas Lumley
R-help (February 2005)
In your indicated example you could probably use substitute() as
effectively.
On Wed, 28 Jun 2006, [EMAIL PROTECTED] wrote:
I am trying to build up a quoted or character expression representing a
component in a list in order to reference it indirectly.
For instance, I have a list that has data I want to pull, and another list
that has character vectors and/or lists of characters containing the names
of the components in the first list.
It seems that the way to do this is as evaluating expressions, but I seem
to be missing something. The concept should be similar to the snippet
below:
For instance:
$x = list(y=list(y1=hello,y2=world),z=list(z1=foo,z2=bar))
$y = quote(x$y$y1)
$eval(y)
[1] hello
but, I'm trying to accomplish this by building up y as a character and
then evaluating it, and having no success.
$y1=paste(x$y$,y1,sep=)
$y1
[1] x$y$y1
How can I evaluate y1 as I did with y previously? or can I?
Much Thanks !
CONFIDENTIALITY NOTICE: This electronic mail transmission (i...{{dropped}}
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--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem running one of the rgl demo scripts...
Duncan Murdoch wrote: Brian Lunergan wrote: Afternoon folks: I'm getting a program crash when I try to run demo(rgl). The following error details result: RGUI caused a stack fault in module NVOPENGL.DLL at 017f:695280f0. Registers: EAX=0002 CS=017f EIP=695280f0 EFLGS=00010246 EBX=0001 SS=0187 ESP=00572000 EBP=004d1208 ECX=042f1f01 DS=0187 ESI=004d1208 FS=5d1f EDX=00442d84 ES=0187 EDI=042f1f3c GS=5d0e Bytes at CS:EIP: 53 56 8b 5c 24 0c 57 83 bb 9c 39 00 00 02 0f 84 Stack dump: 69541be5 004d1208 004d1208 0001 69541bef 0001 004d1208 0001 69541bef 0001 004d1208 0001 69541bef 0001 004d1208 0001 Setup details are: R version: 2.2.1 OS: win98se RGL file name: rgl_0.66.zip It appears to be gagging on an Nvidia opengl driver file, NVIDIA Compatible OpenGL ICD, version 4.12.01.0631. The video card is recorded as: 3DForce2 MX Series,NVIDIA GeForce2 MX (Ver 4.12.01.0631 ,9/20/2000) I also tried this with version 2.3.1 of R with the same results. Anyone have any thoughts or ideas on the subject? Has it occurred any place else? Is there a workaround or solution, or should I perhaps turf the package and forgo its abilities since it appears my system as it stands may not be able to support it? You could try a newer build, available on my web page (http://www.stats.uwo.ca/faculty/murdoch/software). If it dies the same way, you could perhaps try to diagnose what is going wrong and send a patch if it's an rgl bug. Given the age of your video driver (9/20/2000), you might be able to update it and fix a bug there. Just downloaded and installed a new video driver (file the demo originally reporting choking on now showing v4.14.10.8198, December 10, 2005 03:06:00) and things seemed to have settled down. The demo now runs through fully without complaint. -- Brian Lunergan Nepean, Ontario Canada --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0626-2, 2006-06-28 Tested on: 2006-06-28 19:20:04 avast! is copyright (c) 2000-2006 ALWIL Software. http://www.avast.com __ R-help@stat.math.ethz.ch 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] Extracting R plots from MS Word
Hi, I would also like to know how to do this with MS products alone. However, a nice tool to do this is wmf2eps (http://www.wmf2eps.de.vu/). You can paste windows vector graphics into wmf2eps, and it first saves it as EMF (enhanced metafile), before it creates EPS, which is what I use it for. Maybe your publisher will be even more happy if you supply EPS. Best regards, Johannes Ranke * [EMAIL PROTECTED] [EMAIL PROTECTED] [060629 08:30]: Hi, I am revising a paper that I am a co-author of. The figures are plots generated from R but at the moment I do not have the R code that generates them. As this is time critical I would like to slightly abuse the list by asking whether anyone knows how to extract from MS Word into a stand-alone graphics file a plot that was pasted into Word from R (probably as a Windows Metafile, but possibly as a bitmap). I would be very grateful for help with this. Regards, Murray Jorgensen __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Dr. Johannes Ranke [EMAIL PROTECTED] UFT Bremen, Leobenerstr. 1 +49 421 218 8971 D-28359 Bremen http://www.uft.uni-bremen.de/chemie/ranke __ R-help@stat.math.ethz.ch 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] re-direct to more or less
Søren Højsgaard [EMAIL PROTECTED] writes:
Something like
less - function(a){
fn - paste(tempdir(),\\dataframe.txt,sep='',collapse='')
write.table(a, quote=F, file=fn)
system(paste(less ,fn))
}
could perhaps help you (assuming that you have less on your computer). I
agree that it would be very nice to have a built-in version...
Like page(), you mean... ?
:-)
(This goes via file.show, so Windows GUI users get a separate window,
I suppose.)
Regards
Søren
-Oprindelig meddelelse-
Fra: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] På vegne af Mike Wolfgang
Sendt: 29. juni 2006 04:29
Til: R-help list
Emne: [R] re-direct to more or less
Dear list,
sometimes my function generates too much data and shows them
on screen, i cannot view first several lines until program
ends and I have to scroll my mouse up to get them. Is there
any re-direction function in R to pipeline outputs to more
or less type functions?
Thanks
mike
[[alternative HTML version deleted]]
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http://www.R-project.org/posting-guide.html
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--
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] re-direct to more or less
No - not like page(). Page (on windows) gives
structure(list(Sepal.Length = c(5.1, 4.9, 4.7, 4.6, 5, 5.4, 4.6,
5, 4.4, 4.9, 5.4, 4.8, 4.8, 4.3, 5.8, 5.7, 5.4, 5.1, 5.7, 5.1,
5.4, 5.1, 4.6, 5.1, 4.8, 5, 5, 5.2, 5.2, 4.7, 4.8, 5.4, 5.2, .
while the less() function below gives
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa
Regards
Søren
-Oprindelig meddelelse-
Fra: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] På vegne
af Peter Dalgaard
Sendt: 29. juni 2006 10:31
Til: Søren Højsgaard
Cc: Mike Wolfgang; R-help list
Emne: Re: [R] re-direct to more or less
Søren Højsgaard [EMAIL PROTECTED] writes:
Something like
less - function(a){
fn - paste(tempdir(),\\dataframe.txt,sep='',collapse='')
write.table(a, quote=F, file=fn)
system(paste(less ,fn))
}
could perhaps help you (assuming that you have less on your
computer). I agree that it would be very nice to have a
built-in version...
Like page(), you mean... ?
:-)
(This goes via file.show, so Windows GUI users get a separate
window, I suppose.)
Regards
Søren
-Oprindelig meddelelse-
Fra: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] På vegne af
Mike Wolfgang
Sendt: 29. juni 2006 04:29
Til: R-help list
Emne: [R] re-direct to more or less
Dear list,
sometimes my function generates too much data and shows them on
screen, i cannot view first several lines until program
ends and I
have to scroll my mouse up to get them. Is there any re-direction
function in R to pipeline outputs to more
or less type functions?
Thanks
mike
[[alternative HTML version deleted]]
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http://www.R-project.org/posting-guide.html
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PLEASE do read the posting guide!
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--
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:
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Re: [R] Help needed understanding eval,quote,expression
Prof Brian Ripley wrote: You are missing eval(parse(text=)). E.g. x - list(y=list(y1=hello,y2=world),z=list(z1=foo,z2=bar)) (what do you mean by the $ at the start of these lines?) eval(parse(text=x$y$y1)) [1] hello However, bear in mind fortune(parse) If the answer is parse() you should usually rethink the question. -- Thomas Lumley R-help (February 2005) In your indicated example you could probably use substitute() as effectively. On Wed, 28 Jun 2006, [EMAIL PROTECTED] wrote: I am trying to build up a quoted or character expression representing a component in a list in order to reference it indirectly. For instance, I have a list that has data I want to pull, and another list that has character vectors and/or lists of characters containing the names of the components in the first list. It seems that the way to do this is as evaluating expressions, but I seem to be missing something. The concept should be similar to the snippet below: For instance: $x = list(y=list(y1=hello,y2=world),z=list(z1=foo,z2=bar)) $y = quote(x$y$y1) $eval(y) [1] hello but, I'm trying to accomplish this by building up y as a character and then evaluating it, and having no success. $y1=paste(x$y$,y1,sep=) $y1 [1] x$y$y1 How can I evaluate y1 as I did with y previously? or can I? Much Thanks ! if I understand you correctly you can achieve your goal much easier than with eval, parse, substitute and the like: x - list(y=list(y1=hello,y2=world),z=list(z1=foo,z2=bar)) s1 - 'y' s2 - 'y1' x[[s1]][[s2]] i.e. using `[[' instead of `$' for list component extraction allows to use characters for indexing (in other words: x$y == x[['y']]) joerg __ R-help@stat.math.ethz.ch 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] re-direct to more or less
Søren Højsgaard [EMAIL PROTECTED] writes:
No - not like page(). Page (on windows) gives
structure(list(Sepal.Length = c(5.1, 4.9, 4.7, 4.6, 5, 5.4, 4.6,
5, 4.4, 4.9, 5.4, 4.8, 4.8, 4.3, 5.8, 5.7, 5.4, 5.1, 5.7, 5.1,
5.4, 5.1, 4.6, 5.1, 4.8, 5, 5, 5.2, 5.2, 4.7, 4.8, 5.4, 5.2, .
while the less() function below gives
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa
If all else fails, read the manual...: page() has a method= argument.
(It might not be a bad idea to switch the default, though).
-Oprindelig meddelelse-
Fra: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] På vegne
af Peter Dalgaard
Sendt: 29. juni 2006 10:31
Til: Søren Højsgaard
Cc: Mike Wolfgang; R-help list
Emne: Re: [R] re-direct to more or less
Søren Højsgaard [EMAIL PROTECTED] writes:
Something like
less - function(a){
fn - paste(tempdir(),\\dataframe.txt,sep='',collapse='')
write.table(a, quote=F, file=fn)
system(paste(less ,fn))
}
could perhaps help you (assuming that you have less on your
computer). I agree that it would be very nice to have a
built-in version...
Like page(), you mean... ?
:-)
(This goes via file.show, so Windows GUI users get a separate
window, I suppose.)
Regards
Søren
-Oprindelig meddelelse-
Fra: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] På vegne af
Mike Wolfgang
Sendt: 29. juni 2006 04:29
Til: R-help list
Emne: [R] re-direct to more or less
Dear list,
sometimes my function generates too much data and shows them on
screen, i cannot view first several lines until program
ends and I
have to scroll my mouse up to get them. Is there any re-direction
function in R to pipeline outputs to more
or less type functions?
Thanks
mike
[[alternative HTML version deleted]]
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PLEASE do read the posting guide!
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--
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
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Help needed understanding eval,quote,expression
On Thu, 29 Jun 2006, Joerg van den Hoff wrote: Prof Brian Ripley wrote: You are missing eval(parse(text=)). E.g. x - list(y=list(y1=hello,y2=world),z=list(z1=foo,z2=bar)) (what do you mean by the $ at the start of these lines?) eval(parse(text=x$y$y1)) [1] hello However, bear in mind fortune(parse) If the answer is parse() you should usually rethink the question. -- Thomas Lumley R-help (February 2005) In your indicated example you could probably use substitute() as effectively. On Wed, 28 Jun 2006, [EMAIL PROTECTED] wrote: I am trying to build up a quoted or character expression representing a component in a list in order to reference it indirectly. For instance, I have a list that has data I want to pull, and another list that has character vectors and/or lists of characters containing the names of the components in the first list. It seems that the way to do this is as evaluating expressions, but I seem to be missing something. The concept should be similar to the snippet below: For instance: $x = list(y=list(y1=hello,y2=world),z=list(z1=foo,z2=bar)) $y = quote(x$y$y1) $eval(y) [1] hello but, I'm trying to accomplish this by building up y as a character and then evaluating it, and having no success. $y1=paste(x$y$,y1,sep=) $y1 [1] x$y$y1 How can I evaluate y1 as I did with y previously? or can I? Much Thanks ! if I understand you correctly you can achieve your goal much easier than with eval, parse, substitute and the like: x - list(y=list(y1=hello,y2=world),z=list(z1=foo,z2=bar)) s1 - 'y' s2 - 'y1' x[[s1]][[s2]] i.e. using `[[' instead of `$' for list component extraction allows to use characters for indexing (in other words: x$y == x[['y']]) But what he actually asked for was I am trying to build up a quoted or character expression representing a component in a list in order to reference it indirectly. You just typed in x[[s1]][[s2]], not 'built [it] up'. Suppose the specification had been r - x s - c(y, y1) and s was of variable length? Then you need to construct a call similar to x[[y]][[y1]] from r and s. [There was another reason for sticking with $ rather than using [[: the latter makes unnecessary copies in released versions of R.] -- 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 __ R-help@stat.math.ethz.ch 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] re-direct to more or less
Please read the help before replying ...
page(iris, method=print)
does exactly what I understand was asked for.
On Thu, 29 Jun 2006, Søren Højsgaard wrote:
No - not like page(). Page (on windows) gives
structure(list(Sepal.Length = c(5.1, 4.9, 4.7, 4.6, 5, 5.4, 4.6,
5, 4.4, 4.9, 5.4, 4.8, 4.8, 4.3, 5.8, 5.7, 5.4, 5.1, 5.7, 5.1,
5.4, 5.1, 4.6, 5.1, 4.8, 5, 5, 5.2, 5.2, 4.7, 4.8, 5.4, 5.2, .
while the less() function below gives
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa
Regards
Søren
-Oprindelig meddelelse-
Fra: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] På vegne
af Peter Dalgaard
Sendt: 29. juni 2006 10:31
Til: Søren Højsgaard
Cc: Mike Wolfgang; R-help list
Emne: Re: [R] re-direct to more or less
Søren Højsgaard [EMAIL PROTECTED] writes:
Something like
less - function(a){
fn - paste(tempdir(),\\dataframe.txt,sep='',collapse='')
write.table(a, quote=F, file=fn)
system(paste(less ,fn))
}
could perhaps help you (assuming that you have less on your
computer). I agree that it would be very nice to have a
built-in version...
