Re: [R] atan2(1,1i)
On Wed, 29 Mar 2006, Robin Hankin wrote: > Hi guys > > perhaps my original message wasn't so clear. > > My point was that the documentation is inconsistent with the > function. I think it is _your reading_ of the documentation that is inconsistent. An equally plausible reading is that both x and y must be numeric or complex. > How to remedy this? > > (i) add a line to Trig.Rd along the lines of "atan2() will not work > if the first argument > is real and the second argument complex" > > or > (ii) Modify atan2() so that it coerces the first argument to a > complex if necessary. > > > I'd prefer option (ii) but can't see a quick fix. Really? It's a one-line change. BTW, this *really* is an R-devel topic, so please try to use the appropriate list. Suggestions for changes to R get lost in the torrent of R-help extremely easily. And only the designers can say 'but atan2 wasn't originally designed for complex arguments.' but the code suggests otherwise. > > > rksh > > > > > On 28 Mar 2006, at 19:52, Jeff Newmiller wrote: > >> Robin Hankin wrote: >>> Hi >>> >>> ?atan2 says that atan2(y,x)=atan(y/x) for x and y numeric or complex >>> vectors. >>> >>> Well, I would expect atan2(1,1i) to be equal to atan(-1i), but >>> atan2(1,1i) >>> Error in atan2(y, x) : Non-numeric argument to mathematical function >> >> Ravi Varadhan pointed out that you need to make both arguments complex >> to address the error message you obtained... but atan2 wasn't >> originally >> designed for complex arguments. I suspect that what you really want is >> to use the Arg function: >> >>> Arg(1/1i) >> [1] -1.570796 >> >> -- > > > -- > Robin Hankin > Uncertainty Analyst > National Oceanography Centre, Southampton > European Way, Southampton SO14 3ZH, UK > tel 023-8059-7743 > > __ > 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
Re: [R] Spectra for continious time
You cannot observe a time series in continuous time. So either you have regularly spaced observations (and see ?spectrum), or irregular ones (and there may be something in one of the packages for irregular time series, but there is no support in R itself). On Tue, 28 Mar 2006, Martin Albers wrote: > Is there any way to apply a spectra or periodogramm to my time series. > > My first problem is, that I do not know how to get a > spectra/periodogramm for my data. > > I have found time series tools but nothing for spectral analysis. > > My second problem: The time series function I have found, wanted a > discrete timeline, but my timeline is continious. -- 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] psychometrics in R
The hitcounters show a lot of interest. I have now updated http://www.cuddyvalley.org/psychoR/ by putting index files in every (well, almost every) subdirectory. This makes browsing the subdirectories much easier, and it also protects some stuff that nobody needs to see anyway. In addition, the probit package had a major update and is now almost usable. === Jan de Leeuw; Distinguished Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8125 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] .mac: jdeleeuw ++ aim: deleeuwjan ++ skype: j_deleeuw homepages: http://gifi.stat.ucla.edu ++ http://www.cuddyvalley.org - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.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] Skewed t distribution
On 3/28/06, Prof Brian Ripley <[EMAIL PROTECTED]> wrote: > > You need to learn to supply adequate information. The current > version of sn *does* have such an argument, and I was careful to check. > So it seems that you are using an unstated obselete version of sn. > Do ugrade as the posting guide asked you to. Ok, point taken, I just forgot about it and had no way to do it before computations started (I have to work on two machines, and the one with R on it has no access to the internet). My apologies for wasting Your & everyone else's time. rg, konrad -- > "We are what we pretend to be, so we must be careful about what we pretend > to be" > > Kurt Vonnegut Jr. "Mother Night" [[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 plot
On Fri, 24 Mar 2006, Dieter Menne wrote:
> Leonardo D Bacigalupe sheffield.ac.uk> writes:
>
>> I'm trying to plot e.g. fitted vs residuals for each level of the
>> random effects, and i'm getting the same error.
>> I guess this might be a problem of the graphic capabilities of R.
>>
>> Is there any way to obtain those plots?
>>
>> library(nlme)
>> attach(ergoStool)
>> names(ergoStool)
>> [1] "effort" "Type""Subject"
>> m1<-lme(effort~Type,random=~1|Subject)
>> plot(m1,form=resid(.,type="p")~fitted(.)|Subject,abline=0)#resid and
>> fitted for each level of subject
>> Error in as.vector(x, "list") : cannot coerce to vector
>>
>
> I don't believe your idea is wrong, and I don't understand why this does not
> work, but a similar line on page 176 of Pinheiro/Bates does (there, the call
> to
> getData returns non-null). The lines I don't understand in plot.lme are
>
>alist <- lapply(as.list(allV), as.name)
>names(alist) <- allV
> # next line
>alist <- c(as.list(as.name("data.frame")), alist)
>mode(alist) <- "call"
>data <- eval(alist, sys.parent(1))
>
> This code turn up again and again in nlme, but I admit I don't understand what
> it means.
>
> Anybody taking the challenge to dissect it?
It's a bug.
The first two lines sets up a list, in this case, list(Subject=Subject).
The idea is then to call data.frame(Subject=Subject) in the parent
environment, but whenever you see things like
data <- eval(alist, sys.parent(1))
you might want to suspect code copied from S-PLUS. And indeed,
as.list(as.name("data.frame"))
works in S-PLUS but not in R (although just list(as.name("data.frame"))
works in both).
I think the best fix is to make as.list work on symbols, but replacing
as.list by list in plot.lme appears to fix this (that is, it works and the
output appears plausible).
--
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] cat(), Rgui, and support for carriage return \r...
Prof Brian Ripley wrote:
> On Tue, 28 Mar 2006, Duncan Murdoch wrote:
>
>
>>On 3/28/2006 11:00 AM, Prof Brian Ripley wrote:
>>
>>>Rgui now supports \r in the same way as rterm.
>>
>>I notice that there's a slight change to the colour scheme: now the prompt
>>">" is in foreground colour, rather than user colour. This might make sense
>>(it's printed by the system, after all), but it looks a little strange at
>>first.
>
>
> Yes, it was intentional. The problem is that you can now do
>
>
>>cat("abcde\rf")
>
>
> and then the next line will be
>
> f> de
Actually, there is an interest to do so with GUIs, like R Commander or
SciViews-R (although R commander uses its own in/out window by default).
The idea is to work with commands constructed by the GUI, and report the
corresponding command to the console, but to flag them with a "special"
prompt, telling it is different from what the user actually entered.
Something like:
> cat("\rGUI") # Tcl-triggered instruction
would give the following prompt:
GUI>
which is nice if there is a way to append a command in user color just
after it, for instance:
> cat("ls()\n") # Also triggered by Tcl code
giving:
GUI> ls()
with GUI> in foreground colour and ls() in user color.
Perhaps is it not possible, or even, not desirable to get this result
for other situations.
Best,
philippe Grosjean
> with the cursor on the 'd'. There is no longer a left-right divide
> between system output and user input, as you can have output to the right
> of user input. The previous behaviour was to mark as system output all
> the columns up to the 'e' here, so when you started entering new input it
> looked very odd indeed, changing colour in mid-word.
>
> I can change to making the prompt be explicitly regarded as user input,
> which would be backwards compatible and less odd in cases like this.
>
>
>>Duncan Murdoch
>>
>>
>>
>>>On Sun, 19 Mar 2006, Duncan Murdoch wrote:
>>>
>>>
On 3/18/2006 2:39 PM, Duncan Murdoch wrote:
>On 3/17/2006 9:44 AM, Jeffrey Racine wrote:
>
>>Hi, and thanks in advance for your time.
>>
>>Background - I am working on a package and wish to have a routine's
>>progress reported. The routine can take some time, and I would like to
>>inform the user about the routine's progress. I have scoured the
>>archives but to no avail, so would like to solicit input from this list.
>>
>>I am successfully using
>>
>>cat("\rBootstrap replication ", i, " of ", boot.num,)
>>flush.console() # To flush stdout on windows systems
>>
>>which works as expected on *NIX systems and using Rterm under windows.
>>However, under Rgui the carriage return \r is ignored, and I certainly
>>don't want to use the newline escape sequence \n. Under Rgui it appears
>>as
>>
>>Bootstrap replication 1 of 399Bootstrap replication 2 of 399Bootstrap...
>>
>>but I want it to function properly if at all possible.
>>
>>My question is simply whether there is a portable way to implement this
>>so that it works regardless of the R platform the user may be working
>>on?
>>
>>Many thanks for any/all suggestions.
>
>I've just been looking at the source code for this. I think it will be
>relatively easy to make \r in Rgui do a destructive CR (i.e. it will
>return to the start of the line, but clear any existing characters).
>I'll play around a bit and then do that for R-devel.
Oops, this was a bad idea. I did commit the change for a while, but
have reverted it now.
It seems that the help system displays help pages by writing CR LF at
the end of each line; the CR is \r, and my change above caused it to
wipe out the line it had just written. The help pages ended up
completely blank.
I may look into supporting \r as a non-destructive CR, but that's
harder, because it means low-level changes to the console display.
Right now it only writes to the end of the text buffer; this would mean
it would sometimes write to a spot before the end. I don't think it
would be impossible to do, but it will take more time than I have right
now.
Duncan Murdoch
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>>>
>>
>
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[R] load file RData which store in zip file
Dear R users,
My situation:
(1) I have limited workspace for my work harddisk (about 10 GiB).
(2) I have a lot of data files in R workspace (*.RData) which most of
them > 200 MiB. For some reason I zip some of them, for instance
"filename.RData (250 MiB)" to "filename.zip (3MiB)". In this work I
have a lot of more space of my harddisk.
Normally, If I want to use "filename.RData" for my experiment, I can
do it with load("filename.RData").
Then I tried to open/load
> load("filename.zip")
Error: bad restore file magic number (file may be corrupted) -- no data loaded
>
My question:
How can I open/load "filename.zip"? Is there any function to open R
workspace which it store in zip file? I hope some one can give me
advices.
Best, Muhammad Subianto
> version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major2
minor2.1
year 2005
month12
day 20
svn rev 36812
language R
>
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[R] missing value replacement for test data in random forest
HI, I have data set of 3 record with 162 features. when I try to fill out the missing values using rfImpute(), I got kicked out becz: tra.imputed <- rfImpute(tra.na[,-163],tra.na[,163],iter=5,ntree=10) Error in matrix(0, n, n) : cannot allocate vector of length 9 I wonder how to set the parameters(nrnn) for computing the PROXIMITY. thanks iris -Original Message- From: Zhu Ailing Sent: Wed 3/29/2006 11:41 AM To: '[EMAIL PROTECTED]' Cc: Subject: missing value replacement for test data in random forest Hi, In R, how to do missing value replacement for test data in randome forest in the way Breiman decribed. thanks in advance iris __ 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 plot
Prof Brian Ripley <[EMAIL PROTECTED]> writes:
> On Fri, 24 Mar 2006, Dieter Menne wrote:
>
> > Leonardo D Bacigalupe sheffield.ac.uk> writes:
> >
> >> I'm trying to plot e.g. fitted vs residuals for each level of the
> >> random effects, and i'm getting the same error.
> >> I guess this might be a problem of the graphic capabilities of R.
> >>
> >> Is there any way to obtain those plots?
> >>
> >> library(nlme)
> >> attach(ergoStool)
> >> names(ergoStool)
> >> [1] "effort" "Type""Subject"
> >> m1<-lme(effort~Type,random=~1|Subject)
> >> plot(m1,form=resid(.,type="p")~fitted(.)|Subject,abline=0)#resid and
> >> fitted for each level of subject
> >> Error in as.vector(x, "list") : cannot coerce to vector
> >>
> >
> > I don't believe your idea is wrong, and I don't understand why this does not
> > work, but a similar line on page 176 of Pinheiro/Bates does (there, the
> > call to
> > getData returns non-null). The lines I don't understand in plot.lme are
> >
> >alist <- lapply(as.list(allV), as.name)
> >names(alist) <- allV
> > # next line
> >alist <- c(as.list(as.name("data.frame")), alist)
> >mode(alist) <- "call"
> >data <- eval(alist, sys.parent(1))
> >
> > This code turn up again and again in nlme, but I admit I don't understand
> > what
> > it means.
> >
> > Anybody taking the challenge to dissect it?
>
> It's a bug.
Drats, I never even realised that the problem was that it didn't
work...
> The first two lines sets up a list, in this case, list(Subject=Subject).
> The idea is then to call data.frame(Subject=Subject) in the parent
> environment, but whenever you see things like
>
> data <- eval(alist, sys.parent(1))
>
> you might want to suspect code copied from S-PLUS. And indeed,
>
> as.list(as.name("data.frame"))
>
> works in S-PLUS but not in R (although just list(as.name("data.frame"))
> works in both).
Actually, even this works in R:
x <- c("bar","baz")
l <- lapply(x,as.name)
names(l) <- x
as.call(c(quote(data.frame), l))
and in Splus 6.2.1 too, substituting Quote() for quote(). (And Quote()
does actually exist in R too as a compatibility alias for quote())
> I think the best fix is to make as.list work on symbols,
Maybe. It does look to me like bad coding, though: if ever the
argument happens not to be a symbol - an unnamed function, say - there
will be differences between what as.list() and list() does and the
latter is more likely to be as intended. It obviously cannot happen
here, but there are applications where you "rip the head off" a
function call and reuse it to build a new one.
> but replacing
> as.list by list in plot.lme appears to fix this (that is, it works and the
> output appears plausible).
--
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] load file RData which store in zip file
Hi. R can do all of this for you. See ?save.image and especially the
'compress' argument.
/Henrik
On 3/29/06, Muhammad Subianto <[EMAIL PROTECTED]> wrote:
> Dear R users,
> My situation:
> (1) I have limited workspace for my work harddisk (about 10 GiB).
> (2) I have a lot of data files in R workspace (*.RData) which most of
> them > 200 MiB. For some reason I zip some of them, for instance
> "filename.RData (250 MiB)" to "filename.zip (3MiB)". In this work I
> have a lot of more space of my harddisk.
>
> Normally, If I want to use "filename.RData" for my experiment, I can
> do it with load("filename.RData").
>
> Then I tried to open/load
>
> > load("filename.zip")
> Error: bad restore file magic number (file may be corrupted) -- no data loaded
> >
>
> My question:
> How can I open/load "filename.zip"? Is there any function to open R
> workspace which it store in zip file? I hope some one can give me
> advices.
>
>
> Best, Muhammad Subianto
>
> > version
> _
> platform i386-pc-mingw32
> arch i386
> os mingw32
> system i386, mingw32
> status
> major2
> minor2.1
> year 2005
> month12
> day 20
> svn rev 36812
> language 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
>
>
--
Henrik Bengtsson
Mobile: +46 708 909208 (+2h UTC)
__
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Re: [R] load file RData which store in zip file
On Wed, Mar 29, 2006 at 11:44:03AM +0200, Muhammad Subianto wrote: > How can I open/load "filename.zip"? Is there any function to open R > workspace which it store in zip file? I think you have two options: 1) use zip.file.extract() to unzip the file before loading 2) save your data with save.image(file="foo.RData", compress = True) 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
Re: [R] load file RData which store in zip file
On Wed, 29 Mar 2006, Muhammad Subianto wrote:
> Dear R users,
> My situation:
> (1) I have limited workspace for my work harddisk (about 10 GiB).
> (2) I have a lot of data files in R workspace (*.RData) which most of
> them > 200 MiB. For some reason I zip some of them, for instance
> "filename.RData (250 MiB)" to "filename.zip (3MiB)". In this work I
> have a lot of more space of my harddisk.
