[R] Adding new points to a metaMDS ordination ("vegan" pkg)

ced nothing that could be called user-friendly. Code is welcome. BTW, it seems that you didn't use squared chord distance, but just chord distance. Best wishes, Jari Oksanen -- Jari Oksanen <[EMAIL PROTECTED]> __ R-help@stat.math.ethz.ch ma

[R] cca and cca.predict in vegan-what sort of prediction is possible

composition from environmental data, I suggest nonlinear regression (mgcv:::gam with appropriate family, for instance) or some fancier methods. Please note that this kind of specific questions should not be sent to the R News, but to more specialized mailing lists or to the package author dir

Re: [R] Error using mgcv package

1, k=5). See also help in mgcv (?s pointing to ?choose.k) for interpreting argument 'k' which is not directly degrees of freedom. There may be other problems, but this probably fixes tha one you reported above. cheers, jari oksanen > And after deleting df's > > model.gam <

Re: [R] correspondence analysis

you the choice of type?). Another possible source of difference is that corresp gives you "canonical correlations" whereas some other program or function may give you their squares, a.k.a. eigenvalues. Moreover, the sign is arbitrary so that negative and positive scores may be switched bet

Re: [R] biplot package

he name so that you can have biplot.prcomp alongside with your new hyperbiplot.prcomp. (Namespace is an answer to no real problem, but a reason of many new problems.) Somebody already promised to write a biplot method for rda in vegan (howdy Gav), but I haven't heard of this for a long t

Re: [R] R2 always increases as variables are added?

p://www.stats.ox.ac.uk/pub/MASS3/Exegeses.pdf which also touches this issue (page 3) and makes a nice reading anyhow. 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 htt

[R] step in Sweave

behaviour where all trace output is printed without message(). I bet that won't happen, though. Cheers, Jari Oksanen -- Jari Oksanen <[EMAIL PROTECTED]> __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] dist label names

orrectly, and the names are transferred to isoMDS result. Now your isoMDS result should have the labels as rownames to points. Then you can do something: mod <- isoMDS(gog.dist) plot(mod$points, asp=1, type="n") text(mod$points, rownames(mod$points)) I hope this helps. However, it

Re: [R] Help about princomp

owing assumes that 'keep' is a vector which is TRUE for cases you keep, and FALSE for those ignored: pc <- prcomp(x[keep,]) predict(pc, newdata=x) cheers, Jari Oksanen __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailma

Re: [R] Abundance data ordination in R

zeros certaily makes more sense than removing *pairs* of data where species is NA in one site and present in another. There are ways to have something like handling zeros as missing values of various degrees(!), but my decency prohibits me to write about these methods. cheers, jari oksanen __

Re: [R] about hcluster

s are rare, but there may be some alternatives floating around in R. 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.htm

[R] distance metrics

2417, 1105, 5000)] This is slower, of course, but avoids expanding to a matrix. Perhaps a nicer and easier to use (but more opaque) way is to write the function as: getidx <- function(dist, i, j) { dist[idx(i, j, attr(dist, "Size"))] } which can be used with fewer bracket type

Re: [R] RDA and trend surface regression

r: allowing them to be curved allows curved solutions. These arguments are not necessarily valid if you only want to have variance partitioning, or if you use polynomial conditions ("partial out" polynomial effects in Canoco language). In that case it may make sense to use quadratic (or p

[R] RDA and trend surface regression

ormula operators: rda(Helling ~ x + y + I(x*y) + I(x^2) + I(y^2) + I(x*y^2) + I(y*x^2) + I(x^3) + I(y^3)) If you don't have the interaction terms, then it is easier and better (numerically) to use poly(): rda(Helling ~ poly(x, 3) + poly(y, 3)) Another issue is that in my opinion using polyn

Re: [R] something missing in summary()

Number of observations may not be very useful in summary.data.frame, because it varies so little among variables. The R-help message cited above and its follow-ups suggest some ways of locally modifying the code and maintaining the modifications over the upgrades of R. Best wishes, Jari Oksanen _

[R] isoMDS vs. other non-metric non-R routines

cular but about NMDS in general (but he will correct me if my interpretation was wrong). I can imagine cases where non-metric solution works badly, in particular with small data sets. However, that should concern all implementations similarly, and probably it should be visible in Shepard plots (s