Like page(), you mean... ?
:-)
(This goes via file.show, so Windows GUI users get a separate
window, I suppose.)
Regards
Søren
-Oprindelig meddelelse-
Fra: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] På vegne af
Mike Wolfgang
Sendt: 29. juni 2006 04:29
Til: R-help list
Emne: [R] re-direct to more or less
Dear list,
sometimes my function generates too much data and shows them on
screen, i cannot view first several lines until program
ends and I
have to scroll my mouse up to get them. Is there any re-direction
function in R to pipeline outputs to more
or less type functions?
Thanks
mike
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
--
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
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
--
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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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Running R [Broadcast]
You have two choices (AFAIK): 1. Tell configure exactly where to find the readline header files (by something like --with-readline=/where/the/files/are, check configure --help). 2. Compile R without readline; i.e., configure --with-readline=no. Andy _ From: [EMAIL PROTECTED] on behalf of Pramod Anugu Sent: Wed 6/28/2006 4:18 PM To: r-help@stat.math.ethz.ch Subject: Re: [R] Running R [Broadcast] [EMAIL PROTECTED] R-2.3.0]# ./configure checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu loading site script './config.site' loading build specific script './config.site' checking for pwd... /bin/pwd checking whether builddir is srcdir... yes checking for working aclocal... found checking for working autoconf... found checking for working automake... found checking for working autoheader... found checking for working makeinfo... found checking for gawk... gawk checking for egrep... grep -E checking whether ln -s works... yes checking for ranlib... ranlib checking for bison... no checking for byacc... no checking for ar... ar checking for a BSD-compatible install... /usr/bin/install -c checking for sed... /bin/sed checking for less... /usr/bin/less checking for perl... /usr/bin/perl checking whether perl version is at least 5.004... yes checking for dvips... /usr/bin/dvips checking for tex... /usr/bin/tex checking for latex... /usr/bin/latex checking for makeindex... /usr/bin/makeindex checking for pdftex... /usr/bin/pdftex checking for pdflatex... /usr/bin/pdflatex checking for makeinfo... /usr/bin/makeinfo checking for unzip... /usr/bin/unzip checking for zip... /usr/bin/zip checking for gzip... /bin/gzip checking for firefox... /usr/bin/firefox using default browser ... /usr/bin/firefox checking for acroread... no checking for acroread4... no checking for xpdf... no checking for gv... no checking for gnome-gv... no checking for ggv... /usr/bin/ggv checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking whether gcc needs -traditional... no checking how to run the C preprocessor... gcc -E checking for g77... g77 checking whether we are using the GNU Fortran 77 compiler... yes checking whether g77 accepts -g... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking whether __attribute__((visibility())) is supported... yes checking whether gcc accepts -fvisibility... yes checking whether g77 accepts -fvisibility... yes checking for a sed that does not truncate output... /bin/sed checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from gcc object... ok checking for objdir... .libs checking for ranlib... (cached) ranlib checking for strip... strip checking if gcc static flag works... yes checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC checking if gcc PIC flag -fPIC works... yes checking if gcc supports -c -o file.o... yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no configure: creating libtool appending configuration tag CXX to libtool checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m
[R] kmeans clustering
Hello R list members, I'm a bio informatics student from the Leiden university (netherlands). We were asked to make a program with different clustering methods. The problem we are experiencing is the following. we have a matrix with data like the following research1research2research3enz sample1 0.5 0.2 0.4 sample2 0.4 0.4 0.3 sample3 0.7 0.2 0.8 enz now if we use kmeans(matrix,3,20) the clustering method will cluster only on rows by using the columns values as multiple variables. The output from this syntax is for example sample1 = 1 sample2 = 2 sample3 = 3 enz Is there a method that will use the rows and columns as seperate values so that every variable in the matrix will be assigned to a cluster instead of a row. the output then could be interperted as a heatmap. thank you in advance for your time, Richard Mendes __ R-help@stat.math.ethz.ch 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] kmeans clustering
richard mendes wrote: Hello R list members, I'm a bio informatics student from the Leiden university (netherlands). We were asked to make a program with different clustering methods. The problem we are experiencing is the following. we have a matrix with data like the following research1research2research3enz sample1 0.5 0.2 0.4 sample2 0.4 0.4 0.3 sample3 0.7 0.2 0.8 enz now if we use kmeans(matrix,3,20) the clustering method will cluster only on rows by using the columns values as multiple variables. The output from this syntax is for example sample1 = 1 sample2 = 2 sample3 = 3 enz Is there a method that will use the rows and columns as seperate values so that every variable in the matrix will be assigned to a cluster instead of a row. the output then could be interperted as a heatmap. thank you in advance for your time, Richard Mendes __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html You mean something like:? kmeans(dataMatrix,5) ## clustering by rows kmeans(t(dataMatrix),5) ## clustering by attribute HTH, Andrej __ R-help@stat.math.ethz.ch 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] Very slow read.table on Linux, compared to Win2000 [Broad cast]
On Wed, 28-Jun-2006 at 04:43PM -0700, Alberto Murta wrote:
| I have a pentium 4 pc with 256 MB of RAM, so I made a text file, tab
| separated, with column names and 15000 x 483 integers:
|
| system(ls -l teste.txt)
| -rw-r--r-- 1 amurta amurta 16998702 Jun 28 16:08 teste.txt
|
| the time it took to import it was around 15 secs:
|
| system.time(teste - read.delim(teste.txt))
| [1] 15.349 0.244 16.597 0.000 0.000
|
| so I think lack of RAM must not be the main problem.
| Cheers
|
| Alberto
|
|
| version
|_
| platform i386-unknown-freebsd6.1
| arch i386
| os freebsd6.1
| system i386, freebsd6.1
| status
| major 2
| minor 3.1
| year 2006
| month 06
| day01
| svn rev38247
| language R
| version.string Version 2.3.1 (2006-06-01)
Doesn't tell us about your window manager. I'd suspect you're using a
light one.
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_Middle minds discuss events
(:_~*~_:)Small minds discuss people
(_)-(_) . Anon
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
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[R] zero.print in print.table after adding margins
The function addmargins() adds margins to a table, but returns a matrix. But even after converted to a table the print.zero=. option of print.table() does not work: x - sample( 1:7, 20, replace=T ) y - sample( 1:7, 20, replace=T ) tt - table( x, y ) tx - as.table( addmargins( table( x, y ) ) ) print( tt, zero.print=. ) y x 1 2 3 4 5 6 7 1 1 2 2 . . 1 . 2 1 . . 1 . . . 3 . . . . . . 2 4 1 . . . . 1 . 5 1 . 1 . . 1 . 6 . 1 . 1 . . . 7 . . 1 . 1 1 . print( tx, zero.print=. ) y x 1 2 3 4 5 6 7 Sum 11 2 2 0 0 1 0 6 21 0 0 1 0 0 0 2 30 0 0 0 0 0 2 2 41 0 0 0 0 1 0 2 51 0 1 0 0 1 0 3 60 1 0 1 0 0 0 2 70 0 1 0 1 1 0 3 Sum 4 3 4 2 1 4 2 20 Is this a facility of print.table? The attributes() of tt and tx have identical stucture. Best, Bendix -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06 [EMAIL PROTECTED] www.biostat.ku.dk/~bxc __ R-help@stat.math.ethz.ch 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] Mixing grid and base graphics--need help understanding this quirk
Hi Kevin Wright wrote: My setup: Windows 2000, R 2.3.1 When I start a brand new session of R and paste the code below into R, the graphic device shows Some text in the lower left corner. If I paste the code into the command window again, then Some text does not appear in the lower left corner. Why is this? require(grid) par(mfrow=c(1,2)) plot(1:10) plot(-10:1) par(mfrow=c(1,1)) pushViewport(viewport(.04, .04, width=stringWidth(Some text), height=unit(2,lines), name=pagenum, gp=gpar(fontsize=10))) grid.text(Some text, gp=gpar(col=gray30), just=c(left,bottom)) popViewport() Good question! :) Short answer: Traditional and grid graphics are fighting each other for control of the clipping region. Simple fix/workaround: Explicitly set the clipping region for the grid output, like this ... require(grid) par(mfrow=c(1,2)) plot(1:10) plot(-10:1) par(mfrow=c(1,1)) # Requires R = 2.3.0 grid.clip() pushViewport(viewport(.04, .04, width=stringWidth(Some text), height=unit(2,lines), name=pagenum, gp=gpar(fontsize=10))) grid.text(Some text, gp=gpar(col=gray30), just=c(left,bottom)) popViewport() Long answer: The first time you run the code, the pushViewport() call is the first grid operation on the graphics device, so some initial grid set up occurs, *including setting the clipping region to the whole device*. The second time you run the code, the pushViewport() call just inherits the current clipping region (which is the one set by the last traditional plot) so the text gets clipped. You can see this effect, with the following code (the text does not even appear the first time because the grid initialisation occurs before the traditional plots) ... require(grid) grid.newpage() par(mfrow=c(1,2)) plot(1:10) plot(-10:1) par(mfrow=c(1,1)) pushViewport(viewport(.04, .04, width=stringWidth(Some text), height=unit(2,lines), name=pagenum, gp=gpar(fontsize=10))) grid.text(Some text, gp=gpar(col=gray30), just=c(left,bottom)) popViewport() ... so really the problem is that the text should never appear. Interestingly, if you run your original code (text is drawn), then run it again (text is not drawn), then ONLY run the grid part (push, text, pop) the text DOES get drawn! This happens because the popViewport() restores the clipping region of the previous grid viewport (which is the whole device). I need to think a bit more about whether this behaviour can be fixed, whether it should be fixed, or whether the current user beware warning about mixing traditional and grid graphics is sufficient. Paul -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 [EMAIL PROTECTED] http://www.stat.auckland.ac.nz/~paul/ __ R-help@stat.math.ethz.ch 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] Running R [Broadcast]
Liaw, Andy [EMAIL PROTECTED] writes: You have two choices (AFAIK): 1. Tell configure exactly where to find the readline header files (by something like --with-readline=/where/the/files/are, check configure --help). 2. Compile R without readline; i.e., configure --with-readline=no. Andy But first check sequencing - I'm pretty sure that configure can find header files on RedHat if they are there. He's not too good at interpreting his output: --One suggestion was to install readline-devel. But according to the below I already have readline-devel. # find . -iname readline-devel\* find -iname readline-devel\* ./os/4.1/x86_64/RedHat/RPMS/readline-devel-4.3-13.x86_64.rpm #rpm -ivh readline*.rpm Preparing...### [100%] package readline-4.3-13 is already installed and as far as I can see, this means that readline-devel got installed and readline (NOT -devel) was there already. So readline-devel is there now, but wasn't there before. Now did he rerun configure? If so, did it fail with a different message? -- 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 __ R-help@stat.math.ethz.ch 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] zero.print in print.table after adding margins
BXC (Bendix Carstensen) [EMAIL PROTECTED] writes: The function addmargins() adds margins to a table, but returns a matrix. But even after converted to a table the print.zero=. option of print.table() does not work: x - sample( 1:7, 20, replace=T ) y - sample( 1:7, 20, replace=T ) tt - table( x, y ) tx - as.table( addmargins( table( x, y ) ) ) print( tt, zero.print=. ) y x 1 2 3 4 5 6 7 1 1 2 2 . . 1 . 2 1 . . 1 . . . 3 . . . . . . 2 4 1 . . . . 1 . 5 1 . 1 . . 1 . 6 . 1 . 1 . . . 7 . . 1 . 1 1 . print( tx, zero.print=. ) y x 1 2 3 4 5 6 7 Sum 11 2 2 0 0 1 0 6 21 0 0 1 0 0 0 2 30 0 0 0 0 0 2 2 41 0 0 0 0 1 0 2 51 0 1 0 0 1 0 3 60 1 0 1 0 0 0 2 70 0 1 0 1 1 0 3 Sum 4 3 4 2 1 4 2 20 Is this a facility of print.table? The attributes() of tt and tx have identical stucture. It appears to be intentional. print.table has if (is.integer(x) zero.print != 0 any(i0 - !ina x == 0)) xx[i0] - sub(0, zero.print, xx[i0]) and of course, storage.mode(tx) [1] double storage.mode(tt) [1] integer The reason could be that it is not entirely clear what to expect for values that are zero up to round-off. storage.mode(tx) - integer fixes things up. -- 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 __ R-help@stat.math.ethz.ch 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] using rbinom in C code gives me erroneous results... random variable is not random (always zero)...
Dear Listers,
I am trying to use rbinom in my C code, but i always get zeros as output no
matter the probability. Am not sure what I am doing wrong because the function
has worked before. Attached in an example. Noticed that rbinom expects 'n' to
be REAL.
