Please pass along, and apologies for double posting.
We have money to support a student till January 2007 (with a salary of about
1000 euro/month). Most of the work will focus on classification/prediction
using microarray data. The work will involve both methodological research
(mainly
Dear Eleni,
But if every time you remove a variable you pass some test data (ie data
not used to train the model) and base the performance of the new, reduced
model on the error rate on the confusion matrix for the test data, then
this overfitting should not be an issue, right? (unless of
Dear Paul,
I have no direct experience with rpvm, but doing it with rmpi is a piece of
cake. I could provide you with some hints if you want. (I am tempted to ask
why you are using PVM instead of MPI, but this might be the wrong question).
Best,
R.
On Friday 11 August 2006 18:12, Paul Y.
this with rmpi. I use PVM simply because
I picked it up first and it worked well for me. If MPI is the only way to
make use the two processors, I will find out whether it is available or
works in our cluster. Thanks a lot for your response.
Regards,
Paul.
Ramon Diaz-Uriarte wrote:
Dear Paul
Dear Paul,
(I forgot to answer over the weekend). With mpi it is essentially the same.
When using makeCluster, specify the number of slaves. If you have three
machines, and you want each to run two slave processes, just use a 6.
Before that, though, you should tell LAM/MPI how to set up the
Dear Tom,
To add a few things to explore:
- I'd definitely go with LaTeX. Depending on how much formatting control you
want, though, and if your coworkers are reluctant to jump into LaTeX, you
might start with reStructuredText (http://docutils.sourceforge.net/rst.html)
or text2tags
On Wednesday 20 September 2006 17:16, Marc Schwartz (via MN) wrote:
On Wed, 2006-09-20 at 17:03 +0200, Rainer M Krug wrote:
Hi
I heard so much about Emacs and ESS that I decided to try it out - but I
am stuck at the beginning.
Is there anywhere a beginners manual for Emacs ESS to
On Wednesday 20 September 2006 22:21, Iuri Gavronski wrote:
I would like to buy a basic statistics book (experimental design,
sampling, ANOVA, regression, etc.) with examples in R. Or download it
in PDF or html format.
I went to the CRAN contributed documentation, but there were only R
Dear Elizabeth,
When I looked for this a couple of years ago, I found DF's to be discussed in
the book by Pinheiro Bates Mixed effects models for S and S-Plus, as well
as the documentation for SAS's PROC MIXED (I believe that the discussion on
df's on the SAS manual was more complete than on
Dear Erin,
On Tuesday 21 September 2004 06:10, Erin L. Leisz wrote:
hi. i really need help using this program. computer language is a foreign
language to me, and thus, i cannot make heads nor tails of the user manuals
from the website. i need to locate step-by-step examples of simple
If
On Wednesday 22 September 2004 13:07, Ted Harding wrote:
On 22-Sep-04 kan Liu wrote:
Hi, Many thanks for your helpful comments and suggestions. The attached
are the data in both log10 scale and original scale. It would be very
grateful if you could suggest which version of test should be
Dear Cristoph,
I guess you want to assess the error rate of a LDA that has been fitted to a
set of currently existing training data, and that in the future you will get
some new observation(s) for which you want to make a prediction.
Then, I'd say that you want to use the second approach. You
Dear Cristoph, David, Torsten and Bjørn-Helge,
I think that Bjørn-Helge has made more explicit what I had in mind (which I
think is close also to what David mentioned). As well, at the very least, not
placing the PCA inside the cross-validation will underestimate the variance
in the
On Wednesday 05 January 2005 16:29, Thomas Petzoldt wrote:
Douglas Bates wrote:
I'm not sure what model you want to fit here. To specify a random
effect in lme you need both a grouping factor and a model matrix. The
error message indicates that lme is unable to determine a grouping
Dear Rita,
Do you want a package just for yourself, or something useful for others, with
docs, etc? I think the rest of the answers in this thread will help you
create a full fledged package. See also the detailed explanation
in Writing R extensions.
If you just want something quick and dirty
On Wednesday 05 July 2006 10:14, A.J. Rossini wrote:
Greetings!
I have a few colleagues who like the idea of Sweave, but have failed
to become enlightened monks of the One True Editor
(http://www.dina.dk/~abraham/religion/)
Are there any other Microsoft-centric editors or IDEs which have
On Wednesday 05 July 2006 16:05, A.J. Rossini wrote:
On 7/5/06, Ramon Diaz-Uriarte [EMAIL PROTECTED] wrote:
On Wednesday 05 July 2006 10:14, A.J. Rossini wrote:
Greetings!
I have a few colleagues who like the idea of Sweave, but have failed
to become enlightened monks of the One
Dear Peter,
I especially like the VIF (and GVIF) functions in package car, by John Fox.