[R] isoMDS vs. other non-metric non-R routines

x27;maxit') arguments in isoMDS? The default 'tol' is rather slack, and 'maxit' fairly low, since (speculation) the function was written a long time ago when computer were slow, but if you have something better than 75MHz i486, you can try with other values. I have use

[R] isoMDS - high stress value and strange configuration

4 In this case I generated the random configuration using function initMDS of vegan, but you can do that quite well by any other way. Another point (which does not matter here so much) is that isoMDS multiplies stress by 100, so that your stress of 6 would corresponde 0.06 in some other software

Re: [R] question about capscale (vegan)

ou will > see that you have species scores (though their meaning may be hard to > understand if no "comm" provided - see ?capscale) > > I hesitate to call this a bug in capscale() or permutest.cca() (this is > where the error comes from by the way: > > > traceback()

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

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 im

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

m and San Francisco 8240km. In more practical metric of flight time, Baltimore 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 D

Re: [R] Error message with nmds

ly asked. Last thread was on April, 2006. See https://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, Finl

Re: [R] isoMDS and 0 distances

EITHER ORALLY 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://c

Re: [R] isoMDS and 0 distances

the upcoming R release, but that's not released yet.) You may check working with NA: are duplicate points identical in results? Then about replacing zero distances with a tiny number: this has been discussed before in this list, and Ripley said "no, no!". I do it all the time, but

Re: [R] "transparent" background for PDF

play transparent background in PDF. This also concerns transparent background PDF's from 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 __

Re: [R] Ordination of feature film data question

perhaps not the best) choice for co-occurrence 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] Variance for Vector of Constants is Not Zero

sting guide! >> http://www.R-project.org/posting-guide.html > > __ > 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 > -- 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-project.org/posting-guide.html

Re: [R] suppress tick labels

mbers below or beside each tick? Looking at ?axis suggest that you could set labels=FALSE to suppress those. It indeed seems to work, although you get a warning for each omitted tick label (but you must get used to warnings if you plot()). Try: plot(rnorm(20), labels=FALSE) cheers, jari oksanen

Re: [R] modifying code in contributed libraries - changes from versions 1.* to 2.*

970 226-9326 > [[alternative HTML version deleted]] > > __ > 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] open source and R

use Emacs+ESS to edit, test and debug the the function within an R session. That really ruins all decent commenting: comments may be misplaced, and the default formatting of comments is really bad in ESS. So my choice is to uncomment R code, but comment C (and Fortran). cheers, jari oksanen

Re: [R] voronoi

talization), and voronoi.mosaic() in 'tripack' uses .Fortran. cheers, jari oksanen > 2005/11/13, Robert <[EMAIL PROTECTED]>: >> Is there any pure r code to do delaunay or voronoi diagrams? >> Thanks! >> >> - >> >>

Re: [R] error in rowSums:'x' must be numeric

n that intended as rownames is taken as a non-numeric variable. This is such a common problem that an innocent user (not me: I'm no more innocent) would expect R cope with that kind of input format. cheers, jari oksanen -- Jari Oksanen -- Dept Biology,

Re: [R] quadratic form

and it was somewhere between Intel and PowerPC.) 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-project.org/posting-guide.html

[R] Forum of Mac questions (Was: loading packages - mac user)

t;Mac Devolepment" forum that sounds like being "unintelligible to non-programmers"? cheers, jari oksanen -- Jari Oksanen <[EMAIL PROTECTED]> __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help P

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

adings from varimax rotation. However, 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-

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

onential family, although it so often is modelled. I've often seen that species richness (number of species -- or in R-speak 'tokens' -- in a collection) is underdispersed to Poisson, and for a good reason. Even there I'd play safe and use poisson() instead of underdispersed quasipois

Re: [R] Compare two distance matrices

implementation of dissimilarity functions 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], home

Re: [R] indicator value in labdsv

more useful to post to some other mailing group where people are more concerned about indicator species, or to contact the package author directly (I CC this message to him). cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland Ph. +358 8 5531526, cell +

Re: [R] Graphical presentation of logistic regression

ecided 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 --

Re: [R] Document clustering for R

e of these could be the one for you... I would be surprised if cosine index is missing (and if needed, I could 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.et

