Re: [R] R2HTML problem

2010-06-05 Thread Joris Meys
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 it'

Re: [R] (no subject)

2010-06-05 Thread Joris Meys
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 throu

Re: [R] Wilcoxon test output as a table

2010-06-05 Thread Joris Meys
# 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 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 solution and I fou

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

2010-06-05 Thread Joris Meys
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]) } outp

Re: [R] What is the largest in memory data object you've worked with in R?

2010-06-05 Thread Joris Meys
You have to take some things into account : - the maximum memory set for R might not be the maximum memory available - R needs the memory not only for the dataset. Matrix manipulations require frquently double of the amount of memory taken by the dataset. - memory allocation is important when deali

Re: [R] Help on ARFIMA modeling

2010-06-05 Thread Joris Meys
Read the posting guides please and give us a tiny little bit more information. http://www.R-project.org/posting-guide.html Cheers Joris On Sat, Jun 5, 2010 at 4:39 PM, ERIC AIDOO wrote: > Dear R Users, > Please I have applied the arfima  procedure in the forecast package > to my time series data

Re: [R] Prediction in discriminant analysis

2010-06-05 Thread Joris Meys
You use the function "predict" for that. You give a data frame with the new observations, and make sure the variables have exactly the same name. # run example library(MASS) Class <- as.factor(rep(c("A","B","C"),each=30)) X1 <- c(rnorm(30),rnorm(30,3,2),rnorm(30,-3,1)) X2 <- c(rnorm(30,5,3),rnorm

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

2010-06-04 Thread Joris Meys
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 t

Re: [R] Tinn-R keyboard problem

2010-06-04 Thread Joris Meys
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 wrote: > > I have

Re: [R] R with Emacs

2010-06-04 Thread Joris Meys
Emacs ESS : http://ess.r-project.org/ Cheers Joris On Fri, Jun 4, 2010 at 12:55 PM, dhanush 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: > http://r.789695.n4.nabble.com/R-with-Emacs-tp2243022p2

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

2010-06-04 Thread Joris Meys
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 wrote: > Hello! > > My graphs are produced using the "postscript"-option in

Re: [R] save in for loop

2010-06-04 Thread Joris Meys
On a side note: On Thu, May 20, 2010 at 9:43 AM, Ivan Calandra 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 to it. > eval(parse

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

2010-06-04 Thread Joris Meys
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 <- par(mar=c(3.1,

Re: [R] ordinal variables

2010-06-04 Thread Joris Meys
; Honorary Research Fellow > Department of Education > The University of Manchester > Oxford Road, Manchester M13 9PL, UK > Tel. 0044  161 275 3485 > iasonas.lampria...@manchester.ac.uk > > > --- On Thu, 3/6/10, S Ellison wrote: > >> From: S Ellison >> Subject: R

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

2010-06-03 Thread Joris Meys
ly different F statistic > and P-value for the main effect of Zoop and the nested effect of Phyto. > Obviously SPSS is not necessarily the perfect reference, but when using the > Type I SS, the results did agree. Any thoughts on why this might be? Could > the two programs be calculating th

Re: [R] Subsetting for unwanted values

2010-06-03 Thread Joris Meys
> 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 wrote: > > Hi all, >   I have toyed with this for too long today and in the past i used multiple > lines

Re: [R] cumsum function with data frame

2010-06-03 Thread Joris Meys
>> AAO1    2005  2 >> AAO1  2006  4"),header=T) >> >> ddply(Data,.(variable),transform,CUMSUM=cumsum(value)) >> >> >> >> >> - Original Message >> > From: Felipe Carrillo >> > To: Joris Mey

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

2010-06-03 Thread Joris Meys
ke sense from an ecological > perspective, and because the results do change, the order cannot 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. > -- Jori

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

2010-06-03 Thread Joris Meys
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 ne

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

2010-06-03 Thread Joris Meys
he aliasing > warning is replaced by the following error message: > "Error in t(Z) %*% ip : non-conformable arguments" > > That is when I enter this model: > carbonmean<-lm(C.Mean~ Diversity + Zoop + Diversity/Phyto + > Zoop*Diversity/Phyto) > > > > &g

Re: [R] cumsum function with data frame

2010-06-03 Thread Joris Meys
g 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] Problems using gamlss to model zero-inflated and overdispersed count data: "the global deviance is increasing"

2010-06-03 Thread Joris Meys
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 wrote: > See below. > > On Thu, Jun 3, 2010 at 5:35 PM, Gavin Simpson wrote

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

2010-06-03 Thread Joris Meys
See below. On Thu, Jun 3, 2010 at 5:35 PM, Gavin Simpson wrote: > On Thu, 2010-06-03 at 17:00 +0200, Joris Meys wrote: > > On Thu, Jun 3, 2010 at 9:27 AM, Gavin Simpson >wrote: > > > > > > > > vegan is probably not too useful here as the response

Re: [R] Continous variables with implausible transformation?