>
> Normally, If I want to use "filename.RData" for my experiment, I can
> do it with load("filename.RData").
Please try to use the compress=TRUE argument to save(). If you save()ed
uncompressed, you have to load uncompressed, unzip first. There are
unzipping functions in R too, see ?zip.file.extract.
>
> Then I tried to open/load
>
> > load("filename.zip")
> Error: bad restore file magic number (file may be corrupted) -- no data loaded
> >
>
> My question:
> How can I open/load "filename.zip"? Is there any function to open R
> workspace which it store in zip file? I hope some one can give me
> advices.
>
>
> Best, Muhammad Subianto
>
> > version
> _
> platform i386-pc-mingw32
> arch i386
> os mingw32
> system i386, mingw32
> status
> major2
> minor2.1
> year 2005
> month12
> day 20
> svn rev 36812
> language 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
>
--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: [EMAIL PROTECTED]
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Re: [R] load file RData which store in zip file
I apologize for my lack of knowledge. Thank you very much for the suggestions. These are exactly what I was looking for. > ?zip.file.extract Help for 'zip.file.extract' is shown in the browser Maybe I must re-run and re-save again to compress my R workspace. > ?save.image Help for 'save.image' is shown in the browser Regards, Muhammad Subianto On 3/29/06, Philipp Pagel <[EMAIL PROTECTED]> wrote: > On Wed, Mar 29, 2006 at 11:44:03AM +0200, Muhammad Subianto wrote: > > How can I open/load "filename.zip"? Is there any function to open R > > workspace which it store in zip file? > > I think you have two options: > > 1) use zip.file.extract() to unzip the file before loading > > 2) save your data with save.image(file="foo.RData", compress = True) > > 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
Re: [R] load file RData which store in zip file
On Wed, 29 Mar 2006, Henrik Bengtsson wrote:
> Hi. R can do all of this for you. See ?save.image and especially the
> 'compress' argument.
It is nice to know that we anticipated your needs. It is actually even
easier. If you do (using the Rtools or other sources, or on a Unix-alike)
gzip filename.RData
mv filename.RData.gz filename.RData
R will read the compressed file directly (you don't need to rename it, but
it helps keep things tidy).
[As an aside, I wonder whether compress=TRUE should not be the default for
binary save/save.image. It adds little time and may save a lot of disc
space.]
> /Henrik
>
> On 3/29/06, Muhammad Subianto <[EMAIL PROTECTED]> wrote:
>> Dear R users,
>> My situation:
>> (1) I have limited workspace for my work harddisk (about 10 GiB).
>> (2) I have a lot of data files in R workspace (*.RData) which most of
>> them > 200 MiB. For some reason I zip some of them, for instance
>> "filename.RData (250 MiB)" to "filename.zip (3MiB)". In this work I
>> have a lot of more space of my harddisk.
>>
>> Normally, If I want to use "filename.RData" for my experiment, I can
>> do it with load("filename.RData").
>>
>> Then I tried to open/load
>>
>>> load("filename.zip")
>> Error: bad restore file magic number (file may be corrupted) -- no data
>> loaded
>>>
>>
>> My question:
>> How can I open/load "filename.zip"? Is there any function to open R
>> workspace which it store in zip file? I hope some one can give me
>> advices.
--
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] In "step" command, how can I use "scope" parameter
Hi,
My code is:
andeti1 <- read.csv(file='andarai1.csv',head=T,sep=";")
andeti1lm <- lm(formula = valor ~ area+salao+quarto3+play+vaga+frente, data =
andeti1)
step(andeti1lm,direction=c("both"),steps=1000,k=2)
How can I specify "scope" parameter in "step" command?
Thanks.
--
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Rio de Janeiro ICQ 174972645
Pirataria não! Seja livre: Linux
http://www.debian.org
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Re: [R] which function to use to do classification
We have to be careful here. Classification (which is the terminology that the original poster used) is NOT the same as clustering, although the two are often confused. If the original poster wants to do clustering and examine the results for the presence of three clusters, that is fine and there are many methods for clustering that could be used. However, classification will require a different set of tools. If the clustering tools already pointed out are not doing what is needed (that is, that Cao actually is interested in clustering and not classification), then perhaps a further explanation of what the problem would help clarify. Sean On 3/29/06 1:46 AM, "Jacques VESLOT" <[EMAIL PROTECTED]> wrote: > try this (suppose mat is your matrix): > > hc <- hclust(dist(mat,"manhattan"), "ward") > plot(hc, hang=-1) > (x <- identify(hc)) # rightclick to stop > cutree(hc, 3) > > km<- kmeans(mat, 3) > km$cluster > km$centers > > pam(daisy(mat, metric = "manhattan"), k=3, diss=T)$clust > > > > Baoqiang Cao a écrit : > >> Thanks! >> I tried kmeans, the results is not very positive. Anyway, thanks Jacques! >> Please let me know if you have any other thoughts! >> >> Best regards, >>Baoqiang Cao >> >> === At 2006-03-29, 00:08:44 you wrote: === >> >> >> >>> if you want to classify rows or columns, read: >>> ?hclust >>> ?kmeans >>> library(cluster) >>> ?pam >>> >>> >>> Baoqiang Cao a écrit : >>> >>> >>> Dear All, I have a data, suppose it is an N*M matrix data. All I want is to classify it into, let see, 3 classes. Which method(s) do you think is(are) appropriate for this purpose? Any reference will be welcome! Thanks! Best, Baoqiang Cao __ 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 >>> . >>> >>> >> >> = = = = = = = = = = = = = = = = = = = = >> >> Baoqiang Cao >> [EMAIL PROTECTED] >> 2006-03-29 >> >> >> >> > > __ > 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] S3 object
stat stat wrote: > hi all, > > Somewhere I got a phrase - the function returns a S3 object of class > "hclust" - can anyone tell me what is "S3 objects"? Simply an object with a "class" attribute. See chapter "Object-oriented programming" in the R Language Definition manual. Uwe Ligges > > thanks in advance > > - > > > [[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] Plotting shapefiles on existing maps
Dear All,
This is probably a very basic question but:
I have plotted a map of the Barents Sea and surrounding coastline using:
map('worldHires',ylim=c(50,85),xlim=c(5,65),fill=T,resolution=0)
map.axes()
map.scale(x=30,metric=T)
Next, I imported a shapefile with depth contours for the sea:
contours<-read.shape("D://My Documents/BarentsSea.shp",dbf.data=T)
(This is in mercator projection).
Despite extensive searches of the help files and R site, I cannot find a
way to plot the contours onto the map. Does anyone have any suggestions?
Thankyou for you help,
Lillian.
--
Lillian Sandeman
PhD Student
School of Biological Sciences
University of Aberdeen
AB24 2TZ
Tel.: 01224 272648
E-mail: [EMAIL PROTECTED]
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Re: [R] which function to use to do classification
On Wed, 29 Mar 2006, Sean Davis wrote:
We have to be careful here. Classification (which is the terminology that
the original poster used) is NOT the same as clustering, although the two
are often confused.
Well, in one of its two English senses it is the same. From a recent talk
of mine (GfKL30), quoting the Concise Oxford Dictionary:
\emph{Classification} has two senses:
\begin{itemize}
\item `to arrange in classes or categories'
\item `assign (a thing) to a class or category'
\end{itemize}
There is a community (q.v. the International Federation of Classification
Societies and Journal of Classification as well as the entry in the
original Encyclopedia of Statistical Sciences) that meams (almost)
entirely the first sense.
To add to this, the similar words to classification in e.g. French or
German have (I am told) different shades of meaning.
If the original poster wants to do clustering and
examine the results for the presence of three clusters, that is fine and
there are many methods for clustering that could be used. However,
classification will require a different set of tools. If the clustering
tools already pointed out are not doing what is needed (that is, that Cao
actually is interested in clustering and not classification), then perhaps a
further explanation of what the problem would help clarify.
Yes, further explanation would help.
Sean
On 3/29/06 1:46 AM, "Jacques VESLOT" <[EMAIL PROTECTED]> wrote:
try this (suppose mat is your matrix):
hc <- hclust(dist(mat,"manhattan"), "ward")
plot(hc, hang=-1)
(x <- identify(hc)) # rightclick to stop
cutree(hc, 3)
km<- kmeans(mat, 3)
km$cluster
km$centers
pam(daisy(mat, metric = "manhattan"), k=3, diss=T)$clust
Baoqiang Cao a écrit :
Thanks!
I tried kmeans, the results is not very positive. Anyway, thanks Jacques!
Please let me know if you have any other thoughts!
Best regards,
Baoqiang Cao
=== At 2006-03-29, 00:08:44 you wrote: ===
if you want to classify rows or columns, read:
?hclust
?kmeans
library(cluster)
?pam
Baoqiang Cao a écrit :
Dear All,
I have a data, suppose it is an N*M matrix data. All I want is to classify
it into, let see, 3 classes. Which method(s) do you think is(are)
appropriate for this purpose? Any reference will be welcome! Thanks!
Best,
Baoqiang Cao
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.
= = = = = = = = = = = = = = = = = = = =
Baoqiang Cao
[EMAIL PROTECTED]
2006-03-29
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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)
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[R] Monmonier algorithm
Hello list, does anyone know if Monmonier algorithm is available in R? I've checked several spatial libraries, but I didn't find anything related to it. However, there is a huge documentation and I may have missed it. Before coding it, I'd like to be sure it doesn't already exist. Cheers, Thibaut Jombart. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [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] cat(), Rgui, and support for carriage return \r...
On 3/29/2006 2:49 AM, Prof Brian Ripley wrote:
> On Tue, 28 Mar 2006, Duncan Murdoch wrote:
>
>> On 3/28/2006 11:00 AM, Prof Brian Ripley wrote:
>>> Rgui now supports \r in the same way as rterm.
>> I notice that there's a slight change to the colour scheme: now the prompt
>> ">" is in foreground colour, rather than user colour. This might make sense
>> (it's printed by the system, after all), but it looks a little strange at
>> first.
>
> Yes, it was intentional. The problem is that you can now do
>
>> cat("abcde\rf")
>
> and then the next line will be
>
> f> de
>
> with the cursor on the 'd'. There is no longer a left-right divide
> between system output and user input, as you can have output to the right
> of user input. The previous behaviour was to mark as system output all
> the columns up to the 'e' here, so when you started entering new input it
> looked very odd indeed, changing colour in mid-word.
>
> I can change to making the prompt be explicitly regarded as user input,
> which would be backwards compatible and less odd in cases like this.
I'd lean towards backwards compatibility here, but don't have a strong
preference. It's less than perfect that the de is shown as user input,
but fixing that would require a pretty large change to the console code.
Duncan Murdoch
>
>> Duncan Murdoch
>>
>>
>>> On Sun, 19 Mar 2006, Duncan Murdoch wrote:
>>>
On 3/18/2006 2:39 PM, Duncan Murdoch wrote:
> On 3/17/2006 9:44 AM, Jeffrey Racine wrote:
>> Hi, and thanks in advance for your time.
>>
>> Background - I am working on a package and wish to have a routine's
>> progress reported. The routine can take some time, and I would like to
>> inform the user about the routine's progress. I have scoured the
>> archives but to no avail, so would like to solicit input from this list.
>>
>> I am successfully using
>>
>> cat("\rBootstrap replication ", i, " of ", boot.num,)
>> flush.console() # To flush stdout on windows systems
>>
>> which works as expected on *NIX systems and using Rterm under windows.
>> However, under Rgui the carriage return \r is ignored, and I certainly
>> don't want to use the newline escape sequence \n. Under Rgui it appears
>> as
>>
>> Bootstrap replication 1 of 399Bootstrap replication 2 of 399Bootstrap...
>>
>> but I want it to function properly if at all possible.
>>
>> My question is simply whether there is a portable way to implement this
>> so that it works regardless of the R platform the user may be working
>> on?
>>
>> Many thanks for any/all suggestions.
> I've just been looking at the source code for this. I think it will be
> relatively easy to make \r in Rgui do a destructive CR (i.e. it will
> return to the start of the line, but clear any existing characters).
> I'll play around a bit and then do that for R-devel.
Oops, this was a bad idea. I did commit the change for a while, but
have reverted it now.
It seems that the help system displays help pages by writing CR LF at
the end of each line; the CR is \r, and my change above caused it to
wipe out the line it had just written. The help pages ended up
completely blank.
I may look into supporting \r as a non-destructive CR, but that's
harder, because it means low-level changes to the console display.
Right now it only writes to the end of the text buffer; this would mean
it would sometimes write to a spot before the end. I don't think it
would be impossible to do, but it will take more time than I have right
now.
Duncan Murdoch
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>>
>
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[R] warnings
dear list, i have a problem using the adaboost function from the package boost. running the example of leukemia works out very well, but so it does not on my own data. i always get the following 22 warnings: 1: cannot compute exact p-value with ties in: wilcox.test.default(x[which(y == 0)], x[which(y == 1)]) can anybody please help me with the meaning of this warning. thnak you stefan [[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] warnings
Try this: options(warn = 2) Now rerun it and it will fail with an error at the point of the warning and you can issue a: traceback() to find the exact point at which it failed so you can investigate further. On 3/29/06, Sven Schaltenbrand <[EMAIL PROTECTED]> wrote: > dear list, > > i have a problem using the adaboost function from the package boost. > running the example of leukemia works out very well, but so it does not on > my own data. > > i always get the following 22 warnings: > > 1: cannot compute exact p-value with ties in: wilcox.test.default(x[which(y > == 0)], x[which(y == 1)]) > > can anybody please help me with the meaning of this warning. > > thnak you > > stefan > >[[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] warnings
Sven Schaltenbrand wrote: > dear list, > > i have a problem using the adaboost function from the package boost. > running the example of leukemia works out very well, but so it does not on > my own data. > > i always get the following 22 warnings: > > 1: cannot compute exact p-value with ties in: wilcox.test.default(x[which(y > == 0)], x[which(y == 1)]) > > can anybody please help me with the meaning of this warning. As far as I understand, adaboost() uses the Wilcoxon test statistic as some measure to do variable preselection. Since you can adjust how many "features" should be selected, it seems to be less important to obtain *exact* p-values and you can ignore the warning. Nevertheless it makes sense to look into your data where the ties come from ... Uwe Ligges > thnak you > > stefan > > [[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] Monmonier algorithm
On Wed, 29 Mar 2006, Thibaut Jombart wrote: > Hello list, > > does anyone know if Monmonier algorithm is available in R? I've checked > several spatial libraries, but I didn't find anything related to it. > However, there is a huge documentation and I may have missed it. > > Before coding it, I'd like to be sure it doesn't already exist. Googling, I found: http://www-med-physik.vu-wien.ac.at/staff/rub/abstracts/ISCB_2005.pdf which is a poster, and refers to using R for boundary finding, and other software for data management and display. Perhaps the authors are able to help by making code available, the poster looks like a nice example of spatial data analysis. > > Cheers, > > Thibaut Jombart. > > -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [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
[R] ANOVA & BOOTSTRAP
Hello, I'm working on 30 natural populations of Aster amellus L. a threatened plant species. My aim is to see if the population size influence on several fitness trait. I build a multi-factorial ANOVA. The independents variables are altitude, humidity, soil component, maintenance and population density. Unfortunately my data have some heteroscedasticity even after classical transformation. I'm looking for using resampling method or bootstrap to test my multi-factorial Anova. I look on the different packages but I'm not sure to understand the right procedure. Could somebody help me, in giving me an example for testing multi-factorial ANOVA with resampling or bootsrap procedure. Thank you very much. Romain Mayor Assistant Doctorant Université Genève Conservatoire et Jardin botaniques de la Ville de Genève 1 Ch de l'Impératrice CP 60 1292 Chambésy, Geneva, Switzerland tél office : 004122/4185125 tél reception : 004122/4185100 email : [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] [R-pkgs] hybridHclust (new package)
> "Hugh" == Hugh Chipman <[EMAIL PROTECTED]>
> on Tue, 28 Mar 2006 12:17:44 -0400 writes:
Hugh> I'd like to announce the availability of a new library for hybrid
Hugh> hierarchical clustering, "hybridHclust". The library has been
uploaded
Hugh> to CRAN and is now available.
