Re: [R] R version conflict.
Bai Yan [EMAIL PROTECTED] writes: My mistake :( Seems that there's another R installed by root. So when I use .libPaths() there're two of them: .libPaths() [1] /disk/hopper/projects/class/cse514/R/library [2] /usr/lib/R/library How could the second path be enabled then? The R_LIBS have already been set to as the [1] only. If that happens, you're running the installed R, not the one you compiled. You need to run it as /where/you/put/it/bin/R (or bin/R if you're in the toplevel build dir). -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] writing several command line in R console
Hallo
On 4 Mar 2003 at 2:36, Vincent Stoliaroff wrote:
Hi R lovers
I would like to know how to step to the next line in the R console
editor without breaking the continuity of my code more clearly : if
for example I write a function, so far i have to write the all code
inside on the same line wich may become obscure as the function is
more and more complex. I would like to do like in the example of the
manuels:
twosam - function(y1, y2) {
n1 - length(y1); n2 - length(y2)
yb1 - mean(y1); yb2 - mean(y2)s1 - var(y1);s2 -
var(y2) s - ((n1-1)*s1 + (n2-1)*s2)/(n1+n2-2) tst - (yb1 -
yb2)/sqrt(s2*(1/n1 + 1/n2))tst }
all I can do is something like that:
twosam - function(y1, y2) {n1 - length(y1); n2 - length(y2)
+yb1 - mean(y1); yb2 - mean(y2)s1 - var(y1);s2 -
+var(y2) s - ((n1-1)*s1 + (n2-1)*s2)/(n1+n2-2)
+ tst - (yb1 - yb2)/sqrt(s2*(1/n1 + 1/n2))tst }
with the sign + in front of each line
What does this sign mean? and how could I solve my problems
Thanks
Maybe looking to the manuals will be more precise than my
answer.
+ is a continuity sign and means you did not finished your imput
and you shall continue typing your command.
But why you do not use any text ditor for writing functions and
than copy/paste to R command window?
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CheersPetr Pikal
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RE: [R] Embed R in other applications
see the contributed pacakge R2HTML; in case you have access to a databank: RODBC package and the like might also be an option in combination with *.php and/or *.asp-files for web-publishing. I have implemented both and it runs succesfully without any hickups. Updating the data, running R-program as batch via scheduler and outputting directly or writing it first into a databank for further processing. HTH, Bernhard -Original Message- From: Bai Yan [mailto:[EMAIL PROTECTED] Sent: 04 March 2003 06:01 To: [EMAIL PROTECTED] Subject: [R] Embed R in other applications Hello all, I want to create webpages which can display the R results. The first step is essentially getting input from client, generating graphics and returning a page containing those images. What should I do for this? Are there some sources on the web? Any hints will be very helpful. Thanks very much :) Yan __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help -- If you have received this e-mail in error or wish to read our e-mail disclaimer statement and monitoring policy, please refer to http://www.drkw.com/disc/email/ or contact the sender. -- __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] How to estimate or approximate a 3-D surface
Hi On 3 Mar 2003 at 22:03, Feng Zhang wrote: Hey, R-listers Now I am going to estimate or approximate a surface in 3-D space given a large enough number of (x,y,z) data sets. So for these 3-D data points, is it possible to get a surface function, like z=f(x,y) to represent this underlying surface? I am not sure but interp from akima package shall give you an interpolation of your data. Thanks for your time and point. Fred __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help Cheers Petr Pikal [EMAIL PROTECTED] [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Recall: [R] Embed R in other applications
Pfaff, Bernhard would like to recall the message, [R] Embed R in other applications. -- If you have received this e-mail in error or wish to read our e-mail disclaimer statement and monitoring policy, please refer to http://www.drkw.com/disc/email/ or contact the sender. -- __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] R in your pocket on a Sharp Zaurus
R v.1.6.2 is now available for the Sharp SL-5500 Zaurus linux pda. Thanks to the effort of Simon Pickering at Bath University, NA handling is now correct and graphics function fine. It can run on the unexpanded 'out of the box' machine. The FPU emulation can slow some operations a lot, but it can do lowess smoothing on over 10,000 data points in just a few minutes, as good as the 486SX25 I was happy with not that many years ago. And R (+Zaurus) in the hand/jacket pocket is worth any number of laptops in the bush. You'll need R (see http://students.bath.ac.uk/enpsgp/Zaurus/#R), plus a few libraries (from http://ipkgfind.handhelds.org/). To add graphics, you can either run native X-windows - faster - or run X within qtopia (see http://students.bath.ac.uk/enpsgp/Zaurus/#X) for convenience. Stuart PS. At present the help system doesn't function. We're working on this - we're not sure why, but note that in the current compilation, the CONTENTS folders end up empty. All suggestions gratefully received... Dr Stuart Leask MA MRCPsych, Clinical Lecturer in Psychiatry University of Nottingham Dept of Psychiatry, Duncan Macmillan House Porchester Road, Nottingham. NG3 6AA. UK http://www.nottingham.ac.uk/psychiatry/staff/sjl.html __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] tex/pdf?