2010-06-03 Thread Joris Meys
Genentech Nonclinical Biostatistics > -- > 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)) > > --

Re: [R] gam error

2010-06-03 Thread Joris Meys
g 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 contr

Re: [R] function

2010-06-03 Thread Joris Meys
ur attention!! >> >> >> >>[[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 >> h

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

2010-06-03 Thread Joris Meys
parameters or the model maybe > inappropriate > > > > > > > > > > > > Any suggestions on how to proceed with this? > > > > > > Many thanks in advance, > > > > > > > > > Diederik > > > > > > >

Re: [R] ordinal variables

2010-06-03 Thread Joris Meys
lse other than R commander (just writing commands will not > make them happy). > > I hope I am not asking for too much. Hopefully there is a way > > > > > ______ > R-help@r-project.org mailing list > https://stat.ethz.ch/mail

Re: [R] compare results of glms

2010-06-03 Thread Joris Meys
common test statistic in my > field of research), but i reject that due to the small sample size. > > __ > 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 pr

Re: [R] Continous variables with implausible transformation?

2010-06-03 Thread Joris Meys
st > 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 Enginee

Re: [R] gam error

2010-06-03 Thread Joris Meys
> __ > 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, reproduci

Re: [R] function

2010-06-03 Thread Joris Meys
ve 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 > and provide commented, minimal, self-cont

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

2010-06-02 Thread Joris Meys
that's diversity/phyto, zoop or phyto twice in the formula. On Thu, Jun 3, 2010 at 3:00 AM, Joris Meys 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 > w

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

2010-06-02 Thread Joris Meys
y and Zoop. This cannot be correct, however > when I do the model simplification by dropping terms from the models > manually and comparing them using anova(), I get virtually the same > results. > > > > I would appreciate any suggestions for things to try or pointers as to what > I m

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

2010-06-02 Thread Joris Meys
sh_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.10.1 > > > >[[alternative HTML version

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

2010-06-02 Thread Joris Meys
t; Sent from the R help mailing list archive at Nabble.com. > > __ > 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/postin

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

2010-06-02 Thread Joris Meys
0 0 0 0 0 0 0 7 > 571 0 0 0 0 0 0 0 0 0 0 0 8 > 572 0 0 0 0 0 0 0 0 5 0 0 0 > 573 0 0 0 0 0 0 0 0 5 0 0 0 > 574 0 0 0 0 0 0 0 0 13 0 0 0 > 575 0 0 0 0 0 0 0 0 18 0 0 0 > 576 0 0 0 0 0 0 0 0 8 0 0

Re: [R] glmnet strange error message

2010-06-02 Thread Joris Meys
at Nabble.com. > > __ > 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, r

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

2010-06-02 Thread Joris Meys
gt; "02.06.10 07:00 ", "02.06.10 06:00 ", "02.06.10 05:00 ", > > > "02.06.10 04:00 ", "02.06.10 03:00 ", "02.06.10 02:00 ", > > > "02.06.10 01:00 ", "02.06.10 00:00 ", "01.06.10 23

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

2010-06-02 Thread Joris Meys
5:00 ", "01.06.10 14:00 ", > "01.06.10 13:00 ", "01.06.10 05:00 ", "31.05.10 05:00 ", > "30.05.10 05:00 ", "29.05.10 05:00 ", "28.05.10 05:00 ", > "27.05.10 05:00 ") > > > > For sim

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

2010-06-02 Thread Joris Meys
Edifici A. Turmeda > Campus UIB > Ctra. Valldemossa, km. 7,5 > 07122 Palma de Mca. > tel: (+34) 971172987 > fax: (+34) 971173003 > email: arnau@uib.es > URL: http://dmi.uib.es/~arnau <http://dmi.uib.es/%7Earnau> > > > > > > > > > > ______ > R-help

