Re: [R] prcomp eigenvalues

Finally, some popular programs in ecology (your affiliation) use proportional eigenvalues which you can get with: ev/sum(ev) cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa

Re: [R] INDVAL and mvpart

Agnieszka, Package 'mvpart' is documented. In this case, ?rpart.object explains *where* in the rpart object is the membership vector. cheers, jari oksanen On Mon, 2005-08-08 at 16:02 +0200, [EMAIL PROTECTED] wrote: Hi, I'd like to perform Dufrene-Legendre Indicator Species Analysis

Re: [R] invalid 'mode' of argument?

zeros. PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa/ __ R-help

Re: [R] vectors of different length in a matrix

Horn index used in cases where you don't have these identities -- specifically species names. cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa/ __ R-help

Re: [R] vectors of different length in a matrix

On Mon, 2005-08-22 at 16:13 +0300, Jari Oksanen wrote: On Mon, 2005-08-22 at 08:56 -0400, Duncan Murdoch wrote: On 8/22/2005 8:45 AM, Marten Winter wrote: HI! I?ve 3 vectors of different length (a,b,c) and want to arrange them in a matrix a,b,c as rows and the figures

Re: [R] Document clustering for R

write it for you in C, but I don't think that is necessary). cheers, jari oksanen __ 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

Re: [R] Graphical presentation of logistic regression

decided to educate them (I'm not an ESA member, so I wouldn't be educated: therefore 'them' instead of 'us'). The ESA bulletin will be influential in manuscript submitted to the Society journals in the future, and the time for action is now. cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ

Re: [R] Compare two distance matrices

giving compliant results. For Mantel tests you may need ade4 (or some other package that has the same test). cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa

Re: [R] Under-dispersion - a stats question?

' -- in a collection) is underdispersed to Poisson, and for a good reason. Even there I'd play safe and use poisson() instead of underdispersed quasipoisson(). cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland Ph. +358 8 5531526, cell +358 40 5136529, fax +358 8

Re: [R] varimax rotation difference between R and SPSS

, it seems that the raw solutions are identical. cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http

Re: [R] noncommutative addition: NA+NaN != NaN+NA

. I tried this in Linux on Mac iBook G4, and the results were the same: NaN+NA was NaN, just like in MacOS X version. So it looks like a chip issue. However, the RPM built from the src.rpm packages at CRAN failed in some checks in Linux/iBook. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED

RE: [R] isoMDS

probably should use cmdscale. If you know, things are different. Probably isoMDS gives you `better'(TM) results, but it is more complicated to handle. cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland Ph. +358 8 5531526, cell +358 40 5136529, fax +358 8 5531061

Re: [R] isoMDS

I tried, and the results were practically identical with different transformations. So it doesn't matter too much how you change your similarities to dissimilarities, since isoMDS indeed treats them as dissimilarities (but cmdscale treats them as distances). cheers, jari oksanen -- J.Oksanen

Re: [R] Installing packages on OS X

where I solved this in the evening (UTC+3), if you won't get solution before that. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

RE: [R] isoMDS

to avoid the complaint about zero-distances among points. This means that you have some identical points in your data, and isoMDS does not like them. This issue was discussed here in April, 2004 (and many other times). Search archives for the subject question on isoMDS. cheers, jari oksanen -- Jari

Re: [R] getting started on Bayesian analysis

mean(y[1:60]) [1] 0.783 mean(y[41:100]) [1] 0.45 plot(density(uh[,1])) plot(density(uh[,2])) plot(table(uh[,3]), type=h) This was off-topic. So something about business: isn't the (Win)BUGS author working with a R port? cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu

Re: [R] Problem installing source packages on OS X

the g77 path to /usr/local/bin/g77 and so building a package failed in the false claim of missing g77 (yeah, it was in the path). cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo

Re: [R] BUGS and OS X

on how experienced users do bayesian analysis in R would be welcome. You need a guru to guide you. That's the holy tradition in Bayesianism. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch

Re: [R] Signs of loadings from princomp on Windows

investigating. If it's in the eigen, then it dives deep into Fortran, and that may be all you can say. (If your covariance matrices change with repeated calculations, then the problem is deeper). However, sign doesn't matter if there are -- Jari Oksanen [EMAIL PROTECTED

Re: [R] Multi-dimensional scaling

show you most of these and something else, too (perhaps xgvis in the xgobi, if that's installed in your system). Try help.search(multidimensional scaling). cheers, jari oksane -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https

Re: [R] data(eurodist) and PCA ??

