Re: [R] Strange degrees of freedom and SS from car::Anova with type II SS?

ty and the projections used by Anova() break down."). Again, thanks for clarifying my confusion. Best, Ramon > > Best, > John > > - > John Fox, Professor Emeritus > McMaster University > Hamilton, Ontario, Canada

[R] Strange degrees of freedom and SS from car::Anova with type II SS?

(residuals(m_1)^2) - sum(residuals(m_2)^2) -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz ___

Re: [R] On the Design of the R Language

read the posting guide http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > -- > Peter Dalgaard, Professor, > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Email: p

[R] OT: snow socket clusters with VirtualBox and VMware player (Linux host, Win guest)

do in this. However, has anybody been able to run snow and/or snowfall with socket clusters in a similar setup? Best, R. -- Ramon Diaz-Uriarte Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz Phone: +34-91-732-8000 ext. 3

Re: [R] snow makeCluster (makeSOCKcluster) not working in R-2.11

://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 Structural Biology and Biocomputing Programme Spanish National Cancer Centre (C

Re: [R] as.ffdf.data.frame now breaks if using pattern

ame(ffd) > $x > [1] "d:/tmp/fftmp35c34861.ff" > > $y > [1] "d:/tmp/fftmp5be946bb.ff" > > $z > [1] "d:/tmp/fftmp26c49ce.ff" > > Jens > > > -Ursprüngliche Nachricht- > Von: Ramon Diaz-Uriarte > Gesendet: Apr 7, 2010 7:01:23

[R] as.ffdf.data.frame now breaks if using pattern

mand crashes. I wonder if the new behavior is intentional or a bug. If intentional, what is the recommended way of using "pattern" now? Thanks, R. -- Ramon Diaz-Uriarte Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz Phone: +34-

Re: [R] validate (rms package) using step instead of fastbw

Thanks for clarifying it Frank. (Yes, no univariate screening prior to feeding the model to validate. And the "bias correct" I guess is from my spanglish factory of new terminology ;-) Best, R. On Fri, Feb 12, 2010 at 6:26 PM, Frank E Harrell Jr wrote: > Ramon Diaz-Uriarte wrote

Re: [R] validate (rms package) using step instead of fastbw

Frank, let me make sure I understand: On Fri, Feb 12, 2010 at 5:57 PM, Frank E Harrell Jr wrote: > Ramon Diaz-Uriarte wrote: >> >> Dear Frank, >> >> Thanks a lot for your response. And apologies for the question, >> because the answer was obviously in the

Re: [R] validate (rms package) using step instead of fastbw

colleagues is that by doing variable selection, we are actually getting a worse model (as evidenced by the bias-corrected AUC, which is smaller if attempting variable selection). Best, R. On Fri, Feb 12, 2010 at 3:13 PM, Frank E Harrell Jr wrote: > Ramon Diaz-Uriarte wrote: >> &g

[R] validate (rms package) using step instead of fastbw

l. Best, R. P.S. Simple example of fastbw compared to step: library(MASS) ## for stepAIC and bwt data example(birthwt) library(rms) bwt.glm <- glm(low ~ ., family = binomial, data = bwt) bwt.lrm <- lrm(low ~ ., data = bwt) step(bwt.glm) ## same as stepAIC(bwt.glm) fastbw(bwt.lrm) -- Ram

[R] multicore: defunct R processes left

2009 month 11 day05 svn rev50317 language R version.string R version 2.10.0 Patched (2009-11-05 r50317) -- Ramon Diaz-Uriarte Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rd

Re: [R] questions on the ff package

o this? > > Thanks > > Jeff > > __ > R-help@r-project.org 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, min

Re: [R] Best R text editors?

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. >>> >>> __ >>&

Re: [R] Problem with predict.coxph

___ > R-help@r-project.org 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, re

Re: [R] DNAcopy package in R

.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 Phone: +34-91-732-8000 ext

Re: [R] running R-code outside of R

s totally out of line. R. > Mike > > __ > R-help@r-project.org 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, mi

Re: [R] Programming Concepts and Philosophy

___ > R-help@r-project.org 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. > -- R

Re: [R] How can I execute a .R/script file

//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 Nati

Re: [R] ADaCGH package crashes at mpiInit()

___ > R-help@r-project.org 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 Statistical Computin

Re: [R] Calling C code from R...wrapping C structures

> > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > an

Re: [R] permutation test assumption?

33> . > > > > News and news media > > <http://www.agrsci.org/navigation/nyheder_og_presse> . > > > > This email may contain information that is confidential. Any > > use or publication of this email without written permission > > from Faculty of Agricultu

Re: [R] Conditionals for Errors or error flags

t; School for Marine Science and Technology > University of Massachusetts > 200 Mill Road, Suite 325 > Fairhaven, MA 02719 > [EMAIL PROTECTED] > 508-758-6393 > > __ > R-help@r-project.org mailing list > https://stat.

