Re: [R] Ignoring missing elements in data.frame()

Hi, One possible way to get around it is using following idea : X1 - rnorm(10) X2 - rnorm(10) Names - c(X1,X2,X3) Names - Names[Names %in% ls()] n - length(Names) p - 10 #length of each object output - matrix(NA,ncol=n,nrow=p) for(i in 1:n){ output[,i] - get(Names[i]) } output -

Re: [R] Wilcoxon test output as a table

# not tested out - rbind(as.numeric(Wnew),as.numeric(P)) rownames(out) - c(Wnew,P) Cheers On Sat, Jun 5, 2010 at 11:18 PM, Iurie Malai iurie.ma...@gmail.com wrote: Hi! I searched some time ago a way to get the Wilcoxon test results as a table more or less formatted. Nobody told me any

Re: [R] (no subject)

OK, as you're new: 1) this is a list about R, not about statistics. 2) it looks awkwardly much like a homework assignment. People tend to be not really keen on solving those ones. 3) READ THE POSTING GUIDELINES. Seriously, read them. http://www.R-project.org/posting-guide.html As a tip : go

Re: [R] R2HTML problem

Tinn-R is using the R2HTML package itself for communication with R. You could ask JC Faria who wrote Tinn-R what exactly is going on there. You might get more help here : http://sourceforge.net/projects/tinn-r/support Personally, I'd just use a different editor in this case. I love Tinn-R, but

Re: [R] Wilcoxon test output as a table

: Warning in if (nchar(cmd) = width) return(cmd) :  the condition has length 1 and only the first element will be used 2010/6/6 Joris Meys jorism...@gmail.com # not tested out - rbind(as.numeric(Wnew),as.numeric(P)) rownames(out) - c(Wnew,P)        [[alternative HTML version deleted

Re: [R] Creating a maxtrix from conditional prints

Use rbind? Not the most optimal solution, but it should get the job done. # not tested Code example: out - c() for (x in 1:10) { for (y in 1:10) { qui - ifelse((mac[,1] == x) (mac[,5] == y) | (mac[,1] == y) (mac[,5] == x), 1, NA) quo - cbind(mac,qui) qua - subset(quo, qui ==1) if(nrow(qua) ==

Re: [R] Error Bar Issues

you can't refer to an argument within a function call. Try uiw - Saline[,3] plotCI(x=Saline [,1],y=Saline [,2], uiw=uiw, liw=uiw, err=y, pch=21, pt.bg=par(bg), cex=1.5, lty=1, type=o, gap=0, sfrac=0.005, xlim=c(-21,340),xaxp=c(-20,320,11), xlab=Time (min), ylim=c(0,12), yaxp=c(0,12,11),

Re: [R] ordinal variables

, Manchester M13 9PL, UK Tel. 0044  161 275 3485 iasonas.lampria...@manchester.ac.uk --- On Thu, 3/6/10, S Ellison s.elli...@lgc.co.uk wrote: From: S Ellison s.elli...@lgc.co.uk Subject: Re: [R] ordinal variables To: Joris Meys jorism...@gmail.com, Iasonas Lamprianou lampria...@yahoo.com Cc: r

Re: [R] Handling of par() with variables

I think you misunderstand the working of par(). If you set new parameters, R allows you to store the old parameters simultaneously. Take a look at : par(no.readonly=T) oldpar - par(mar=c(1,1,1,1),tck=0.02) par(no.readonly=T) par(oldpar) par(no.readonly=T) So your line : newpar -

Re: [R] save in for loop

On a side note: On Thu, May 20, 2010 at 9:43 AM, Ivan Calandra ivan.calan...@uni-hamburg.de wrote: Thanks to all of you for your answers! ... Tao, I don't understand why you have backslashes before file and after .rda. I guess it's something about regular expression, but I'm still very new

Re: [R] ps-output and LaTeX/DVIPS/PS2PDF - Greek letters disappear

That's a problem of LateX and Ubuntu, not R : https://bugs.launchpad.net/ubuntu/+source/poppler/+bug/319495 You'll have more luck on an Ubuntu list or forum. Cheers Joris On Fri, Jun 4, 2010 at 11:47 AM, Steffen Uhlig steffen.uh...@htw-saarland.de wrote: Hello! My graphs are produced using