Hugh> The library implements a hybrid of top-down and bottom-up hierarchical
Hugh> clustering.
(3 times... .gh... ) and why do you think the mailing list is called
R- *packages* ???
Please do
for(i in 1:20)
cat("It's a package!\n")
Martin
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[R] bug in pictex() (package:grDevices)
running
pictex()
plot(1:11,(-5:5)^2, type='b', main="Simple_Example_Plot")
dev.off()
(as in the pictex example, but with underscores instead of spaces).
the TeX file contains
\put {Simple_Example_Plot} [lB] <0.00pt,0.00pt> at 124.00 275.33
the underscores have a special meaning in TeX, so they should be quoted
or converted to dashes.
--
Sam Steingold (http://www.podval.org/~sds) on Fedora Core release 4 (Stentz)
http://www.iris.org.il http://www.openvotingconsortium.org
http://pmw.org.il http://www.palestinefacts.org http://www.memri.org
Just because you're paranoid doesn't mean they AREN'T after you.
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Re: [R] non parametric MANOVA
Jose: You might want to check out the multiresponse permutation procedure (MRPP) family of statistics as they can perform permutation tests of common distributions among groups of multivariate response data or perform tests of equality of multivariate means among groups (i.e., a permutation version of MANOVA). Note the former hypothesis test is more general than a test of multivariate means as it detects multiple forms of difference in distributions (shifts in medians, dispersion, both). I don't know whether any of this has been programmed in R. You can obtain a simple user friendly implementation in the USGS Blossom software (www.fort.usgs.gov/products/software/blossom/blossom.asp) or obtain the raw Fortran programs from Paul Mielke's web site at Colorado State University Statistics Department. Brian Brian S. Cade U. S. Geological Survey Fort Collins Science Center 2150 Centre Ave., Bldg. C Fort Collins, CO 80526-8818 email: [EMAIL PROTECTED] tel: 970 226-9326 "Jose David Gomez" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 03/28/2006 07:20 AM To R-help@stat.math.ethz.ch cc Subject [R] non parametric MANOVA Dear colleagues, has anyone an idea how to carry out a nonparametric manova for comparing K groups? has anyone a good package of non-parametric stats? Thank you for your help. -- José David Gómez Químico Farmacéutico Universidad Nacional [[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 [[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] load file RData which store in zip file
Prof Brian Ripley <[EMAIL PROTECTED]> writes: > [As an aside, I wonder whether compress=TRUE should not be the default for > binary save/save.image. It adds little time and may save a lot of disc > space.] Here's one user who thinks that is a great idea. I often have to remind developers who contribute packages to Bioconductor to use the compress=TRUE option to save(). I think it is a sensible default. + seth __ 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] QIC from gee() or geese()
Hello, Is it possible to derive Pan's QIC (2001 Biometrics 57:120) from either a fitted gee() object in the gee package or from a geese() fit in the geepack package? If so, would anyone be kind enough to provide me with code to do so? I realize that QIC is part of the output from yags() but I would like to use one of the other functions. Thanks. Richard __ 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] which function to use to do classification
>On Wed, 29 Mar 2006, Sean Davis wrote:
>
>> We have to be careful here. Classification (which is the terminology that
>> the original poster used) is NOT the same as clustering, although the two
>> are often confused.
>
>Well, in one of its two English senses it is the same. From a recent talk
>of mine (GfKL30), quoting the Concise Oxford Dictionary:
>
>\emph{Classification} has two senses:
>
>\begin{itemize}
>\item `to arrange in classes or categories'
>\item `assign (a thing) to a class or category'
>\end{itemize}
>
>There is a community (q.v. the International Federation of Classification
>Societies and Journal of Classification as well as the entry in the
>original Encyclopedia of Statistical Sciences) that meams (almost)
>entirely the first sense.
>
>To add to this, the similar words to classification in e.g. French or
>German have (I am told) different shades of meaning.
>
>
>> If the original poster wants to do clustering and
>> examine the results for the presence of three clusters, that is fine and
>> there are many methods for clustering that could be used. However,
>> classification will require a different set of tools. If the clustering
>> tools already pointed out are not doing what is needed (that is, that Cao
>> actually is interested in clustering and not classification), then perhaps a
>> further explanation of what the problem would help clarify.
>
>Yes, further explanation would help.
My intension is to arrange all the samples in classes. As a non-native English
speaker, I should have checked the word before I actually use it to express
myself. The quoting makes perfect sense to me. Appreciate!
Thank you Jacques and Martin, your comments and suggestion are well received!
Best,
Baoqiang Cao
>
>> Sean
>>
>>
>> On 3/29/06 1:46 AM, "Jacques VESLOT" <[EMAIL PROTECTED]> wrote:
>>
>>> try this (suppose mat is your matrix):
>>>
>>> hc <- hclust(dist(mat,"manhattan"), "ward")
>>> plot(hc, hang=-1)
>>> (x <- identify(hc)) # rightclick to stop
>>> cutree(hc, 3)
>>>
>>> km<- kmeans(mat, 3)
>>> km$cluster
>>> km$centers
>>>
>>> pam(daisy(mat, metric = "manhattan"), k=3, diss=T)$clust
>>>
>>>
>>>
>>> Baoqiang Cao a �crit :
>>>
Thanks!
I tried kmeans, the results is not very positive. Anyway, thanks Jacques!
Please let me know if you have any other thoughts!
Best regards,
Baoqiang Cao
=== At 2006-03-29, 00:08:44 you wrote: ===
> if you want to classify rows or columns, read:
> ?hclust
> ?kmeans
> library(cluster)
> ?pam
>
>
> Baoqiang Cao a �crit :
>
>
>
>> Dear All,
>>
>> I have a data, suppose it is an N*M matrix data. All I want is to
>> classify
>> it into, let see, 3 classes. Which method(s) do you think is(are)
>> appropriate for this purpose? Any reference will be welcome! Thanks!
>>
>> Best,
>> Baoqiang Cao
>>
>>
>>
>>
>>
>> __
>> 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
>>
>>
>>
> .
>
>
= = = = = = = = = = = = = = = = = = = =
Baoqiang Cao
[EMAIL PROTECTED]
2006-03-29
>>>
>>> __
>>> 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
>>
>
>--
>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
= = = = = = = = = = = = = = = = = = = =
Baoqiang Cao
[EMAIL PROTECTED]
2006-03-29
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R crashes during 'eigen'
> It looks like there might be a bug in the symmetry detection routine of
> eigen. When I do
>
> eigen(M, symmetric=FALSE)
>
> it works fine.
- but the matrix is symmetric, which seems to be correctly detected
(since eigen() hangs whether symmetric=TRUE is supplied or not).
> Eigenvalues (after omitting their imaginary parts, which
> are essentially zeros) are the same as the ones obtained with EISPACK to
> within a small multiple of machine epsilon.
>
> However, the eigenvector matrices seem different ! This happens on
> R-2.2.1-patched and R-2.3.0 (both compiled from daily snapshots).
- This is OK isn't it? All the non-zero eigenvalues are the same for this
matrix, so the eigenvectors can't be uniquely defined, can they?
best,
Simon
>- Simon Wood, Mathematical Sciences, University of Bath, Bath BA2 7AY
>- +44 (0)1225 386603 www.maths.bath.ac.uk/~sw283/
>
> Andy
>
> PS. My system is Windows 2000 on a Xeon CPU. I use precompiled Pentium 4
> Rblas DLL from CRAN, but the same thing happens with standard Rblas.
>
> __
> Andy Jaworski
> 518-1-01
> Process Laboratory
> 3M Corporate Research Laboratory
> -
> E-mail: [EMAIL PROTECTED]
> Tel: (651) 733-6092
> Fax: (651) 736-3122
>
>
>
> "C.J.Albers"
> <[EMAIL PROTECTED]
> ac.uk> To
> Sent by:
> [EMAIL PROTECTED] cc
> at.math.ethz.ch
>Subject
>[R] R crashes during 'eigen'
> 03/28/2006 10:01
> AM
>
>
>
>
>
>
>
>
> Hi all,
>
> Hi,
>
> When I want to compute the eigenvalues & eigenvectors of a specific
> matrix, R crashes (i.e. it stops responding to any input). I've tried it
> with different versions of R (2.1.1, 2.2.0, 2.2.1) - all with crashing
> as result.
>
> What I did before the crash was:
>
> M <- as.matrix(read.table("thematrix",header=T))
> eigen(M)
>
> If, instead of eigen(M), I use eigen(M, EISPACK=T), R doesn't crash. So,
> I know a workaround my problem, but still don't understand why R
> crashes. Could anyone explain this?
> In case someone wants to download my matrix to see where it goes wrong,
> it can be downloaded from http://mcs.open.ac.uk/cja235/thematrix
> (warning: obviously, R might crash so save your unsaved work first).
>
> thanks,
> Casper Albers
>
>
> [[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
>
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] aggregate function....
Dear R users, I have some trouble with the aggregate function. Here are my data > daf S_id AF_Class count... R_gc_percent S_length 5 82644971 30 0.4835678 6 826449737 0.4835678 8 82645541 31 0.5138894 9 82645542 11 0.5138894 10 826455431 0.5138894 for a given S_id, I would like to select the line corresponding to the max count. To perform this, I used: > aggregate(daf,list(daf$S_id),max) Group.1S_id AF_Class count... R_gc_percent S_length 1 8264497 82644973 30 0.4835678 2 8264554 82645543 31 0.5138894 which is ok for the count. But I realized that max function is also applied to AF_class (should be 1 and 1 instead of 3 and 3), so it seems that aggregate is not the appropriate function for that I want to do. Is there any other function I could use instead? Best whishes, Stéphane. -- == Stephane CRUVEILLER Ph. D. Genoscope - Centre National de Sequencage Atelier de Genomique Comparative 2, Rue Gaston Cremieux CP 5706 91057 Evry Cedex - France Phone: +33 (0)1 60 87 84 58 Fax: +33 (0)1 60 87 25 14 EMails: [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
[R] Help with the zero.weights option of plotMA3by2 function in Limma package
Dear all, trying to get some insights in a data set resulting from a microarray experiment, I used the Limma package and its graphical function plotMA and plotMA3by2. I am wondering if there might be a problem with the zero.weights option. Here are the command lines I have tried, and their results > plotMA(RGflag2[,1], zero.weights=TRUE) I got a graphical display, with all data plotted for the first array of my data set named RGflag2. RGflag2 includes weights (2 possible values: 0 and 1). > plotMA(RGflag2[,1], zero.weights=FALSE) When I use this one, I get a plot but some data are missing ( not displayed), which is correct, given the option zero.weights=FALSE However, when I tried to use plotMA3by2 > plotMA3by2(RGflag2, prefix="zero weights included", zero.weights=TRUE) > plotMA3by2(RGflag2, prefix="zero weights excluded", zero.weights=FALSE) the images I obtain are identical and correspond to plots without data having a 0 as weight value, whatever the setting (TRUE or FALSE). In other words, individually the zero.weights option gives the expected results, but when dealing with a batch of plots with the plotMA3by2 it is like it stays by default on the zero.weights=FALSE. Could anyone know if I am doing something wrong or misunderstanding the function zero.weights in the plotMA3by2 ? Thank you, Florian PS: thanks to the creator of R and the packages, by the way. __ 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] SNP array analysis
Hi Does anyone who uses R know if there are any new R packages available - I imagine under Bioconductor - that process SNP microarray data and determine copy number and Loss of heterozygosity? Thanks Natalie Twine -- __ 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 crashes during 'eigen'
> "Simon" == Simon Wood <[EMAIL PROTECTED]>
> on Wed, 29 Mar 2006 16:14:14 +0100 (BST) writes:
>> It looks like there might be a bug in the symmetry detection routine of
>> eigen. When I do
>>
>> eigen(M, symmetric=FALSE)
>>
>> it works fine.
Simon> - but the matrix is symmetric, which seems to be correctly detected
Simon> (since eigen() hangs whether symmetric=TRUE is supplied or not).
>> Eigenvalues (after omitting their imaginary parts, which
>> are essentially zeros) are the same as the ones obtained with EISPACK to
>> within a small multiple of machine epsilon.
>>
>> However, the eigenvector matrices seem different ! This happens on
>> R-2.2.1-patched and R-2.3.0 (both compiled from daily snapshots).
Simon> - This is OK isn't it? All the non-zero eigenvalues are the same for
this
Simon> matrix, so the eigenvectors can't be uniquely defined, can they?
Indeed, you are right, Simon.
But anyway the fact is that the LAPACK based eigen seems to end
in an infinite loop, and I can confirm the behavior for at least
R 2.2.1, R-patched and R-devel (aka "2.3.0 alpha") with the "R
builtin" versions of BLAS and LAPACK and also with Atlas.
Seems quite a bad story to me at the moment.
I assume that octave (or matlab) which are also based on BLAS +
LAPACK internally can eigen-decompose the matrix correctly?
Could anyone check this (without much effort) for us?
Thanks in advance,
Martin Maechler, ETH Zurich
Simon> best,
Simon> Simon
>> - Simon Wood, Mathematical Sciences, University of Bath, Bath BA2 7AY
>> - +44 (0)1225 386603 www.maths.bath.ac.uk/~sw283/
>>
>> Andy
>>
>> PS. My system is Windows 2000 on a Xeon CPU. I use precompiled Pentium
4
>> Rblas DLL from CRAN, but the same thing happens with standard Rblas.
>>
>> __
>> Andy Jaworski
>> 518-1-01
>> Process Laboratory
>> 3M Corporate Research Laboratory
>> -
>> E-mail: [EMAIL PROTECTED]
>> Tel: (651) 733-6092
>> Fax: (651) 736-3122
>>
>>
>>
>> "C.J.Albers"
>> <[EMAIL PROTECTED]
ac.uk> To
>> Sent by:
>> [EMAIL PROTECTED] cc
>> at.math.ethz.ch
>> Subject
>> [R] R crashes during 'eigen'
>> 03/28/2006 10:01
>> AM
>>
>>
>>
>>
>>
>>
>>
>>
>> Hi all,
>>
>> Hi,
>>
>> When I want to compute the eigenvalues & eigenvectors of a specific
>> matrix, R crashes (i.e. it stops responding to any input). I've tried it
>> with different versions of R (2.1.1, 2.2.0, 2.2.1) - all with crashing
>> as result.
>>
>> What I did before the crash was:
>>
>> M <- as.matrix(read.table("thematrix",header=T))
>> eigen(M)
>>
>> If, instead of eigen(M), I use eigen(M, EISPACK=T), R doesn't crash. So,
>> I know a workaround my problem, but still don't understand why R
>> crashes. Could anyone explain this?