Regards, Vumani
R 2.3.1 (2006-06-01)
Windows XP
Gcc
/* Called this file binom.c and then ran rcmd shlib on it */#include
R.h#include Rmath.h#include math.h#include Rdefines.hSEXP binomial(SEXP
r, SEXP n, SEXP p){ int i; SEXP out; PROTECT(out =
allocVector(REALSXP,INTEGER(r)[0])); for(i = 0; i INTEGER(r)[0]; ++i){
REAL(out)[i] = rbinom(REAL(n)[0],REAL(p)[0]); } Rprintf(%d %f
%f\n,INTEGER(r)[0],REAL(n)[0],REAL(p)[0]); UNPROTECT(1); return(out);}
### used theses line in R
dyn.load(binom.dll).Call(binomial,as.integer(10),as.double(1),as.double(0.4))dyn.unload(binom.dll)
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Re: [R] Extracting R plots from MS Word
Click the graphic, press ctrl-C to copy it to the clipboard and then using ctrl-V paste it into mspaint or Xnview (free, find it via google) or other graphics program and then save it from there. Which program will work will depend on the format of the image. Another possibility is to save the Word file in HTML format. In Word, choose File | SaveAs and choose the Save As Type to be Web Page. That will create an HTML file plus it will create a folder with one file per image. On 6/29/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi, I am revising a paper that I am a co-author of. The figures are plots generated from R but at the moment I do not have the R code that generates them. As this is time critical I would like to slightly abuse the list by asking whether anyone knows how to extract from MS Word into a stand-alone graphics file a plot that was pasted into Word from R (probably as a Windows Metafile, but possibly as a bitmap). I would be very grateful for help with this. Regards, Murray Jorgensen __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Very slow read.table on Linux, compared to Win2000 [Broad cast]
On Wednesday 28 June 2006 15:45, Patrick Connolly wrote: On Wed, 28-Jun-2006 at 04:43PM -0700, Alberto Murta wrote: | I have a pentium 4 pc with 256 MB of RAM, so I made a text file, tab | | separated, with column names and 15000 x 483 integers: | system(ls -l teste.txt) | | -rw-r--r-- 1 amurta amurta 16998702 Jun 28 16:08 teste.txt | | the time it took to import it was around 15 secs: | system.time(teste - read.delim(teste.txt)) | | [1] 15.349 0.244 16.597 0.000 0.000 | | so I think lack of RAM must not be the main problem. | Cheers | | Alberto | | version | |_ | platform i386-unknown-freebsd6.1 | arch i386 | os freebsd6.1 | system i386, freebsd6.1 | status | major 2 | minor 3.1 | year 2006 | month 06 | day01 | svn rev38247 | language R | version.string Version 2.3.1 (2006-06-01) Doesn't tell us about your window manager. I'd suspect you're using a light one. I'm using KDE 3.5.2 (a not so light one) and running R in emacs. -- Alberto G. Murta IPIMAR - Institute of Fisheries and Marine Research Avenida de Brasilia; 1449-006 Lisboa; Portugal Tel: +351 213027120; Fax: +351 213015948 __ R-help@stat.math.ethz.ch 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] re-direct to more or less
The first few lines or last few lines of an object can often be viewed like this: head(iris) tail(iris) On 6/28/06, Mike Wolfgang [EMAIL PROTECTED] wrote: Dear list, sometimes my function generates too much data and shows them on screen, i cannot view first several lines until program ends and I have to scroll my mouse up to get them. Is there any re-direction function in R to pipeline outputs to more or less type functions? Thanks mike [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Extracting R plots from MS Word
Another way to do this is with OpenOffice (OO). Read the Word file into OO Writer. Cut the figure. Open OO Draw. Click Paste, and the figure appears in Draw. Save it as EPS, or whatever you like. This works for both EMF and WMF. * [EMAIL PROTECTED] [EMAIL PROTECTED] [060629 08:30]: As this is time critical I would like to slightly abuse the list by asking whether anyone knows how to extract from MS Word into a stand-alone graphics file a plot that was pasted into Word from R (probably as a Windows Metafile, but possibly as a bitmap). -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron Editor: Judgment and Decision Making (http://journal.sjdm.org) __ R-help@stat.math.ethz.ch 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 rbinom in C code gives me erroneous results... random variable is not random (always zero)...
Your text has lost almost all the carriage returns: please do as we ask
and not send HTML code.
You appear not to be initializing the random seed in your code: the manual
says:
The C code behind @R{}'s @[EMAIL PROTECTED] functions can be accessed by
including the header file @file{Rmath.h}; @xref{Distribution
functions}. Those calls generate a single variate and should also be
enclosed in calls to @code{GetRNGstate} and @code{PutRNGstate}.
Why have you not done so?
On Thu, 29 Jun 2006, Vumani Dlamini wrote:
Dear Listers,
I am trying to use rbinom in my C code, but i always get zeros as output no
matter the probability. Am not sure what I am doing wrong because the
function has worked before. Attached in an example. Noticed that rbinom
expects 'n' to be REAL.
Regards, Vumani
R 2.3.1 (2006-06-01)
Windows XP
Gcc
/* Called this file binom.c and then ran rcmd shlib on it */#include
R.h#include Rmath.h#include math.h#include Rdefines.hSEXP
binomial(SEXP r, SEXP n, SEXP p){ int i; SEXP out; PROTECT(out =
allocVector(REALSXP,INTEGER(r)[0])); for(i = 0; i INTEGER(r)[0]; ++i){
REAL(out)[i] = rbinom(REAL(n)[0],REAL(p)[0]); } Rprintf(%d %f
%f\n,INTEGER(r)[0],REAL(n)[0],REAL(p)[0]); UNPROTECT(1); return(out);}
### used theses line in R
dyn.load(binom.dll).Call(binomial,as.integer(10),as.double(1),as.double(0.4))dyn.unload(binom.dll)
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--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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[R] Package Spatialkernel Annocement
Hi, A new R package spatialkernel has been accepted by CRAN. Spatialkernel focuses on implementation of kernel regression methods proposed in Diggle P.J. et al (2005), J. R. Stat. Soc. C, 54, 3, 645-658 and kernel density estimation of inhomogeneous Poisson point process with edge-correction proposed by M. Berman and P.J. Diggle (1989), J. R. Stat. Soc, B, 51, 81–92, for an arbitrary polygonal area. The package source and Windows binary are available at http://www.maths.lancs.ac.uk/~zhengp1/spatialkernel/ Examples in spatialkernel-package shows a quick run of some basic functionality. Sorry for the wrong linked URL address at CRAN archives. Best wishes -- Dr Pingping Zheng Department of Mathematics and Statistics Fylde College Lancaster University Lancaster LA1 4YF UK __ R-help@stat.math.ethz.ch 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] numerical integration problem
Hi,
I have got problems integrating the following function using integrate:
lambdat-function(t){
tempT-T[k,][!is.na(T[k,])]#available values from k-th row of matrix T
tempJ-J[k,][!is.na(J[k,])]
hg-length(tempT[tempT=t tempJ==0])#counts observations satisfing the
conditions
ag-length(tempT[tempT=t tempJ==1])
lambdaXY[hg+1,ag+1]#takes values from a 10x10 matrix
}
I keep receiving this message:
1: longer object length
is not a multiple of shorter object length in: tempT = t
2: longer object length
is not a multiple of shorter object length in: tempT = t tempJ == 0
What I suspect is that the integrate function submits the whole vector of
points at which the integral is to be evaluated at once. For my function to be
integrated it would rather have to be evaluated at each point after another in
a loop of some kind.
Can you think of a way to solve this problem without me having to write the
integrating procedure from scratch (I have no idea about FORTRAN and this is
what the integrate description refers to)?
Thank you.
Kind Regards,
Lukasz Szczepanski
Student
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Re: [R] numerical integration problem
przeszczepan wrote:
Hi,
I have got problems integrating the following function using integrate:
lambdat-function(t){
tempT-T[k,][!is.na(T[k,])]#available values from k-th row of matrix T
tempJ-J[k,][!is.na(J[k,])]
hg-length(tempT[tempT=t tempJ==0])#counts observations satisfing the
conditions
ag-length(tempT[tempT=t tempJ==1])
lambdaXY[hg+1,ag+1]#takes values from a 10x10 matrix
}
I keep receiving this message:
1: longer object length
is not a multiple of shorter object length in: tempT = t
2: longer object length
is not a multiple of shorter object length in: tempT = t tempJ ==
0
What I suspect is that the integrate function submits the whole vector of
points at which the integral is to be evaluated at once. For my function to
be integrated it would rather have to be evaluated at each point after
another in a loop of some kind.
You suspect correctly. Best to read ?integrate too.
Can you think of a way to solve this problem without me having to write the
integrating procedure from scratch (I have no idea about FORTRAN and this is
what the integrate description refers to)?
Just put a for-loop in your function to iterate over t.
n - length(t)
hg - ag - vector(numeric, n)
for(i in seq(n)) {
hg[i] - length(tempT[tempT = t[i] tempJ == 0])
ag[i] - length(tempT[tempT = t[i] tempJ == 1])
}
I doubt this will work because integrate is expecting a vector of
n=length(t) from lambdat. The last line of the function returns a nxn
matrix. Please submit data to run the function plus your call to
integrate in any subsequent postings.
HTH,
--sundar
Thank you.
Kind Regards,
Lukasz Szczepanski
Student
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Re: [R] numerical integration problem
On 6/29/2006 7:38 AM, Sundar Dorai-Raj wrote:
przeszczepan wrote:
Hi,
I have got problems integrating the following function using integrate:
lambdat-function(t){
tempT-T[k,][!is.na(T[k,])]#available values from k-th row of matrix T
tempJ-J[k,][!is.na(J[k,])]
hg-length(tempT[tempT=t tempJ==0])#counts observations satisfing the
conditions
ag-length(tempT[tempT=t tempJ==1])
lambdaXY[hg+1,ag+1]#takes values from a 10x10 matrix
}
I keep receiving this message:
1: longer object length
is not a multiple of shorter object length in: tempT = t
2: longer object length
is not a multiple of shorter object length in: tempT = t tempJ ==
0
What I suspect is that the integrate function submits the whole vector of
points at which the integral is to be evaluated at once. For my function to
be integrated it would rather have to be evaluated at each point after
another in a loop of some kind.
You suspect correctly. Best to read ?integrate too.
Can you think of a way to solve this problem without me having to write the
integrating procedure from scratch (I have no idea about FORTRAN and this is
what the integrate description refers to)?
Just put a for-loop in your function to iterate over t.
Or use Vectorize().
vlambdat - Vectorize(lambdat)
should give a function that can be passed to integrate(), assuming that
lambdat works when given a length 1 vector as input.
Duncan Murdoch
n - length(t)
hg - ag - vector(numeric, n)
for(i in seq(n)) {
hg[i] - length(tempT[tempT = t[i] tempJ == 0])
ag[i] - length(tempT[tempT = t[i] tempJ == 1])
}
I doubt this will work because integrate is expecting a vector of
n=length(t) from lambdat. The last line of the function returns a nxn
matrix. Please submit data to run the function plus your call to
integrate in any subsequent postings.
HTH,
--sundar
Thank you.
Kind Regards,
Lukasz Szczepanski
Student
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Re: [R] Running R
Thank you Andy for your suggestion. I used the method 2 and was able to go upto Step 8. But When I type R # R Fatal error: unable to open the base package 1. Tell configure exactly where to find the readline header files (by something like --with-readline=/where/the/files/are, check configure --help). 2. Compile R without readline; i.e., configure --with-readline=no. Andy 1. gunzip R-patched.tar.gz 2. tar -xvf R-patched.tar 3. changed the directory to the newly created directory R-patched 4. Typed ./configure 5. Typed make 6. Make check 7. make check-all 8. Typed make install *9. Typed R __ R-help@stat.math.ethz.ch 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] specify y axis values
Dear All, I am looking how to specify the values on the y axis and x axis for a curve function. example: curve(2*x + 3, 0,10) gives me a range of x axis in (0,2,4,6,8,10) amd for yaxis (5,10,15,20). How to do in order to have the x axis in (0,1,2,3,4,5,6,7,8,9,10) and y axis in (5,6,7,8,.., 10). Thanks a lot, Bernard - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Problems using na.include
Hi I am having problems using na.action=na.include in a nlme call. Basically I am trying to run a particular model without including any covariates but my dataset does include some covariates (factors) with missing values. My understanding from the Pinheiro and Bates book is that one would use na.action=na.include in order to treat the missing values as another factor level and then one can also use naPattern to specify which rows must be excluded from the calculation of the objective function. I have tried this but keep getting error messages about being unable to find the object or the function na.include. I have also tried to replicate the particular Phenobarbital example verbatim from the book but am getting the same error message. Could it be that my version of the nlme package is outdated? I also cannot find any help on na.include... Thanks Greg __ R-help@stat.math.ethz.ch 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] boxplot of subset of factors, in an order of my choice
Hi Folks, Say I am working with the following data set: testResults: studtestscore 1 1 fTest 43 2 1 rTest 39 3 1 gTest 43 4 2 fTest 23 5 2 rTest 33 6 2 gTest 41 . . . N n gTest 47 I would like to generate a boxplot of rTest only. Here is what I have done after reading the data in and attaching the object. test - factor(test) Now when I try boxplot(score ~ test, subset = test==rTest) 1. I still see the tick marks for the other factors on the x-axis although no data are plotted. Can I eliminate these extra markers (and the space for these faactors) and just have the tick marker and the label for rTest? 2. I would also like to be able to rearrange the tests as they appear from left to right on the graph. I read the hints and help about reorder.factor but it does not seem to be the solution in this case. I am wanting to re-order the boxes without any logic (statistical anyways). Can this be done? Thanks in advance, Sumit __ R-help@stat.math.ethz.ch 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] boxplot of subset of factors, in an order of my choice [B roadcast]
1. Use something like with(testResults, boxplot(score[test == rTest])) 2. testResults$test - factor(as.character(testResults$test), levels=c(rTest, gTest, fTest)) [Substitute any order you like in the last line.] Andy From: Sumitrajit Dhar Hi Folks, Say I am working with the following data set: testResults: studtestscore 1 1 fTest 43 2 1 rTest 39 3 1 gTest 43 4 2 fTest 23 5 2 rTest 33 6 2 gTest 41 . . . N n gTest 47 I would like to generate a boxplot of rTest only. Here is what I have done after reading the data in and attaching the object. test - factor(test) Now when I try boxplot(score ~ test, subset = test==rTest) 1. I still see the tick marks for the other factors on the x-axis although no data are plotted. Can I eliminate these extra markers (and the space for these faactors) and just have the tick marker and the label for rTest? 2. I would also like to be able to rearrange the tests as they appear from left to right on the graph. I read the hints and help about reorder.factor but it does not seem to be the solution in this case. I am wanting to re-order the boxes without any logic (statistical anyways). Can this be done? Thanks in advance, Sumit __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] lmer - Is this reasonable output?