(I'm assuming you are dealing with [generalized] linear models).
HTH,
R.
On Wednesday 05 July 2006 17:16, Peter Lauren wrote:
Is there a colinearty function implemented in R? I
have tried
Dear All,
I found Andy Liaw's suggestion about using a NUMA (instead of SMP) kernel when
running R on amd64 with 1 CPU
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/35109.html
A couple of questions:
1. Is this still the case with the newer dual-core opterons (e.g., the 275 et
al.,
I started using LyX; it is very straightforward. Then, I started exporting to
LaTeX and playing around with the LaTeX file (I found it faster than using
LyX, and could take my file anywhere they had something that could manipulate
text ---emacs, vim, nedit, whatever).
Googling you'll find
Dear All,
I was writing a small wrapper to bootstrap a classification algorithm, but if
we generate the indices in the usual way as:
bootindex - sample(index, N, replace = TRUE)
there is a non-zero probability that all the samples belong to only
one class, thus leading to problems in the
On Wednesday 20 April 2005 00:17, array chip wrote:
Hi all,
In Tibshirani's PNAS paper about nearest shrunken
centroid analysis of microarrays (PNAS vol 99:6567),
they used cross validation to choose the amount of
shrinkage used in the model, and then test the
performance of the model with
Dear Giordano,
Library Hmisc, by Frank Harrell, contains several functions for imputation
which I have found extremely useful.
Best,
R.
On Tuesday 26 April 2005 11:58, Giordano Sanchez wrote:
Hello,
Thanks for the instructive responses. But two questions arise.
Firstable I can't manage
Dear Uwe,
Yes, sure, I understand how to install to another directory. I think I was not
very clear, because my doubt is whether I should do that, or if it is OK to
install to the very same place where Debian left the previous installation.
By doing the later I save myself having to reinstall
On Friday 06 May 2005 09:48, Prof Brian Ripley wrote:
On Fri, 6 May 2005, Uwe Ligges wrote:
Diaz.Ramon wrote:
Dear All,
I've got into the habit of installing R from the precompiled Debian
binaries, including many of the packages from the r-cran-* Debian
packages, and later building
Dear Gareth,
?coxph.control (which we are told to check from ?coxph) contains an argument
for maxiter.
Best,
R.
On Tuesday 26 August 2003 13:51, Gareth Hughes wrote:
How can I specify the maximum number of iterations in coxph
whilst also specifying my model?? I can't find any on-line
Dear All,
I have been using the randomForest package for a couple of difficult
prediction problems (which also share p n). The performance is good, but
since all the variables in the data set are used, interpretation of what is
going on is not easy, even after looking at variable importance
Dear Andy,
Thanks a lot for your message.
This is quite a hazardous game. We've been burned by this ourselves. I'll
send you a paper we submitted on variable selection for random forest
off-line. (Those who are interested, let me know.)
Thanks!
The basic problem is that when you select
Dear All,
I think there is a typo in the documentation for coxph (library survival).
The help says:
eps: convergence threshold. Iteration will continue until the
relative change in the log-likelihood is less than eps.
Default is .0001.
However, if I do coxph.control() I
Dear Bill,
You can obtain marginal tests using
anova(your.lme.object, type = marginal)
(If you are going to compare output, note that marginal tests when using
non-orthogonal contrasts ---SAS and treatment--- might give you unexpected
results, last time I checked).
R.
On Thursday 11
Since Spencer Graves already answered the factorial questions, I'll try to
answer one of the other two:
On Monday 15 December 2003 05:17, [EMAIL PROTECTED] wrote:
To anyone who can help,
Intelligent question (1) I keep on trying to fit a linear mixed model in R
using 'lme(y~fxd.dsgn, data =
This is strange; the sir for R I know (in package dr on CRAN, from S.
Weisberg), last time I checked (about a year ago?) was able to handle
multivariate responses. In fact, p. 6 of the documentation shows an example
of SIR with a bivariate response, and I tried it, and it works.
Best,
R.
On
Dear Martin,
I'd suggest you check the DESCRIPTION file and ask the author(s) of the
package (e.g., a package might be related to a tech report which might, now,
be in press, or whatever).
Best,
R.
On Monday 09 February 2004 15:21, Martin Henry H. Stevens wrote:
How do I cite a package
On Tuesday 07 November 2006 15:56, Randall C Johnson [Contr.] wrote:
Hello everyone,
I've been fiddling around with the snow and Rmpi packages on my new Intel
Mac, and have run into a few problems. When I make a cluster on my machine,
both slaves start up just fine, and everything works as
On Tuesday 07 November 2006 19:28, Randall C Johnson [Contr.] wrote:
On 11/7/06 11:28 AM, Ramon Diaz-Uriarte [EMAIL PROTECTED] wrote:
On Tuesday 07 November 2006 15:56, Randall C Johnson [Contr.] wrote:
Hello everyone,
I've been fiddling around with the snow and Rmpi packages on my new
On Thursday 23 November 2006 15:44, Prof Brian Ripley wrote:
Try this:
gannet% cat month.R
x - commandArgs()
print(x[length(x)])
gannet% R --slave --args January month.R
[1] January
Is the above
R --slave --args January month.R
the preferred way of using it?