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

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

vector elements had identities ("names") originally, then you should stack your data so that entries with the same identity go to the same column. It is difficult to imagine Horn index used in cases where you don't have these identities -- specifically species nam

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

You shouldn't forge your data: the function handles 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/ ___

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 Indica

Re: [R] prcomp eigenvalues

o the sum of squares, and you can get these by es <- (nrow(x) - 1) * ev 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, Finla

Re: [R] ellipse -confidence interval

of ellipse package (see ordiellipse there). Some people are hypersensitive to "principle" components (beware). cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo

Re: [R] plot(corresp(data)...)

You have three rows, and you can get only 2d with corresp. You can use scatterplot3d or rgl functions for 3d plotting (both in packages with the same name) after you get data where you have more than two axes. These figures easily get illegible, though. cheers (again), jari oksanen -- Jari O

Re: [R] plot(corresp(data)...)

lp me, send me source if you can! What's wrong with the biplot function that is used in the example of corresp help page? That is: biplot(corresp(data,nf=2)) It seems to give a legible plot with your data (that you named data, a bad idea). At least in my screen. cheers, jari oksanen -- Jari

Re: [R] Uses of isoMDS()

sted) > before there's a chance that things will become clear. > And take care that Kruskal, too, is in your local library when MASS arrives: the book does not tell you which of Kruskal's alternative stresses is used, but you got to compare the equation

Re: [R] A long digression on packages

sts starts a discussion in a certain forum, you shall not divert it to another forum where it may be hidden by most readers, perhaps even by the originator of the thread. cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ R-help@stat.math.ethz.

Re: [R] R GUI for Linux?

ch more user friendly than it used to be some decade ago. 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] R annoyances

de breakage even in base R) was caused by the same kind of political correctness. Please Mr R, keep it like it used to be... 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-project.org/posting-guide.html

Re: [R] cmdscale: missing dimnames in R 2.1.0

tr(*, "dimnames")=List of 2 > ..$ : NULL > ..$ : NULL > > I miss the names of the cities. What can I do? > You can use R 2.1.0-patched where this is fixed. cheers, jari oksanen -- Jari Oksanen <[EMAIL PROTECTED]> _

Re: [R] tcl/tk problem

ou have to register to use their services). I'm not sure how grasper works, but it may be that you must start X11 yourself in Mac R before calling grasper. But before this, you probably have some installation to do. You can find F For Mac OS X FAQ from the Help entry of the upper panel in R.ap

Re: [R] libz library missing while installing RMySQL

d probably need zlib-devel as well (this is FC3). So they are system level libraries that come with SuSe instead of R packages. cheers, jari oksanen -- Jari Oksanen <[EMAIL PROTECTED]> __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.

Re: [R] Pca loading plot lables

and: plot(pr$loadings, type="n") text(pr$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 o

Re: [R] results from sammon()

= 0.500 stress after 30 iters: 0.07838, magic = 0.500 stress after 40 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

Re: [R] results from sammon()

need to give more details if you want to get 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] 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] Very Slow Gower Similarity Function

for loops 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 guid

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

my case this happened when I tried 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@st

Re: [R] Factor Analysis Biplot

ee this, you may try: unclass(eurofood$loadings) print(eurofuud$loadings, cutoff=0) 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 mai

Re: [R] R binaries for UMBUTU Linux?

you can do this fairly safely (the general problem is a potential conflict 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.

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

ly, it says that "sdev" are standard deviations). cheers, jari 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/ _

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

y removed the effect of x... In orthogonal case the coefficient for x would be 0. Residuals are equal in these two models: > range(residuals(mod) - residuals(mod2)) [1] -2.797242e-17 5.551115e-17 But, of course, fitted values are not equal, since you fit the mod2 to the residuals af

Re: [R] Principle Component Analysis in R

principal than others. Wouldn't original data do? 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] How to do such MDS in R

be easy to port 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 Ok

Re: [R] Significance of Principal Coordinates

ture. Let's hope so. The old truth is that most data sets have 2.5 dimensions (Kruskal): those two that you can show in a printed plot, and that half a dimension that you must explain away in the text. Wouldn't that be a sufficient solution? cheers, jari oksanen -- Jari Oksanen <[

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

you use labdsv ord <- isoMDS(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

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

Re: [R] Reconstructing Datasets

though. Library 'vegan' can do this automatically for PCA run with function 'rda', but there the scaling of raw results is non-conventional (though "biplot"). 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] How to set up number of prin comp.