I'm estimating two models for data with n = 179 with four clusters (21, 70, 36, and 52) named siteid. I'm estimating a logistic regression model with random intercept and another version with random intercept and random slope for one of the independent variables. fit.1 - lmer(glaucoma~(1|siteid)+x1 +x2,family=binomial,data=set1,method=ML, control=list(usePQL=FALSE,msVerbose=TRUE)) Generalized linear mixed model fit using PQL Formula: glaucoma ~ (1 | siteid) + x1 + x2 Data: set1 Family: binomial(logit link) AIC BIClogLik deviance 236.7448 249.4944 -114.3724 228.7448 Random effects: Groups NameVariance Std.Dev. siteid (Intercept) 0.05959 0.24411 number of obs: 179, groups: siteid, 4 Estimated scale (compare to 1) 0.464267 Fixed effects: Estimate Std. Error z value Pr(|z|) (Intercept) -2.213779 0.688158 -3.2170 0.001296 ** x1 0.609028 0.293250 2.0768 0.037818 * x2 0.025027 0.009683 2.5846 0.009749 ** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) x1 x1 -0.871 x2 -0.372 -0.024 ranef(fit.1) An object of class “ranef.lmer” [[1]] (Intercept) 1 -0.05053772 2 -0.21592157 3 0.36643051 4 -0.04141520 fit.2 - lmer(glaucoma~(x1|siteid)+x1 +x2,family=binomial,data=set1,method=ML, control=list(usePQL=FALSE,msVerbose=TRUE)) Generalized linear mixed model fit using PQL Formula: glaucoma ~ (x1 | siteid) + x1 + x2 Data: set1 Family: binomial(logit link) AIC BIClogLik deviance 239.3785 258.5029 -113.6893 227.3785 Random effects: Groups NameVariance Std.Dev. Corr siteid (Intercept) 0.059590 0.24411 x1 0.013079 0.11436 0.000 number of obs: 179, groups: siteid, 4 Estimated scale (compare to 1) 0.4599856 Fixed effects: Estimate Std. Error z value Pr(|z|) (Intercept) -2.2137787 0.6911360 -3.2031 0.001360 ** x1 0.6090279 0.2995553 2.0331 0.042042 * x2 0.0250268 0.0097569 2.5650 0.010316 * --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) x1 x1 -0.854 x2 -0.372 -0.023 ranef(fit.2) An object of class “ranef.lmer” [[1]] (Intercept) x1 1 -0.05534800 0.009265667 2 -0.16991678 -0.052723584 3 0.27692026 0.137597965 4 0.01648737 -0.062232012 Note that the fixed coefficient estimates are identical for both models and they are exactly equal to what glm gives ignoring the sites (but the standard errors given by lmer are definitely larger - which would seem reasonable). The se's for the fixed factors differ slightly between the two models. Note also that the estimated random effect sd for siteid intercept is identical for both models. I ran both models using PROC NLMIXED in SAS. It gives be similar estimates but not identical for the fixed effects and random effects. The confidence intervals on the random effects for each site are very large. Am I getting these results because I don't really need to fit a random effect for siteid? The estimated random effects for slope seem to say that siteid matters. When I plot the data for each site with smoothing splines it indicates reasonably different patterns between sites. I don't think these models are that complicated and I have a reasonable amount of data. I fit the fixed and random curves to the separate sites (along with separate glm estimates for each site). As would be expected, the random curves lie between the fixed effect curve and the glm curve. But there seems to be a lot of shrinkage toward the fixed effect curve. (The fixed effect curve fits the smoothing spline curve for all sites combined very closely.) If I specify method=ML and use PQL, I get similar fixed effect estimates (but not identical to glm). The random intercept sd about doubles. I think SAS NLMIXED uses an approximation to the likelihood so that may explain some of the differences. One other thing that seems odd to me is the random intercept sd for site id. It equals 0.24411 in both models. If I change x1 to, say x3 (an entirely different variable), I still get 0.24411. However, the random slope sd does change. I just want to make sure I'm fitting a reasonable model and getting reasonable estimates. Rick B. __ R-help@stat.math.ethz.ch 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] lmer - Is this reasonable output?
Hello Rick, some comments below: o in lmer(), 'method = ML' and its counterpart REML refer to the case of linear mixed models; for GLMMs the methods currently available are PQL and Laplace. The control argument 'usePQL = FALSE' can be used when 'method = Laplace', and in fact specifies not to use PQL as a refinement to the initial values. o SAS proc NLMIXED performs (adaptive) Gaussian Quadrature and is conceptually closer to 'method = Laplace' in lmer(); for PQL you have to use proc GLIMMIX. o for GLMMs both lmer() and NLMIXED work with an approximation to the observed data likelihood, since this likelihood involves an integral with no closed-form solution (except from very specific cases). o with only 4 clusters I think it'd be difficult to estimate variance components; If you want to correct for site, you could just put it as an ordinary covariate in your logistic regression. I hope my comments help. 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: Rick Bilonick [EMAIL PROTECTED] To: R Help r-help@stat.math.ethz.ch Sent: Thursday, June 29, 2006 3:52 PM Subject: [R] lmer - Is this reasonable output? I'm estimating two models for data with n = 179 with four clusters (21, 70, 36, and 52) named siteid. I'm estimating a logistic regression model with random intercept and another version with random intercept and random slope for one of the independent variables. fit.1 - lmer(glaucoma~(1|siteid)+x1 +x2,family=binomial,data=set1,method=ML, control=list(usePQL=FALSE,msVerbose=TRUE)) Generalized linear mixed model fit using PQL Formula: glaucoma ~ (1 | siteid) + x1 + x2 Data: set1 Family: binomial(logit link) AIC BIClogLik deviance 236.7448 249.4944 -114.3724 228.7448 Random effects: Groups NameVariance Std.Dev. siteid (Intercept) 0.05959 0.24411 number of obs: 179, groups: siteid, 4 Estimated scale (compare to 1) 0.464267 Fixed effects: Estimate Std. Error z value Pr(|z|) (Intercept) -2.213779 0.688158 -3.2170 0.001296 ** x1 0.609028 0.293250 2.0768 0.037818 * x2 0.025027 0.009683 2.5846 0.009749 ** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) x1 x1 -0.871 x2 -0.372 -0.024 ranef(fit.1) An object of class “ranef.lmer” [[1]] (Intercept) 1 -0.05053772 2 -0.21592157 3 0.36643051 4 -0.04141520 fit.2 - lmer(glaucoma~(x1|siteid)+x1 +x2,family=binomial,data=set1,method=ML, control=list(usePQL=FALSE,msVerbose=TRUE)) Generalized linear mixed model fit using PQL Formula: glaucoma ~ (x1 | siteid) + x1 + x2 Data: set1 Family: binomial(logit link) AIC BIClogLik deviance 239.3785 258.5029 -113.6893 227.3785 Random effects: Groups NameVariance Std.Dev. Corr siteid (Intercept) 0.059590 0.24411 x1 0.013079 0.11436 0.000 number of obs: 179, groups: siteid, 4 Estimated scale (compare to 1) 0.4599856 Fixed effects: Estimate Std. Error z value Pr(|z|) (Intercept) -2.2137787 0.6911360 -3.2031 0.001360 ** x1 0.6090279 0.2995553 2.0331 0.042042 * x2 0.0250268 0.0097569 2.5650 0.010316 * --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) x1 x1 -0.854 x2 -0.372 -0.023 ranef(fit.2) An object of class “ranef.lmer” [[1]] (Intercept) x1 1 -0.05534800 0.009265667 2 -0.16991678 -0.052723584 3 0.27692026 0.137597965 4 0.01648737 -0.062232012 Note that the fixed coefficient estimates are identical for both models and they are exactly equal to what glm gives ignoring the sites (but the standard errors given by lmer are definitely larger - which would seem reasonable). The se's for the fixed factors differ slightly between the two models. Note also that the estimated random effect sd for siteid intercept is identical for both models. I ran both models using PROC NLMIXED in SAS. It gives be similar estimates but not identical for the fixed effects and random effects. The confidence intervals on the random effects for each site are very large. Am I getting these results because I don't really need to fit a random effect for siteid? The estimated random effects for slope seem to say that siteid matters. When I plot the data for each site with smoothing splines it indicates reasonably different patterns between sites. I don't think these models are that complicated and I have a reasonable amount of data. I fit the fixed and random curves to the separate sites (along with separate
[R] function in boot
Dear R users:
I'm trying to use boot function under the package boot to run some
bootstrapping.
Basically, I have a df as follows. (The data is simplified for illustrative
purpose.)
V1 V2 V3
1 2 3
4 5 7
3 5 2
Say that I want bootrap among (V1,V2,V3) for 1000 times and calculate the
average of them, ie., v_bar still has lenght of 3. I think my question is
really how to write bf function below.
bf - function(d,f)
{
gp1 - 1:3 #indicate random draw from three series
dmean - apply(d[,gp1]*f[gp1],1,mean)
}
a - boot(df,bf, R=1000, stype=f)
Any help or suggestions? Many thanks.
Yihsu
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Re: [R] smoothing splines and degrees of freedom
The help page for 'smooth.spline' says the argument 'df' is 'the desired equivalent number of degrees of freedom (trace of the smoother matrix).' It also explains that the output of 'smooth.spline' includes a component 'fit', and two components of 'fit' are 'knot' and 'coef'. To learn more, you can run the examples, examine 'str(cars.spl)' and the other objects produced by those examples. You can also read more in the references cited there. If you would like further help from this group, please submit another question, preferably after first reading the posting guide! www.R-project.org/posting-guide.html. There is substantial but anecdotal evidence to suggest that posts more consistent with that guide tend to get better answers quicker. For example, if the above does NOT answer your question, I believe you would have gotten a better reply if you had provided a simple, self-contained example, rather than having me rely on one from the 'example' section of the 'smooth.spline' help page. Hope this helps. Spencer Graves Steven Shechter wrote: Hi, If I set df=2 in my smooth.spline function, is that equivalent to running a linear regression through my data? It appears that df=# of data points gives the interpolating spline and that df = 2 gives the linear regression, but I just want to confirm this. Thank you, Steven __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] multivariate normality test
Hello, Could someone help me to explain the VERY big difference in applying two tests on multivariate normality: library(mvnormtest) data(EuStockMarkets) mshapiro.test(t(EuStockMarkets[15:29,1:4])) Shapiro-Wilk normality test data: Z W = 0.8161, p-value = 0.005955 and library(energy) mvnorm.etest( EuStockMarkets[15:29,1:4] ) Energy test of multivariate normality: estimated parameters data: x, sample size 15, dimension 4, replicates 999 E-statistic = 1.0041, p-value = 0.2482 Many thanks, Rem __ R-help@stat.math.ethz.ch 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 needed understanding eval,quote,expression
Great help, thanks to both of you. I actually think I get it.
I think I was locked into eval(expression ... ) as the solution. I did
search the archives for this question, but it must not have clicked with
me.The Thomas Lumley R-help (February 2005) was on the money. I was
missing the power flexibility of the [[ operation. It is certainly more
direct.
I do believe this pattern will satisfy my original problem.
x = list(y=list(y1=hello,y2=world),z=list(z1=foo,z2=bar))
ids = list( zIds=c(z1,z2),yIds=c(y1,y2))
str=y1
x$y[[str]]
[1] hello
btw: I set my prompt to $, so the first post, the $ at the beginning of
the line was the prompt. apologies for the confusion.
cheers.
Prof Brian Ripley [EMAIL PROTECTED]
06/29/2006 04:06 AM
To
Joerg van den Hoff [EMAIL PROTECTED]
cc
[EMAIL PROTECTED], r-help@stat.math.ethz.ch
Subject
Re: [R] Help needed understanding eval,quote,expression
On Thu, 29 Jun 2006, Joerg van den Hoff wrote:
Prof Brian Ripley wrote:
You are missing eval(parse(text=)). E.g.
x - list(y=list(y1=hello,y2=world),z=list(z1=foo,z2=bar))
(what do you mean by the $ at the start of these lines?)
eval(parse(text=x$y$y1))
[1] hello
However, bear in mind
fortune(parse)
If the answer is parse() you should usually rethink the question.
-- Thomas Lumley
R-help (February 2005)
In your indicated example you could probably use substitute() as
effectively.
On Wed, 28 Jun 2006, [EMAIL PROTECTED] wrote:
I am trying to build up a quoted or character expression representing
a
component in a list in order to reference it indirectly.
For instance, I have a list that has data I want to pull, and another
list
that has character vectors and/or lists of characters containing the
names
of the components in the first list.
It seems that the way to do this is as evaluating expressions, but I
seem
to be missing something. The concept should be similar to the snippet
below:
For instance:
$x = list(y=list(y1=hello,y2=world),z=list(z1=foo,z2=bar))
$y = quote(x$y$y1)
$eval(y)
[1] hello
but, I'm trying to accomplish this by building up y as a character and
then evaluating it, and having no success.
$y1=paste(x$y$,y1,sep=)
$y1
[1] x$y$y1
How can I evaluate y1 as I did with y previously? or can I?
Much Thanks !
if I understand you correctly you can achieve your goal much easier than
with
eval, parse, substitute and the like:
x - list(y=list(y1=hello,y2=world),z=list(z1=foo,z2=bar))
s1 - 'y'
s2 - 'y1'
x[[s1]][[s2]]
i.e. using `[[' instead of `$' for list component extraction allows to
use
characters for indexing (in other words: x$y == x[['y']])
But what he actually asked for was
I am trying to build up a quoted or character expression representing
a
component in a list in order to reference it indirectly.
You just typed in x[[s1]][[s2]], not 'built [it] up'. Suppose the
specification had been
r - x
s - c(y, y1)
and s was of variable length? Then you need to construct a call similar
to x[[y]][[y1]] from r and s.
[There was another reason for sticking with $ rather than using [[: the
latter makes unnecessary copies in released versions of R.]