Re: [R] R with Emacs

Emacs ESS : http://ess.r-project.org/ Cheers Joris On Fri, Jun 4, 2010 at 12:55 PM, dhanush dhana...@gmail.com wrote: I want to know how Emacs works with R. can anyone provide me a link or manual to read? Thank you -- View this message in context:

Re: [R] Tinn-R keyboard problem

Tinn-R works with SDI. Make sure you have both the settings in R and the Rprofile.site correct. If the bug persists with the latest version of Tinn-R, look for help on : http://sourceforge.net/projects/tinn-r/support Cheers Joris On Fri, Jun 4, 2010 at 11:56 AM, dhidh23061972

[R] package mgcv inconsistency in help files? cyclic P-spline cs not cyclic?

Dear all, I'm a bit stunned by the behaviour of a gam model using cyclic P-spline smoothers. I cannot provide the data, as I have about 61.000 observations from a time series. I use the following model : testgam - gam(NO~s(x)+s(y,bs=cs)+s(DD,bs=cs)+s(TT),data=Final) The problem lies with the

Re: [R] function

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. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department

Re: [R] gam error

-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics

Re: [R] Continous variables with implausible transformation?

/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87

Re: [R] compare results of glms

. __ 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. -- Joris Meys Statistical Consultant Ghent University Faculty

Re: [R] ordinal variables

http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000

Re: [R] Problems using gamlss to model zero-inflated and overdispersed count data: the global deviance is increasing

%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http

Re: [R] function

]] __ 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. -- Joris Meys Statistical Consultant Ghent University Faculty

Re: [R] gam error

commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be

Re: [R] Continous variables with implausible transformation?

-- But you wrote linear+ square. Don't you mean: lrm(Y~x+x^2) --- I believe this is the same as lrm(Y ~ x). You must protect the x^2 via lrm(Y ~ x + I(x^2)) -- -- Joris Meys Statistical Consultant Ghent University

Re: [R] Problems using gamlss to model zero-inflated and overdispersed count data: the global deviance is increasing

See below. On Thu, Jun 3, 2010 at 5:35 PM, Gavin Simpson gavin.simp...@ucl.ac.ukwrote: On Thu, 2010-06-03 at 17:00 +0200, Joris Meys wrote: On Thu, Jun 3, 2010 at 9:27 AM, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: vegan is probably not too useful here as the response is univariate

Re: [R] Problems using gamlss to model zero-inflated and overdispersed count data: the global deviance is increasing

Correction : That should give some clarity on the question whether it is the optimization of GAMLSS that goes wrong, or whether the problem is inherent to the data. On Thu, Jun 3, 2010 at 7:00 PM, Joris Meys jorism...@gmail.com wrote: See below. On Thu, Jun 3, 2010 at 5:35 PM, Gavin Simpson

Re: [R] cumsum function with data frame

, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http

Re: [R] Nested ANOVA with covariate using Type III sums of squares

enter this model: carbonmean-lm(C.Mean~ Diversity + Zoop + Diversity/Phyto + Zoop*Diversity/Phyto) On Wed, Jun 2, 2010 at 6:05 PM, Joris Meys jorism...@gmail.com wrote: that's diversity/phyto, zoop or phyto twice in the formula. On Thu, Jun 3, 2010 at 3:00 AM, Joris Meys jorism

Re: [R] Nested ANOVA with covariate using Type III sums of squares

I see where my confusion comes from. I counted 4 levels of Phyto, but you have 8, being 4 in every level of Diversity. There's your aliasing. table(Diversity,Phyto) Phyto Diversity M1 M2 M3 M4 P1 P2 P3 P4     H  0  0  0  0  6  6  6  6     L  6  6  6  6  0  0  0  0 There's no

Re: [R] Nested ANOVA with covariate using Type III sums of squares

be ignored from a statistical perspective. Finally, I have tried using the Type II SS and received similar warnings. Do you have a recommendations? Anita. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics

Re: [R] cumsum function with data frame

),header=T) ddply(Data,.(variable),transform,CUMSUM=cumsum(value)) - Original Message From: Felipe Carrillo mazatlanmex...@yahoo.com To: Joris Meys jorism...@gmail.com; n.via...@libero.it n.via...@libero.it Cc: r-help@r-project.org Sent: Thu, June 3, 2010 11:28:58 AM Subject: Re

Re: [R] Subsetting for unwanted values

PcToAdd_-Pc[!(Pc %in% Pc.X)] PcToAdd_ [1] Res Os Gov Rur PcToAdd_-subset(Pc,!(Pc %in% Pc.X)) PcToAdd_ [1] Res Os Gov Rur On Fri, Jun 4, 2010 at 1:52 AM, LCOG1 jr...@lcog.org wrote: Hi all,   I have toyed with this for too long today and in the past i used multiple lines of code to

Re: [R] Nested ANOVA with covariate using Type III sums of squares

helpful. Anita. On Thu, Jun 3, 2010 at 4:25 PM, Joris Meys jorism...@gmail.com wrote: I see where my confusion comes from. I counted 4 levels of Phyto, but you have 8, being 4 in every level of Diversity. There's your aliasing. table(Diversity,Phyto) Phyto Diversity M1 M2 M3 M4 P1

Re: [R] storing output data from a loop that has varying row numbers

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. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering

Re: [R] Seeking help on Vectorize()

-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. -- Joris Meys Statistical Consultant Ghent University Faculty

Re: [R] how to label the som notes by the majority vote

. if a note has 3 objects mapped to it (the temperature are 30, 40, 30), then I want the 30 be labeled on the note. the right plot is the mapping plot, I want it to be labeled by only one temperature. Thanks so much! On Tue, Jun 1, 2010 at 5:36 PM, Joris Meys jorism...@gmail.com

Re: [R] Problems using gamlss to model zero-inflated and overdispersed count data: the global deviance is increasing

. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http://helpdesk.ugent.be/e

Re: [R] regexpr mystery can not remove trailing spaces

http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent

Re: [R] compute the associate vector of distances between leaves in a binary non-rooted tree

://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. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied

Re: [R] regexpr mystery can not remove trailing spaces

sub('[:space:]', '', bbb[1]) [1] 02.06.10 1240 I also tried Matt's suggestion but it did not help. Regards Petr Joris Meys jorism...@gmail.com napsal dne 02.06.2010 14:35:19: Could you provide us with dput(becva$V1[1])? Cheers Joris On Wed, Jun 2, 2010 at 2:07 PM, Petr PIKAL

Re: [R] regexpr mystery can not remove trailing spaces

and put it to single variable. I also reinstalled R to recent R-devel sub('\\w+$', '', bbb[1]) [1] 02.06.10 12:40 sub('[:space:]', '', bbb[1]) [1] 02.06.10 1240 I also tried Matt's suggestion but it did not help. Regards Petr Joris Meys jorism

Re: [R] glmnet strange error message

the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links

Re: [R] why the dim gave me different results

do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control

Re: [R] nnet: cannot coerce class c(terms, formula) into a data.frame

. __ 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. -- Joris Meys Statistical

Re: [R] Use apply only on non-missing values

PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process

Re: [R] Nested ANOVA with covariate using Type III sums of squares

/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. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics

Re: [R] Nested ANOVA with covariate using Type III sums of squares

that's diversity/phyto, zoop or phyto twice in the formula. On Thu, Jun 3, 2010 at 3:00 AM, Joris Meys jorism...@gmail.com wrote: That's what one would expect with type III sum of squares. You have Phyto twice in your model, but only as a nested factor. To compare the full model with a model

Re: [R] storing output data from a loop that has varying row numbers

. __ 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. -- Joris Meys Statistical Consultant Ghent University Faculty

Re: [R] storing output data from a loop that has varying row numbers

-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be

Re: [R] storing output data from a loop that has varying row numbers

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. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department

Re: [R] storing output data from a loop that has varying row numbers

Sorry, forgot to add the sel. This is the first line, then just run the rest. sel - as.factor(paste(seal_dist[,10],-,seal_dist[,5],sep=)) cheers Joris On Tue, Jun 1, 2010 at 4:56 PM, Joris Meys jorism...@gmail.com wrote: Is this what you're looking for? seal_list - split(seal_dist,sel