>> In case someone wants to download my matrix to see where it goes wrong,
>> it can be downloaded from http://mcs.open.ac.uk/cja235/thematrix
>> (warning: obviously, R might crash so save your unsaved work first).
>>
>> thanks,
>> Casper Albers
>>
>>
>> [[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
>>
Simon> __
Simon> R-help@stat.math.ethz.ch mailing list
Simon> https://stat.ethz.ch/mailman/listinfo/r-help
Simon> 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] aggregate function....
try 'by':
> x
S_id AF_Class count... R_gc_percent S_length
5 82644971 30 0.4835678
6 826449737 0.4835678
8 82645541 31 0.5138894
9 82645542 11 0.5138894
10 826455431 0.5138894
> do.call('rbind', by(x, x$S_id, function(y) y[which.max(y$AF_Class),]))
S_id AF_Class count... R_gc_percent S_length
8264497 826449737 0.4835678
8264554 826455431 0.5138894
>
On 3/29/06, Stephane CRUVEILLER <[EMAIL PROTECTED]> wrote:
>
> Dear R users,
>
> I have some trouble with the aggregate function. Here are my data
>
> > daf
> S_id AF_Class count... R_gc_percent S_length
> 5 82644971 30 0.4835678
> 6 826449737 0.4835678
> 8 82645541 31 0.5138894
> 9 82645542 11 0.5138894
> 10 826455431 0.5138894
>
> for a given S_id, I would like to select the line corresponding to the
> max count. To perform this, I used:
> > aggregate(daf,list(daf$S_id),max)
> Group.1S_id AF_Class count... R_gc_percent S_length
> 1 8264497 82644973 30 0.4835678
> 2 8264554 82645543 31 0.5138894
>
> which is ok for the count. But I realized that max function is also
> applied
> to AF_class (should be 1 and 1 instead of 3 and 3), so it seems that
> aggregate is not the appropriate function for that I want to do. Is
> there any other function I could use instead?
>
> Best whishes,
>
>
> Stéphane.
> --
> ==
> Stephane CRUVEILLER Ph. D.
> Genoscope - Centre National de Sequencage
> Atelier de Genomique Comparative
> 2, Rue Gaston Cremieux CP 5706
> 91057 Evry Cedex - France
> Phone: +33 (0)1 60 87 84 58
> Fax: +33 (0)1 60 87 25 14
> EMails: [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
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390 (Cell)
+1 513 247 0281 (Home)
What the problem you are trying to solve?
[[alternative HTML version deleted]]
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Re: [R] graphing and scrolling
in regards to the dynamic resizing, one would think that
commands like
plot.default {package:graphics} does it, as I am exploring other
commands from graphics it seams like tkrplot may not be needed,
I am
not sure as I just started with graphics in R, maybe a better
way to
go is call TclTk from R but not sure how, or even save the data
to an
output file and run TclTk independently.
what do you think?
I have done it both ways, you can see examples of using the R graphics
window (which can be resized) with a Tk control box in several of the
functions in the TeachingDemos package (run.cor2.examp for example).
Unfortunatly when working in windows there is a tendancy for the R
window to jump in front of the Tk window which I find annoying, you can
get past this by running R with the SDI switch, but I favor the tkrplot
approach now (The TeachingDemos examples will be changing at some point
to allow either option). This is less of an issue on Unix, I have no
idea about macs.
This is starting to get into details rather than general R discussion so
future discussion may be better as just e-mails rather than involving
the discussion list.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
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Re: [R] R crashes during 'eigen'
Taking that matrix, stripping out the quoted row and column i.d.s and
entering it into MATLAB R14 (7.01) as M, I get from the eig(M) operation:
E = eig(M)
E =
-0.
-0.
-0.
-0.
-0.
-0.
-0.
-0.
-0.
-0.
-0.
-0.
-0.
-0.
-0.
-0.
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
7.4486
>>
I presume this is the expected output (i.e. all non-zero eigenvalues the
same, 7.4486).
Regards,
Mike
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Martin Maechler
Sent: 29 March 2006 17:02
To: Simon Wood
Cc: r-help@stat.math.ethz.ch; [EMAIL PROTECTED]
Subject: Re: [R] R crashes during 'eigen'
> "Simon" == Simon Wood <[EMAIL PROTECTED]>
> on Wed, 29 Mar 2006 16:14:14 +0100 (BST) writes:
>> It looks like there might be a bug in the symmetry detection routine
of
>> eigen. When I do
>>
>> eigen(M, symmetric=FALSE)
>>
>> it works fine.
Simon> - but the matrix is symmetric, which seems to be correctly
detected
Simon> (since eigen() hangs whether symmetric=TRUE is supplied or not).
>> Eigenvalues (after omitting their imaginary parts, which
>> are essentially zeros) are the same as the ones obtained with EISPACK
to
>> within a small multiple of machine epsilon.
>>
>> However, the eigenvector matrices seem different ! This happens on
>> R-2.2.1-patched and R-2.3.0 (both compiled from daily snapshots).
Simon> - This is OK isn't it? All the non-zero eigenvalues are the same
for this
Simon> matrix, so the eigenvectors can't be uniquely defined, can they?
Indeed, you are right, Simon.
But anyway the fact is that the LAPACK based eigen seems to end in an
infinite loop, and I can confirm the behavior for at least R 2.2.1,
R-patched and R-devel (aka "2.3.0 alpha") with the "R builtin" versions of
BLAS and LAPACK and also with Atlas.
Seems quite a bad story to me at the moment.
I assume that octave (or matlab) which are also based on BLAS + LAPACK
internally can eigen-decompose the matrix correctly?
Could anyone check this (without much effort) for us?
Thanks in advance,
Martin Maechler, ETH Zurich
Simon> best,
Simon> Simon
>> - Simon Wood, Mathematical Sciences, University of Bath, Bath BA2 7AY
>> - +44 (0)1225 386603 www.maths.bath.ac.uk/~sw283/
>>
>> Andy
>>
>> PS. My system is Windows 2000 on a Xeon CPU. I use precompiled
Pentium 4
>> Rblas DLL from CRAN, but the same thing happens with standard Rblas.
>>
>> __
>> Andy Jaworski
>> 518-1-01
>> Process Laboratory
>> 3M Corporate Research Laboratory
>> -
>> E-mail: [EMAIL PROTECTED]
>> Tel: (651) 733-6092
>> Fax: (651) 736-3122
>>
>>
>>
>> "C.J.Albers"
>> <[EMAIL PROTECTED]
ac.uk> To
>> Sent by:
>> [EMAIL PROTECTED] cc
>> at.math.ethz.ch
>> Subject
>> [R] R crashes during 'eigen'
>> 03/28/2006 10:01
>> AM
>>
>>
>>
>>
>>
>>
>>
>>
>> Hi all,
>>
>> Hi,
>>
>> When I want to compute the eigenvalues & eigenvectors of a specific
>> matrix, R crashes (i.e. it stops responding to any input). I've tried
it
>> with different versions of R (2.1.1, 2.2.0, 2.2.1) - all with
crashing
>> as result.
>>
>> What I did before the crash was:
>>
>> M <- as.matrix(read.table("thematrix",header=T))
>> eigen(M)
>>
>> If, instead of eigen(M), I use eigen(M, EISPACK=T), R doesn't crash.
So,
>> I know a workaround my problem, but still don't understand why R
>> crashes. Could anyone explain this?
>> In case someone wants to download my matrix to see where it goes
wrong,
>> it can be downloaded from http://mcs.open.ac.uk/cja235/thematrix
>> (warning: obviously, R might crash so save your unsaved work first).
>>
>> thanks,
>> Casper Albers
>>
>>
>> [[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-gu
Re: [R] atan2(1,1i)
Prof Brian Ripley wrote: > [...] > And only the designers can say > > 'but atan2 wasn't originally designed for complex arguments.' > > but the code suggests otherwise. I was not referring to the _coding_ of the function... I was referring to the _design_. The design of the "atan2" function preceeds the existence of the "R" software package by decades, and it was created to get around the limitations of the "atan" function for extracting the angular component of a polar coordinate from rectangular coordinates. Applications of this function with complex arguments remain obscure, while its use in obtaining the argument of a complex number is not. Regardless of obscurity, given that the "R" version does support complex numbers, I agree with Robin that it should accept any combination of numeric and complex parameters, and I concur with you that this suggestion belongs on the developers list. >> On 28 Mar 2006, at 19:52, Jeff Newmiller wrote: >> >>> Robin Hankin wrote: >>> Hi ?atan2 says that atan2(y,x)=atan(y/x) for x and y numeric or complex vectors. Well, I would expect atan2(1,1i) to be equal to atan(-1i), but > atan2(1,1i) Error in atan2(y, x) : Non-numeric argument to mathematical function >>> >>> >>> Ravi Varadhan pointed out that you need to make both arguments complex >>> to address the error message you obtained... but atan2 wasn't >>> originally >>> designed for complex arguments. I suspect that what you really want is >>> to use the Arg function: >>> Arg(1/1i) >>> >>> [1] -1.570796 -- --- Jeff NewmillerThe . . Go Live... DCN:<[EMAIL PROTECTED]>Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k __ 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] Sub-vector
Dear list, Given a vector of logical values, say >a <- c(TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE) Are there any R functions that can tell whether there are two or more "TRUE" in a row in this vector? Thanks, Wuming __ 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] Sub-vector
Wuming, which(a) will identify the TRUE values and sum(a) will tell you how many TRUE values there are. David -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Wuming Gong Sent: 29 March 2006 18:21 To: r-help@stat.math.ethz.ch Subject: [R] Sub-vector * Please Note : This message was received from the Internet * _ Dear list, Given a vector of logical values, say >a <- c(TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE) Are there any R functions that can tell whether there are two or more "TRUE" in a row in this vector? Thanks, Wuming __ 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 __ This message might contain confidential information. If it has been sent to you in error please do not forward it or copy it or act upon its contents, but report it to [EMAIL PROTECTED] Schroders has the right lawfully to record, monitor and inspect messages between its employees and any third party. Your messages shall be subject to such lawful supervision as Schroders deems to be necessary in order to protect its information, its interests and its reputation. Schroders prohibits and takes steps to prevent its information systems from being used to view, store or forward offensive or discriminatory material. If this message contains such material please report it to [EMAIL PROTECTED] Schroders does not normally accept or offer business instructions via email unless prior agreements are in place. Any action that you might take upon this message might be at your own risk. Schroder Investment Management Limited 31 Gresham Street London EC2V 7QA Authorised and regulated by the Financial Services Authority. Schroder Investment Management Limited is entered on the FSA register under the following register number: 119348 Registered Office 31 Gresham Street London EC2V 7QA Registered number 1893220 VAT registration number 243 8687 30 __ 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] Sub-vector
Try this: with(rle(a), any(lengths[values]>1)) On 3/29/06, Wuming Gong <[EMAIL PROTECTED]> wrote: > Dear list, > > Given a vector of logical values, say > > >a <- c(TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE) > > Are there any R functions that can tell whether there are two or more > "TRUE" in a row in this vector? > > Thanks, > > Wuming > > __ > 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] Sub-vector
On Thu, 30 Mar 2006, Wuming Gong wrote: > Dear list, > > Given a vector of logical values, say > > >a <- c(TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE) > > Are there any R functions that can tell whether there are two or more > "TRUE" in a row in this vector? ?rle (a very useful function) aa <- rle(a) any(aa$values & aa$lengths > 1) > > Thanks, > > Wuming > > __ > 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 > -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [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
[R] Lmer BLUPS: was(lmer multilevel)
Paul: I may have found the issue (which is similar to your conclusion). I checked using egsingle in the mlmRev package as these individuals are strictly nested in this case: library(mlmRev) library(nlme) fm1 <- lme(math ~ year, random=~1|schoolid/childid, egsingle) fm2 <- lmer(math ~ year +(1|schoolid:childid) + (1|schoolid), egsingle) Checking the summary of both models, the output is exactly the same w.r.t. the fixed effects, variance components, standard errors etc. The prior two lines of code fit the same models. However, the following does not generate similar output: head(coef(fm2)[[1]]) (Intercept) year 2020:273026452 -0.30213394 0.7461233 2020:273030991 0.41469885 0.7461233 2020:273059461 -0.07443003 0.7461233 2020:278058841 0.61676579 0.7461233 2020:292017571 0.29529524 0.7461233 2020:292020281 -1.03811716 0.7461233 > head(coef(fm1, level=2)) (Intercept) year 2020/273026452 0.3248913 0.7461233 2020/273030991 1.0417241 0.7461233 2020/273059461 0.5525952 0.7461233 2020/278058841 1.2437910 0.7461233 2020/292017571 0.9223205 0.7461233 2020/292020281 -0.4110920 0.7461233 Although they are similar for schools: > head(coef(fm1, level=1)) (Intercept) year 2020 -0.1534565 0.7461233 2040 -0.6985680 0.7461233 2180 -1.0621073 0.7461233 2330 -0.6262567 0.7461233 2340 -1.0090541 0.7461233 2380 -0.6095037 0.7461233 > head(coef(fm2)[[2]]) (Intercept) year 2020 -0.1534566 0.7461233 2040 -0.6985681 0.7461233 2180 -1.0621072 0.7461233 2330 -0.6262567 0.7461233 2340 -1.0090541 0.7461233 2380 -0.6095037 0.7461233 I checked a bit further to see if there was any pattern to the differences: tt <- cbind(coef(fm1, level=2)[1], coef(fm2)[[1]][1]) tt$dif <- tt[,1] - tt[,2] There is clearly a systematic pattern to the difference between the two. Now, when you go and look at the random effects head(ranef(fm2)[[2]]) You can see that this is the value that is not being added in to the coefficients in lmer() and this accounts for the difference. So, these need to be added in for now. I hope this helps, Harold My question relates to problems that I'm having matching lme and lmer examples in P&B. using Matix 0.995 In the Oxide example in p167-170 I can't get the level 2 coefficient estimates to match the fm1Oxide model in lme is data(Oxide,package="nlme") lme(Thickness~1,Oxide) which I translate in Lmer syntax to fm3Oxide<-lmer(Thickness~ (1|Lot)+(1|Lot:Wafer),data=Oxide) #or alternatively which gives the same result Oxide$LW<-with(Oxide,Lot:Wafer)[drop=TRUE] fm4Oxide<-lmer(Thickness~ (1|Lot)+(1|LW),data=Oxide) however if you look at say Lot 8, lme gives 81993.767 8/11993.677 8/21995.170 8/31990.693 while lmer gives coef(fm3Oxide) 81993.767 8:1 2000.062 8:2 2001.555 8:3 1997.078 To me this looks like lmer in not including the lot random effect (8= -6.385129, Intercept 2000.153 ). Is this because I'm not specifying the model correctly? Thanks Paul [[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] nlme for groupedData with inner and outer factors
1. Have you read Pinheiro and Bates (2000) Mixed-Effects Models in S and S-Plus (Springer)? If no, I believe your study of that book will be well rewarded; mine has. 2. If you've looked at Pinheiro and Bates and still have questions about this, PLEASE do read the posting guide! "www.R-project.org/posting-guide.html", especially the bit about developing a toy example that is as simple as you can make it that still illustrates your question. I've solved many of my own problems doing this, and I've answered many questions for people on this list dealing with functions I've not previously used. You could help people like me by providing a few lines of R code that we could copy from your email, paste into R and replicate what you see. hope this helps, spencer graves Dan Bebber wrote: > Hello, > > I am having trouble specifying a suitable nlme model. > My data structure is described by > > gd <- groupedData(ppath ~ lcut | exp, outer = ~ bait, inner = ~ weight, data > = d) > > i.e. the response (ppath) of several subjects (sub) was measured at levels > of a continuous variable (lcut). Subjects were given either of one level of > a factor (bait), and all subjects were measured at two levels of another > factor (weight). Therefore bait varies among subjects and weight varies > within subjects. > > The relationship ppath ~ cut for each subject and weight appear to follow a > logistic curve, with xmid and scal affected by bait and weight. There is > also a random effect of subject on xmid and scal. > > Any help with formulating the correct model would be greatly appreciated. > > Many thanks, > Dan Bebber > > Department of Plant Sciences > University of Oxford > > p.s. Part of my data are shown below: > > sublcut ppath bait weight > 1 pv1_ 0.0 1.01 0 > 2 pv1_ 0.1 0.8277738211 0 > 3 pv1_ 0.2 0.3801025021 0 > 4 pv1_ 0.3 0.2091518781 0 > 5 pv1_ 0.4 0.0769293041 0 > 6 pv1_ 0.5 0.0656815641 0 > 7 pv1_ 0.6 0.0206701081 0 > 8 pv1_ 0.7 0.0128170211 0 > 9 pv1_ 0.8 0.0086615141 0 > 10 pv1_ 0.9 0.0115683231 0 > 11 pv19 0.0 1.01 0 > 12 pv19 0.1 0.6683902911 0 > 13 pv19 0.2 0.3433184621 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 __ 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] R for Windows crash on new laptop
I'm trying to use a contributed package (rmetasim) to generate simulated
genetic datasets. My scripts work fine when I run them on a Sun
workstation running Solaris 7 and when I run them on a ~4 year old
laptop PC that I have. However, when I run them on my new laptop (Dell
Latitude D410 purchased in August 2005), the simulation will run for a
short (variable) period of time, then R crashes. When it crashes, I
either get an Application Popup that says
'The instruction at "0x5ad71531" referenced memory at "0x0014". The
memory could not be "read".',
or I simply get the popup saying that RGUI has experienced a problem,
would I like to send a report to Microsoft. When the latter happens, an
event log is generated that says
'Fauling application rgui.exe, version 2.30.37590.0, fauling module
ntdll.dll, version 5.1.2600.2180, fault address 0x0001888f.'