Hello,
I'm having some problems, now with building libraries/packages. Actually, with making
pdf- or latex-files. So, everyting is ok, I can generate latex-files ('.tex') using 'R
CMD Rdconv -t tex', but apparently, it are not valid latex-files (no 'documentclass',
no 'body' etc). How come? Do I have to add these things manually?
Kurt.
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RE: [R] log axis assignment
From: Jeremy Z Butler [mailto:[EMAIL PROTECTED]
Surely I should be able to set the
ylog option to T using another object (logaxis).
for (n in colnames(raw))
{
if(n==pH){logaxis-T} else {logaxis-F}
plot(full.age,raw[,n],type=n,ylog=logaxis)
...
}
What (probably) will work is:
if(n==pH){logaxis-Y} else {logaxis-}
plot(full.age,raw[,n],type=n,log=logaxis)
The plot-argument log takes which axis that shuld be logaritmic.
Morten
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Re: [R] tex/pdf?
On Tue, 4 Mar 2003, Kurt Sys wrote:
I'm having some problems, now with building libraries/packages.
Actually, with making pdf- or latex-files. So, everyting is ok,
I can generate latex-files ('.tex') using 'R CMD Rdconv -t tex',
but apparently, it are not valid latex-files (no 'documentclass',
no 'body' etc). How come? Do I have to add these things manually?
No, you use help(offline=TRUE) or R CMD Rd2dvi (which is documented in
R-exts).
Please wrap your lines in emails
--
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] How to estimate or approximate a 3-D surface
Have you tried looking at packages mgcv or gss? Now I am going to estimate or approximate a surface in 3-D space given a large enough number of (x,y,z) data sets. So for these 3-D data points, is it possible to get a surface function, like z=f(x,y) to represent this underlying surface? Simon _ Simon Wood [EMAIL PROTECTED]www.stats.gla.ac.uk/~simon/ Department of Statistics, University of Glasgow, Glasgow, G12 8QQ Direct telephone: (0)141 330 4530 Fax: (0)141 330 4814 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] How to estimate or approximate a 3-D surface
Locfit has worked well for me. http://cm.bell-labs.com/cm/ms/departments/sia/project/locfit/ Stuart Dr Stuart Leask MA MRCPsych, Clinical Lecturer in Psychiatry University of Nottingham Dept of Psychiatry, Duncan Macmillan House Porchester Road, Nottingham. NG3 6AA. UK http://www.nottingham.ac.uk/psychiatry/staff/sjl.html - Original Message - From: Simon Wood [EMAIL PROTECTED] To: Feng Zhang [EMAIL PROTECTED] Cc: R-Help [EMAIL PROTECTED] Sent: Tuesday, March 04, 2003 9:55 AM Subject: Re: [R] How to estimate or approximate a 3-D surface Have you tried looking at packages mgcv or gss? Now I am going to estimate or approximate a surface in 3-D space given a large enough number of (x,y,z) data sets. So for these 3-D data points, is it possible to get a surface function, like z=f(x,y) to represent this underlying surface? Simon _ Simon Wood [EMAIL PROTECTED]www.stats.gla.ac.uk/~simon/ Department of Statistics, University of Glasgow, Glasgow, G12 8QQ Direct telephone: (0)141 330 4530 Fax: (0)141 330 4814 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] writing several command line in R console
Petr Pikal [EMAIL PROTECTED] writes:
I would like to know how to step to the next line in the R console
editor without breaking the continuity of my code more clearly : if
for example I write a function, so far i have to write the all code
inside on the same line wich may become obscure as the function is
more and more complex. I would like to do like in the example of the
manuels:
twosam - function(y1, y2) {
n1 - length(y1); n2 - length(y2)
yb1 - mean(y1); yb2 - mean(y2)s1 - var(y1);s2 -
var(y2) s - ((n1-1)*s1 + (n2-1)*s2)/(n1+n2-2) tst - (yb1 -
yb2)/sqrt(s2*(1/n1 + 1/n2))tst }
...
+ is a continuity sign and means you did not finished your imput
and you shall continue typing your command.
But why you do not use any text ditor for writing functions and
than copy/paste to R command window?
I'm not sure if and how it works on Windows, but on Unix one of the
better kept secrets of the readline library is that you can embed
newlines by typing ctr-V ctr-J, e.g.
x - matrix(c(1,2,3,
4,5,6,
7,8,9), 3)
The nice thing is that it allows you to recall the entire command and
edit it (I don't think it survives being saved to the history file
though). If you have ever had to correct a typo in an expression that
has been split over 8 lines, you'll know what I mean:
up,up,up,up,up,up,up,up,RET,
up,up,up,up,up,up,up,up,RET,
up,up,up,up,up,up,up,up,RET,
up,up,up,up,up,up,up,up,fix typo,RET,
up,up,up,up,up,up,up,up,RET,
up,up,up,up,up,up,up,up,RET,
up,up,up,up,up,up,up,up,RET,
up,up,up,up,up,up,up,up,RET
--
O__ Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Re: [R] How to estimate or approximate a 3-D surface
On Tue, 4 Mar 2003, Stuart Leask wrote: Locfit has worked well for me. http://cm.bell-labs.com/cm/ms/departments/sia/project/locfit/ Unfortunately it has not been updated for current versions of R: it also writes diagnostic output to stderr which is not shown on GUI versions of R (especially on Windows). There is a version in the Devel area on CRAN. Package akima is the most obvious choice for interpolation. For smoothing, there are all the various spatial packages (and package fields) as well as mgcv and gss already mentioned. -- 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 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Parallel programming using R
Dear All, For my regression problem(thousand dependents by thousand predictors by hundred months observations), I prefer to parallel computation in R. Is it possible to parallel programming using R as using C and Fortran? Cheers, Lun __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] tex/pdf?