Re: [R] Help on aggregate method

University __ 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. -- Joris

Re: [R] storing output data from a loop that has varying row numbers

. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http

Re: [R] R-help spam detection; please help the moderators

out of a string using regular expressions? From: Joris Meys jorism...@gmail.com To: Gabor Grothendieck ggrothendi...@gmail.com Cc: R mailing list r-help@r-project.org Content-Type: multipart/alternative; boundary=000e0cd2295481515c0487a6b3be --000e0cd2295481515c0487a6b3be Content-Type: text/plain

Re: [R] as.date

, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http

Re: [R] Issue with assigning text to matrix

read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control

Re: [R] any doc to understand arima state space model?

, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http

Re: [R] BreastCancer Dataset for Classification in kknn

guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B

Re: [R] regexpr help (match.length=0)

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. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department

Re: [R] how to label the som notes by the majority vote

, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http

Re: [R] Linear Discriminant Analysis in R

the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure

Re: [R] about heatmap

-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. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience

Re: [R] What does LOESS stand for?

, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be

Re: [R] missing values in autocorelation

-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9

Re: [R] How to delete the previously saved workspace restored

. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http://helpdesk.ugent.be/e

Re: [R] Problems with apply

commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be

Re: [R] Linear Discriminant Analysis in R

. __ 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. -- Joris Meys Statistical Consultant Ghent University Faculty

Re: [R] difference in sort order linux/Windows (R.2.11.0)

. __ 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. -- Joris Meys Statistical Consultant Ghent University

Re: [R] clustering in R

guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B

Re: [R] Handing significance digits

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. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department

[R] How to get values out of a string using regular expressions?

gives something I can use, but it still requires a lot of list manipulation afterwards to get the right vector. Is there an option or a function I'm missing somewhere? Cheers Joris -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied

Re: [R] anova post hoc tests

__ 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. -- Joris Meys

Re: [R] Linear Discriminant Analysis in R

, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer

Re: [R] How to get values out of a string using regular expressions?

at 8:21 AM, Joris Meys jorism...@gmail.com wrote: Dear all, I have a vector of filenames which begins like this : X - c(OrthoP1_DNA_str.aln, OrthoP10_DNA_str.aln, OrthoP100_DNA_str.aln, OrthoP101_DNA_str.aln, OrthoP102_DNA_str.aln, OrthoP103_DNA_str.aln, OrthoP104_DNA_str.aln

Re: [R] Matrix interesting question!

commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be

Re: [R] leave-one-out cross validation

, 5/26/10, Joris Meys jorism...@gmail.com wrote: From: Joris Meys jorism...@gmail.com Subject: Re: [R] validation logistic regression To: azam jaafari azamjaaf...@yahoo.com Cc: r-help@r-project.org Date: Wednesday, May 26, 2010, 5:00 AM Hi, first of all, you shouldn't backtransform your

Re: [R] clustering in R

, or a matrix (of distances) or an object which can be coerced to such a matrix using as.matrix() On Fri, May 28, 2010 at 6:34 AM, Joris Meys jorism...@gmail.comwrote: As Tal said. Next to that, I read that column1 (and column2?) are supposed to be seen as factors, not as numerical variables. Did you

Re: [R] clustering in R

being my original dataset as according to the documentaion on dist() For the default method, a dist object, or a matrix (of distances) or an object which can be coerced to such a matrix using as.matrix() On Fri, May 28, 2010 at 6:34 AM, Joris Meys jorism...@gmail.comwrote: As Tal said

Re: [R] clustering in R

. Because obviously the data frame changes again with that. Any ideas on how to do that? On Fri, May 28, 2010 at 4:13 PM, Joris Meys jorism...@gmail.com wrote: errr, forget about the output of dput(q), but keep it in mind for next time. f = dist(t(q)) hclust(f,method=single) it's as simple