--
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
CONFIDENTIALITY NOTICE: This electronic mail transmission (i...{{dropped}}
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Re: [R] Problems using na.include
Greg Distiller wrote: Hi I am having problems using na.action=na.include in a nlme call. Basically I am trying to run a particular model without including any covariates but my dataset does include some covariates (factors) with missing values. My understanding from the Pinheiro and Bates book is that one would use na.action=na.include in order to treat the missing values as another factor level and then one can also use naPattern to specify which rows must be excluded from the calculation of the objective function. The approach of adding new categories for missing values has been shown to be highly problematic, completely changing the interpretation of the predictor and causing biases. See an article by Werner Vach on this in the Encyclopedia of Biostatistics. I have tried this but keep getting error messages about being unable to find the object or the function na.include. I have also tried to replicate the particular Phenobarbital example verbatim from the book but am getting the same error message. Could it be that my version of the nlme package is outdated? I also cannot find any help on na.include... Thanks Greg __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch 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] Problems Creating an R package
Hi all,
When I check my package using Rcmd check ..\myPackage\R.mykg on Windows in
Command Prompt, this is what get:-
* using log directory 'C:/R/bin/R.getdata.Rcheck'
* using Version 2.3.1 (2006-06-01)
* checking for file 'R.getdata/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R.getdata' version '1.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'R.getdata' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory 'src' contains no source files.
* checking R files for syntax errors ... ERROR
Syntax error in file 'R/ConnectionFactory.R'
Q1. What should I put in 'src'. I did put two of my source .R files, it
still does not work.
Q2. This is what I get if I source R/ConnectionFactory.R.
Error in parse(file, n = -1, NULL, ?) : syntax error at
5: }
6: , .env =
These are the contents of R/ConnectionFactory.R.
ConnectionFactory -
structure(function()
{
extend(Object(), ConnectionFactory)
}
, .env = environment, class = c(Class, Object), ...instanciationTime =
structure(1151521420.604, class = c(POSIXt,
POSIXct)), formals = c(public, class), modifiers = c(public,
class)
Please note that this file is one that was automatically generated in
R.mykg/R. My source file ConnectionFactory.R has the actual R code which
sources just fine.
I will greatly appreciate any help! Thank you.
Aarti
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Re: [R] Extracting R plots from MS Word
On Thu, Jun 29, 2006 at 05:15:08PM +1200, [EMAIL PROTECTED] wrote: I am revising a paper that I am a co-author of. The figures are plots generated from R but at the moment I do not have the R code that generates them. As this is time critical I would like to slightly abuse the list by asking whether anyone knows how to extract from MS Word into a stand-alone graphics file a plot that was pasted into Word from R (probably as a Windows Metafile, but possibly as a bitmap). Open the doc file in OpenOffice, save in sxw format (openoffice's old native format), unpack the file with unzip and find the figure in the resulting directory. I'm not sure if and how this works with the new odt format used by openoffice now, but sxw will work. cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ R-help@stat.math.ethz.ch 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] initializing table and filling it out
Hi everyone,
I'm writting a script that will open multiple files in a single folder
and then will do some calculations to finally save everything in a big table.
So here is the pseudo code
#read all files in the given directory
myfiles -list.files(c:\\myDir)
#initialize table
???
#loop through files
for(f in myfiles[-1]) {
netMat - read.table( f, sep )
netMat -as.matrix(netMat)
# calculate the needed Stats
gden(netMat)-density
centralization(netMat, degree) - Gdegree
centralization(netMat, betweenness) - Gbetweenness
centralization(netMat, closeness) - Gcloseness
#store into table
}
So my questions are two
First how can I initialize the table (it will be a 4 X 1001 table) without
filling it out first.
Second how can I store each value in the table (i.e. in each round I'll be
adding one full column with density and the 3 different centralizations)?
thks
-Cuau
-
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Re: [R] superimposing histograms con't
Bill == Bill Shipley [EMAIL PROTECTED]
on Wed, 28 Jun 2006 15:53:35 -0400 writes:
Bill Earlier, I posted the following question:
Bill I want to superimpose histograms from three
Bill populations onto the same graph, changing the shading
Bill of the bars for each population. After consulting the
Bill help files and the archives I cannot find out how to
Bill do this (seemly) simple graph. To be clear, I want
Bill - a single x axis (from -3 to 18)
Bill - three groups of bars forming the histograms of each population
Bill (they will not overlap much, but this is a detail)
Bill - the bars from each histogram having different
Bill shadings or other visually distinguishing features.
Bill Gabor Grothendieck [EMAIL PROTECTED] pointed
Bill to some code to to this but I have found another way
Bill that works even easier.
Bill hist(x[sel1],xlim=c(a,b),ylim=c(A,B)) - this plots the histogram for
the
Bill first group (indexed by sel1) but with an x axis and a y axis that
spans the
Bill entire range.
Bill par(new=T) - to keep on the same graph
Bill hist(x[sel2],main=Null,xlab=NULL,ylab=NULL,axes=F) -superimposes the
second
Bill histogram
Bill par(new=T) - to keep on the same graph
Bill hist(x[sel3],main=Null,xlab=NULL,ylab=NULL,axes=F) -superimposes the
third
Bill histogram
Hmm, the above does not work (because of 'Null' instead of 'NULL')
but even if you fix that, I'm pretty sure you get pretty wrong
plots.
par(new = TRUE) is quite often a bad choice.
In the present case, plot 2 and 3 use different
coordinate systems than plot 1.
The correct solution -- apart from using lattice::histogram()
with the correct 'superpose' panel is really to make use of the
fact that
1) hist() returns a histogram (S3) object which is plotted by
2) plot.histogram() which has a nice help page even though
the funcion is namespace-hidden.
Here's a reproducible solution --- with quite a bit of extra
code in order to show two ``colorizations'' for overplotting,
in particular one with ``transparent colors'' :
##MM: construct reproducible example data
set.seed(1)
x - c(rnorm(50), (rnorm(60) +3.5), (rnorm(40) +3.5 + 3))
str(grouping - factor(c(rep(1,50), rep(2,60), rep(3,40
(n.gr - length(table(grouping))) # 3
xr - range(x)
## Compute all three histograms objects but without plotting:
histL - tapply(x, grouping, hist, plot = FALSE)
maxC - max(print( sapply(lapply(histL, [[, counts), max)) ) # 14 15 15
pdf(3histo.pdf, version = 1.4) # = 1.4 is needed
## or try the default x11()
if((TC - transparent.cols - .Device %in% c(pdf, png))) {
cols - hcl(h = seq(30, by=360 / n.gr, length = n.gr), l = 65,
alpha = 0.5) ## transparency
} else {
h.den - c(10, 15, 20)
h.ang - c(45, 15, -30)
}
## Plots the histogram for the
## first group (indexed by sel1) but with an x axis and a y axis that spans the
## entire range.
if(TC) {
plot(histL[[1]], xlim = xr, ylim= c(0, maxC), col = cols[1],
xlab = x, main = 3 Histograms of 3 Selections from 'x')
} else
plot(histL[[1]], xlim = xr, ylim= c(0, maxC), density = h.den[1], angle =
h.ang[1],
xlab = x, main = Histogram of 3 selections from 'x')
## Using density instead of color make these *add*
if(!transparent.cols) {
for(j in 2:n.gr)
plot(histL[[j]], add = TRUE, density = h.den[j], angle = h.ang[j])
} else { ## use semi-translucent colors (available only for PDF = 1.4 and PNG
devices):
for(j in 2:n.gr)
plot(histL[[j]], add = TRUE, col = cols[j])
}
if(.Device == pdf) { ## you have set it above
dev.off()
system(gv 3histo.pdf )## or use 'acroread' ; 'xpdf' does not show
transparent colors...
}
1 ##--- Martin Maechler, ETH Zurich
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Re: [R] Problems Creating an R package
Hi Aarti
src/ if you have source files in C or Fortran.
R/for the R sources.
If you have no C or Fortran files, you should delete the src/ directory.
The syntax error in your R function is simply that the , is on a new
line so R thinks that the line above is complete.
Hope it helps
Thomas P.
Aarti Dahiya wrote:
Hi all,
When I check my package using Rcmd check ..\myPackage\R.mykg on Windows in
Command Prompt, this is what get:-
* using log directory 'C:/R/bin/R.getdata.Rcheck'
* using Version 2.3.1 (2006-06-01)
* checking for file 'R.getdata/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R.getdata' version '1.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'R.getdata' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory 'src' contains no source files.
* checking R files for syntax errors ... ERROR
Syntax error in file 'R/ConnectionFactory.R'
Q1. What should I put in 'src'. I did put two of my source .R files, it
still does not work.
Q2. This is what I get if I source R/ConnectionFactory.R.
Error in parse(file, n = -1, NULL, ?) : syntax error at
5: }
6: , .env =
These are the contents of R/ConnectionFactory.R.
ConnectionFactory -
structure(function()
{
extend(Object(), ConnectionFactory)
}
, .env = environment, class = c(Class, Object), ...instanciationTime =
structure(1151521420.604, class = c(POSIXt,
POSIXct)), formals = c(public, class), modifiers = c(public,
class)
Please note that this file is one that was automatically generated in
R.mykg/R. My source file ConnectionFactory.R has the actual R code which
sources just fine.
I will greatly appreciate any help! Thank you.
Aarti
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Re: [R] superimposing histograms con't
Jeff == Jeff Miller [EMAIL PROTECTED] on Wed, 28 Jun 2006 16:20:39 -0400 writes: Jeff I was just thinking about this last night. Jeff I would like to do the same but WITH overlapping. Jeff For example, I graph 2 sets of count data. Say the Jeff bars for the 1`s overlap...I would like to show that Jeff with a different shading for the group that has the Jeff higher frequency. For example, it could be black up to Jeff a frequency of 5 followed by diagonal-dashes from 5-7 Jeff representing the higher frequency of a second group. Just 5 minutes ago, I've posted a reply to Bill's message containing R code which I think also solves the above problem. Solving overlapping visually either by (old style) shading or by (new style) transparent colors -- unfortunately only available on pdf(version = 1.4), png(), and quartz(), AFAIK. Martin Maechler __ R-help@stat.math.ethz.ch 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] initializing table and filling it out
If you use lapply you don't have to set up the storage area.
Here is an example. I have used textConnection with character
strings to make this reproducible but you can replace conn with
a vector of filenames,
# test data
Lines1 -
1 2
3 4
Lines2 -
11 12
13 14
conn - list(textConnection(Lines1), textConnection(Lines2))
# this is code
f - function(f) with(read.table(f), c(a = mean(V1), b = sd(V2)))
do.call(rbind, lapply(conn, f))
On 6/29/06, Cuau [EMAIL PROTECTED] wrote:
Hi everyone,
I'm writting a script that will open multiple files in a single folder
and then will do some calculations to finally save everything in a big table.
So here is the pseudo code
#read all files in the given directory
myfiles -list.files(c:\\myDir)
#initialize table
???
#loop through files
for(f in myfiles[-1]) {
netMat - read.table( f, sep )
netMat -as.matrix(netMat)
# calculate the needed Stats
gden(netMat)-density
centralization(netMat, degree) - Gdegree
centralization(netMat, betweenness) - Gbetweenness
centralization(netMat, closeness) - Gcloseness
#store into table
}
So my questions are two
First how can I initialize the table (it will be a 4 X 1001 table) without
filling it out first.
Second how can I store each value in the table (i.e. in each round I'll be
adding one full column with density and the 3 different centralizations)?
thks
-Cuau
-
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Re: [R] Problems Creating an R package
On Thu, 29 Jun 2006, Thomas Petzoldt wrote:
Hi Aarti
src/ if you have source files in C or Fortran.
R/for the R sources.
If you have no C or Fortran files, you should delete the src/ directory.
The syntax error in your R function is simply that the , is on a new
line so R thinks that the line above is complete.
R does know it is waiting for a ')'. The error is exactly where it says, at
6: , .env =
and of course
, .env = environment, class = c(Class, Object), ...instanciationTime =
^
which is not valid R.
Hope it helps
Thomas P.
Aarti Dahiya wrote:
Hi all,
When I check my package using Rcmd check ..\myPackage\R.mykg on Windows in
Command Prompt, this is what get:-
* using log directory 'C:/R/bin/R.getdata.Rcheck'
* using Version 2.3.1 (2006-06-01)
* checking for file 'R.getdata/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R.getdata' version '1.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'R.getdata' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory 'src' contains no source files.
* checking R files for syntax errors ... ERROR
Syntax error in file 'R/ConnectionFactory.R'
Q1. What should I put in 'src'. I did put two of my source .R files, it
still does not work.
Q2. This is what I get if I source R/ConnectionFactory.R.
Error in parse(file, n = -1, NULL, ?) : syntax error at
5: }
6: , .env =
These are the contents of R/ConnectionFactory.R.
ConnectionFactory -
structure(function()
{
extend(Object(), ConnectionFactory)
}
, .env = environment, class = c(Class, Object), ...instanciationTime =
structure(1151521420.604, class = c(POSIXt,
POSIXct)), formals = c(public, class), modifiers = c(public,
class)
Please note that this file is one that was automatically generated in
R.mykg/R. My source file ConnectionFactory.R has the actual R code which
sources just fine.
I will greatly appreciate any help! Thank you.