Mail from [EMAIL PROTECTED], sent on Tuesday March 4
2003 at 09:42 (GMT+):
On Tue, 4 Mar 2003, Kurt Sys wrote:
I'm having some problems, now with building
libraries/packages. Actually, with making pdf- or
latex-files. So, everyting is ok, I can generate
latex-files ('.tex') using 'R CMD Rdconv -t tex', but
apparently, it are not valid latex-files (no
'documentclass', no 'body' etc). How come? Do I have to
add these things manually?
No, you use help(offline=TRUE) or R CMD Rd2dvi (which is
documented in R-exts).
Ok... tnx. Was a stupid question. Should have found that myself...
Kurt.
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[R] Instability in package gld in R?
Dear All, Is there anyone using package gld in R? I have managed to load this package into Splus. I found that in some cases the use of this package will cause Splus to crash and R to hang, I am not sure why but this is just an example: qgl(c(0,1),45.23587,0.2363868,-1.5,0) Which means the functon ranges from -Inf to Inf, however if you put: pgl(150,45.23587,0.2363868,-1.5,0) Then Splus will crash and R will hang. There are other examples in dgl that also causes R to hang and Splus to quit. I think this may have to do with using numerical methods to approximate the distribution function of gld. Does anyone have any ideas about how to fix this problem or correct this difficulty? Steve. ** Steve Su ([EMAIL PROTECTED]) PhD student. School of Accountancy School of Mathematical Sciences Queensland University of Technology Postal Address: Steve Su, School of Accountancy, QUT, PO Box 2434, Brisbane, Queensland, Australia, 4000. Phone: +61 7 3864 2017 Fax:+61 7 3864 1812 Mobile: 0421 840 586 . _--_|\ / QUT \_.--._/ v ** [[alternate HTML version deleted]] __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] error using try() and coxph()
Dear all,
I'm experiencing some problems in using the following code to perform
simulations with Cox models (using coxph() in survival package):
for(i in 1:1000){
dd-#simulate the dataframe
o0-try(coxph(Surv(start,stop,status)~x,data=dd))
o1-try(coxph(Surv(start,stop,status)~x+x:stop,data=dd))
o2-try(coxph(Surv(start,stop,status)~x+x:poly(stop,2),data=dd))
}
The error (both in Rgui and in batch mode) causes R to crash immediately
with a DOS message like Error in survival.dll
Using coxph() without try() simulation stops because sometimes the model may
be not fitted, I get the explicit error message. Therefore I suspect that
the problem depends on using try(coxph()). Also note that using
try(arima()) for a similar problem works well.
versions: survival 2.9-4 and R 1.5.1 on WinMe
I know I should update R, but I wonder whether the problem depends on the
old version
Could anyone suggest me anything?
cheers,
vito
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[R] Unit root test for panel data
Dear Sir/Madam, I need to apply IPS, Fischer or any other more contemporary panel data unit root test. I would be glad if you could inform me whether there are r-modules which can perform these tests. I thank you very much in advance for your precious time and interest. Yours Sincerely, Cenktan zyldrm __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] How to modify XML documents and save changes
Again, Stephen is right on the mark with his explanation of modifying
the XML objects and needing to put the modified values back into the
containing structure. Trees graphs are slightly cumbersome in the S
language since it is not a reference-based language. There are some
tricks one can use that are in the XML package for indexing them with
a cursor, but these are (currently) only for use when constructing a
tree from scratch within S.
A little cumbersome, but doable. One other option is to use xmlEventParse
and write a handler that would add the element after the one you're
interested in. I hope there is a better way, but haven't seen it yet. :-(
Here there is some good news. xmlEventParse is extremely low-level
relative to xmlTreeParse and typically used for efficiency in
minimizing the amount of storage used when parsing the contents of an
XML document. The idea is that an S function gets invoked when an XML
tag is opened, and another when it is closed.
xmlTreeParse() can also be used in this event-driven style
programming. When the XML parser encounters the close of a tag, it
looks for a suitable S function to invoke specified in the handlers
argument of xmlTreeParse. If there is an element in that list of
functions whose name matches the tag name, it is invoked. Thus if you
programmatically want to augment/modify the contents of an XML node,
you can supply a function that operates on that node. The function
can return the resulting updated node and it will be inserted into the
overall tree as one would expect.
So, suppose one wants to _always_ add a node
Norm/Norm
to each tagname/tagname node, you can use the following
myFun - function(node,...) {
node - append.XMLNode(node, xmlNode(Norm))
node
}
and then use this in the command
xmlTreeParse(file.xml, handlers = list(tagname = myFun), asTree = TRUE)
One can also use XSL to do this, either directly from the command
line or from S via the Sxslt package.