I tend to use
R
Thanks.
R.
On Thursday 23 November 2006 16:32, Prof Brian Ripley wrote:
On Thu, 23 Nov 2006, Ramon Diaz-Uriarte wrote:
On Thursday 23 November 2006 15:44, Prof Brian Ripley wrote:
Try this:
gannet% cat month.R
x - commandArgs()
print(x[length(x)])
gannet% R --slave --args
On Tuesday 28 November 2006 16:03, Tom Backer Johnsen wrote:
I have been looking at the documentation and the output from the
functions princomp() and factanal(), and found them somewhat difficult
to understand. This is probably due to differences in respect to what
I am used to with respect
On Friday 01 December 2006 13:23, Millo Giovanni wrote:
Dear List,
the advent of multicore machines in the consumer segment makes me wonder
whether it would, at least in principle, be possible to divide a
computational task into more slave R processes running on the different
cores of the
Dear All,
I've read Thomas Lumley's fortune If the answer is parse() you should usually
rethink the question.. But I am not sure it that also applies (and why) to
other situations (Lumley's comment
http://tolstoy.newcastle.edu.au/R/help/05/02/12204.html
was in reply to accessing a list).
On Friday 05 January 2007 19:21, Peter Dalgaard wrote:
Ramon Diaz-Uriarte wrote:
Dear All,
I've read Thomas Lumley's fortune If the answer is parse() you should
usually rethink the question.. But I am not sure it that also applies
(and why) to other situations (Lumley's comment
http
Statistics
South San Francisco, CA 94404
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Ramon Diaz-Uriarte
Sent: Friday, January 05, 2007 10:02 AM
To: r-help; [EMAIL PROTECTED]
Subject: [R] eval(parse(text vs. get when accessing a function
Dear All
- function(x, fpost) {
calledf - eval(parse(text = paste(f., fpost, sep = )))
calledf(x)
## the thousands of calls to calledf go here
}
R.
On 1/5/07, Ramon Diaz-Uriarte [EMAIL PROTECTED] wrote:
On Friday 05 January 2007 19:35, Bert Gunter wrote:
??
Or to add to what Peter Dalgaard
. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Ramon
Diaz-Uriarte
Sent: Friday, January 05, 2007 11:41 AM
To: Peter Dalgaard
Cc: r-help; [EMAIL
On 1/6/07, Thomas Lumley [EMAIL PROTECTED] wrote:
On Fri, 5 Jan 2007, Ramon Diaz-Uriarte wrote:
I see, this is direct way of dealing with the problem. However, you first
need
to build the f list, and you might not know about that ahead of time. For
instance, if I build a function so
On 1/6/07, Brian Ripley [EMAIL PROTECTED] wrote:
On Sat, 6 Jan 2007, Ramon Diaz-Uriarte wrote:
(...)
cvFunct - function(whatever, genefiltertype, whateverelse) {
internalGeneSelect - eval(parse(text = paste(geneSelect,
genefiltertype, sep
-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz
__
R-help
of OOP (nor of S4 classes); in
this case, in particular, it seems there is a lot of scaffolding in
the code above (the counterpoint to the structure?) and, regarding
scoping rules, I prefer to think about them explicitly (I find it much
simpler than inheritance).
Best,
R.
Ramon Diaz-Uriarte
- function(x) UseMethod(f)
f(structure(10, class = a))
[1] 11
attr(,class)
[1] a
On 1/6/07, Ramon Diaz-Uriarte [EMAIL PROTECTED] wrote:
Hi Martin,
On 1/6/07, Martin Morgan [EMAIL PROTECTED] wrote:
Hi Ramon,
It seems like a naming convention (f.xxx) and eval(parse
On Friday 19 January 2007 03:30, Frank E Harrell Jr wrote:
Like kile for LaTeX, Linux/KDE's kate editor is an excellent editor for
R, with easy code submission to a running R process. Syntax
highlighting is good. I have not been able to figure out two things:
- how to automatically
On Friday 19 January 2007 14:12, Frank E Harrell Jr wrote:
Ramon Diaz-Uriarte wrote:
On Friday 19 January 2007 03:30, Frank E Harrell Jr wrote:
Like kile for LaTeX, Linux/KDE's kate editor is an excellent editor for
R, with easy code submission to a running R process. Syntax
highlighting
Hi Dirk,
On Friday 19 January 2007 15:39, Dirk Eddelbuettel wrote:
Ramon, Frank,
Great discussion. Nothing like an editor feud over morning coffee. Just
kidding.