Re: [R] data frame manipulation change elements meeting criteria

, something like : if(trade$Trade.Status==DEL)switch(.) I would like to avoid the loop . From: Joris Meys [mailto:jorism...@gmail.com] Sent: Wednesday, May 26, 2010 9:15 PM To: arnaud Gaboury Cc: r-help@r-project.org Subject: Re: [R] data frame manipulation change elements meeting

Re: [R] data frame manipulation change elements meeting criteria

NULL $Net.Charges..sum. NULL That's certainly not what I want. From: Joris Meys [mailto:jorism...@gmail.com] Sent: Thursday, May 27, 2010 8:43 AM To: arnaud Gaboury Cc: r-help@r-project.org Subject: Re: [R] data frame manipulation change elements meeting criteria The loop is due

Re: [R] data frame manipulation change elements meeting criteria

want !! From: Joris Meys [mailto:jorism...@gmail.com] Sent: Thursday, May 27, 2010 10:38 AM To: arnaud Gaboury Cc: r-help@r-project.org Subject: Re: [R] data frame manipulation change elements meeting criteria Off course. You put in a matrix to sapply, but sapply is for vectors. You want

Re: [R] cluster analysis and supervised classification: an alternative to knn1?

-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m

Re: [R] cluster analysis and supervised classification: an alternative to knn1?

Joris Meys jorism...@gmail. com To Sent by: abanero gdevi...@xtel.it r-help-boun...@r- cc project.org r-help

Re: [R] summary of arima model in R

the significancy of intervention regressors,rather than see the goodness of fit of time series itself. Thanks On 5/26/10, Joris Meys jorism...@gmail.com wrote: Check http://cran.r-project.org/doc/contrib/Ricci-refcard-ts.pdf for some ideas on testing time series in R. I'd go with the acf

Re: [R] validation logistic regression

and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be

Re: [R] Calculation time of isoMDS and the optimal number of dimensions

, On Tue, May 25, 2010 at 1:00 PM, Joris Meys jorism...@gmail.com wrote: Dear all, I'm running a set of nonparametric MDS analyses, using a wrapper for isoMDS, on a 800x800 distance matrix. I noticed that setting the parameter k to larger numbers seriously increases the calculation time

Re: [R] Calculation time of isoMDS and the optimal number of dimensions

, but it is perfectly valid for any kind of distance matrix. thanks again for your insights. Cheers Joris On Wed, May 26, 2010 at 9:34 AM, Gavin Simpson gavin.simp...@ucl.ac.ukwrote: On Tue, 2010-05-25 at 19:00 +0200, Joris Meys wrote: Dear all, I'm running a set of nonparametric MDS analyses

Re: [R] (no subject)

code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http

Re: [R] condition apply to elements of a data frame column

: Joris Meys [mailto:jorism...@gmail.com] Sent: Wednesday, May 26, 2010 2:48 PM To: arnaud Gaboury Cc: r-help@r-project.org Subject: Re: [R] (no subject) What exactly are you trying to do? If you want to know which position is wrong, try : if (sum(u$POSITION==0)0) cat(WARNING:POSITION

[R] stress function in isoMDS

that transformation within isoMDS? Kind regards Joris -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be

Re: [R] cluster analysis and supervised classification: an alternative to knn1?

-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. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience

Re: [R] how to avoid a subset of a matrix to become a column vector

do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control

Re: [R] data frame manipulation change elements meeting criteria

__ 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. -- Joris Meys Statistical Consultant Ghent

Re: [R] error variable names are limited to 256 bytes when sourcing code

/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87

Re: [R] R editor

. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http

Re: [R] Linear Discriminant Analysis in R

-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9

Re: [R] More efficient way to use ifelse()? - A follow up

On Wed, May 26, 2010 at 9:04 PM, Ian Dworkin idwor...@msu.edu wrote: # Dennis Murphy suggested switch.. I have not gotten it working yet.. elevation.DM - switch(Population, CO= 2169, CN = 1121, Ga = 500, KO = 2500, Mw = 625, Ng = 300 ) -- Joris Meys Statistical Consultant Ghent University

Re: [R] Fill a matrix using logical arguments?

guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B

Re: [R] Need Help! Poor performance about randomForest for large data

-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 joris.m

Re: [R] R eat my data

-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. -- Joris Meys Statistical Consultant Ghent University Faculty

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