If one only wants to modify particular tagname elements, it is
probably easiest to read the entire tree and modify it directly.
For people familiar with other XML parsers, the default xmlTreeParse
behaves like DOM and xmlEventParse behaves likes SAX. With handlers,
xmlTreeParse() provides a hybrid parser for XML somewhere between DOM
and SAX.
D.
Stephen C. Upton wrote:
Steffen,
As with most R objects, you're basically putting a copy of the R object into
the new object. Any operation or function you apply to that object does not
affect the original. Same goes for append.xmlNode - you're appending to the
original and getting back another structure that is the original plus the
new node. Finally, saveXML works on an object of XMLInternalDocument and doc
(the object returned by xmlTreeParse) is a XMLDocument object.
Here's one suggestion:
1. Read in the doc object as you've done, but manipulate the structure as
you would any other R object, e.g.,
QTListNode [[1]] -
append.xmlNode(QTListNode[[1]],xmlNode(name=Norm,attrs=NULL))
2. you then need to modify that node within the root with this new, modified
node, e.g. (assume I've assigned root - xmlRoot(doc)),
root[[whateverindextagnameis]] - QTListNode[[1]]
(I use the index here rather than the name, since it's unique - if you use a
name,e.g., root[[tagname]], that just adds a list element to root with
name tagname)
3. to write out, use write with toString.XMLNode,
write(toString.XMLNode(root, file=out.xml)
Since this is probably a little cumbersome, suggest writing a function to do
the finding, appending, and replacement.
A little cumbersome, but doable. One other option is to use xmlEventParse
and write a handler that would add the element after the one you're
interested in. I hope there is a better way, but haven't seen it yet. :-(
HTH
steve
Steffen Durinck wrote:
Dear,
I want to read XML documents, add child nodes to some elements and store
everything back as an XML document.
I've tryed the following:
doc - xmlTreeParse(file.xml)
QTListNode-xmlElementsByTagName(xmlRoot(doc)[[1]],tagname)
append.xmlNode(QTListNode[[1]],newXMLNode(name =Norm, attrs = NULL))
saveXML(doc, file = out.xml, compression = 0, indent=T)
This doesn't seem to work.
Can anyone help?
Thanks,
Steffen
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--
___
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Bell Labs, Lucent Technologiesoffice: (908)582-3217
700 Mountain Avenue, Room 2C-259 fax:(908)582-3340
Murray Hill, NJ 07974-2070
http://cm.bell-labs.com/stat/duncan
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[R] linear model with arma errors
Dear all, I'm looking for how can I estimate a linear model with ar(ma) errors : y(t)=a*X(t)+e(t) with P(B)e(t)=Q(B)u(t) where u is a white noise and P, Q are some polynomes. Could you help me ? Grégory Benmenzer __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Wavelets correlation test
Hello, I use wavethresh packages to perform wavelet analysis. In particular, I would like to compare 2 signals (vectors) after a wavelet decomposition. I would like to use cor.test function, but this function acts on the entire vector values. I plan to perform a cor.test on each level of the wavelet decomposition, say N. So I will have at the end of a first step N results of cor.test. How can I deal with this N results to have an answer globaly ? A lot of this code is already implemented in an alternative wavelet analysis package for R (waveslim). There, I have placed code to compute multiscale covariance/correlation estimates that may also be a function of lag. This would provide a correlation coefficient (or autocorrelation sequence) per scale. Approximate confidence intervals for these estimates are also available, there might be a reference in wave.covariance or wave.correlation -- I can't remember. The papers of interest are: - Whitcher, Guttorp, Percival (2000). Wavelet analysis of covariance with application to atmospheric time series, JGR 105 (D11), 14,941-14,962. - Serroukh and Walden (2000). Wavelet scale analysis of bivariate time series I: Motivation and estimation, Journal of Nonparametric Statistics, 13 (1), 1-36. - Gencay, Selcuk, Whitcher (2001). An Introduction to Wavelets and Other Filtering Methods in Finance and Economics, Academic Press. I think it would be difficult to make a statement for the whole series. Some scales may agree and some scales may not. What is the scientific question you are trying to answer? cheers... Brandon -- Senior Researcher in Imaging GlaxoSmithKline Research Statistics Unit New Frontiers Science Park (South) Third Avenue, Harlow CM19 5AW phone: +44 (0)127 963 1285 United Kingdom fax:+44 (0)127 964 4004 [EMAIL PROTECTED] -- __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] linear model with arma errors
That's discussed in Pinhiero and Bates, Mixed Effects Models in S and S-Plus. I don't have the book in my hand now, so I can't tell you exactly where to find it. However, I'm pretty confident that it can be done in lme. Spencer Graves Gregory BENMENZER wrote: Dear all, I'm looking for how can I estimate a linear model with ar(ma) errors : y(t)=a*X(t)+e(t) with P(B)e(t)=Q(B)u(t) where u is a white noise and P, Q are some polynomes. Could you help me ? Grégory Benmenzer __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] suggestion for addition to R-lang.texi
Stephen Eglen [EMAIL PROTECTED] writes:
Small suggestion for the documentation:
Should the = operator for assignments, described on
http://developer.r-project.org/equalAssign.html, now be included in
the operator table in doc/manual/R-lang.texi? If so, one possibility
could be after lines 1096/7:
@item @code{-}
@tab Left assignment, binary
@item @code{=}
@tab Left assignment, binary
Also, where is the best place to send suggestions of this nature? I
didn't want to send it to r-bugs, since it is not a bug.