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

2010-06-02 Thread Joris Meys
(unstable) (2010-04-25 r51820)" > > on Windows > > Regards > Petr > > __ > 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/po

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

2010-06-02 Thread Joris Meys
proceed with this? > > Many thanks in advance, > > > Diederik > > > Diederik Strubbe > Evolutionary Ecology Group > Department of Biology > University of Antwerp > Groenenborgerlaan 171 > 2020 Antwerpen, Belgium > tel: +32 3 265 3464 > > >[

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

2010-06-02 Thread Joris Meys
the temperature. > 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! > > > > > > > > > > > >

Re: [R] Seeking help on Vectorize()

2010-06-02 Thread Joris Meys
789 > [5,]89 10 > > > I get exactly what I want. Where I am making fault? > > Thanks, > > > >[[alternative HTML version deleted]] > > > __ > R-help@r-project.org mailing list > https://stat.e

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

2010-06-02 Thread Joris Meys
__ > 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 Mey

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

2010-06-01 Thread Joris Meys
ct)], > main="Mapping plot") > > > > > -- > Sincerely, > Changbin > -- > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide

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

2010-06-01 Thread Joris Meys
e posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-hel

Re: [R] BreastCancer Dataset for Classification in kknn

2010-06-01 Thread Joris Meys
ble 'Id' converted to a factor > > I tried the codes with other datasets in mlbench package and most of them > working. That is the mistake here for this particular dataset and how can I > solve it? > > Thanks > Nitin > >[[alternative HTML version dele

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

2010-06-01 Thread Joris Meys
> 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...@uge

Re: [R] Issue with assigning text to matrix

2010-06-01 Thread Joris Meys
NA NA NA NA NA > NA > > [151] NA NA NA NA NA NA NA NA NA NA NA NA NA NA > NA > > [166] NA NA NA NA NA NA NA NA NA NA NA NA NA NA > NA > > [181] NA NA NA NA NA NA NA NA NA NA NA NA

Re: [R] as.date

2010-06-01 Thread Joris Meys
l/10"), CREATED.DATE = structure(c(18395, 18395, > 18396, 18396, 18392, 18392), class = "Date"), QUANITY = c(1, > 1, -1, -1, 1, 1), CLOSING.PRICE = c("81.2000", "81.2000", "503.6000", > "503.6000", "13.8900", "13.8900&quo

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

2010-06-01 Thread Joris Meys
orism...@gmail.com Message-ID: Subject: Re: [R] How to get values out of a string using regular expressions? From: Joris Meys To: Gabor Grothendieck Cc: R mailing list Content-Type: multipart/alternative; boundary=000e0cd2295481515c0487a6b3be --000e0cd2295481515c0487a6b3be Content-Type: text/

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

2010-06-01 Thread Joris Meys
'", "'P1'", "'Q1'", "'Q2'", "'Q3'", >"'R1.1'", "'R1'", "'R2'", "'R3.1'", "'R3'", "'R4.1'&qu

Re: [R] Help on aggregate method

2010-06-01 Thread Joris Meys
gt; Stella Pachidi > Master in Business Informatics student > Utrecht 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-p

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

2010-06-01 Thread Joris Meys
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 wrote: > Is this what you're looking for? > > seal

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

2010-06-01 Thread Joris Meys
-SEL_DAY[SEL_DAY[,5]==s,] >print(paste("HR", s, "of 11")) >indx <- subset(SEL_HR, SEL_HR$DIST == 0) >SEL_HR$TO_ID <- indx$ID[match(SEL_HR$TO, indx$TO)] > DIST_LOOP[i,]<-SEL_HR >} >} > &g

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

2010-06-01 Thread Joris Meys
$TO_ID <- indx$ID[match(SEL_HR$TO, indx$TO)] > DIST_LOOP[i,]<-SEL_HR >} >} > > But storing the data in the DIST_LOOP matrix doesn't work, I am just told > in > another post that a list might be better than a matrix? > > I hope this makes mor

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

2010-06-01 Thread Joris Meys
//r.789695.n4.nabble.com/storing-output-data-from-a-loop-that-has-varying-row-numbers-tp2238396p2238396.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list >

Re: [R] Problems with apply

2010-05-31 Thread Joris Meys
ror message. Attached is the data I am using. Any idea of why > this is happening? > > Thank you > > Felipe Parra > > ______ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the p

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

2010-05-31 Thread Joris Meys
.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 6

Re: [R] missing values in autocorelation

2010-05-31 Thread Joris Meys
elp@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 Univ

Re: [R] What does LOESS stand for?