In both types of errors, the memory addresses listed are different every
time a crash occurs.
I experience this problem primarily when attempting to simulate large
datasets. My script saves the 'landscape' (the object being simulated)
every 100 time steps. When R crashes, I can start it back up, reload
the last landscape saved before the crash, and continue simulating from
there. Thus, there appears to be nothing wrong with the landscapes I'm
simulating.
I've been in contact with the author of the contributed package I'm
using, and he has been unable to find any bugs in the package or
reproduce the error. The bug seems to be platform specific since, as I
mentioned, I'm able to run my scripts crash-free on other computers.
However, I've tried running my scripts on another computer that is
nearly identical to mine (a Dell D610 purchased in August 2005), and
experience the same problems on that computer. I've tried running my
scripts from a command window using 'R --vanilla', and experience the
same problems. I've tried using the development version of R
(R-2.3.0alpha) and experience the same problems.
In reading other bug reports I found that some people have had crashes
caused by buggy video drivers. I've updated my video drivers, but it
didn't help. However, I was only able to upgrade to the newest version
of the video driver; I haven't been able to find an alternative driver
to work with my display adapter. The display adapter used by my
computer is the mobile Intel 915GM/GMS,910GML Express Chipset.
I'm running R 2.2.1 (though I've tried R 2.0.1 and 2.3.0alpha and had
the same problem). The machine on which I've had problems is a Dell
Latitude D410 laptop running Windows XP Pro SP2, 2GHz Pentium processor
with 1GB of RAM. The output of the R command 'version' is;
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major2
minor2.1
year 2005
month12
day 20
svn rev 36812
language R
The exact sequence of commands I type, after launching the Rgui, is as
follows:
>library(rmetasim)
>source("ArchI_burnin_NOdensdep-mod.R")
The script I'm running (which obviously requires that the package
'rmetasim' be installed) follows. Beware that the script takes about 15
minutes to run on my old computer (the one on which it doesn't crash.
For what it's worth, that computer is a Dell Latitude C400 running
Windows XP Pro SP2, 866 MHz Pentium III processor, 512 MB of RAM). Any
suggestions would be greatly appreciated.
#ArchI_burnin_NOdensdep-mod.R#
habitats <- 1
carrycap <- 7500
stages <- 5
rland <- NULL
numreps <- 2
numsteps <- 50
stepsize <- 100
runlength <- numsteps*stepsize
rland <- new.landscape.empty()
rland <- new.intparam.land(rland, h = habitats, s = stages, totgen =
runlength)
rland <- new.switchparam.land(rland, mp = 1)
rland <- new.floatparam.land(rland)
#life history matrices at zero population density
SZ <- matrix (c(0.730, 0, 0, 0, 0,
0.210, 0, 0, 0, 0,
0, 0.470, 0, 0.946, 0,
0, 0, 0.946, 0, 0,
0, 0.470, 0, 0, 0.954), nrow=5, byrow = T)
RZ <- matrix (c(0, 0, 0, .94, 0,
0, 0, 0, 0, 0,
0, 0, 0, 0, 0,
0, 0, 0, 0, 0,
0, 0, 0, 0, 0), nrow = 5, byrow = T)
M <- matrix (c(0, 0, 0, 0, 0,
0, 0, 0, 0, 0,
0, 0, 0, 0, 0,
0, 0, 0, 0, 1,
0, 0, 0, 0, 0), nrow = 5, byrow = T)
rland <- new.local.demo(rland,SZ,RZ,M)
rland <-
new.epoch.island(rland,0,c(0,0,0,0,0),c(0,0,0,0,0),0,c(0,0,0,0,0),c(0,0,0,0,0),
0,c(0,0,0,0,0),c(0,0,0,0,0), carry = rep(carrycap,habitats))
rland <- new.locus(rland, type = 1, ploidy = 2, transmission = 0,
numalleles = 1, mutationrate = 0.001)
rland <- new.locus(rland, type = 1, ploidy = 2, transmission = 0,
numalleles = 1, mutationrate = 0.001)
rland <- new.locus(rland, type = 1, ploidy = 2, transm
Re: [R] Optim and likelihood computations
For general maxiimum likelihood estimation, have you considered the function "mle" in library(stats4)? I've learned some things (a) reading the documentation for "mle" and for other topics listed under "See Also" and (b) working the "Examples" in the documentation. Regarding AR structures, there are many capabilities for time series in R scattered in numerous packages. Since you are new to R, have you read Venables and Ripley (2002) Modern Applied Statists with S (Springer)? Ch. 14 deals with time series. I highly recommend this book for R in general, and this chapter provides a reasonable introduction to a few of the time series capabilities in the base R distribution. Beyond that, have you worked through the vignettes associated with the "zoo" package? If no, you might find that quite useful. [Are you aware that edit(vignette(...)) will provide a script file with the R code discussed in the vignette, which can be viewed in Adobe Acrobat while you are working throught the examples line by line, modifying them, etc.? I've found this to be very useful. If you use XEmacs, "edit(vignette(...))" may not work. Instead, try Stangle(vignette(...)$file). This will copy the R code to a file in the working directory, which you can then open.] I've also found the dse bundle and its vignettes very interesting and usefulfor time series. Beyond that, you might try the Rmetrics project (www.rmetrics.org). I expect that other questions will occur to you in the process of reviewing or trying to apply some of the material I just suggested. Please feel free to post other questions to this list -- but please first also review the posting guide! "www.R-project.org/posting-guide.html"; doing so might increase your chances of getting useful answers quicker. hope this helps. spencer graves [EMAIL PROTECTED] wrote: > Hello everyone. > > I want to write some likelihood functions to use with optim. For example > AR-structures, I have written a couple of functions that appear to get the > job done. But, since I am new to R, I wanted to ask if there are any > references in this topic. > > Thanks in advance, > > *** > Antonio Paredes > USDA- Center for Veterinary Biologics > Biometrics Unit > 510 South 17th Street, Suite 104 > Ames, IA 50010 > (515) 232-5785 > > > [[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] Recall for parent
What's the best way to simulate Recall for parent function?
Consider this one-time recursive code:
alwaysEven <- function(x) {
handleOdd <- function(x) {
alwaysEven(x-1)# use Recall-like here
}
return(if (x %% 2) handleOdd(x) else x)
}
any2even <- alwaysEven
rm(alwaysEven)
any2even(3)
--
SIGSIG -- signature too long (core dumped)
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[R] Message to R-help
From: [EMAIL PROTECTED] Reply-to: [EMAIL PROTECTED] Subject: S-PLUS 8 Beta Program Time to go out: As soon as possible Dear R-help readers, As Insightful announced at the DSC2005 meeting in Seattle, the next release of S-PLUS will introduce a new package system. Our goal is to provide package authors the means to create cutting-edge statistical methods currently available either as R packages or as S-PLUS library sections and deliver them to the entire community of S-PLUS and R users. In this release of S-PLUS, we plan to implement many low-level utility functions with the same API as R. Just as many R functions originated in S-PLUS, we plan on re-implementing many R functions in S-PLUS to provide S-PLUS users the ability to create packages of their work and distribute them to others as R users have done for many years. In the future, we expect package authors will be able to create a single package that will run in both environments. The actual package system would be a port of the R package system code, which furthers the exchangeability of S-PLUS and R code. The ported code will be available in a GPL library called Rcompat To demonstrate that R packages can now be ported to S-PLUS, we have - with the permissions of the authors - ported several R packages to run as S-PLUS packages. We are planning to make these packages available for download from an Insightful-hosted website (called csan.insightful.com for consistency with the CRAN site of R packages). The license terms of the source packages will always be respected, and these packages will all be available under their original open-source license. Any improvements to open-source packages, whether by Insightful or by others, will remain open-source. Our intent will be to grow the list of open-source, cross-system-compatible packages over time. While most existing R packages will not run automatically in S-PLUS, with some effort, a user should be able to port an existing R package to an S-PLUS package. More important, by using functions and interfaces now available in both systems, a user should be able to create a single package that will run in both S-PLUS and R in the future. (The judicious use of some system-specific if(is.R()) statement will help to this end.) As a proof of concept, we are developing a package that will run on both systems. In the future, we hope to post this package on both CSAN and CRAN sites. We are also working to provide S-PLUS library sections from our research group as S-PLUS packages that would also work in R. Our work on the S-PLUS package functionality is ongoing. We expect to begin beta testing in April. We invite R package authors who are interested in testing their packages in S-PLUS to participate in the beta test. As a beta participant, you will receive a beta version of S-PLUS that will be fully functional until the end of the beta period. You will also be able to send input to the development team regarding the S-PLUS package system. If you are a package author, and you are interested in participating in the beta test, see the full details on the S-PLUS 8 beta test and complete the registration form at the Insightful website: http://www.insightful.com/support/splus8beta/ Best regards from the S-PLUS product management team, Patrick Aboyoun (S-PLUS Platform) Michael O'Connell (Life Sciences) David Smith (Finance) [[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] Recall for parent
Here are two ways:
# method 1. nest an extra alwaysEven
alwaysEven <- function(x) {
alwaysEven <- function(x) {
handleOdd <- function(x) {
alwaysEven(x-1)# use Recall-like here
}
return(if (x %% 2) handleOdd(x) else x)
}
alwaysEven(x)
}
any2even <- alwaysEven
rm(alwaysEven)
any2even(3)
# method 2. sys.function
alwaysEven <- function(x) {
handleOdd <- function(x) {
sys.function(1)(x-1)# use Recall-like here
}
return(if (x %% 2) handleOdd(x) else x)
}
any2even <- alwaysEven
rm(alwaysEven)
any2even(3)
On 3/29/06, Paul Roebuck <[EMAIL PROTECTED]> wrote:
> What's the best way to simulate Recall for parent function?
> Consider this one-time recursive code:
>
> alwaysEven <- function(x) {
>handleOdd <- function(x) {
>alwaysEven(x-1)# use Recall-like here
>}
>
>return(if (x %% 2) handleOdd(x) else x)
> }
> any2even <- alwaysEven
> rm(alwaysEven)
> any2even(3)
>
> --
> SIGSIG -- signature too long (core dumped)
>
> __
> 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
>
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[R] S-PLUS 8 beta program [repost]
[Sorry about the duplicate posting; this one comes from the correct address. Please respond to me with any questions about this -- David.] Dear R-help readers, As Insightful announced at the DSC2005 meeting in Seattle, the next release of S-PLUS will introduce a new package system. Our goal is to provide package authors the means to create cutting-edge statistical methods currently available either as R packages or as S-PLUS library sections and deliver them to the entire community of S-PLUS and R users. In this release of S-PLUS, we plan to implement many low-level utility functions with the same API as R. Just as many R functions originated in S-PLUS, we plan on re-implementing many R functions in S-PLUS to provide S-PLUS users the ability to create packages of their work and distribute them to others as R users have done for many years. In the future, we expect package authors will be able to create a single package that will run in both environments. The actual package system would be a port of the R package system code, which furthers the exchangeability of S-PLUS and R code. The ported code will be available in a GPL library called Rcompat To demonstrate that R packages can now be ported to S-PLUS, we have - with the permissions of the authors - ported several R packages to run as S-PLUS packages. We are planning to make these packages available for download from an Insightful-hosted website (called csan.insightful.com for consistency with the CRAN site of R packages). The license terms of the source packages will always be respected, and these packages will all be available under their original open-source license. Any improvements to open-source packages, whether by Insightful or by others, will remain open-source. Our intent will be to grow the list of open-source, cross-system-compatible packages over time. While most existing R packages will not run automatically in S-PLUS, with some effort, a user should be able to port an existing R package to an S-PLUS package. More important, by using functions and interfaces now available in both systems, a user should be able to create a single package that will run in both S-PLUS and R in the future. (The judicious use of some system-specific if(is.R()) statement will help to this end.) As a proof of concept, we are developing a package that will run on both systems. In the future, we hope to post this package on both CSAN and CRAN sites. We are also working to provide S-PLUS library sections from our research group as S-PLUS packages that would also work in R. Our work on the S-PLUS package functionality is ongoing. We expect to begin beta testing in April. We invite R package authors who are interested in testing their packages in S-PLUS to participate in the beta test. As a beta participant, you will receive a beta version of S-PLUS that will be fully functional until the end of the beta period. You will also be able to send input to the development team regarding the S-PLUS package system. If you are a package author, and you are interested in participating in the beta test, see the full details on the S-PLUS 8 beta test and complete the registration form at the Insightful website: http://www.insightful.com/support/splus8beta/ Best regards from the S-PLUS product management team, Patrick Aboyoun (S-PLUS Platform) Michael O'Connell (Life Sciences) David Smith (Finance) -- David M Smith <[EMAIL PROTECTED]> Senior Product Manager, Insightful Corp, Seattle WA Tel: +1 (206) 802 2360 Fax: +1 (206) 283 6310 __ 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] Plotting shapefiles on existing maps
> From: [EMAIL PROTECTED]
>
> I have plotted a map of the Barents Sea and surrounding coastline using:
>
> map('worldHires',ylim=c(50,85),xlim=c(5,65),fill=T,resolution=0)
> map.axes()
> map.scale(x=30,metric=T)
>
> Next, I imported a shapefile with depth contours for the sea:
>
> contours<-read.shape("D://My Documents/BarentsSea.shp",dbf.data=T)
>
> (This is in mercator projection).