It could easily be considered one... There is a Documentation category
in the bug repository, so why not?
BTW, I wonder: why did your mail come with sender r-help-bounces
instead of the usual r-help-admin and confuse my mail filter?
--
O__ Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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[R] r-help-bounces and r-devel-bounces e-mail?
Hi all, Just curious on the sudden change in the e-mail address coming from r-help and r-devel today. They are indicated as being [EMAIL PROTECTED] and [EMAIL PROTECTED] Any clues? I just noticed that my e-mail filter rule suddenly stopped putting these messages in their respective folders this morning (my time). Regards, Marc __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] r-help-bounces and r-devel-bounces e-mail?
Any clues? I just noticed that my e-mail filter rule suddenly stopped putting these messages in their respective folders this morning (my time). I believe they're upgrading the Mailman software that runs the list. __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] suggestion for addition to R-lang.texi
Peter Dalgaard BSA [EMAIL PROTECTED] writes: BTW, I wonder: why did your mail come with sender r-help-bounces instead of the usual r-help-admin and confuse my mail filter? Mailman upgrade? best, -tony -- A.J. RossiniRsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics [EMAIL PROTECTED] FHCRC/SCHARP/HIV Vaccine Trials Net [EMAIL PROTECTED] -- http://software.biostat.washington.edu/ FHCRC:Tu: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX (CHANGE: monday/wednesday/friday locations are completely unpredictable.) __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] r-help-bounces and r-devel-bounces e-mail?
-Original Message- From: Charles Annis, P.E. [mailto:[EMAIL PROTECTED] Sent: Tuesday, March 04, 2003 11:06 AM To: 'Jeff Gentry'; 'Marc Schwartz' Cc: [EMAIL PROTECTED] Subject: RE: [R] r-help-bounces and r-devel-bounces e-mail? You need to add [EMAIL PROTECTED] to your filtering rules to augment your current rule, [EMAIL PROTECTED] Charles Annis, P.E. Easy enough to do of course. Just curious if this was a temporary (as Jeff note suggests) or a permanent change. The 'bounces' suggests a problem, which raised my suspicions. From Peter Dalgaard's reply earlier, it would seem to be unexpected. I wasn't sure if I had perhaps missed an announcement somewhere. Thanks, Marc __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] r-help-bounces and r-devel-bounces e-mail?
JeffG == Jeff Gentry [EMAIL PROTECTED]
on Tue, 4 Mar 2003 11:53:13 -0500 (EST) writes:
Any clues? I just noticed that my e-mail filter rule suddenly stopped
putting these messages in their respective folders this morning (my
time).
JeffG I believe they're upgrading the Mailman software that runs the list.
Exactly. They := { (our head sys.admin.), me }
The new mailman (2.1.1 instead of 2.0.13) has quite a few new
features; particularly it says it allows unsubscribing without a
password --- something which will hopefully save quite a bit of
my time {from answering e-mails of people who are not patient
enough to read a page on the web to its end}.
I'm sorry we overlooked the change from
Sender: list[EMAIL PROTECTED]
to
Sender: list[EMAIL PROTECTED]
BTW: I think there are still some new problems that we hadn't
seen on the testing machine on which we tried everything.
But now is past the end of the working day around here...
Please send more feedback directly to me, aka [EMAIL PROTECTED]
Regards,
Martin Maechler [EMAIL PROTECTED] http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum LEO C16Leonhardstr. 27
ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
phone: x-41-1-632-3408 fax: ...-1228
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[R] implementing ecological models in R
Hi all, we found, that R is not only *the* superior data analysis, graphics and statistics package, but it is also a general tool for implementing, running and teaching ecological models. Last week we held our second course Modelling in Limnology using R. Some material (code and docs) was produced for this purpose and may be interesting to someone else, so I put the tutorial Konstruktion ökologischer Modelle mit der Open Source Software R on my homepage. The tutorial covers * a short introduction, * some simple regression models, * the modelling of populations with ODEs (thanks to Woodrow Sezter!), * some basic lake modelling stuff and * some basic individual-based techniques (population dynamics, movement, Conway's game of life, an individual-based predator-prey model). All examples are given in full source code. The tutorial is in German language, but possibly someone may be interested to work together with me on an English version in the future. It is work in progress, so please excuse typos and mistakes (some PDF errors are already known). On the other hand, I would be very glad about remarks and constructive criticism. The tutorial can be found on http://www.tu-dresden.de/fghhihb/petzoldt/zeugs.html together with an absolutely preliminary version of an accompanying library (the name simecol may be changed soon). Thank you for your feedback! Many thanks to all the people who are making the R-project possible! Thomas -- Thomas PetzoldtTel. +49-351-463 3 4954 Dresden University of Technology Fax +49-351-463 3 7108 Institute for Hydrobiology [EMAIL PROTECTED] 01062 Dresden http://www.tu-dresden.de/fghhihb/petzoldt/ __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] r-help-bounces and r-devel-bounces e-mail?