)[trip, trip] Athens Rome Milan Athens 0 817 2282 Rome 8170 586 Milan2282 586 0 817 + 586 [1] 1403 I thought that World is non-Euclidean, but not that obviously. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED

Re: [R] biplot.princomp with loadings only

the arrows text(1.1*X, rownames(X), col=red, xpd=T) Cheers, jari okanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting

Re: [R] How to use a matrix in pcurve?

oksanen -- Jari Oksanen, Oulu, Finland __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

Re: [R] persp(), scatterplot3d(), ... argument

On Wed, 2004-10-27 at 11:11, Uwe Ligges wrote: Jari Oksanen wrote: On Wed, 2004-10-27 at 10:04, Uwe Ligges wrote: This is a larger problem if 1. one of the underlying functions does not have ... 2. you want to relay arguments to two or more underlying functions, and 3. you

Re: [R] ploting an ellipse keeps giving errors

' there. It could be useful to use argument specified in the help page. Section 'Details' of ?ellipse explains the parametrization. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] ploting an ellipse keeps giving errors

On Wed, 2004-10-27 at 12:04, Jari Oksanen wrote: On Wed, 2004-10-27 at 11:34, Sun wrote: library (ellipse) Here's your problem! See below. shape1 = c (1, 0, 0,1) dim(shape1) = c(2,2) ellipse (center = c(0,0), shape = shape1, radius = 1) = Error

Re: [R] biplot drawing conc ellipses

for loadings, Moreover, scaling of results is different. It seems that the only thing you can do is to write your sweet on biplot function. cheers, jari oksanen -- Jari Oksanen -- Oulu, Finland. But, Mousie, thou art no thy lane, In proving foresight may be vain; The best-laid schemes o' mice an 'men

Re: [R] rgl on Mac OS

, you may install libpng as well. cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r

Re: [R] gdist and gower distance

, and Euclidean distances are method 2. Gower's original paper is available through http://www.jstor.org/ (Biometrics Vol. 27, No. 4, p. 857-871; 1971). cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https

Re: [R] R works on Fedora Core 3

is just cute here: tiny, sharp, fast graphics window.) Has the options()printcmd reappeared, so that dev.print() works without changing default options? cheers, jazza -- Jari Oksanen, Oulu, Finland __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch

Re: [R] CDs for R?

that Ubuntu will be one R version off again). I guess the lag is even worse in packages. cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] CDs for R?

On Wed, 2004-11-17 at 16:54, Dirk Eddelbuettel wrote: On Wed, Nov 17, 2004 at 08:25:54AM +0200, Jari Oksanen wrote: On 16 Nov 2004, at 23:39, (Ted Harding) wrote: Now comes my suggestion to CRAN maintainer: this all would be easier, if you would produce a CD image file ('iso

Re: [R] Running R from CD?

in the help browser window. Go to chapter 7. Some Suggestions for Instructors which tells you how to make a live CD of R in Windows. I haven't tried this, since I don't have Windows, but I sure will when I got to be an instructor in a Windows class. cheers, jari oksanen -- Jari Oksanen [EMAIL

Re: [R] How to insert one element into a vector?

, and I'm happy that Peter Dalgaard didn't know that 'append' inserts: it gives some hope to us ordinary mortals. cheers, jazza -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] The hidden costs of GPL software?

useful quite easily. All of us who have had the frustration of searching for a forgotten function would be grateful. You mean SOM? -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

Re: [R] A basic question

oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

Re: [R] can't install r package on debian due to linker problem

stable R version 2.0.1 gcc 2.95.4-14 g77 2.95.4-14 binutils 2.12.90.0.1-4 cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http

Re: [R] step.gam

/lab5.html. You may find some useful hints here, as Dave is partial to the traditional S-plus gam as well. cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa

Re: [R] Protocol for answering basic questions

or a Forum (these are words I've seen, but I wouldn't visit places like this, talking about my g-g-generation). cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] depth constrained cluster

onedimensional or chronologically constrained clustering and 2dim or spatially constrained clustering. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] Protocol for answering basic questions

discussion instead of a public call to a private discussion. cheers, jari oksanen -- Jari Oksanen -- Oulu, Finland. But, Mousie, thou art no thy lane, In proving foresight may be vain; The best-laid schemes o' mice an 'men, Gang aft agley, An'lea'e us nought but grief an' pain, For promis'd joy

Re: [R] How about a mascot for R?