>
> Despite extensive searches of the help files and R site, I cannot find a
> way to plot the contours onto the map. Does anyone have any suggestions?
>
It is not clear to me exactly what you are having difficulty with, but
if you are able to produce a contour plot from that data, then note that
both contour() and map() have an "add" argument, so as long as the axis
limits are conformant (i.e. both longitude/latitude) you can add one
plot to the other.
Perhaps the trick is in converting your contours data into
longitude/latitude form for the x and y components.
Hope this helps,
Ray Brownrigg
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Re: [R] S-PLUS 8 beta program [repost]
This is an excellent initiative! But how can you integrate GPL code in a software that is not GPL? As far as I understand it, GPL is a contaminant license, imposing to the whole software to be GPL too (or providing at least similar freedom). I have no doubt that you solved this problem. I am just curious about the solution you found. Best regards, Philippe Grosjean ..<°}))>< ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Pentagone (3D08) ( ( ( ( (Academie Universitaire Wallonie-Bruxelles ) ) ) ) ) 8, av du Champ de Mars, 7000 Mons, Belgium ( ( ( ( ( ) ) ) ) ) phone: + 32.65.37.34.97, fax: + 32.65.37.30.54 ( ( ( ( (email: [EMAIL PROTECTED] ) ) ) ) ) ( ( ( ( (web: http://www.umh.ac.be/~econum ) ) ) ) ) http://www.sciviews.org ( ( ( ( ( .. David Smith wrote: > [Sorry about the duplicate posting; this one comes from the correct address. > Please respond to me with any questions about this -- David.] > > Dear R-help readers, > > As Insightful announced at the DSC2005 meeting in Seattle, the next > release of S-PLUS will introduce a new package system. Our goal is to provide > package authors the means to create cutting-edge statistical methods > currently available either as R packages or as S-PLUS library sections and > deliver them to the entire community of S-PLUS and R users. > > In this release of S-PLUS, we plan to implement many low-level > utility functions with the same API as R. Just as many R functions originated > in S-PLUS, we plan on re-implementing many R functions in S-PLUS to provide > S-PLUS users the ability to create packages of their work and distribute them > to others as R users have done for many years. In the future, we expect > package authors will be able to create a single package that will run in both > environments. The actual package system would be a port of the R package > system code, which furthers the exchangeability of S-PLUS and R code. The > ported code will be available in a GPL library called Rcompat > > To demonstrate that R packages can now be ported to S-PLUS, we have - > with the permissions of the authors - ported several R packages to run as > S-PLUS packages. We are planning to make these packages available for > download from an Insightful-hosted website (called csan.insightful.com for > consistency with the CRAN site of R packages). The license terms of the > source packages will always be respected, and these packages will all be > available under their original open-source license. Any improvements to > open-source packages, whether by Insightful or by others, will remain > open-source. Our intent will be to grow the list of open-source, > cross-system-compatible packages over time. > > While most existing R packages will not run automatically in S-PLUS, > with some effort, a user should be able to port an existing R package to an > S-PLUS package. More important, by using functions and interfaces now > available in both systems, a user should be able to create a single package > that will run in both S-PLUS and R in the future. (The judicious use of some > system-specific if(is.R()) statement will help to this end.) As a proof of > concept, we are developing a package that will run on both systems. In the > future, we hope to post this package on both CSAN and CRAN sites. We are also > working to provide S-PLUS library sections from our research group as S-PLUS > packages that would also work in R. > > Our work on the S-PLUS package functionality is ongoing. We expect to > begin beta testing in April. We invite R package authors who are interested > in testing their packages in S-PLUS to participate in the beta test. As a > beta participant, you will receive a beta version of S-PLUS that will be > fully functional until the end of the beta period. You will also be able to > send input to the development team regarding the S-PLUS package system. If > you are a package author, and you are interested in participating in the beta > test, see the full details on the S-PLUS 8 beta test and complete the > registration form at the Insightful website: > > > http://www.insightful.com/support/splus8beta/ > > > Best regards from the S-PLUS product management team, > > Patrick Aboyoun (S-PLUS Platform) > Michael O'Connell (Life Sciences) > David Smith (Finance) > > -- > David M Smith <[EMAIL PROTECTED]> > Senior Product Manager, Insightful Corp, Seattle WA > Tel: +1 (206) 802 2360 > Fax: +1 (206) 283 6310 > > __ > 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, RMysql, and MySQL 5 Decimal Type Support
That is interesting to find out since on RMySQL module site (http://stat.bell-labs.com/RS-DBI/download/) it says the following for the latest version: "RMySQL 0.5-7 built with R 2.2.1 and MySQL 5.0.18" which is now obviously not entirely true, seeing as how that is what I am using. :) It there any type of release schedule for a new RMySQL? Also, I tried coercing the vector into a numeric but get the following: (this is just a simple example) >grdata = dbGetQuery(connection, "select 2 as age, 2.5 as hours"); >attach(grdata); >test = as.numeric(grdata["hours"]); Error in as.double.default(grdata["hours"]) : unimplemented type 'character' in 'asReal' I can run the same command on the age (2) value with no errors. It just does not like the 2.5 at all! -Original Message- From: David James [mailto:[EMAIL PROTECTED] Sent: Tuesday, March 28, 2006 11:08 PM To: Jason Trimble Cc: r-help@stat.math.ethz.ch Subject: Re: [R] R, RMysql, and MySQL 5 Decimal Type Support Hi, MySQL data type 246 is the new (as of version 5.0?) fixed precision DECIMAL type, which doesn't map to any existing R type. In most cases, I believe, it is imported as an R character vector, and you can just coerce it to numeric, i.e., to floating point precision. Next version of RMySQL will address this issue, and comments regarding what would be a suitable R type for SQL fixed DECIMALs are welcome. -- David Jason Trimble wrote: > Hi, > > > > Whenever I have a MySQL query that returns a Decimal result to R I get > the following warning in R: > > > > Warning message: > > RS-DBI driver warning: (unrecognized MySQL field type 246 in column 1) > > > > I get this for a simple query like "SELECT 2, 2.5" !! > > > > I am using: > > R ver 2.1.1 > > RMySQL ver. 0.5-7 > > DBI ver. 0.1-10 > > MySQL Ver 14.12 Distrib 5.0.18. > > > > Please Help! > > Jason > > > > [[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] conflicts Var names
Dear R users I have read somewhere which I don't remember that some variable names are not to be used for conflict avoidance. and those were (c, q, T, F, T) I ran this > conflicts(detail=TRUE) $.GlobalEnv [1] "ts" $"package:methods" [1] "body<-" $"package:stats" [1] "ts" $"package:base" [1] "body<-" I don't note ts was in the list of to-avoid "oh I think it was some tips and tricks relating to R". at this point, it is recommended to rename my ts variable in my code? thank you - [[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] S-PLUS 8 beta program [repost]
The GPL code is available as separately-downloaded packages for S-PLUS, as has been done for many years. My own Oswald library for S-PLUS was published under the GPL in 1997, for example, and many other authors produce open-source libraries for S-PLUS under a variety of licenses. The only difference is that they will be packaged as, well, packages rather than libraries. # David Smith -- David M Smith <[EMAIL PROTECTED]> Senior Product Manager, Insightful Corp, Seattle WA Tel: +1 (206) 802 2360 Fax: +1 (206) 283 6310 Insightful Corporation (www.insightful.com) provides analytical solutions for text and data using S-PLUS, Insightful Miner, InFact and consulting services. > -Original Message- > From: Philippe Grosjean [mailto:[EMAIL PROTECTED] > Sent: Wednesday, March 29, 2006 1:06 PM > To: David Smith > Cc: r-help@stat.math.ethz.ch > Subject: Re: [R] S-PLUS 8 beta program [repost] > > > This is an excellent initiative! But how can you integrate > GPL code in a > software that is not GPL? As far as I understand it, GPL is a > contaminant license, imposing to the whole software to be GPL too (or > providing at least similar freedom). I have no doubt that you solved > this problem. I am just curious about the solution you found. > Best regards, > > Philippe Grosjean > > ..<°}))>< > ) ) ) ) ) > ( ( ( ( (Prof. Philippe Grosjean > ) ) ) ) ) > ( ( ( ( (Numerical Ecology of Aquatic Systems > ) ) ) ) ) Mons-Hainaut University, Pentagone (3D08) > ( ( ( ( (Academie Universitaire Wallonie-Bruxelles > ) ) ) ) ) 8, av du Champ de Mars, 7000 Mons, Belgium > ( ( ( ( ( > ) ) ) ) ) phone: + 32.65.37.34.97, fax: + 32.65.37.30.54 > ( ( ( ( (email: [EMAIL PROTECTED] > ) ) ) ) ) > ( ( ( ( (web: http://www.umh.ac.be/~econum > ) ) ) ) ) http://www.sciviews.org > ( ( ( ( ( > .. > > David Smith wrote: > > [Sorry about the duplicate posting; this one comes from the > correct address. > > Please respond to me with any questions about this -- David.] > > > > Dear R-help readers, > > > > As Insightful announced at the DSC2005 meeting in > Seattle, the next > > release of S-PLUS will introduce a new package system. Our > goal is to provide > > package authors the means to create cutting-edge statistical methods > > currently available either as R packages or as S-PLUS > library sections and > > deliver them to the entire community of S-PLUS and R users. > > > > In this release of S-PLUS, we plan to implement many low-level > > utility functions with the same API as R. Just as many R > functions originated > > in S-PLUS, we plan on re-implementing many R functions in > S-PLUS to provide > > S-PLUS users the ability to create packages of their work > and distribute them > > to others as R users have done for many years. In the > future, we expect > > package authors will be able to create a single package > that will run in both > > environments. The actual package system would be a port of > the R package > > system code, which furthers the exchangeability of S-PLUS > and R code. The > > ported code will be available in a GPL library called Rcompat > > > > To demonstrate that R packages can now be ported to > S-PLUS, we have - > > with the permissions of the authors - ported several R > packages to run as > > S-PLUS packages. We are planning to make these packages > available for > > download from an Insightful-hosted website (called > csan.insightful.com for > > consistency with the CRAN site of R packages). The license > terms of the > > source packages will always be respected, and these > packages will all be > > available under their original open-source license. Any > improvements to > > open-source packages, whether by Insightful or by others, > will remain > > open-source. Our intent will be to grow the list of open-source, > > cross-system-compatible packages over time. > > > > While most existing R packages will not run > automatically in S-PLUS, > > with some effort, a user should be able to port an existing > R package to an > > S-PLUS package. More important, by using functions and > interfaces now > > available in both systems, a user should be able to create > a single package > > that will run in both S-PLUS and R in the future. (The > judicious use of some > > system-specific if(is.R()) statement will help to this > end.) As a proof of > > concept, we are developing a package that will run on both > systems. In the > > future, we hope to post this package on both CSAN and CRAN > sites. We are also > > working to provide S-PLUS library sections from our > research group as S-PLUS > > packages that would also work in R. > > > > Our work on the S-PLUS package functionality is > ongoing. We expect to > > begin beta testing in April. We invite R package authors > who are interested >
Re: [R] S-PLUS 8 beta program [repost]
David Smith wrote: > The GPL code is available as separately-downloaded packages for S-PLUS, as > has been done for many years. My own Oswald library for S-PLUS was published > under the GPL in 1997, for example, and many other authors produce > open-source libraries for S-PLUS under a variety of licenses. The only > difference is that they will be packaged as, well, packages rather than > libraries. > > # David Smith Thank you for the explanation. The fact that GPL code is distributed *separately* from S-PLUS is the key point here. PhG __ 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] April Course***R/S-plus Fundamentals and Programming Techinques (San Francisco and New York)
XLSolutions Corporation (www.xlsolutions-corp.com) is proud to announce 2-day "R/S-plus Fundamentals and Programming Techniques" at 2 locations this April www.xlsolutions-corp.com/Rfund.htm San Francisco - April 27th-28th, 2006 New York City - April 24th-25th, 2006 Reserve your seat now at the early bird rates! Payment due AFTER the class Course Description: This two-day beginner to intermediate R/S-plus course focuses on a broad spectrum of topics, from reading raw data to a comparison of R and S. We will learn the essentials of data manipulation, graphical visualization and R/S-plus programming. We will explore statistical data analysis tools,including graphics with data sets. How to enhance your plots, build your own packages (librairies) and connect via ODBC,etc. We will perform some statistical modeling and fit linear regression models. Participants are encouraged to bring data for interactive sessions With the following outline: - An Overview of R and S - Data Manipulation and Graphics - Using Lattice Graphics - A Comparison of R and S-Plus - How can R Complement SAS? - Writing Functions - Avoiding Loops - Vectorization - Statistical Modeling - Project Management - Techniques for Effective use of R and S - Enhancing Plots - Using High-level Plotting Functions - Building and Distributing Packages (libraries) - Connecting; ODBC, Rweb, Orca via sockets and via Rjava Interested in R/Splus Advanced course? email us. Email us for group discounts. Email Sue Turner: [EMAIL PROTECTED] Phone: 206-686-1578 Visit us: www.xlsolutions-corp.com/training.htm Please let us know if you and your colleagues are interested in this classto take advantage of group discount. Register now to secure your seat! Interested in R/Splus Advanced course? email us. Cheers, Elvis Miller, PhD Manager Training. XLSolutions Corporation 206 686 1578 www.xlsolutions-corp.com [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
[R] calcualtign a trailing 12 column mean in a dataframe?
I have a dataframe of 25 columns and 100,000 rows called testdf. I wish to build a new dataframe, with 14 columns and 100,000 rows. I wish the new dataframe to have the trailing 12 column mean. That is, I want column 1 of the new dataframe to have soemthing like: ( mean(testdf[,1:12],na.rm=T) What is the best way to accomplish this? __ 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] S-PLUS 8 beta program [repost]
Correct: I'm not an attorney, but I've read the GPL. It clearly says that if you have software that has functionality independent of GPL code, the GPL applies to the code you use to connect to GPL code not to your original code. Thus, Insightful would have to make publicly available anything special they do to link to GPL code that they can't reasonably claim works for other purposes. However, they are not required to reveal other parts of their source code. hope this helps, spencer graves Philippe Grosjean wrote: > David Smith wrote: > >>The GPL code is available as separately-downloaded packages for S-PLUS, as >>has been done for many years. My own Oswald library for S-PLUS was published >>under the GPL in 1997, for example, and many other authors produce >>open-source libraries for S-PLUS under a variety of licenses. The only >>difference is that they will be packaged as, well, packages rather than >>libraries. >> >># David Smith > > > Thank you for the explanation. The fact that GPL code is distributed > *separately* from S-PLUS is the key point here. > > PhG > > __ > 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] Data assimilation / inverse modeling in R
Hello,
I'm trying to find out if something has been written in R regarding data
assimilation and inverse modeling.
These searches do not return anything that look like Kalman filter
variations (EK, SEEK, ROEK, etc.)
help.search("assimilation")
help.search("inverse model")
Regards,
**
AVIS DE NON-RESPONSABILITE: Ce document transmis par courrie...{{dropped}}
__
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[R] Random effects ANOVA?