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Martin
Maechler
Sent: Tuesday, March 04, 2003 11:42 AM
To: [EMAIL PROTECTED]
Subject: Re: [R] r-help-bounces and r-devel-bounces e-mail?
JeffG == Jeff Gentry [EMAIL PROTECTED]
on Tue, 4 Mar 2003 11:53:13 -0500 (EST) writes:
Any clues? I just noticed that my e-mail filter rule
suddenly stopped
putting these messages in their respective folders this
morning (my
time).
JeffG I believe they're upgrading the Mailman software
that runs the list.
Exactly. They := { (our head sys.admin.), me }
The new mailman (2.1.1 instead of 2.0.13) has quite a few new
features; particularly it says it allows unsubscribing without
a password --- something which will hopefully save quite a bit
of my time {from answering e-mails of people who are not
patient enough to read a page on the web to its end}.
I'm sorry we overlooked the change from
Sender: list[EMAIL PROTECTED]
to
Sender: list[EMAIL PROTECTED]
BTW: I think there are still some new problems that we hadn't
seen on the testing machine on which we tried everything.
But now is past the end of the working day around here...
Please send more feedback directly to me, aka [EMAIL PROTECTED]
Regards,
Martin Maechler [EMAIL PROTECTED]
Martin,
Thanks for the clarifications. Most importantly thanks for your energy
in maintaining and continuously improving the lists!
Best regards,
Marc
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[R] tseries contains a class for irregularly spaced time series
A new version of tseries (0.9-10) has been uploaded to CRAN. The new version contains the class irts for irregularly spaced time series. Irregular time series are basically time series where each observation (uni- or multivariate) has a time-stamp represented by an object of class POSIXct. It provides some basic functionality such as reading and writing irregular time series from files, or plotting, printing, subscripting, and interpolating irregular time series. This is a first version of the class irts and I very much welcome feedback. best Adrian -- Dr. Adrian Trapletti Phone : +41 (0) 1 994 5631 Trapletti Statistical Computing Mobile: +41 (0)76 370 5631 Wildsbergstrasse 31 Fax : +41 (0) 1 994 5631 CH-8610 UsterEmail : mailto:[EMAIL PROTECTED] Switzerland WWW : http://trapletti.homelinux.com __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Sample size and stepAIC, step, or AIC
Do any R functions incorporate a sample sample size correction (e.g., Burnham and Anderson 1998). Thanks, Hank Stevens Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/botany/bot/henry.html http://www.muohio.edu/ecology __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] problem at installing Rade
Hi! I try to install the R version of ade4 on a linux (suse7.3) box with R 1.6.2 (from rpm) and get /usr/local/bin/R INSTALL ade4_1.00.tar.gz tar: /usr/local/lib/libpthread.so.0: version `GLIBC_2.2' not found (required by /lib/librt.so.1) ERROR: cannot extract package from 'ade4_1.00.tar.gz' But I actually have glibc 2.2.4 (at least this is what my suse's Yast conf. tool tells me, perhaps there is a more direct way of checking it?) Having used the rpm for R, should I use the rpm for ade4? Thanks Dr. Agustin Lobo Instituto de Ciencias de la Tierra (CSIC) Lluis Sole Sabaris s/n 08028 Barcelona SPAIN tel 34 93409 5410 fax 34 93411 0012 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Parallel programming using R
Thank you very much for the information of RPvm and RMPI packages. I got them. Best regards, Lun From: M.Kondrin [EMAIL PROTECTED] To: lun li [EMAIL PROTECTED] CC: R-Help [EMAIL PROTECTED] Subject: Re: [R] Parallel programming using R Date: Tue, 04 Mar 2003 14:25:02 -0800 lun li wrote: Dear All, For my regression problem(thousand dependents by thousand predictors by hundred months observations), I prefer to parallel computation in R. Is it possible to parallel programming using R as using C and Fortran? Cheers, Lun __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help Look up RPvm and RMPI packages Good luck ... __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Disregard:problem at installing Rade
Excuses to the list, this problem is a peculiarity of my system that I (thought) had solved, but after installing a (non-R) package seems to be here again. Agus Dr. Agustin Lobo Instituto de Ciencias de la Tierra (CSIC) Lluis Sole Sabaris s/n 08028 Barcelona SPAIN tel 34 93409 5410 fax 34 93411 0012 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Sample size and stepAIC, step, or AIC
They use AIC as defined by its author, Akaike. With good reason: `sample size' is not a well-defined concept in general, and the R functions are general. Most people call the adjusted (I hesitate to call it `corrected') version `AICC'. I believe the `clarified' 2002 edition of Burnham Anderson uses AIC_c. (It's easy to set up problems, e.g, a binomial glm, in which the number of observations relevant to each parameter differs radically. They occur in real life too.) On Tue, 4 Mar 2003, Martin Henry H. Stevens wrote: Do any R functions incorporate a sample sample size correction (e.g., Burnham and Anderson 1998). -- 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 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] (no subject)
On Tue, 4 Mar 2003, Usman Shehu wrote: It is possible I run R on MINGW32 MSYS? If so how do I configure the MSYS to do that. MSYS is an environment for building Unix packages under Windows. R runs under Windows: you don't need Unix-emulation tools to run it. We have a much more reliable set of Unix-emulation tools to build it, selected from Cygwin (of which MSYS is a derivative, anyway). -- 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 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] How to extract R{i} from lme object?