Aarti
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--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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[R] R server
Hi, I just installed R in Windows, it seems to me that R is a standalone desktop application. Do you know if R has its server version which could handle multi-users, have several distinct R sessions and their own variables in Unix or Windows? I saw OpenStatServer, RStatServer available, can those handle multi-sessions? Thanks Mike [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] R server
One approach would be to install R on a unix machine and let other machines connect to it via a standard X server. There might be other approaches though Gabor On Thu, Jun 29, 2006 at 12:05:40PM -0400, Li, Mike wrote: Hi, I just installed R in Windows, it seems to me that R is a standalone desktop application. Do you know if R has its server version which could handle multi-users, have several distinct R sessions and their own variables in Unix or Windows? I saw OpenStatServer, RStatServer available, can those handle multi-sessions? Thanks Mike [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Csardi Gabor [EMAIL PROTECTED]MTA RMKI, ELTE TTK __ R-help@stat.math.ethz.ch 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] specify y axis values
?axis curve(2*x + 3, 0,10,xaxt='n',yaxt='n') axis(1, at=seq(0,10)) axis(2, at=seq(5,10)) On 6/29/06, Marc Bernard [EMAIL PROTECTED] wrote: Dear All, I am looking how to specify the values on the y axis and x axis for a curve function. example: curve(2*x + 3, 0,10) gives me a range of x axis in (0,2,4,6,8,10) amd for yaxis (5,10,15,20). How to do in order to have the x axis in (0,1,2,3,4,5,6,7,8,9,10) and y axis in (5,6,7,8,.., 10). Thanks a lot, Bernard - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Jim Holtman Cincinnati, OH +1 513 646 9390 (Cell) +1 513 247 0281 (Home) What is the problem you are trying to solve? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Internet Problem in R
Hi, I have a student who's R seems to be unable to connect to the internet. I have verified that her computer has internet access that's working fine, but that R is not able to establish connections. For example, she cannot download packages for R from the URL site, cannot source webpages, or read.table from a webpage (all of these give errors of not being able to establish a connection). Right now I have shown her how to manually download the zip file for the package and install it from the local file, but she wants Bioconductor -- the instructions for which seem to require the usual internet access. Does anyone have any troubleshooting suggestions? (I've never had problems with the internet interface with R, so I don't even know where to start to try to fix it or even diagnose the problem). Could a firewall have this effect? Wireless? Her computer is running version R.2.3.1, on a Windows XP. Thanks, Elizabeth Purdom __ R-help@stat.math.ethz.ch 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] Internet Problem in R
It could well be a firewall issue. Try adding --internet2 as argument to Rgui.exe in the target field of the shortcut for Rgui. Andy From: Elizabeth Purdom Hi, I have a student who's R seems to be unable to connect to the internet. I have verified that her computer has internet access that's working fine, but that R is not able to establish connections. For example, she cannot download packages for R from the URL site, cannot source webpages, or read.table from a webpage (all of these give errors of not being able to establish a connection). Right now I have shown her how to manually download the zip file for the package and install it from the local file, but she wants Bioconductor -- the instructions for which seem to require the usual internet access. Does anyone have any troubleshooting suggestions? (I've never had problems with the internet interface with R, so I don't even know where to start to try to fix it or even diagnose the problem). Could a firewall have this effect? Wireless? Her computer is running version R.2.3.1, on a Windows XP. Thanks, Elizabeth Purdom __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Biobass, SAGx, and Jonckheere-Terpstra test
Hi list, I tried to load the package SAGx and failed because it complains it's looking for the Biobass which is not there. Then I looked up the package list and Biobass is not found. I'm trying to run the Jonckheere-Terpstra test and from what I see in the R archive, SAGx is the only place it's been implemented. library(SAGx) Loading required package: multtest Loading required package: survival Loading required package: splines Loading required package: sma Error in loadNamespace(i, c(lib.loc, .libPaths())) : there is no package called 'Biobase' Error: package/namespace load failed for 'SAGx' Horace W. Tso __ R-help@stat.math.ethz.ch 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] RCOM Package
Hi list, I just installed the rcom package and tried to read/give out some values from/to Excel. Altogether it works great... but nevertheless I don't know how the syntax works or in other words: Which command needs which parameters? Is there somwhere a manual about this package with good examples? I've read the Package description... but there are not really good descriptions/examples. I know the following parameters/commands: #Connect to the active Workbook excel - comGetObject(Excel.Application) #Set the active sheet sheet - comGetProperty(excel,ActiveSheet) #Set a specific sheet sheet - comGetProperty(excel,Worksheets,WorksheetXY) #Create a new Worksheet comInvoke(comGetProperty(excel,Worksheets),Add) #Define a range in a defined sheet range1 - comGetProperty(sheet,Range,A1,A20) #Read out this range from Excel val1 - as.double(comGetProperty(range1,Value)) #Give back the results to Excel comSetProperty(range1,Value,val1) Some of my questions are: - How can I rename a worksheet? - How can I define the name of a new worksheet? - How can I delete a worksheet? - How can I connect to a specific Workbook, if more than one is opened? - ... Can someone help me? Thanks, Thomas __ R-help@stat.math.ethz.ch 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] RCOM Package
Go into Excel, turn on macro recording, perform whatever operations you want and look at whatever code is generated for you. On 6/29/06, Thomas Sudler [EMAIL PROTECTED] wrote: Hi list, I just installed the rcom package and tried to read/give out some values from/to Excel. Altogether it works great... but nevertheless I don't know how the syntax works or in other words: Which command needs which parameters? Is there somwhere a manual about this package with good examples? I've read the Package description... but there are not really good descriptions/examples. I know the following parameters/commands: #Connect to the active Workbook excel - comGetObject(Excel.Application) #Set the active sheet sheet - comGetProperty(excel,ActiveSheet) #Set a specific sheet sheet - comGetProperty(excel,Worksheets,WorksheetXY) #Create a new Worksheet comInvoke(comGetProperty(excel,Worksheets),Add) #Define a range in a defined sheet range1 - comGetProperty(sheet,Range,A1,A20) #Read out this range from Excel val1 - as.double(comGetProperty(range1,Value)) #Give back the results to Excel comSetProperty(range1,Value,val1) Some of my questions are: - How can I rename a worksheet? - How can I define the name of a new worksheet? - How can I delete a worksheet? - How can I connect to a specific Workbook, if more than one is opened? - ... Can someone help me? Thanks, Thomas __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Cointegration Test in R
Hello! I'm using the blrtest() function in the urca package to test cointegration relationships. Unfortunately, the hypothesis (restrictions on beta) specifies the same restriction on all cointegration vectors. Is there any possibility to specify different restrictions on the cointegration vectors? Are there any other packages in R using cointegration tests? Thanks and best regards. Dennis Heidemann [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Biobass, SAGx, and Jonckheere-Terpstra test
It is *Biobase*. That is part of BioC (www.bioconductor.org), although I agree that it should make clear where to get non-CRAN packages. (Worse: SAGx used not to require it, and only the update to the most recent version does.) On Thu, 29 Jun 2006, Horace Tso wrote: Hi list, I tried to load the package SAGx and failed because it complains it's looking for the Biobass which is not there. Then I looked up the package list and Biobass is not found. I'm trying to run the Jonckheere-Terpstra test and from what I see in the R archive, SAGx is the only place it's been implemented. library(SAGx) Loading required package: multtest Loading required package: survival Loading required package: splines Loading required package: sma Error in loadNamespace(i, c(lib.loc, .libPaths())) : there is no package called 'Biobase' Error: package/namespace load failed for 'SAGx' Horace W. Tso __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- 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 __ R-help@stat.math.ethz.ch 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] How to use a for loop to generate two sequences
Hi R users, Hope the question is not too simple: How to use a for loop to generate two lists as below: testlist - list(test1, test2, ..., test1000) stringlist - list(test1,test2,...,test1000) Thanks Xiaohua __ R-help@stat.math.ethz.ch 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 to use a for loop to generate two sequences
On Thu, 29 Jun 2006, Xiaohua Dai wrote: Hi R users, Hope the question is not too simple: How to use a for loop to generate two lists as below: testlist - list(test1, test2, ..., test1000) stringlist - list(test1,test2,...,test1000) I don't know why you would want to use a for loop: stringlist-as.list(paste(test,1:1000,sep=)) testlist-lapply(stringlist, as.name) -thomas __ R-help@stat.math.ethz.ch 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] cat and positioning of the output
Hello R users!
I like to use cat in a loop. I know, loops are not the best way in R ... but
my question: It is possible to overwrite the expression Reading row: i in
each iteration of the loop (print out in the below loop on the screen) or
more particulary to overwrite the counter i.
for(i in 1:header$M){
cat(Reading row: , i)
SparseIndex[[i]] - readBin( con, integer(), n=MIndexNumber[i], size=4 )
SparseSignal[[i]] - readBin( con, numeric(), n=MIndexNumber[i], size=4 )
}
Many thanks
J?rn Schulz.
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Re: [R] cat and positioning of the output
On Windows XP this works for me:
for(i in 1:3) { if (i 1) cat(\b); cat(i); flush.console();
Sys.sleep(1) }; cat(\n)
It displays 1, then it overwrites it with 2 and then overwrites that with 3.
On 6/29/06, J?rn Schulz [EMAIL PROTECTED] wrote:
Hello R users!
I like to use cat in a loop. I know, loops are not the best way in R ... but
my question: It is possible to overwrite the expression Reading row: i in
each iteration of the loop (print out in the below loop on the screen) or
more particulary to overwrite the counter i.
for(i in 1:header$M){
cat(Reading row: , i)
SparseIndex[[i]] - readBin( con, integer(), n=MIndexNumber[i], size=4 )
SparseSignal[[i]] - readBin( con, numeric(), n=MIndexNumber[i], size=4 )
}
Many thanks
J?rn Schulz.
--
View this message in context:
http://www.nabble.com/cat-and-positioning-of-the-output-tf1869521.html#a5109359
Sent from the R help forum at Nabble.com.
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Re: [R] cat and positioning of the output
=?ANSI_X3.4-1968?Q?J=3Frn_Schulz?= wrote:
Hello R users!
I like to use cat in a loop. I know, loops are not the best way in R ... but
my question: It is possible to overwrite the expression Reading row: i in
each iteration of the loop (print out in the below loop on the screen) or
more particulary to overwrite the counter i.
In package svMisc (SciViews bundle):
?progress
example(progress)
Best,
Philippe Grosjean
for(i in 1:header$M){
cat(Reading row: , i)
SparseIndex[[i]] - readBin( con, integer(), n=MIndexNumber[i], size=4 )
SparseSignal[[i]] - readBin( con, numeric(), n=MIndexNumber[i], size=4 )
}
Many thanks
J?rn Schulz.
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Re: [R] cat and positioning of the output
=?ANSI_X3.4-1968?Q?J=3Frn_Schulz?= wrote:
Hello R users!
I like to use cat in a loop. I know, loops are not the best way in R ... but
my question: It is possible to overwrite the expression Reading row: i in
each iteration of the loop (print out in the below loop on the screen) or
more particulary to overwrite the counter i.
for(i in 1:header$M){
cat(Reading row: , i)
SparseIndex[[i]] - readBin( con, integer(), n=MIndexNumber[i], size=4 )
SparseSignal[[i]] - readBin( con, numeric(), n=MIndexNumber[i], size=4 )
}
Many thanks
J?rn Schulz.
On a UNIX terminal, adding '\r' will cause the cursor to go back to the
beginning of the same line. I can't speak for Windows.
e.g.
for ( i in 1:10 ) { cat(Number,i,\r); Sys.sleep(1) }; cat(\n)
-Dan
--
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Re: [R] cat and positioning of the output
Dan Gunter wrote:
=?ANSI_X3.4-1968?Q?J=3Frn_Schulz?= wrote:
Hello R users!
I like to use cat in a loop. I know, loops are not the best way in R ... but
my question: It is possible to overwrite the expression Reading row: i in
each iteration of the loop (print out in the below loop on the screen) or
more particulary to overwrite the counter i.
for(i in 1:header$M){
cat(Reading row: , i)
SparseIndex[[i]] - readBin( con, integer(), n=MIndexNumber[i], size=4 )
SparseSignal[[i]] - readBin( con, numeric(), n=MIndexNumber[i], size=4 )
}
Many thanks
J?rn Schulz.
On a UNIX terminal, adding '\r' will cause the cursor to go back to the
beginning of the same line. I can't speak for Windows.
e.g.
for ( i in 1:10 ) { cat(Number,i,\r); Sys.sleep(1) }; cat(\n)
-Dan
It works, but I don't like much strange things that can happen with \r
because the caret is located at the beginning of the line. Look at what
happens if you forgot the latests 'cat(\n)'. Also, note that for RGui
under windows, you must use flush.console(). So:
for (i in 1:10) {
cat(Number,i,\r)
flush.console()
Sys.sleep(1)
}
cat(\n)
does the job. The alternative is to use \b repeatedly, which is done
in progress() indeed.
Best,
Philippe Grosjean
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Re: [R] cat and positioning of the output
It works on Windows (rgui.exe) with this change:
for ( i in 1:10 ) { cat(Number,i,\r); flush.console(); Sys.sleep(1)
}; cat(\n)
MHP
on 6/29/2006 4:33 PM Dan Gunter said the following:
=?ANSI_X3.4-1968?Q?J=3Frn_Schulz?= wrote:
Hello R users!
I like to use cat in a loop. I know, loops are not the best way in R ... but
my question: It is possible to overwrite the expression Reading row: i in
each iteration of the loop (print out in the below loop on the screen) or
more particulary to overwrite the counter i.
for(i in 1:header$M){
cat(Reading row: , i)
SparseIndex[[i]] - readBin( con, integer(), n=MIndexNumber[i], size=4 )
SparseSignal[[i]] - readBin( con, numeric(), n=MIndexNumber[i], size=4 )
}
Many thanks
J?rn Schulz.
On a UNIX terminal, adding '\r' will cause the cursor to go back to the
beginning of the same line. I can't speak for Windows.
e.g.
for ( i in 1:10 ) { cat(Number,i,\r); Sys.sleep(1) }; cat(\n)
-Dan
--
Michael Prager, Ph.D.
Southeast Fisheries Science Center
NOAA Center for Coastal Fisheries and Habitat Research
Beaufort, North Carolina 28516
** Opinions expressed are personal, not official. No
** official endorsement of any product is made or implied.
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[R] Passing argument in nested function calls
Please, do not ask why you would do this. I have simplified my complicated
code to just the basic problem occuring to be able to make it easier to
understand the actual problem.
I have two function getArgs() and extractArgs() - code and test results
provided below.
I test them using getArgs(id = 's1002') from the command line.
getArgs() prints the name of the argument as id and the actual argument as
s1002, which is correct.
But, when I call extractArgs() from within getArgs() passing value of passed
(stored in passed, passed is created from paste(names(args),=,
sQuote(args))); extractArgs() treats the value of passed as a string id =
's1002' and treats the whole thing as one argument. So, it prints
args[[1]] as the whole thing id = 's1002', but prints blank for
names(args[[1]]), obviously beacuse it cannot find a name for the argument.