Hi all -- So I have a very simple dataset, which consists of 60 subjects, who watched one of three videos, drank one of two drinks, and completed a task. The response variable is the time to complete the task. The ANOVA command is simple enough: anova(aov(time ~ drink * video, data = df)); However, the videos were randomly selected; I need to use the random effects model for them. So I tried anova(aov(time ~ drink + Error(video), data = df)); This gives me a "no applicable method for 'anova'" error. The command aov works, but doesn't give me anything I can interpret effectively. Is there a simpler command I should be using? Am I doing something wrong? -- Chris __ 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] which function to use to do classification
In addition to Brian's comment, Gordon's book, already in 2nd edition, is all about clustering, but the title is simply `Classification'. Andy From: Sean Davis > > We have to be careful here. Classification (which is the > terminology that the original poster used) is NOT the same as > clustering, although the two are often confused. If the > original poster wants to do clustering and examine the > results for the presence of three clusters, that is fine and > there are many methods for clustering that could be used. > However, classification will require a different set of > tools. If the clustering tools already pointed out are not > doing what is needed (that is, that Cao actually is > interested in clustering and not classification), then > perhaps a further explanation of what the problem would help clarify. > > Sean > > > On 3/29/06 1:46 AM, "Jacques VESLOT" <[EMAIL PROTECTED]> wrote: > > > try this (suppose mat is your matrix): > > > > hc <- hclust(dist(mat,"manhattan"), "ward") > > plot(hc, hang=-1) > > (x <- identify(hc)) # rightclick to stop > > cutree(hc, 3) > > > > km<- kmeans(mat, 3) > > km$cluster > > km$centers > > > > pam(daisy(mat, metric = "manhattan"), k=3, diss=T)$clust > > > > > > > > Baoqiang Cao a écrit : > > > >> Thanks! > >> I tried kmeans, the results is not very positive. Anyway, thanks > >> Jacques! Please let me know if you have any other thoughts! > >> > >> Best regards, > >>Baoqiang Cao > >> > >> === At 2006-03-29, 00:08:44 you wrote: === > >> > >> > >> > >>> if you want to classify rows or columns, read: > >>> ?hclust > >>> ?kmeans > >>> library(cluster) > >>> ?pam > >>> > >>> > >>> Baoqiang Cao a écrit : > >>> > >>> > >>> > Dear All, > > I have a data, suppose it is an N*M matrix data. All I > want is to > classify it into, let see, 3 classes. Which method(s) do > you think > is(are) appropriate for this purpose? Any reference will be > welcome! Thanks! > > Best, > Baoqiang Cao > > > > > --- > - > > __ > 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 > > > > >>> . > >>> > >>> > >> > >> = = = = = = = = = = = = = = = = = = = = > >> > >> Baoqiang Cao > >> [EMAIL PROTECTED] > >> 2006-03-29 > >> > >> > >> > >> > > > > __ > > 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
Re: [R] R for Windows crash on new laptop - corrected script
I realized that the script I included in my original post (see below)
was written for an older version of rmetasim and will not work with the
current version. The only change that need be made to get my script to
run with the latest release of rmetasim is to change the command
'simulate.landscape()' to 'sim.landscape()'. My apologies to anyone who
tried to use my script and ran into problems.
Cheers, Karen
>> -Original Message-
>> From: [EMAIL PROTECTED] [mailto:r-help-
>> [EMAIL PROTECTED] On Behalf Of Karen Martien
>> Sent: Wednesday, March 29, 2006 11:07 AM
>> To: r-help@stat.math.ethz.ch
>> Subject: [R] R for Windows crash on new laptop
>>
>> I'm trying to use a contributed package (rmetasim) to generate simulated
>> genetic datasets. My scripts work fine when I run them on a Sun
>> workstation running Solaris 7 and when I run them on a ~4 year old
>> laptop PC that I have. However, when I run them on my new laptop (Dell
>> Latitude D410 purchased in August 2005), the simulation will run for a
>> short (variable) period of time, then R crashes. When it crashes, I
>> either get an Application Popup that says
>>
>> 'The instruction at "0x5ad71531" referenced memory at "0x0014". The
>> memory could not be "read".',
>>
>> or I simply get the popup saying that RGUI has experienced a problem,
>> would I like to send a report to Microsoft. When the latter happens, an
>> event log is generated that says
>>
>> 'Fauling application rgui.exe, version 2.30.37590.0, fauling module
>> ntdll.dll, version 5.1.2600.2180, fault address 0x0001888f.'
>>
>> In both types of errors, the memory addresses listed are different every
>> time a crash occurs.
>>
>> I experience this problem primarily when attempting to simulate large
>> datasets. My script saves the 'landscape' (the object being simulated)
>> every 100 time steps. When R crashes, I can start it back up, reload
>> the last landscape saved before the crash, and continue simulating from
>> there. Thus, there appears to be nothing wrong with the landscapes I'm
>> simulating.
>>
>> I've been in contact with the author of the contributed package I'm
>> using, and he has been unable to find any bugs in the package or
>> reproduce the error. The bug seems to be platform specific since, as I
>> mentioned, I'm able to run my scripts crash-free on other computers.
>> However, I've tried running my scripts on another computer that is
>> nearly identical to mine (a Dell D610 purchased in August 2005), and
>> experience the same problems on that computer. I've tried running my
>> scripts from a command window using 'R --vanilla', and experience the
>> same problems. I've tried using the development version of R
>> (R-2.3.0alpha) and experience the same problems.
>>
>> In reading other bug reports I found that some people have had crashes
>> caused by buggy video drivers. I've updated my video drivers, but it
>> didn't help. However, I was only able to upgrade to the newest version
>> of the video driver; I haven't been able to find an alternative driver
>> to work with my display adapter. The display adapter used by my
>> computer is the mobile Intel 915GM/GMS,910GML Express Chipset.
>>
>> I'm running R 2.2.1 (though I've tried R 2.0.1 and 2.3.0alpha and had
>> the same problem). The machine on which I've had problems is a Dell
>> Latitude D410 laptop running Windows XP Pro SP2, 2GHz Pentium processor
>> with 1GB of RAM. The output of the R command 'version' is;
>>
>> platform i386-pc-mingw32
>> arch i386
>> os mingw32
>> system i386, mingw32
>> status
>> major2
>> minor2.1
>> year 2005
>> month12
>> day 20
>> svn rev 36812
>> language R
>>
>> The exact sequence of commands I type, after launching the Rgui, is as
>> follows:
>>
>> >library(rmetasim)
>> >source("ArchI_burnin_NOdensdep-mod.R")
>>
>> The script I'm running (which obviously requires that the package
>> 'rmetasim' be installed) follows. Beware that the script takes about 15
>> minutes to run on my old computer (the one on which it doesn't crash.
>> For what it's worth, that computer is a Dell Latitude C400 running
>> Windows XP Pro SP2, 866 MHz Pentium III processor, 512 MB of RAM). Any
>> suggestions would be greatly appreciated.
>>
>> ##
>> ##
>> #ArchI_burnin_NOdensdep-mod.R#
>>
>> habitats <- 1
>> carrycap <- 7500
>> stages <- 5
>> rland <- NULL
>> numreps <- 2
>> numsteps <- 50
>> stepsize <- 100
>> runlength <- numsteps*stepsize
>>
>> rland <- new.landscape.empty()
>> rland <- new.intparam.land(rland, h = habitats, s = stages, totgen =
>> runlength)
>> rland <- new.switchparam.land(rland, mp = 1)
>> rland <- new.floatparam.land(rland)
>>
>> #life history matrices at zero population density
>> SZ <- matrix (c(0.730, 0, 0, 0, 0,
>>0.210, 0, 0, 0, 0,
>>0, 0.470, 0, 0.946, 0,
>>0, 0, 0.946, 0, 0,
>>0, 0.470, 0, 0, 0.954)
Re: [R] calcualtign a trailing 12 column mean in a dataframe?
While we wait for others to provide the best way, here's one way (if I understand your question correctly): numrows <- 10 x <- rnorm(25 * numrows) dat <- as.data.frame(matrix(x, nc = 25)) newdat <- as.data.frame(matrix(0, nr = numrows, nc = 14)) for(j in 1:14) newdat[, j] <- rowMeans(dat[, j:(j + 11)], na.rm = TRUE) Peter Ehlers r user wrote: > I have a dataframe of 25 columns and 100,000 rows > called “testdf”. > > I wish to build a new dataframe, with 14 columns and > 100,000 rows. > > I wish the new dataframe to have the “trailing 12 > column” mean. That is, I want column 1 of the new > dataframe to have soemthing like: > > “( mean(testdf[,1:12],na.rm=T)” > > What is the best way to accomplish this? > > __ > 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] missing value replacement for test data in random forest
The current randomForest package stores the entire proximity matrix (3 x 3 in your case), which is needed for imputation. Breiman and Cutler's Fortran code stores the largest nrnn element of each row. If you really want to do it that way, use the Fortran version. Andy From: Zhu Ailing > > HI, > I have data set of 3 record with 162 features. when I > try to fill out the missing values using rfImpute(), I got > kicked out becz: > tra.imputed <- rfImpute(tra.na[,-163],tra.na[,163],iter=5,ntree=10) > Error in matrix(0, n, n) : cannot allocate vector of length 9 > > I wonder how to set the parameters(nrnn) for computing the > PROXIMITY. thanks iris > > -Original Message- > From: Zhu Ailing > Sent: Wed 3/29/2006 11:41 AM > To: '[EMAIL PROTECTED]' > Cc: > Subject: missing value replacement for test data in > random forest > > > Hi, > > In R, how to do missing value replacement for test data > in randome forest in the way Breiman decribed. > > thanks in advance > > iris > > __ > 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] S-PLUS 8 beta program [repost]
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[R] access list component names with lapply
I have a question regarding accessing the names of list
components when applying a function with lapply.
Here is an example that demonstrates what I'd like to do.
I have a list like this one:
mylist <- list(a=letters[1:10], b=letters[10:1], c=letters[1:3])
Now I would like to append the names of the list components to their
corresponding vectors with the c() function. I thought this could
be done like in the following command, but it doesn't:
lapply(mylist, function(x) { c(names(x), x) } )
I know how to do this in a for loop, but lapply runs so much faster over
large lists.
Any help on this simple problem will be highly appreciated.
Thomas
--
Thomas Girke
1008 Noel T. Keen Hall
University of California
Riverside, CA 92521
Ph: 951-827-2469
Fax: 951-827-4437
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Re: [R] access list component names with lapply
Try this:
lapply(names(mylist), function(nm) c(nm, mylist[[nm]]))
On 3/29/06, Thomas Girke <[EMAIL PROTECTED]> wrote:
> I have a question regarding accessing the names of list
> components when applying a function with lapply.
>
> Here is an example that demonstrates what I'd like to do.
>
> I have a list like this one:
>
>mylist <- list(a=letters[1:10], b=letters[10:1], c=letters[1:3])
>
> Now I would like to append the names of the list components to their
> corresponding vectors with the c() function. I thought this could
> be done like in the following command, but it doesn't:
>
>lapply(mylist, function(x) { c(names(x), x) } )
>
> I know how to do this in a for loop, but lapply runs so much faster over
> large lists.
>
> Any help on this simple problem will be highly appreciated.
>
> Thomas
>
>
> --
> Thomas Girke
> 1008 Noel T. Keen Hall
> University of California
> Riverside, CA 92521
>
> Ph: 951-827-2469
> Fax: 951-827-4437
>
> __
> 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
>
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Re: [R] predict.glmmPQL Problem
Please try again after upgrading to the versions of R and MASS.
If you still have a problem, PLEASE do read the posting guide!
"www.R-project.org/posting-guide.html" before you submit another post.
Most of the people who donate their time to answer questions on this
listserve are more likely to answer a question if it is simple and
completely self contained -- including a very brief toy example that
they can copy from an email into R and reproduce the problem. If they
can't do that, they are less likely to understand your question and
therefore less likely to produce a useful answer -- and less likely to
bother to even read carefully your question.
hope this helps,
spencer graves
rsubcriber wrote:
> Dear all,
>
> for a cross-validation I have to use predict.glmmPQL() , where the
> formula of
> the corresponding glmmPQL call is not given explicitly, but constructed
> using as.formula.
> However, this does not work as expected:
>
> x1<-rnorm(100); x2<-rbinom(100,3,0.5); y<-rpois(100,2)
> mydata<-data.frame(x1,x2,y)
>
> library(MASS)
> # works as expected
> model1<-glmmPQL(y~x1, ~1 | factor(x2), family=poisson, data=mydata)
> predict(model1, newdata=mydata, type="response")
>
> f<-as.formula(paste("y", "~","x1"))
> # predict does not work:
> # Error in mCall[["fixed"]][-2] : object is not subsettable
> model2<-glmmPQL(f, ~1 | factor(x2), family=poisson, data=mydata)
> predict(model2, newdata=mydata, type="response")
>
> Has anyone an idea what goes wrong?
> I am using R 2.0.1 under Windows 2000.
>
> Thanks,
> Anneke
>
> __
> R-help@stat.math.ethz.ch mailing list
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> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
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Re: [R] How do I report coefficients of categorical fixed effects in a publication?
Have you read Pinheiro and Bates (2000) Mixed-Effects Models in S and S-Plus (Springer)? The figures and tables in this book should give you some ideas that you can adapt to summarizing the results of fits to nonnormal data. If you've tried this and still have questions for this listserve, PLEASE do read the posting guide! "www.R-project.org/posting-guide.html" then submit another post after trying some of the things suggested in the posting guide. In particular, if your question includes a self-contained example that someone can copy from your email into R and try a few things in less than 60 seconds, I believe you will increase your chances of getting useful replies quickly. hope this helps, spencer graves Tracy Feldman wrote: > To whom it may concern: > > I recently used lmer (for non-normally distributed data and mixed effects, > using the Laplace method). All 3 of my fixed effects were categorical, > including two ordered factors and one unordered factor. In my tables, I > currently report the number of observations for the response variable, and > both the degrees of freedom and Chi Square values from tests of reduced > models against the full model. > > However, I would also like to include some indication of the magnitude and > direction of the change in each fixed effect (and interaction effects) as a > function of the response variable. Is this done with the "estimate +/- SE" > of fixed effects in the summary of the fitted model? Either way, I am > confused with how to report these effects succinctly, especially because for > categorical variables, each category has its own estimated effect. What is a > reasonable way to do this? Or should I just avoid it entirely? > > I really appreciate your time and help. Please reply to [EMAIL PROTECTED] > or [EMAIL PROTECTED] > > Sincerely, > Tracy S. Feldman > > > - > > [[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] yaxis for plot(density(...))
Hi R users I have a question for yaxis for plot(density(...)). plot(density(rnorm(100,.25,0.0701361)),xlim=c(-.5,1),col="red",xlab="",main="") I expected that yaxis is a probabilty (from 0 to 1) but it wasn't I got 1 to 5 or 6 on yaxis. How do I interpret yaxis values ? Thanks TM __ 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] predict.glmmPQL Problem
I have found a similar problem when constructing formulae and passing
them to glmmPQL. My solution was to use do.call(glmmPQL,...). See ?do.call.
HTH,
Simon.
pencer Graves wrote:
> Please try again after upgrading to the versions of R and MASS.
>
> If you still have a problem, PLEASE do read the posting guide!
> "www.R-project.org/posting-guide.html" before you submit another post.
> Most of the people who donate their time to answer questions on this
> listserve are more likely to answer a question if it is simple and
> completely self contained -- including a very brief toy example that
> they can copy from an email into R and reproduce the problem. If they
> can't do that, they are less likely to understand your question and
> therefore less likely to produce a useful answer -- and less likely to
> bother to even read carefully your question.