Hi, lme() users,
Can some one tell me how to do this.
I model Orthodont with the same G for random
variables, but different R{i}'s for boys and girls, so
that I can get sigma1_square_hat for boys and
sigma2_square_hat for girls.
The model is Y{i}=X{i}beta + Z{i}b + e{i}
b ~ iid N(0,G) and e{i} ~ iid N(0,R{i}) i=1,2
orth.lme - lme(distance ~ Sex * age, data=Orthodont,
random=~age|Subject, weights=varIdent(form=~1|Sex),
method=ML)
I can see the numbers I need from summary(), but how
can I extract them? I tried several functions in nlme,
but I cannot find a correct one.
Peng
Peng Liu
--
Peng Liu |
Division of Statistics|
Northern Illinois University |
De Kalb, IL 60115, USA|
E-mail: [EMAIL PROTECTED] |
--
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Re: [R] How to extract R{i} from lme object?
Peng wrote:
Hi, lme() users,
Can some one tell me how to do this.
I model Orthodont with the same G for random
variables, but different R{i}'s for boys and girls, so
that I can get sigma1_square_hat for boys and
sigma2_square_hat for girls.
The model is Y{i}=X{i}beta + Z{i}b + e{i}
b ~ iid N(0,G) and e{i} ~ iid N(0,R{i}) i=1,2
orth.lme - lme(distance ~ Sex * age, data=Orthodont,
random=~age|Subject, weights=varIdent(form=~1|Sex),
method=ML)
I can see the numbers I need from summary(), but how
can I extract them? I tried several functions in nlme,
but I cannot find a correct one.
Peng
Peng,
Is this what you need?
R data(Orthodont)
R orth.lme - lme(distance ~ Sex * age,
+ data=Orthodont,
+ random=~age|Subject,
+ weights=varIdent(form=~1|Sex),
+ method=ML)
R orth.lme$modelStruct$varStruct
Variance function structure of class varIdent representing
MaleFemale
1.000 0.4112708
R rcov.unscaled - as.matrix(orth.lme$modelStruct$reStruct[[1]])
R rcov.scaled - rcov.unscaled * orth.lme$sigma^2
R Stdev - sqrt(diag(rcov.scaled))
R Stdev
(Intercept) age
1.7914848 0.1408001
R
If there's nesting, look for more elements in $reStruct.
Regards,
Sundar
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Re: [R] How to extract R{i} from lme object?
--- Sundar Dorai-Raj [EMAIL PROTECTED] wrote:
Peng wrote:
Hi, lme() users,
Can some one tell me how to do this.
I model Orthodont with the same G for random
variables, but different R{i}'s for boys and
girls, so
that I can get sigma1_square_hat for boys and
sigma2_square_hat for girls.
The model is Y{i}=X{i}beta + Z{i}b + e{i}
b ~ iid N(0,G) and e{i} ~ iid N(0,R{i}) i=1,2
orth.lme - lme(distance ~ Sex * age,
data=Orthodont,
random=~age|Subject,
weights=varIdent(form=~1|Sex),
method=ML)
I can see the numbers I need from summary(), but
how
can I extract them? I tried several functions in
nlme,
but I cannot find a correct one.
Peng
Peng,
Is this what you need?
R data(Orthodont)
R orth.lme - lme(distance ~ Sex * age,
+ data=Orthodont,
+ random=~age|Subject,
+ weights=varIdent(form=~1|Sex),
+ method=ML)
R orth.lme$modelStruct$varStruct
Variance function structure of class varIdent
representing
MaleFemale
1.000 0.4112708
Sundar,
Thanks a lot!
In the above model, I assume the error term for boy
has iid N(0, sigma1), and that for girl has iid
N(0,sigma2). I hope that I wrote the correct lme(). If
so, what I want is:
(1/unique(attributes(orth.lme$modelStruct$varStruct)$weights)*orth.lme$sigma)^2
[1] 2.6292575 0.4447223
, where 2.629 for boys, and 0.445 for girls.
I am still wondering whether there is a function like
getVarCov(), so that I can get R var-cov matrix
directly. I looked through the function list of nlme,
but I cannot find.
Peng
R rcov.unscaled -
as.matrix(orth.lme$modelStruct$reStruct[[1]])
R rcov.scaled - rcov.unscaled * orth.lme$sigma^2
R Stdev - sqrt(diag(rcov.scaled))
R Stdev
(Intercept) age
1.7914848 0.1408001
R
If there's nesting, look for more elements in
$reStruct.