2010-05-31 Thread Joris Meys
/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 A

Re: [R] about heatmap

2010-05-31 Thread Joris Meys
__ > 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

Re: [R] Linear Discriminant Analysis in R

2010-05-31 Thread Joris Meys
ot;), class = "data.frame", row.names = c(NA, > -671L)) > > > Thank you once more for your help. I really can not say it enough. > > ps. original files i work with are attached. > > Cobbler. > > http://r.789695.n4.nabble.com/file/n2236083/3dMaskDump.txt 3dMask

Re: [R] Linear Discriminant Analysis in R

2010-05-29 Thread Joris Meys
Nabble.com. > > __ > 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, reproducib

Re: [R] clustering in R

2010-05-28 Thread Joris Meys
rupts and > hclust doesnt want to recognize it anyore again. 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 wrote: > >> errr, forget about the output of dput(q), but keep it in mind for

Re: [R] clustering in R

2010-05-28 Thread Joris Meys
--- >>> >>> >>> >>> >>> On Fri, May 28, 2010 at 9:04 PM, Ayesha Khan < >>> ayesha.diamond...@gmail.com> wrote: >>> >>>> Thanks Tal & Joris! >

Re: [R] clustering in R

2010-05-28 Thread Joris Meys
t; On Fri, May 28, 2010 at 9:04 PM, Ayesha Khan < >> ayesha.diamond...@gmail.com> wrote: >> >>> Thanks Tal & Joris! >>> I created my distance matrix distA by using the dist() function in R >>> manipulating my output in order to get a matrix. >>&g

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

2010-05-28 Thread Joris Meys
4140036 -1783225921 1484611221 1365746860 -346485118 > [31] 1206044253 1201793367 956757054 350214264 -1324711077 > . > . > . > please help me > > Thanks alot > > --- On Wed, 5/26/10, Joris Meys wrote: > > > From: Joris Meys > Subject: Re: [R] validation logis

Re: [R] Matrix interesting question!

2010-05-28 Thread Joris Meys
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 get values out of a string using regular expressions?

2010-05-28 Thread Joris Meys
gt; On Fri, May 28, 2010 at 8:21 AM, Joris Meys 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", > >

Re: [R] Linear Discriminant Analysis in R

2010-05-28 Thread Joris Meys
from the R help mailing list archive at Nabble.com. > > __ > 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 p

Re: [R] anova post hoc tests

2010-05-28 Thread Joris Meys
> Dr. Iasonas Lamprianou > > > > > __ > 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, minima

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

2010-05-28 Thread Joris Meys
lit(X,"\\d+") [[1]] [1] "OrthoP" "_DNA_str.aln" which gives me exactly what I want to throw away. So : > strsplit(X,"\\D+") [[1]] [1] "" "1" [[2]] [1] "" "10" gives something I can use, but it still requires a

Re: [R] Handing significance digits

2010-05-28 Thread Joris Meys
ternative 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 > and provide commented, minimal

Re: [R] clustering in R

2010-05-28 Thread Joris Meys
esha Khan > > MS Bioengineering > Dept. of Bioengineering > Rice University, TX > >[[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE

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

2010-05-28 Thread Joris Meys
nabble.com/difference-in-sort-order-linux-Windows-R-2-11-0-tp2234251p2234251.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the pos

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

2010-05-27 Thread Joris Meys
t; > steve_fried...@nps.gov > Office (305) 224 - 4282 > Fax (305) 224 - 4147 > > > > Joris Meys > com> To > Sent by: abanero > r-help-bo

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

2010-05-27 Thread Joris Meys
x can be used with a number of different methods. And you're right, randomForest doesn't handle categorical variables either. So I haven't been of great help here... Cheers Joris On Thu, May 27, 2010 at 1:25 PM, abanero wrote: > > Hi, > > thank you Joris and Ulrich