If I call extractArgs(id = 's1002') from the command line, it works just
fine, prints the name of the argument as id and the actual argument as
s1002, which is correct.
How do I fix the problem so that when extractArgs() is called within
getArgs(), it behaves the same way as getArgs() and extracts the argument
and argument name? Can we unstring passed or change it into another mode?
I'll appreciate any help or pointers. Thanks. Aarti
getArgs - function(...)
{
cat(\nEntering getArgs()\n\n)
args - list(...)
cat(In getArgs(), names(args[1]) is )
cat(names(args[1]))
cat( and args[[1]] is )
cat(args[[1]])
cat(\n)
passed - paste(names(args),=, sQuote(args))
extractArgs(passed)
cat(Exiting getArgs()\n\n)
}
extractArgs - function(...)
{
cat(\nEntering extractArgs()\n\n)
args - list(...)
cat(In extractArgs(), names(args[1]) is )
cat(names(args[1]))
cat( and args[[1]] is )
cat(args[[1]])
cat(\n)
cat(\nExiting extractArgs()\n\n)
}
Test:
getArgs(id = 's1002')
Entering getArgs()
In getArgs(), names(args[1]) is id and args[[1]] is s1002
Entering extractArgs()
In extractArgs(), names(args[1]) is and args[[1]] is id = 's1002'
Exiting extractArgs()
Exiting getArgs()
extractArgs(id = 's1002')
Entering extractArgs()
In extractArgs(), names(args[1]) is id and args[[1]] is s1002
Exiting extractArgs()
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Re: [R] Transform Normal Dist to ArcTan Dist
Luis Cota luis.cota at avmltd.com writes: I have a set of data that is distributed normally. How can I transform this data to fit an ArcTan distribution? [[alternative HTML version deleted]] __ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html we need more information. This is a stats question more than an R question, and there isn't enough context here to know either (1) what arctangent distribution you're talking about (it may be the Cauchy/ t-distribution with 1 df, or it may be something else) or (2) why you want to transform the distribution, and whether it's a sensible thing to do in the first place ... (see what the posting guide has to say about statistical questions ...) Ben Bolker __ R-help@stat.math.ethz.ch 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] help with coxme
Hi there, I have a question on fitting data by coxme. In particular I want to fit a random intercept and random slope cox model. Using the rats dataset as an example, I generated another covariate x2 and want to specify a random slope for x2. Here is my code: x2=matrix(rep(runif(50), 3), 50, 3) x2=as.vector(t(x2)) rats2=cbind(rats, x2) But when I used the coxme function as follows, it gave an error message. What is the right way to do it? Thanks a lot! coxme(Surv(time, status) ~ rx+x2, data=rats2, random=~ (1+x2)|litter ) Lei Liu Assistant Professor Division of Biostatistics and Epidemiology Dept. of Public Health Sciences School of Medicine University of Virginia 3181 Hospital West Complex Charlottesville, VA 22908-0717 1-434-982-3364 (o) 1-434-806-8086 (c) [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] Passing argument in nested function calls
getArgs should be:
getArgs - function(...) extractArgs(...)
# test
extractArgs(x = 3)
getArgs(x = 3)
On 6/29/06, Aarti Dahiya [EMAIL PROTECTED] wrote:
Please, do not ask why you would do this. I have simplified my complicated
code to just the basic problem occuring to be able to make it easier to
understand the actual problem.
I have two function getArgs() and extractArgs() - code and test results
provided below.
I test them using getArgs(id = 's1002') from the command line.
getArgs() prints the name of the argument as id and the actual argument as
s1002, which is correct.
But, when I call extractArgs() from within getArgs() passing value of passed
(stored in passed, passed is created from paste(names(args),=,
sQuote(args))); extractArgs() treats the value of passed as a string id =
's1002' and treats the whole thing as one argument. So, it prints
args[[1]] as the whole thing id = 's1002', but prints blank for
names(args[[1]]), obviously beacuse it cannot find a name for the argument.
If I call extractArgs(id = 's1002') from the command line, it works just
fine, prints the name of the argument as id and the actual argument as
s1002, which is correct.
How do I fix the problem so that when extractArgs() is called within
getArgs(), it behaves the same way as getArgs() and extracts the argument
and argument name? Can we unstring passed or change it into another mode?
I'll appreciate any help or pointers. Thanks. Aarti
getArgs - function(...)
{
cat(\nEntering getArgs()\n\n)
args - list(...)
cat(In getArgs(), names(args[1]) is )
cat(names(args[1]))
cat( and args[[1]] is )
cat(args[[1]])
cat(\n)
passed - paste(names(args),=, sQuote(args))
extractArgs(passed)
cat(Exiting getArgs()\n\n)
}
extractArgs - function(...)
{
cat(\nEntering extractArgs()\n\n)
args - list(...)
cat(In extractArgs(), names(args[1]) is )
cat(names(args[1]))
cat( and args[[1]] is )
cat(args[[1]])
cat(\n)
cat(\nExiting extractArgs()\n\n)
}
Test:
getArgs(id = 's1002')
Entering getArgs()
In getArgs(), names(args[1]) is id and args[[1]] is s1002
Entering extractArgs()
In extractArgs(), names(args[1]) is and args[[1]] is id = 's1002'
Exiting extractArgs()
Exiting getArgs()
extractArgs(id = 's1002')
Entering extractArgs()
In extractArgs(), names(args[1]) is id and args[[1]] is s1002
Exiting extractArgs()
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Re: [R] How to use a for loop to generate two sequences
A vector of character strings: nm - paste(test, 1:1000, sep = ) A list whose components are the objects: test1, test2, ... lapply(nm, get) or if you do it this way the list will have 'test1', 'test2', ... as the component names: L - sapply(paste(test, 1:1000, sep = ), get, simplify = FALSE) and then names(L) gives the vector of names. Also note that apropos(^test[0-9]+) will give a vector of object names corresponding to objects in the current workspace whose names are test followed by a number. On 6/29/06, Xiaohua Dai [EMAIL PROTECTED] wrote: Hi R users, Hope the question is not too simple: How to use a for loop to generate two lists as below: testlist - list(test1, test2, ..., test1000) stringlist - list(test1,test2,...,test1000) Thanks Xiaohua __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Reporting ppr fits and using them externally.
A couple days of detective work have gone along way to reveal how one
may
recover the actual knots and coefficients of the splines used in ppr.
It's not finished yet, but I may be due some mid-course correction.
First, ... I was asked, ... why?
On Jun 27, 2006, at 11:50 PM, Prof Brian Ripley wrote:
It is normal to report smooth curves via plots of smooth curves.
There are examples for ppr in MASS4 p.241 (referenced on the help
page). This is done by the plot() method.
Please do consult the references in the documentation: those who
very carefully documented these tools put them there because they
do give additional information.
This reading and plotting of course was all done before contacting r-
help.
The plots of the smooth curves will be used to communicate with most
readers of our
publication. However, reviewers for J. Geophysical Research and
Atmospheric Environment
will require specifics of the fit performed. We hope that the
results will be used
to greatly improve our understanding of smog ozone formation, and for
field use,
the pure spline fit is required, unencumbered by the ~2000 fitted
points of our estimation
data set.
So, we have found that (my colleague Bob E's words)
Both smooth.spline and ppr, with spline or gcvspline option,
eventually come to a call to qsbart.f. Therefore, find out
which parameters ppr is using in the qsbart call, and
determine which parameters to smooth.spline cause the
same arguments to qsbart.
From ppr, qsbart is called from at
the end of the chain (some wrappers left out):
ppr - smart1 - {subfit, fulfit} - onetrm - oneone - supsmu -
spline - qsbart
Nearly all the code in the fortran routines deals with the
supersmoother case.
smooth.spline (stats/R/smspline.R) calls subroutine spline directly.
I have found that qsbart is in this file /library/stats/src/
sbart.c
and that the inputs and outputs seem to be clearly documented at the
beginning
of the code:
/* A Cubic B-spline Smoothing routine.
The algorithm minimises:
(1/n) * sum ws(i)^2 * (ys(i)-sz(i))^2 + lambda* int
( s(x) )^2 dx
lambda is a function of the spar which is assumed to be between
0 and 1
INPUT
-
penalt A penalty 1 to be used in the gcv criterion
dofoff either `df.offset' for GCV or `df' (to be matched).
nnumber of data points
ys(n)vector of length n containing the observations
ws(n)vector containing the weights given to each data point
xs(n)vector containing the ordinates of the observations
ssw `centered weighted sum of y^2'
nk number of b-spline coefficients to be estimated
nk = n+2
knot(nk+4) vector of knot points defining the cubic b-spline
basis.
To obtain full cubic smoothing splines one might
have (provided the xs-values are strictly increasing)
spar penalised likelihood smoothing parameter
isparindicating if spar is supplied (ispar=1) or to be
estimated
lspar, uspar lower and upper values for spar search; 0.,1. are
good values
tol, eps used in Golden Search routine
isetup setup indicator [initially 0
icritindicator saying which cross validation score is to
be computed
0: none ; 1: GCV ; 2: CV ; 3: 'df matching'
ld4 the leading dimension of abd (ie ld4=4)
ldnk the leading dimension of p2ip (not referenced)
OUTPUT
--
coef(nk) vector of spline coefficients
sz(n)vector of smoothed z-values
lev(n) vector of leverages
crit either ordinary or generalized CV score
spar if ispar != 1
lspar == lambda (a function of spar and the design)
iter number of iterations needed for spar search (if
ispar != 1)
ier error indicator
ier = 0 ___ everything fine
ier = 1 ___ spar too small or too big
problem in cholesky decomposition
These are returned to the calling FORTRAN code (we should note the
need to
respect FORTRAN-C array and call conventions).
So it remains for us to find either the results of the last call to
qsbart.f
made from subroutine spline (n, x, y, w, smo, edf) in the ppr.f
code spline
subroutine spline (n, x, y, w, smo, edf)
c
c--
c
c input:
cn : number of observations.
cx(n) : ordered abscissa values.
cy(n) : corresponding ordinate (response) values.
cw(n) : weight for each (x,y) observation.
c output:
c smo(n) : smoothed ordinate (response) values.
c edf : equivalent degrees of freedom
c
c--
Note that coefficients are not passed back up from here.
The predict method in subroutine pppred(np,x,smod,y,sc)
Re: [R] NLME Fitting
I'm not certain what you want, but it sounds like the answer might be in '?nlme' help page. Toward the end, it describes the 'Value' returned as follows: an object of class 'nlme' representing the nonlinear mixed-effects model fit. Generic functions such as 'print', 'plot' and 'summary' have methods to show the results of the fit. See 'nlmeObject' for the components of the fit. The functions 'resid', 'coef', 'fitted', 'fixed.effects', and 'random.effects' can be used to extract some of its components. Also, 'str' might help you find what you want. Spencer Graves p.s. If you'd like further help from this listserve, PLEASE do read the posting guide! www.R-project.org/posting-guide.html. This might help you write a question so it is easier for others to understand, thereby increasing the chances for a quick and useful reply. F Monadjemi wrote: Dear Reader, Is it possible to extract the random part of nlme fitting analysis (non linear mixed effect model) i.e.sigma(b), in R? Thank you for respond Farinaz __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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 to use a for loop to generate two sequences
I followed your method but there was an error on FUN get: nm - paste(test, 1:1000, sep = ) lapply(nm, get) Error in get(x, envir, mode, inherits) : variable test1 was not found L - sapply(paste(test, 1:1000, sep = ), get, simplify = FALSE) Error in get(x, envir, mode, inherits) : variable test1 was not found But lapply(nm, as.name) worked well. Are there any problem with my R env? traceback() 2: FUN(X[[1]], ...) 1: lapply(nm, get) sessionInfo() Version 2.3.1 (2006-06-01) i386-pc-mingw32 attached base packages: [1] methods stats graphics grDevices utils datasets [7] base win.version() [1] Windows XP Professional (build 2600) Service Pack 2.0 Thanks Xiaohua On 6/30/06, Gabor Grothendieck [EMAIL PROTECTED] wrote: A vector of character strings: nm - paste(test, 1:1000, sep = ) A list whose components are the objects: test1, test2, ... lapply(nm, get) or if you do it this way the list will have 'test1', 'test2', ... as the component names: L - sapply(paste(test, 1:1000, sep = ), get, simplify = FALSE) and then names(L) gives the vector of names. Also note that apropos(^test[0-9]+) will give a vector of object names corresponding to objects in the current workspace whose names are test followed by a number. On 6/29/06, Xiaohua Dai [EMAIL PROTECTED] wrote: Hi R users, Hope the question is not too simple: How to use a for loop to generate two lists as below: testlist - list(test1, test2, ..., test1000) stringlist - list(test1,test2,...,test1000) Thanks Xiaohua __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Extracting R plots from MS Word
Thanks to all those who responded to my request about extracting R plots from MS Word. I decided to try Gabor Grothendieck's second suggestion and saved the Word document as html. (I may yet try some of the other suggestions.) Saving the .doc as .htm indeed produced a folder with many of the images in .gif form. However some of my images seemed to be described by files with .wmz or .emz extensions. I am not quite sure how to change these into .gif or .eps or anything useful! Cheers, Murray Jorgensen Click the graphic, press ctrl-C to copy it to the clipboard and then using ctrl-V paste it into mspaint or Xnview (free, find it via google) or other graphics program and then save it from there. Which program will work will depend on the format of the image. Another possibility is to save the Word file in HTML format. In Word, choose File | SaveAs and choose the Save As Type to be Web Page. That will create an HTML file plus it will create a folder with one file per image. On 6/29/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi, I am revising a paper that I am a co-author of. The figures are plots generated from R but at the moment I do not have the R code that generates them. As this is time critical I would like to slightly abuse the list by asking whether anyone knows how to extract from MS Word into a stand-alone graphics file a plot that was pasted into Word from R (probably as a Windows Metafile, but possibly as a bitmap). I would be very grateful for help with this. Regards, Murray Jorgensen __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Extracting R plots from MS Word
I think these are zipped emf and wmf files. Google for emz extension. On 6/29/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Thanks to all those who responded to my request about extracting R plots from MS Word. I decided to try Gabor Grothendieck's second suggestion and saved the Word document as html. (I may yet try some of the other suggestions.) Saving the .doc as .htm indeed produced a folder with many of the images in .gif form. However some of my images seemed to be described by files with .wmz or .emz extensions. I am not quite sure how to change these into .gif or .eps or anything useful! Cheers, Murray Jorgensen Click the graphic, press ctrl-C to copy it to the clipboard and then using ctrl-V paste it into mspaint or Xnview (free, find it via google) or other graphics program and then save it from there. Which program will work will depend on the format of the image. Another possibility is to save the Word file in HTML format. In Word, choose File | SaveAs and choose the Save As Type to be Web Page. That will create an HTML file plus it will create a folder with one file per image. On 6/29/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi, I am revising a paper that I am a co-author of. The figures are plots generated from R but at the moment I do not have the R code that generates them. As this is time critical I would like to slightly abuse the list by asking whether anyone knows how to extract from MS Word into a stand-alone graphics file a plot that was pasted into Word from R (probably as a Windows Metafile, but possibly as a bitmap). I would be very grateful for help with this. Regards, Murray Jorgensen __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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 to use a for loop to generate two sequences
On 6/29/06, Xiaohua Dai [EMAIL PROTECTED] wrote: I followed your method but there was an error on FUN get: nm - paste(test, 1:1000, sep = ) lapply(nm, get) Error in get(x, envir, mode, inherits) : variable test1 was not found L - sapply(paste(test, 1:1000, sep = ), get, simplify = FALSE) Error in get(x, envir, mode, inherits) : variable test1 was not found But lapply(nm, as.name) worked well. Are there any problem with my R env? These are different things. Using as.name gives you a list of names but I am assuming you are looking for a list of the objects themselves so you need to have those objects defined. Here is a reproducible example: test1 - test2 - 1 sapply(paste(test, 1:2, sep = ), get, simplify = FALSE) $test1 [1] 1 $test2 [1] 1 traceback() 2: FUN(X[[1]], ...) 1: lapply(nm, get) sessionInfo() Version 2.3.1 (2006-06-01) i386-pc-mingw32 attached base packages: [1] methods stats graphics grDevices utils datasets [7] base win.version() [1] Windows XP Professional (build 2600) Service Pack 2.0 Thanks Xiaohua On 6/30/06, Gabor Grothendieck [EMAIL PROTECTED] wrote: A vector of character strings: nm - paste(test, 1:1000, sep = ) A list whose components are the objects: test1, test2, ... lapply(nm, get) or if you do it this way the list will have 'test1', 'test2', ... as the component names: L - sapply(paste(test, 1:1000, sep = ), get, simplify = FALSE) and then names(L) gives the vector of names. Also note that apropos(^test[0-9]+) will give a vector of object names corresponding to objects in the current workspace whose names are test followed by a number. On 6/29/06, Xiaohua Dai [EMAIL PROTECTED] wrote: Hi R users, Hope the question is not too simple: How to use a for loop to generate two lists as below: testlist - list(test1, test2, ..., test1000) stringlist - list(test1,test2,...,test1000) Thanks Xiaohua __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Trellis.par.set/ family/ global change font?