$rotation[, 1:4] # The four first loadings Also, loadings(pc) should work 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@sta

Re: [R] eigen vector question

ne functions: loadings <- function(x) UseMethod("loadings") loadings.princomp <- function (x) x$loadings loadings.prcomp <- function(x) structure(x$rotation, class="loadings") 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] R + MacOSX + Emacs(XEmacs) + ESS

different versions, both work graphically 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

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, inst

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

(saving in disk space is more considerable of course). So are there plans for binary Linux packages for other distros than Debian so that people could use the non-devel piece of R only? cheers, jari oksanen -- Jari Oksanen <[EMAIL PROTECTED]> __ R-he

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

binary if you don't want to see the trouble of installing X-Code and g77. However, it failed with missing 'gtools' upon loading. cheers, jari oksanen > On Wed, 9 Feb 2005, Theresa Talley wrote: > > > Hi- > > I've been trying to install the hier.part package on > &

Re: [R] randomisation

Windows binary is not available at CRAN since the package fails R CMD check in Windows (so you shouldn't check the package but just use 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, 2

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

gl' library assumes that 'libpng' 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 'j

Re: [R] Bootstrapped eigenvector

;- pc$loadings[ ,k] sol <- sweep(sol, 2, reve, "*") out <- out + ifelse(res > 0, sol <= 0, sol >= 0) } out/permutations } With typical chemical data, you should pass option cor = TRUE to princomp. Another issue is whether you should use

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

hing? > Saving a plot from a menu bar (click "save") saves a plot 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 w

Re: [R] printing PCA scores

arentheses in the original help file] So this is what you asked 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] (no subject)

On the other hand, I find it extremely hard to find a reason to find a reason to use detrended CCA. It seems to destroy everything... cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mail

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

somewhere else 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/l

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

sitting by your computer. Another efficiency issue 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]&

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

ms, and negative eigenvalues are unrelated. So you 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 Bio

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

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

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

up is: Stümpke, H. 1957. Bau und Leben der Rhinogradentia. Gustav Fischer 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

Re: [R] Importing vector graphics into R

was made of polygons instead of lines, and we couldn't change line widths for horizontal lines only in panel headers. This is what pstoedit gives for version info: pstoedit: version 3.33 / DLL interface 108 (build Oct 17 2003 - release build) : Copyright (C) 1993 - 2003 Wolfgang Glu

Re: [R] Gam() function in R

irst question of deciding the smoothness, and explains how elegantly 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:

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

ing Finn which helps to explain this attitude). With this attitude, you could pick a gray, mouse-like nocturnal bird 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, Ou

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

o Pat Burns): > > http://www.accesscom.com/~alvaro/alien/thepics/alien102_.jpg It seems that tastes for movies vary. I've never liked movies about ecologically non-sustainable and energetically impossible life forms. The current sub-theme brings to my mind something completely diff

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

x27;m at my office. You can have a look at the image at http://cc.oulu.fi/~jarioksa/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 ___

Re: [R] Protocol for answering basic questions

tion. In several cases the solutions to the problem remain private as well. After all, the purpose of the mailing list is a public 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

Re: [R] depth constrained cluster

sgrain/fr/labo/. his package seems to have both onedimensional or chronologically constrained clustering and 2dim or spatially constrained clustering. cheers, jari oksanen -- Jari Oksanen <[EMAIL PROTECTED]> __ [EMAIL PROTECTED] mailing list https://

Re: [R] Protocol for answering basic questions

a Usenet newsgroup a generation thing. I think some of the younger users would prefer a Wiki 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

Re: [R] step.gam

ss validation? Dave Roberts discusses R/S-plus (or mgcv/gam package level) gam fitting in ecological context at http://labdsv.nr.usu.edu/splus_R/lab5/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

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

y hints will be very much appreciated. > > i'm running: > > debian 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]> __ [

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