>
> hope this helps,
> spencer graves
>
> rsubcriber wrote:
>
>
>> Dear all,
>>
>> for a cross-validation I have to use predict.glmmPQL() , where the
>> formula of
>> the corresponding glmmPQL call is not given explicitly, but constructed
>> using as.formula.
>> However, this does not work as expected:
>>
>> x1<-rnorm(100); x2<-rbinom(100,3,0.5); y<-rpois(100,2)
>> mydata<-data.frame(x1,x2,y)
>>
>> library(MASS)
>> # works as expected
>> model1<-glmmPQL(y~x1, ~1 | factor(x2), family=poisson, data=mydata)
>> predict(model1, newdata=mydata, type="response")
>>
>> f<-as.formula(paste("y", "~","x1"))
>> # predict does not work:
>> # Error in mCall[["fixed"]][-2] : object is not subsettable
>> model2<-glmmPQL(f, ~1 | factor(x2), family=poisson, data=mydata)
>> predict(model2, newdata=mydata, type="response")
>>
>> Has anyone an idea what goes wrong?
>> I am using R 2.0.1 under Windows 2000.
>>
>> Thanks,
>> Anneke
>>
>> __
>> 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
>
>
--
Simon Blomberg, B.Sc.(Hons.), Ph.D, M.App.Stat.
Centre for Resource and Environmental Studies
The Australian National University
Canberra ACT 0200
Australia
T: +61 2 6125 7800 email: Simon.Blomberg_at_anu.edu.au
F: +61 2 6125 0757
CRICOS Provider # 00120C
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[R] Can someone please help me understand this? (Was Re: calling R's optimization routines from C)
Dear list,
Can someone please help me here? Is it not possible to use the R library for
optimization and other routines calling from C?
Thank you!!
AarEm Trotter
--- Globe Trotter <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I have read R's Writing Extensions manual and am still confused about how to
> use some of the routines there when I call from C. Specifically, I am writing
> a
> little test function which I will optimize using the nmmin function which
> underlies R's optim() with Nelder-Mead. I guess I wonder what library/header
> files I should be using. I was using R_ext/Applic.h and linking with libR but
> I
> can not get it to work. (Btw, I am using RHEL4/FC4 Linux).
>
> The function is very simple: all it does is calculate the sum of squared
> differences from a parameter, so the minimizer will be the mean.
>
> Actually, here is my code:
>
> #include
> #include
>
> #include
>
> typedef struct {
> double *X;
> int n;
> } MyData;
>
> double myfunc(int m, double *par, void *ex)
> {
> MyData *mydata = ex;
> double *X = mydata->X;
> int n = mydata->n;
> double mu = par[0];
> double sum = 0.0;
> int i;
>
> for (i=0; i double t = X[i] - mu;
> sum += t*t;
> }
> return sum;
> }
>
> int main(void)
> {
> int i,n=1, trace=1, maxit=100, fail, fncount;
> double *par, abstol=0.0001, intol=.0001, alpha=1, beta=.5, gamma=2, *xin,
> *x,
>
> Fmin;
>
> MyData ex;
>
> par=malloc(n*sizeof(double));
> xin=malloc(n*sizeof(double));
> x=malloc(n*sizeof(double));
>
> par[0]=5;
> xin[0]=5;
>
> ex.n=5;
>
> ex.X=malloc(ex.n*sizeof(double));
>
> for(i=0;i
> nmmin(n,xin,x,&Fmin,myfunc,&fail,abstol,intol,&ex,alpha,
> beta,gamma,trace,&fncount,maxit);
> free(par);
> free(x);
> free(xin);
> free(ex.X);
> return 0;
> }
>
>
> I compile using the following:
>
> gcc -o testex testex.c -std=c99 -Wall -pedantic -I/usr/lib/R/include
> -L/usr/lib/R/lib -lm -lR
>
> Which actually compiles without error, but I get Segmentation fault when I
> run
> it.
>
> Clearly, I am doing something wrong. Can someone please provide suggestions?
>
> Many thanks and best wishes,
> Aaarem
>
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Re: [R] yaxis for plot(density(...))
Probabilities can't be greater than 1 but densities can. On 3/29/06, Taka Matzmoto <[EMAIL PROTECTED]> wrote: > Hi R users > I have a question for yaxis for plot(density(...)). > > plot(density(rnorm(100,.25,0.0701361)),xlim=c(-.5,1),col="red",xlab="",main="") > > I expected that yaxis is a probabilty (from 0 to 1) but it wasn't > > I got 1 to 5 or 6 on yaxis. > > How do I interpret yaxis values ? > > Thanks > > TM > > __ > 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] new to the list - problems with non-solid lines in eps export - problem fixed!
Hi Uwe, thanks for the reply! I used postscript() instead of dev.copy2eps(), but the problem remained; furthermore, its the same on the screen and in a physical print. After some more testing, I figured out that I can produce the desired output if I do not use the pre-defined line type "dotted", as in lines(LL[1:251], type="l", lwd=1, lty="dotted"), but rather define an own line type as in lines(LL[1:251], type="l", lwd=1, lty="11"). With this, dotted lines in the eps output look nice. So, thanks again for your help, Gregor Am Sonntag, 26. März 2006 15:16 schrieb Uwe Ligges: > Gregor Volberg wrote: > > Dear all, > > I am new to this list and, unfortunately, could not provide help to > > anyone as yet. I hope I can do so in the future, though! Until then, I am > > grateful for helpful hints from you more experienced users. > > > > For use in an upcoming publication, I generated an eps figure from my > > x11 window under Debian Linux with dev.copy2eps. It contains 28 line > > plots with 2 lines each, one solid and one dotted (they show > > event-related brain potentials in two different conditions, if this is of > > interest for someone). The plots are arranged in a window with width=5 > > inch and height = 6 inch, so single plots are quite small. > > Now the problem: When I include the file in Latex or other word > > processing programs, the dotted line is almost unreadable. The whole > > waveform consists of, say, 20 dots, which hardly form a curve. The same > > problem occurs under MS Windows with dev.copy2eps(). However, when I > > directly plot the device under Windows, the dotted lines are nice. Thus, > > the problem is presumably special to eps "export". > > I know that I could do an easy workaround by using thick/thin lines or > > black/grey ones, but publication offices say that such lines are hard to > > distinguish for the reader in the final print version. Also, I searched > > this list for something like "high resolution plots", but I learend that > > eps as a vector format does not have a fixed resolution (and thus no > > option to make ist "higher"). Plotting the figure to another device (png, > > bmp) reveals the expected curves, but bitmaps are often not accepted. > > Does anyone have a hint, or does anyone have the same problem? Thank you > > in advance for your help! > > 1. Use postscript() directly rather than the way through dev.copy2eps() > (which should work as well, but let us exclude it for further reference). > > 2. Print the resulting postscript physically rather than looking at it > on the screen. Omitting some points might be caused by some settings of > your postscript viewer. > > Uwe Ligges > > > Gregor > > > > > > P.S.: The dotted lines are not fuzzy, but "stretched" in the way that the > > point are to far away from each other to appear continuos. The same is > > with other non-solid lines (dashed etc). -- Dr. rer. nat. Gregor Volberg <[EMAIL PROTECTED]> Institute for Experimental Psychology University of Regensburg Universitätsstraße 31 D-93053 Regensburg Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html pgpWlIkKOMOWG.pgp Description: PGP signature __ 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 about for loop?
Hello useRs,
I can't figure out how can I store a data frame of values of X and D from
this loop:
Z <- c(1:10)
for (i in 1:(length(Z)-2))
{D <- x[1:(2+i)];
X <- paste("x",sep="",i)
print (X)
print (D)
}
Thank You,
Andris Jankevics
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[R] Plotting a segmented function
This might be a trivial question, but I would appreciate if anybody could suggest an elegant way of plotting a function such as the following (a simple distribution function): F(x) = 0 if x<=0 =(x^2)/2 if 02 This is just an example. In this case it is a continuous function. But how to do it in general in an elegant way. I've done the following: x1 <- seq(-1,0,.01) f1 <- rep(0,101) x2 <- seq(0,1,.01) f2 <- 0.5*(x2^2) x3 <- seq(1,2,.01) f3 <- (2*x3)-(0.5*(x3^2))-1 x4 <- seq(2,3,.01) f4 <- rep(1,101) x <- c(x1,x2,x3,x4) F <- c(f1,f2,f3,f4) plot(x,F,type='l') But this seems very cumbersome. Any help is much appreciated. Thanks Jacob Jacob L van Wyk Department of Statistics University of Johannesburg APK P O Box 524 Auckland Park 2006 South Africa Tel: +27-11-489-3080 Fax: +27-11-489-2832 __ 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] Plotting a segmented function
Jacob van Wyk wrote:
> This might be a trivial question, but I would appreciate if anybody
> could suggest an elegant way of plotting a function such as the
> following (a simple distribution function):
> F(x) = 0 if x<=0
>=(x^2)/2 if 0=2x-((x^2)/2)-1 if 1=1 if x>2
> This is just an example. In this case it is a continuous function. But
> how to do it in general in an elegant way.
> I've done the following:
> x1 <- seq(-1,0,.01)
> f1 <- rep(0,101)
> x2 <- seq(0,1,.01)
> f2 <- 0.5*(x2^2)
> x3 <- seq(1,2,.01)
> f3 <- (2*x3)-(0.5*(x3^2))-1
> x4 <- seq(2,3,.01)
> f4 <- rep(1,101)
> x <- c(x1,x2,x3,x4)
> F <- c(f1,f2,f3,f4)
> plot(x,F,type='l')
>
> But this seems very cumbersome.
> Any help is much appreciated.
Define a function such as
f <- function(x){
(x>2) +
(2*x-((x^2)/2)-1) * ((1 < x) & (x <= 2)) +
((x^2)/2) * ((0 < x) & (x <= 1))
}
curve(f, from = -1, to = 3)
> Thanks
> Jacob
>
>
> Jacob L van Wyk
> Department of Statistics
> University of Johannesburg APK
> P O Box 524
> Auckland Park 2006
> South Africa
> Tel: +27-11-489-3080
> Fax: +27-11-489-2832
>
> __
> R-help@stat.math.ethz.ch mailing list
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Re: [R] conflicts Var names
Fred J. wrote: > Dear R users > > I have read somewhere which I don't remember that some variable names > are not to be used for conflict avoidance. and those were (c, q, T, F, > T) > I ran this > > conflicts(detail=TRUE) > $.GlobalEnv > [1] "ts" > > $"package:methods" > [1] "body<-" > > $"package:stats" > [1] "ts" > > $"package:base" > [1] "body<-" > > I don't note ts was in the list of to-avoid "oh I think it was some > tips and tricks relating to R". at this point, it is recommended to > rename my ts variable in my code? Well, it is nice to avoid such names, but since R distinguishes functions vs. data, you can live with it if you are aware of the problem. Uwe Ligges > thank you > > > - > > [[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] Plotting a segmented function
You could try nested ifelse statements, something like (untested) x <- seq(-1, 3, 0.1) y <- ifelse( x <= 3, ifelse( x <= 2, ifelse( x <= 1, ifelse( x <= 0, 0, x^2/2), 2 * x - (x^2/2) -1), 1) ) plot(x, y) ** This might be a trivial question, but I would appreciate if anybody could suggest an elegant way of plotting a function such as the following (a simple distribution function): F(x) = 0 if x<=0 =(x^2)/2 if 02 This is just an example. In this case it is a continuous function. But how to do it in general in an elegant way. I've done the following: x1 <- seq(-1,0,.01) f1 <- rep(0,101) x2 <- seq(0,1,.01) f2 <- 0.5*(x2^2) x3 <- seq(1,2,.01) f3 <- (2*x3)-(0.5*(x3^2))-1 x4 <- seq(2,3,.01) f4 <- rep(1,101) x <- c(x1,x2,x3,x4) F <- c(f1,f2,f3,f4) plot(x,F,type='l') But this seems very cumbersome. Any help is much appreciated. Thanks Jacob -- Ken Knoblauch Inserm U371 Cerveau et Vision Dept. of Cognitive Neuroscience 18 avenue du Doyen Lépine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 http://www.lyon.inserm.fr/371/ __ 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] Question about for loop?
Andris Jankevics wrote:
> Hello useRs,
>
> I can't figure out how can I store a data frame of values of X and D from
> this loop:
>
> Z <- c(1:10)
>
> for (i in 1:(length(Z)-2))
> {D <- x[1:(2+i)];
> X <- paste("x",sep="",i)
> print (X)
> print (D)
> }
Assign them as elements of a list, for example.
For further reference what a list is:
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
Uwe Ligges
>
> Thank You,
>
> Andris Jankevics
>
> __
> 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
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Re: [R] Random effects ANOVA?
I think you want print or summary rather than anova. anova() is not very useful for aov() models even without error strata. The point of the aov classes is that they present the results of lm() fits in ways which are more conventional for designed experiments, including giving conventional ANOVA tables without recourse to anova(). I didn't follow how the videos were chosen. Random effects apply when the 'treatments' were chosen from a large population (which might apply if each subject watched (on separate occasions) three videos chosen randomly from a larger pool), and if the interest is in the variability of the response over videos in the pool. If subjects were observed more than once then I suspect you most likely want a random effect for subjects. What I guess is more likely is that you have 60 measurements on 60 subjects, each of whom was assigned one video and one drink. Then there appear to be no random effects, and the problem caused by randomly selecting videos is that the experiment is likely to be unbalanced (since each video is not going to be selected 20 times by chance). aov() is primarily intended for balanced designs, and interpretation is tricky without balance (see the warnings on its help page). There are many loose ends hindering offering help by email, and the best advice is to consult a statistician face-to-face about an appropriate analysis. On Wed, 29 Mar 2006, Chris Bergstresser wrote: > Hi all -- > >So I have a very simple dataset, which consists of 60 subjects, > who watched one of three videos, drank one of two drinks, and > completed a task. The response variable is the time to complete the > task. The ANOVA command is simple enough: anova(aov(time ~ drink * > video, data = df)); > > However, the videos were randomly selected; I need to use the > random effects model for them. So I tried anova(aov(time ~ drink + > Error(video), data = df)); This gives me a "no applicable method for > 'anova'" error. > > The command aov works, but doesn't give me anything I can interpret > effectively. Is there a simpler command I should be using? Am I > doing something wrong? > > -- Chris -- 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] symbols plot
before getting scolded for submitting a (non-)bug report: when using the 'symbols' function for plotting boxplot data (i.e. using 'boxplots' symbols), I noted that the x/y-position of the symbols is associated with the center of the box. while this is obviously natural for a usual plotting symbol (say a circle or a rectangle), it is probably not desired if one uses the 'boxplots' symbols: looking at such a plot, probably everyone will assume that y-position is that of the median within the box (in other words: that one can read off the values of the medians from the y-axis). the current behaviour is counter-intuitive, I believe, if the distributions are asymmetrical (and the median is not centered in it's box). (I even think, that such plots are misinterpreted easily: think what happens if the median lies very near one of the hinges in one box and is centered in another one within the same plot and the medians are actually the same) in short: I think the 'boxplots' should not be centered at the specified y-coordinates but rather drawn with a y-coordinate of y + bxh * (0.5 - bxm) where bxh and bxm are the second and fifths column of the 'boxplots' matrix. in this way, the median position is identical to the specified y-coordinate. at the very least, I think, the manpage should explicitely state that all symbols (including boxplots) are positioned with their geometrical center at the specified coordinates. right or wrong? regards, 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