Background: OS: Linux Ubuntu Dapper 6.06 release: R 2.3.1 editor: GNU Emacs 21.4.1 front-end: ESS 5.2.3 - Colleagues I have a rather complicated trellis plot that a journal editor has requested I edit and change all the fonts to times. I'd like to change all fonts globally for the plot, as in par(family=serif) for non-trellis plots. Various experiments with trellis.par.set after reading the help page have not solved the problem for me. Even doing the local change trellis.par.set(par.xlab.text=list(cex=1.5, family=serif)) does not change the font to times for xlab (I mean my syntax is wrong, not that there is a bug). So I'm obviously misreading the help page or just missing the meaning. Any suggestions? Thanks Sam Sam McClatchie, Oceanography subprogram South Australian Aquatic Sciences Centre PO Box 120, Henley Beach 5022 Adelaide, South Australia email [EMAIL PROTECTED] Cellular: 0431 304 497 Telephone: (61-8) 8207 5448 FAX: (61-8) 8207 5481 Research home page http://www.members.iinet.net.au/~s.mcclatchie/ /\ ...xX(° °)Xx / \\ (((° (((° ...xX(°O°)Xx [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] lme convergence
Does anyone know how to obtain the 'returnObject' from an 'lme' run that fails to converge? An argument of this name is described on the 'lmeControl' help page as, a logical value indicating whether the fitted object should be returned when the maximum number of iterations is reached without convergence of the algorithm. Default is 'FALSE'. Unfortunately, I've so far been unable to get it to work, as witnessed by the following modification of an example from the '?lme' help page: library(nlme) fm1 - lme(distance ~ age, data = Orthodont, +control=lmeControl(msMaxIter=1)) Error in lme.formula(distance ~ age, data = Orthodont, control = lmeControl(msMaxIter = 1)) : iteration limit reached without convergence (9) fm1 Error: object fm1 not found fm1 - lme(distance ~ age, data = Orthodont, +control=lmeControl(msMaxIter=1, + returnObject=TRUE)) Error in lme.formula(distance ~ age, data = Orthodont, control = lmeControl(msMaxIter = 1, : iteration limit reached without convergence (9) fm1 Error: object fm1 not found I might be able to fix the problem myself, working through the 'lme' code line by line, e.g., using 'debug'. However, I'm not ready to do that just now. Best Wishes, Spencer Graves Ravi Varadhan wrote: Use try to capture error messages without breaking the loop. ?try -- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: [EMAIL PROTECTED] Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html -- -Original Message- From: [EMAIL PROTECTED] [mailto:r-help- [EMAIL PROTECTED] On Behalf Of Pryseley Assam Sent: Wednesday, June 28, 2006 12:18 PM To: R-Users Subject: [R] lme convergence Dear R-Users, Is it possible to get the covariance matrix from an lme model that did not converge ? I am doing a simulation which entails fitting linear mixed models, using a for loop. Within each loop, i generate a new data set and analyze it using a mixed model. The loop stops When the lme function does not converge for a simulated dataset. I want to inquire if there is a method to suppress the error message from the lme function, or better still, a way of going about this issue of the loop ending once the lme function does not converge. Thanks in advance, Pryseley - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] aggregate data.frame by one column
Hi, everyone, I have a data.frame named eva like this: IND PARTNO VC1 EO1 EO2 EO3 EO4 EO5 114 114001 2 5 4 4 5 4 114 114001 2 4 4 4 4 4 114 114001 2 4 NA NA NA NA 112 112002 2 3 3 6 2 6 112 112002 2 1 1 3 4 4 112 112003 2 6 6 6 5 6 112 112003 2 5 7 6 6 6 112 112003 2 6 6 6 4 5 114 114004 2 2 3 3 2 4 114 114004 2 5 3 4 4 2 114 114004 2 NA NA NA NA NA 113 113005 2 5 5 6 6 5 113 113005 2 7 7 4 7 6 111 111006 2 5 7 7 7 7 112 112007 2 7 7 7 2 2 112 112007 2 6 6 6 1 2 112 112007 2 7 6 6 2 2 111 111008 2 4 1 3 1 4 111 111008 2 3 1 5 3 2 This is only a small part of the whole data. PARTNO is a digit variable and I want to use it as a group variable to aggreate other variables. What I want to get looks like this: IND PARTNO NUM VC1 EO1 EO2 EO3 EO4 EO5 114 114001 3 2 4.3 4 4 4.5 4 112 112002 2 2 2 2 4.5 3 5 112 112003 3 2 5.7 6.3 6 5 5.7 114 114004 3 2 3.5 3 3.5 3 3 113 113005 2 2 6 6 5 6.5 5.5 111 111006 1 2 5 7 7 7 7 112 112007 3 2 6.7 6.3 6.3 1.7 2 111 111008 2 2 3.5 1 4 2 3 NUM is a newly added variable which indicates the case number of each group grouped by PARTNO. I have two questions on this manipulation. The first is how to get the newly added variable NUM. I have no idea on this question. The second is how to average other variables by group. If there are NA, I want the average operation is done on other cases. For example, the variable EO1 has values of 2, 5, and NA on case 114004. What I have done is aggregate(eva[,-2], by=eva[,-2], mean) But it seems because there are NAs, the aggregate cannot process. Because the NA values are not a small part, I cannot use imputation methods. I'm not sure whether my operation is right. Does anyone have any suggestion on the two problems? Thanks in advance! __ R-help@stat.math.ethz.ch 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] Trellis.par.set/ family/ global change font?
On 6/29/06, McClatchie, Sam (PIRSA-SARDI) [EMAIL PROTECTED] wrote: Background: OS: Linux Ubuntu Dapper 6.06 release: R 2.3.1 editor: GNU Emacs 21.4.1 front-end: ESS 5.2.3 - Colleagues I have a rather complicated trellis plot that a journal editor has requested I edit and change all the fonts to times. I'd like to change all fonts globally for the plot, as in par(family=serif) for non-trellis plots. Various experiments with trellis.par.set after reading the help page have not solved the problem for me. Even doing the local change trellis.par.set(par.xlab.text=list(cex=1.5, family=serif)) does not change the font to times for xlab (I mean my syntax is wrong, not that there is a bug). So I'm obviously misreading the help page or just missing the meaning. Any suggestions? Lattice uses 'fontfamily' rather than 'family' (borrowed from grid, I suppose). I don't think there's a way to set the family globally. You might try trellis.par.set(grid.pars = list(fontfamily = serif)) but I'm not sure if that will work. -Deepayan __ R-help@stat.math.ethz.ch 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] aggregate data.frame by one column
Hi Wei-Wei, try this: eva.agg - aggregate(x = list( VC1=eva$VC1, EO1=eva$EO1, EO2=eva$EO2, EO3=eva$EO3, EO4=eva$EO4, EO5=eva$EO5 ), by = list(PARTNO=eva$PARTNO), FUN = mean, na.rm = TRUE) eva.agg$NUM - aggregate(eva$PARTNO, list(eva$PARTNO), length) Cheers Andrew On Fri, Jun 30, 2006 at 10:54:47AM +0800, Guo Wei-Wei wrote: Hi, everyone, I have a data.frame named eva like this: IND PARTNO VC1 EO1 EO2 EO3 EO4 EO5 114 114001 2 5 4 4 5 4 114 114001 2 4 4 4 4 4 114 114001 2 4 NA NA NA NA 112 112002 2 3 3 6 2 6 112 112002 2 1 1 3 4 4 112 112003 2 6 6 6 5 6 112 112003 2 5 7 6 6 6 112 112003 2 6 6 6 4 5 114 114004 2 2 3 3 2 4 114 114004 2 5 3 4 4 2 114 114004 2 NA NA NA NA NA 113 113005 2 5 5 6 6 5 113 113005 2 7 7 4 7 6 111 111006 2 5 7 7 7 7 112 112007 2 7 7 7 2 2 112 112007 2 6 6 6 1 2 112 112007 2 7 6 6 2 2 111 111008 2 4 1 3 1 4 111 111008 2 3 1 5 3 2 This is only a small part of the whole data. PARTNO is a digit variable and I want to use it as a group variable to aggreate other variables. What I want to get looks like this: IND PARTNO NUM VC1 EO1 EO2 EO3 EO4 EO5 114 114001 3 2 4.3 4 4 4.5 4 112 112002 2 2 2 2 4.5 3 5 112 112003 3 2 5.7 6.3 6 5 5.7 114 114004 3 2 3.5 3 3.5 3 3 113 113005 2 2 6 6 5 6.5 5.5 111 111006 1 2 5 7 7 7 7 112 112007 3 2 6.7 6.3 6.3 1.7 2 111 111008 2 2 3.5 1 4 2 3 NUM is a newly added variable which indicates the case number of each group grouped by PARTNO. I have two questions on this manipulation. The first is how to get the newly added variable NUM. I have no idea on this question. The second is how to average other variables by group. If there are NA, I want the average operation is done on other cases. For example, the variable EO1 has values of 2, 5, and NA on case 114004. What I have done is aggregate(eva[,-2], by=eva[,-2], mean) But it seems because there are NAs, the aggregate cannot process. Because the NA values are not a small part, I cannot use imputation methods. I'm not sure whether my operation is right. Does anyone have any suggestion on the two problems? Thanks in advance! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Andrew Robinson Department of Mathematics and StatisticsTel: +61-3-8344-9763 University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599 Email: [EMAIL PROTECTED] http://www.ms.unimelb.edu.au __ R-help@stat.math.ethz.ch 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] aggregate data.frame by one column
Hi Andrew, Thank you very much! It works so well than I can expect. All the best, Wei-Wei 2006/6/30, Andrew Robinson [EMAIL PROTECTED]: Hi Wei-Wei, try this: eva.agg - aggregate(x = list( VC1=eva$VC1, EO1=eva$EO1, EO2=eva$EO2, EO3=eva$EO3, EO4=eva$EO4, EO5=eva$EO5 ), by = list(PARTNO=eva$PARTNO), FUN = mean, na.rm = TRUE) eva.agg$NUM - aggregate(eva$PARTNO, list(eva$PARTNO), length) Cheers Andrew __ R-help@stat.math.ethz.ch 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] Empirical CDF
Good day everyone, I want to assess the error when fitting a Gram-Charlier CDF to some data 'ws', that is, I want to calculate: Err = |ecdf(ws) - GCh_ser(ws)| The problem is, I cannot get the F(x) values from the ecdf. 'Summary(ecdf())' returns some of the x-axis values, but how do you get the F(x) values? Thank you for any help you can provide. Regards, Augusto Augusto Sanabria. MSc, PhD. Mathematical Modeller Risk Research Group Geospatial Earth Monitoring Division Geoscience Australia (www.ga.gov.au) Cnr. Jerrabomberra Av. Hindmarsh Dr. Symonston ACT 2609 Ph. (02) 6249-9155 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