/mascot.html I think this is a copyright picture, and it cannot be used freely as a mascot (and will disappear soon from this address). cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo

Re: [R] How about a mascot for R?

. I've never liked movies about ecologically non-sustainable and energetically impossible life forms. The current sub-theme brings to my mind something completely different: http://www.hundland.com/posters/t/TheTalentedMr.Ripley.jpg. cheers, jari o. -- Jari Oksanen [EMAIL PROTECTED

Re: [R] How about a mascot for R?

as a mascot. Naturally, this is none of my business, so you should not let this message influence your opinion (it wouldn't anyway). cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r

Re: [R] Gam() function in R

this is done in mgcv:::gam (gam:::gam has another set of tools and philosophy). If you happened to use gam:::gam, then you have to look at another explanation. cheers, jari oksanen From: Liaw, Andy [mailto:[EMAIL PROTECTED] Sent: Sunday, December 05, 2004 11:34 PM To: 'Janice Tse'; [EMAIL

Re: [R] Importing vector graphics into R

/ DLL interface 108 (build Oct 17 2003 - release build) : Copyright (C) 1993 - 2003 Wolfgang Glunz cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

RE: [R] How about a mascot for R?

Verlag, Stuttgart The English translation is The Snouters: Form and life of the Rhinogrades . The University of Chicago Press (1981). Google will found more info for those who don't have acces to these books. cheers, jaRi oksanen -- Jari Oksanen [EMAIL PROTECTED

RE: [R] How about a mascot for R?

On Wed, 2004-12-08 at 17:01, Jari Oksanen wrote: I just wait for someone jumping off and saying this is off-topic and you should stop posting to this list -- and I'm afraid it could happen just at this point. Just to make it clear and to avoid misunderstanding: I was trying to reach

RE: [R] How about a mascot for R?

On Wed, 2004-12-08 at 17:01, Jari Oksanen wrote: I just wait for someone jumping off and saying this is off-topic and you should stop posting to this list -- and I'm afraid it could happen just at this point. Just to make it clear and to avoid misunderstanding: I was trying to reach

Re: [R] How to circumvent negative eigenvalues in the capscale function

need more memory or an operating system with better memory handling. You may try with some Linux live-cd (such as Quantian) where you can use R in Linux without installing Linux in your hard drive. cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland email [EMAIL

Re: [R] Switching to Mac, suggestions? (was switching to linux)

than in R. By the way, Ubuntu GNU/Linux works nicely in Mac, with blas who knows about the vector processor in G4. cheers, jazza -- Jari Oksanen, Oulu, Finland __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] Switching to Mac, suggestions? (was switching to linux)

in Mac is that graphics are superb in Mac. The default plot (quartz) is small but sharp. It used to scale instantly when you changed its size, but this deteriorated in 2.0 series. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED

Re: [R] printing PCA scores

for. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ 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

Re: [R] MacOS X and vectorized files (emf, wmf,...)

in pdf which is vectorized graphic format native to MacOS X. Further, dev.copy2eps() work normally, as do postcript() and pdf() devices. See appropriate help pages. Native MS Windows formats (such as wmf) may not work, but who needs them? cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED

Re: [R] Bootstrapped eigenvector

cor = TRUE to princomp. Another issue is whether you should use this method. Opinions may be divided here, but I'll let that to the proper Statistician to comment on. Best wishes, Jari Oksanen -- Jari Oksanen [EMAIL PROTECTED] __ R-help

Re: [R] Problem installing Hmisc (more info)

' to be in a different place that I had it. For instance, Darwin's Fink installs stuff in a unique place called /sw. Perhaps that's the problem? However, ideally MacOS software should work 'jus anywhere' (and 'just work') like they say in ads. cheers, jari oksanen -- Jari Oksanen, Oulu, Finland

Re: [R] randomisation

it). The Mac binary is not available at CRAN since the whole Mac binary package system seems to be dysfunctional (there is nothing after Jan 19, 2005). cheers, jari oksanen __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] installing package hier.part on Mac OSX

. cheers, jari oksanen On Wed, 9 Feb 2005, Theresa Talley wrote: Hi- I've been trying to install the hier.part package on my mac (OSX 10.3.7) and it is not working for some reason. I am downloading the package source called : hier.part_1.0.tar.gz. When I try to auto install from

Re: [R] Failure of update.packages()

Debian so that people could use the non-devel piece of R only? cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ 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

Re: [R] Failure of update.packages()