Regards,
Sundar
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Re: [R] Parallel programming using R
On Tue, 04 Mar 2003, lun li told this: Thank you very much for the information of RPvm and RMPI packages. I got them. You might want to wait for a few days for snow (Simple Network of Workstations) package to reach CPAN. Or download it from here, http://www.stat.uiowa.edu/~luke/R/cluster/cluster.html Cheers, Michael __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] logistic regression for repeated measurement
Dear R-users (B (BI need your help. (BI have a data set which was collected from (Ban experiment of one between- and one (Bwithin-subject design. And the response (Bdata is coded by success(1)/failure(0). (B (BThe experiment had two groups of subjects: (BThe one was experimental, and the (Bother, control. The experimental group (Bgot a task training, and both groups of subjects (Bwere tested twice, once before the training (Band once after the training. at the same time. (BI like to examine the effect of training by (Bdetecting an interaction effect of the group and (Btests. (BNow, it seems glm is not appropriate to this (Bsituation since it does not deal with stratified (Berrors. (B (BCould you lead me to appropriate functions? (BSincerely (B--- (BHiroto Miyoshi $B;09%90?M(B (B[EMAIL PROTECTED] (B (B__ (B[EMAIL PROTECTED] mailing list (Bhttp://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] logistic regression for repeated measurement
On Wed, 5 Mar 2003 11:14:37 +0900 Hiroto Miyoshi [EMAIL PROTECTED] wrote: Dear R-users I need your help. I have a data set which was collected from an experiment of one between- and one within-subject design. And the response data is coded by success(1)/failure(0). The experiment had two groups of subjects: The one was experimental, and the other, control. The experimental group got a task training, and both groups of subjects were tested twice, once before the training and once after the training. at the same time. I like to examine the effect of training by detecting an interaction effect of the group and tests. Now, it seems glm is not appropriate to this situation since it does not deal with stratified errors. Could you lead me to appropriate functions? Sincerely --- Hiroto Miyoshi [EMAIL PROTECTED] There are several ways to go. GEE is one, random effects models another. One other approach is to install the Hmisc and Design packages (http://hesweb1.med.virginia.edu/biostat/s) and do (assume id is the unique subject identifier): f - lrm(y ~ x1 + x2*x3 + ..., x=T, y=T) # working independence model g - robcov(f, id) # cluster sandwich variance adjustment h - bootcov(f, id, B=100) # cluster bootstrap adjustment summary(g) # etc. -- Frank E Harrell Jr Prof. of Biostatistics Statistics Div. of Biostatistics Epidem. Dept. of Health Evaluation Sciences U. Virginia School of Medicine http://hesweb1.med.virginia.edu/biostat __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] How to draw several plots in one figure?
Hey, I want to draw several plots sequently, but have to make them dispaly in one figure. So how to achieve this? Thanks. Fred __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] How to draw several plots in one figure?
Thanks, Su. But I want to plot the several plots in the same x-y axis setting, not in multiple subplots. - Original Message - From: Steve Su [EMAIL PROTECTED] To: Feng Zhang [EMAIL PROTECTED] Sent: Wednesday, March 05, 2003 12:29 AM Subject: Re: [R] How to draw several plots in one figure? Dear Fred, try par(mfrow=c(2,2)) for example, gives four plots per page. Also try trellis plots. Steve. - Original Message - From: Feng Zhang [EMAIL PROTECTED] To: R-Help [EMAIL PROTECTED] Sent: Wednesday, March 05, 2003 4:05 PM Subject: [R] How to draw several plots in one figure? Hey, I want to draw several plots sequently, but have to make them dispaly in one figure. So how to achieve this? Thanks. Fred __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] How to draw several plots in one figure?
One way is to make inital plot: plot() Then build other data into the plot using: lines() points() etc. see help files for those Alternatively: set par(new=T) then plot again and the device wont be cleared J. From: Feng Zhang [EMAIL PROTECTED] To: Steve Su [EMAIL PROTECTED] CC: R-Help [EMAIL PROTECTED] Subject: Re: [R] How to draw several plots in one figure? Date: Wed, 5 Mar 2003 00:35:00 -0600 Thanks, Su. But I want to plot the several plots in the same x-y axis setting, not in multiple subplots. - Original Message - From: Steve Su [EMAIL PROTECTED] To: Feng Zhang [EMAIL PROTECTED] Sent: Wednesday, March 05, 2003 12:29 AM Subject: Re: [R] How to draw several plots in one figure? Dear Fred, try par(mfrow=c(2,2)) for example, gives four plots per page. Also try trellis plots. Steve. - Original Message - From: Feng Zhang [EMAIL PROTECTED] To: R-Help [EMAIL PROTECTED] Sent: Wednesday, March 05, 2003 4:05 PM Subject: [R] How to draw several plots in one figure? Hey, I want to draw several plots sequently, but have to make them dispaly in one figure. So how to achieve this? Thanks. Fred __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
BSOD with ESS[R] under win2000
I have had a visit from our windows buddy the BSOD twice in one day when running R1.6.2 under ESS5.1.24 on a win2000 platform. I wasn't doing anything special, just moving or resizing the emacs window, although I did have 4 or 5 emacs windows open at the time. Has anyone else observed this problem? Thanks, Darryl. __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