Not at the editor flame war stage yet (nobody mentioned vim :-).
On 19 January 2007 at 11:18, Ramon Diaz-Uriarte wrote
Hi Marc,
Thanks a lot for the detailed explanation! I'll give it a try. (But
still, why emacs23? what is missing in v. 21 that you get in 23?).
Best,
R.
On 1/19/07, Marc Schwartz [EMAIL PROTECTED] wrote:
On Fri, 2007-01-19 at 16:09 +0100, Ramon Diaz-Uriarte wrote:
snip
I had problems
script to build it. Let me know.
Let me try with the debian packages, and if I have problems, I'll
definitely start bugging you. Thanks a lot for your help!
Best,
R.
Best regards,
Marc
On Sat, 2007-01-20 at 03:59 +0100, Ramon Diaz-Uriarte wrote:
Hi Marc,
Thanks a lot
On 1/20/07, Marc Schwartz [EMAIL PROTECTED] wrote:
On Sat, 2007-01-20 at 11:20 +0100, Ramon Diaz-Uriarte wrote:
On 1/20/07, Marc Schwartz [EMAIL PROTECTED] wrote:
xft anti-aliasing is incorporated into the version 23 unicode trunk.
So it looks great on a hi-res LCD panel. Without xft
read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz
On 1/20/07, Peter Dalgaard [EMAIL PROTECTED] wrote:
Ramon Diaz-Uriarte wrote:
Hi Marc,
Thanks a lot for the detailed explanation! I'll give it a try. (But
still, why emacs23? what is missing in v. 21 that you get in 23?).
Best,
R.
Ability to load files with UTF-8 characters
On 1/22/07, Dirk Eddelbuettel [EMAIL PROTECTED] wrote:
On 22 January 2007 at 00:05, Ramon Diaz-Uriarte wrote:
| On 1/20/07, Dirk Eddelbuettel [EMAIL PROTECTED] wrote:
| Just confirms my suspicion that even after all these years, I barely
| scratched the surface of ess. That '2+ years' old
and provide commented, minimal, self-contained, reproducible code.
--
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz
__
R-help@stat.math.ethz.ch mailing
]]
__
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
and provide commented, minimal, self-contained, reproducible code.
--
Ramon Diaz-Uriarte
list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
.
--
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read
.
--
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read
://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National
, reproducible code.
--
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman
sockets, etc,
directly from R.
However, Simon's comment about better ways of R-to-R communication
made me wonder if this idea really makes sense. What is the catch?
Have other people tried similar approaches?
Thanks,
R.
--
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology
On 4/9/07, Simon Urbanek [EMAIL PROTECTED] wrote:
On Apr 7, 2007, at 10:56 AM, Ramon Diaz-Uriarte wrote:
Dear All,
The clients.txt file of the latest Rserve package, by Simon
Urbanek, says, regarding its R client,
(...) a simple R client, i.e. it allows you to connect to Rserve
the subscript, and then call those objects back
into the main script, which seems like a very slow and onerous way to
do it.
Would Rserve do what I'm looking for?
On 4/7/07, Ramon Diaz-Uriarte [EMAIL PROTECTED] wrote:
Dear All,
The clients.txt file of the latest Rserve package, by Simon
---or PVM--- add. ).
HTH,
R.
On 4/7/07, Ramon Diaz-Uriarte [EMAIL PROTECTED] wrote:
Dear All,
The clients.txt file of the latest Rserve package, by Simon Urbanek,
says, regarding its R client,
(...) a simple R client, i.e. it allows you to connect to Rserve from
R itself. It is very
to
do it.
Would Rserve do what I'm looking for?
On 4/7/07, Ramon Diaz-Uriarte [EMAIL PROTECTED] wrote:
Dear All,
The clients.txt file of the latest Rserve package, by Simon
Urbanek,
says, regarding its R client,
(...) a simple R client, i.e. it allows you to connect
On 4/10/07, AJ Rossini [EMAIL PROTECTED] wrote:
On Monday 09 April 2007 23:02, Ramon Diaz-Uriarte wrote:
(Yes, maybe I should check snowFT, but it uses PVM, and I recall a
while back there was a reason why we decided to go with MPI instead of
PVM).
There is no reason that you can't run
On 4/11/07, AJ Rossini [EMAIL PROTECTED] wrote:
On Tuesday 10 April 2007 23:17, Ramon Diaz-Uriarte wrote:
Of course, you are right there. I think that might still be the case.
At the time we made our decision, and decided to go for MPI, MPI 2 was
already out, and MPI seemed more like
code.
--
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
.
--
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE
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