On 10 Feb 2005, at 19:26, Peter Dalgaard wrote: [EMAIL PROTECTED] writes: Quoting Jari Oksanen [EMAIL PROTECTED]: On Thu, 2005-02-10 at 13:52 +0100, Peter Dalgaard wrote: I M S White [EMAIL PROTECTED] writes: Can anyone explain why with latest version of R (2.0.1) on FC3, installed from R-2.0.1-0

Re: [R] R + MacOSX + Emacs(XEmacs) + ESS

without X11. ESS installs quite smoothly. Depending on your configuration, you may have to use ESC for Meta instead of Alt of some other systems. So start R in ESS using ESC-R. (The emacs that comes with MacOS X also is GNU Emacs, but works only within terminal window.) cheers, jari oksanen -- Jari

Re: [R] eigen vector question

oksanen -- Jari Oksanen [EMAIL PROTECTED] __ 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

Re: [R] How to set up number of prin comp.

with prcomp. I think I'll write functions as.prcomp.princomp and as.princomp.prcomp someday. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] Reconstructing Datasets

). cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ 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

Re: [R] Reconstructing Datasets

On Wed, 2005-03-02 at 08:30 +0200, Jari Oksanen wrote: On Tue, 2005-03-01 at 20:30 +, Laura Quinn wrote: Hi, Is it possible to recreate smoothed data sets in R, by performing a PCA and then reconstructing a data set from say the first 2/3 EOFs? I've had a look in the help pages

Re: [R] Multidimensional Scaling (MDS) in R

(dis) plot(ord$points, asp = 1, type=n) text(ord$points, rownames(ord$points) The posting guide tells you to make package specific questions to the package author directly. In this case, the package author does not read R-News. cheers, jari oksanen On 8 Mar 2005, at 19:43, Isaac Waisberg wrote

Re: [R] Significance of Principal Coordinates

a dimension that you must explain away in the text. Wouldn't that be a sufficient solution? cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] How to do such MDS in R

the software into R, but I think the license does not allow this. The hardest bit would be to change the output into R. I suggest you dig up SINDSCAL somewhere -- it could be in netlib -- and compile it yourself. Gnu g77 is quite OK. cheers, jari oksanen -- Jari Oksanen, Oulu, Finland

Re: [R] Principle Component Analysis in R

because people with Factor Analysis background expect this. However, I would be worried if I got results like this, and would not use Princip*al* Components at all, since none of the components seems to be any more principal than others. Wouldn't original data do? cheers, jari oksanen -- Jari

Re: [R] two methods for regression, two different results

5.551115e-17 But, of course, fitted values are not equal, since you fit the mod2 to the residuals after removing the effect of x... cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch

Re: [R] weird results w/ prcomp-princomp

oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland Ph. +358 8 5531526, cell +358 40 5136529, fax +358 8 5531061 email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch

Re: [R] Error message with nmds

://stat.ethz.ch/pipermail/r-help/2006-April/092598.html and answers. You may also use RSiteSearch with keyword isoMDS to find other (and older) threads. cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa

Re: [R] 2 Courses Near You - (1) Introduction to R/S+ programming: Microarrays Analysis and Bioconductor, (2) R/Splus Fundamentals and Programming Techniques

is closest (OUL - BWI 12h55min), but Boston and Chicago are not much further away (OUL - BOS 14h00min, OUL-CHI 14h15min). cheers, jari oksanen Probably some football related metric: FIFA WM takes place in Dortmund and commercials say something like the world is our guest ... Now, let's

Re: [R] MDS with missing data?

Dear Context Grey, On 15 Jun 2006, at 6:42, context grey wrote: I will be applying MDS (actually Isomap) to make a psychological concept map of the similarities between N concepts. So actually, how do you do isomap? RSiteSearch gave me one hit of isomap. I only ask, because I've

Re: [R] MDS with missing data?

On Thu, 2006-06-15 at 07:13 +0300, Jari Oksanen wrote: 1) use nonmetric/gradient descent MDS which seems to allow missing data, or Not the isoMDS function in MASS. if N(N-1) is a problem, then nonmetric MDS may not be the solution. Sorry for the wrong information: isoMDS does handle

Re: [R] Ordination of feature film data question

data in movies. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ 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

Re: [R] transparent background for PDF

other programmes than R. This experience is from Linux Mac (pdf) and PP in Mac (never tried that with PowerPoint on Linux...). cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

Re: [R] isoMDS and 0 distances

was to drop duplicates, but then there still is a weighting issue, and isoMDS does not have weights argument. cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa

Re: [R] isoMDS and 0 distances

OR IN WRITING, IS C PROHIBITED WITHOUT WRITTEN PRERMISSION OF C BELL LABORATORIES. CKYST-2A AUGUST, 1977 cheers, jari oksanen -- Jari Oksanen -- Biologian laitos, Oulun yliopisto, 90014 Oulu sposti [EMAIL PROTECTED], kotisivu http://cc.oulu.fi/~jarioksa

Re: [R] environmental data as vector in PCA plots

with a pdf document which discusses PCA scaling in prcomp, princomp, rda (of vegan) and Canoco (of Cajo ter Braak), and even hints how to get the minus scalings that the author doesn't approve. cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ [EMAIL

Re: [R] BIO-ENV procedure

that someone can implement the method. Your post is not sufficient to know what should be there. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] BIO-ENV procedure

it. The missing pieces are the harmonic rank correlation (if you think that's essential) and automating variable selection. Somebody could do them (not me, though). cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list

Re: [R] Factor loadings and principal component plots

On Tue, 2004-05-04 at 09:56, Prof Brian Ripley wrote: On 4 May 2004, Jari Oksanen wrote: On Tue, 2004-05-04 at 09:34, Prof Brian Ripley wrote: Yes, but princomp is the recommended way, not prcomp. But the documentation seems to recommend prcomp: For numerical accuracy

Re: [R] Factor loadings and principal component plots

. A preferred method of calculation is to use 'svd' on 'x', as is done in 'prcomp'. Just confused, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] Common principle components

to do the analysis you need. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

[R] distance in the function kmeans

with your original dissimilarity. Cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

Re: [R] privileged slots,

without warning, and your code may be broken anytime. Just be prepared. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http

Re: [R] running R UNIX in a mac computer

to run the same svd-heavy test code. Another reason seemed to be that the Fortran compiler produces much slower code in Linux than in MacOS X (difference about 20%). cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list

Re: [R] can't get text to appear over individual panels in multi-panel plot

oksanen -- Jari Oksanen, Oulu, Finland __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

Re: [R] can't get text to appear over individual panels in multi-panel plot

On Fri, 2004-06-18 at 09:28, Jari Oksanen wrote: On 18 Jun 2004, at 8:26, Deepayan Sarkar wrote: On Thursday 17 June 2004 22:57, Patrick Bennett wrote: yes, i can reproduce that same graph when i print to the pdf-device. but the panel titles do not appear when I print to the Quartz

RE: [R] Maxima/minima of loess line?

need to supply constant values for those in optimize, or for simultaneous search in all use optim or nlm. cheers, jari oksanen From: Fredrik Karlsson Dear list, I've produced a loess line that I would like to investigate in terms of local/global maxima and minima. How would you

Re: [R] integrate function

mathematics (Maple is available for Linux, at least). It may be that you still have to work to get the solution you need, even with snappy tools like that. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https

Re: [R] R binaries for UMBUTU Linux?

in version naming which may lead to conflicts in upgrades, but I think this is OK with R). So you may get the latest Debian (testing) packages -- as soon as they get through the jungle of dependencies and appear in Debian. cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu

Re: [R] Factor Analysis Biplot

) cheers, J -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] R2.0.1 for Mac OS X 10.3 problem

Thomas Yee's VGAM and then removed the package.) cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa/ __ R-help@stat.math.ethz.ch mailing list https

Re: [R] Very Slow Gower Similarity Function

is the problem, but I couldn't figure out how to get rid of them. cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ 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

Re: [R] Very Slow Gower Similarity Function

On 18 Apr 2005, at 20:36, Anon. wrote: Jari Oksanen wrote: On 18 Apr 2005, at 19:10, Tyler Smith wrote: Hello, I am a relatively new user of R. I have written a basic function to calculate the Gower similarity function. I was motivated to do so partly as an excercise in learning R, and partly

Re: [R] results from sammon()

help. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ 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

Re: [R] results from sammon()

iters: 0.07754, magic = 0.500 stress after 50 iters: 0.07710, magic = 0.500 stress after 60 iters: 0.07681, magic = 0.500 stress after 70 iters: 0.07663, magic = 0.500 stress after 80 iters: 0.07653, magic = 0.500 cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED

Re: [R] Pca loading plot lables

$loadings, rownames(pr$loadings), xpd=TRUE) abline(h=0); abline(v=0) If you really want to have Axis 2 as horizontal, then you must replace all pr$loadings pieces with pr$loadings[,2:1]. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ R-help

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