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

2010-05-27 Thread Joris Meys
)],switch,Sell="Buy",Buy="Sell") > > > tradenews > Sell > "Buy" > > Not really what I want !! > > From: Joris Meys [mailto:jorism...@gmail.com] > Sent: Thursday, May 27, 2010 10:38 AM > To: arnaud Gaboury > Cc: r-help@r-projec

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

2010-05-27 Thread Joris Meys
t; NULL > > $Instrument.Long.Name > NULL > > $Delivery.Prompt.Date > NULL > > $Buy.Sell..Cleared. > [1] "Buy" > > $Volume > [1] "Buy" > > $Price > NULL > > $Net.Charges..sum. > NULL > > That's certainly not what I w

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

2010-05-26 Thread Joris Meys
e any way to combine if() and switch() in one line? In my case, > 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 &

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

2010-05-26 Thread Joris Meys
f Physical Geography and Quaternary Geology > Stockholm University > 106 91 Stockholm > Sweden > > +46(0)8 674 7568 > +46(0)76 7158975 > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help >

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

2010-05-26 Thread Joris Meys
00 ) Cheers Joris On Wed, May 26, 2010 at 9:04 PM, Ian Dworkin wrote: > > # Dennis Murphy suggested switch.. I have not gotten it working yet.. > > elevation.DM <- switch(Population, "CO"= 2169, "CN" = 1121, "Ga" = > 500, "KO" = 2500, &quo

Re: [R] Linear Discriminant Analysis in R

2010-05-26 Thread Joris Meys
p://r.789695.n4.nabble.com/Linear-Discriminant-Analysis-in-R-tp2231922p2231922.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help >

Re: [R] R editor

2010-05-26 Thread Joris Meys
ide 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] error "variable names are limited to 256 bytes" when sourcing code

2010-05-26 Thread Joris Meys
>>col="orange", >>lty=3) >>} >># Add MEDIAN line >>if (plot.med == TRUE) { >>lines(hh.wealth.quantiles$

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

2010-05-26 Thread Joris Meys
quot;. > If trade$Trade.Status=="INS", do nothing > I tried to work around with ifelse, but don't know how to deal with so many > conditions. > > Any help is appreciated. > > TY > > __

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

2010-05-26 Thread Joris Meys
___ > 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. > --

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

2010-05-26 Thread Joris Meys
6p2231656.html > Sent from the R help mailing list archive at Nabble.com. > > __ > 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,

[R] stress function in isoMDS

2010-05-26 Thread Joris Meys
. " How do I have to see 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

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

2010-05-26 Thread Joris Meys
s false in fact (minimum of one element different from > zero). > > > > > > > From: 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 y

Re: [R] (no subject)

2010-05-26 Thread Joris Meys
e correct way to pass the various arguments. > > Any help is appreciated > > > > > *** > Arnaud Gaboury > Mobile: +41 79 392 79 56 > BBM: 255B488F > > __ > R-help@r-project.org mailing list > h

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

2010-05-26 Thread Joris Meys
u're right. It might be written for community data, 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 wrote: > On Tue, 2010-05-25 at 19:00 +0200, Joris Meys wrote: > > Dear all, >

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

2010-05-26 Thread Joris Meys
ris, > > On Tue, May 25, 2010 at 1:00 PM, Joris Meys 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 ser

Re: [R] validation logistic regression

2010-05-26 Thread Joris Meys
rnative 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 > and provide commented, mi

Re: [R] summary of arima model in R

2010-05-26 Thread Joris Meys
gnificancy of > intervention regressors,rather than see the goodness of fit of time > series itself. > > Thanks > > On 5/26/10, Joris Meys wrote: > > Check http://cran.r-project.org/doc/contrib/Ricci-refcard-ts.pdf for > some > > ideas on testing time series in R. I'd

Re: [R] R eat my data

2010-05-25 Thread Joris Meys
; >> > >>> dim(gene_name) > >>> > >> [1] 10683 > >> > >> > >> -- > >> > > > > > > David Winsemius, MD > > West Hartford, CT > > > > > > > -- > Sincerely, > Changbin > -- &g

Re: [R] File normalization

2010-05-25 Thread Joris Meys
> spec...@stat.berkeley.edu > > > > > > > On Tue, 25 May 2010, Joris Meys wrote: > > Scale is written to do that IF you want to normalize according to the mean >> and the sd. For any other form of normalization, apply or sweep con

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