Re: [R] Help with 'memory not mapped'

s) > >> 4: eval.with.vis(ei, envir) > >> 5: source("rrprogv1_2.R") > >> 6: eval.with.vis(expr, envir, enclos) > >> 7: eval.with.vis(ei, envir) > >> 8: source("mariam1_2.R") > >> > >> Possible actions: >

Re: [R] Help with 'memory not mapped'

> R-help@r-project.org 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 Statistical Com

Re: [R] R_alloc with structures with "flexible array members"

5 AM, Dirk Eddelbuettel <[EMAIL PROTECTED]> wrote: > > Hi Ramon, > > > On 5 March 2008 at 22:00, Ramon Diaz-Uriarte wrote: > | Yes, of course! You are right. What a silly mistake on my part! I was > | using a standalone program for development of functions, debugging, &

Re: [R] R_alloc with structures with "flexible array members"

Humm... but I mistakenly thought I was assuming almost nothing. R. On Wed, Mar 5, 2008 at 10:38 PM, Jeffrey Horner <[EMAIL PROTECTED]> wrote: > Ramon Diaz-Uriarte wrote on 03/05/2008 03:00 PM: > > > Dear Prof. Ripley, > > > > Yes, of course! You are right. What

Re: [R] R_alloc with structures with "flexible array members"

On Wed, 5 Mar 2008, Ramon Diaz-Uriarte wrote: > > > Dear Jeff, > > > > Thanks for the suggestion. However, something is still not working. > > This is a simple example: > > > > *** start C > > #include > &

Re: [R] R_alloc with structures with "flexible array members"

de -I/usr/share/R/include -L/usr/lib/R/lib -lR ex7.c and the ./a.out segfaults when I use R_alloc (not with malloc). Best, R. On Wed, Mar 5, 2008 at 5:23 PM, Jeffrey Horner <[EMAIL PROTECTED]> wrote: > Ramon Diaz-Uriarte wrote on 03/05/2008 04:25 AM: > > > > Dear All, >

[R] R_alloc with structures with "flexible array members"

eof(struct sequence)); but both result in segmentation faults. Should I just keep using malloc (and free at end)? Thanks, R. -- Ramon Diaz-Uriarte Statistical Computing Team Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http:

Re: [R] using zlib (was compress data on read, decompress on write)

Dear Prof. Ripley, Thanks for your reply. I think I understand now. Best, R. On Fri, Feb 29, 2008 at 7:36 PM, Prof Brian Ripley <[EMAIL PROTECTED]> wrote: > On Fri, 29 Feb 2008, Ramon Diaz-Uriarte wrote: > > > Dear All, > > > > > I think I am confused

[R] using zlib (was compress data on read, decompress on write)

ke creative use of serialization > to do the compression. > > > On Thu, 28 Feb 2008, Ramon Diaz-Uriarte wrote: > > > Dear All, > > > > I'd like to be able to have R store (in a list component) a compressed > > data set, and then write it out uncompresse

Re: [R] compress data on read, decompress on write

Thanks, Greg. Yes, I'd store the compressed stuff as a raw data type. Best, R. On Thu, Feb 28, 2008 at 11:54 PM, Gregory Warnes <[EMAIL PROTECTED]> wrote: > > You might look at storing the data using R's "raw" data type... > > -G > > > >

Re: [R] compress data on read, decompress on write

ties to do internal (gzip) > compression and decompression (e.g. see the end of > src/main/connections.c), and you could make creative use of serialization > to do the compression. > > > On Thu, 28 Feb 2008, Ramon Diaz-Uriarte wrote: > > > Dear All, > > > > I'

Re: [R] compress data on read, decompress on write

this affords great compression ratios, depending on the size > and degree of sparseness of the matrix. > > -Christos > > > > > -Original Message- > > From: [EMAIL PROTECTED] > > [mailto:[EMAIL PROTECTED] On Behalf Of Ramon Diaz-Uriarte > > Sent: Thu

[R] compress data on read, decompress on write

d then use readBin, etc, from R. But, if I can, I'd like to avoid our C code having to call zlib, etc, so as to make our package easily portable. Thanks, R. -- Ramon Diaz-Uriarte Statistical Computing Team Structural Biology and Biocomputing Programme Spanish National Cancer Cen

Re: [R] Any mountain clustering method in R?

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

Re: [R] how to wait after plotting in BATCH mode?

you. > > -- > kind regards, > > Jonas Stein <[EMAIL PROTECTED]> > > __ > R-help@r-project.org 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,

Re: [R] Normalizing data

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. > > > > > > -- > Jim Holtman > Cincinnati, OH >

Re: [R] Linux editor for R+LaTeX, but not Emacs

gt; 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 Span