Re: [R] tcl/tk problem

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.app or through CRAN. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch

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

this is fixed. 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

, 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] A long digression on packages

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.ch mailing

Re: [R] Uses of isoMDS()

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 against Kruskal's. cheers, jari oksanen

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

)) 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 Oksanen [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

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

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 Oksanen [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r

Re: [R] ellipse -confidence interval

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/r-help PLEASE do read the posting guide! http://www.R

Re: [R] USA map

, type=n) map(worldHires,Norway, add=TRUE) map(worldHires,Norway, add=TRUE, exact=TRUE, col=red) By the way, where is Estonia? Couln't find it with any strings I could imagine. Some R core developers have frequented Estonia, so it would be nice to have that in the map. cheers, jari oksanen -- Jari

Re: [R] basic question

into R, which, but in Dave's words That concept is completely foreign to windows people of course, so it's pretty much useless. It may be that you have to wait until Dave Roberts lectures on these methods again, since then he may have to finish up the package. cheers, jari oksanen -- Jari Oksanen

Re: [R] citing a package?

documentation in CRAN. If citing URL is allowed in the journal, this is a place to point. cheers, jari oksanen -- J.Oksanen, Oulu, Finland. Object-oriented programming is an exceptionally bad idea which could only have originated in California. E. Dijkstra

Re: [R] Odd behaviour of step (and stepAIC)?

function where this ordering was done, but I was not clever enough to instantly know how to change the behaviour. cheers, jari oksanen On 19 Mar 2004, at 17:25, Anon. wrote: I can only assume I'm betraying my ignorance here, but this is not what I would expect. I'm getting the following from

Re: [R] Fwd: MDS problems [ajtee@ajtee.uklinux.net]

that you did this dirty trick. 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

Re: [R] calculate length of gradient ?

better than PCA, even with short gradients so you don't need axis lengths. Please read the posting guide (about messages that should be sent to the list vs. to the package authors). cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ [EMAIL PROTECTED

Re: [R] StepAIC

decide how to order terms in formulae. cheers, jari oksanen (Oulu) __ [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] question on isoMDS

- unique(test.bc) The name of the function may be confusing: what's `unique' in removing zeros? However, the following seems to hold: dist(unique(x)) == unique(dist(x)) which would justify the name. The previous discussion mentioned some dirty tricks, too. cheers, jari oksanen On Mon, 2004-04-12

Re: [R] (no subject)

, but I can't find it in his (or Casgrain's) web pages. However, his package was called R long before Ihaka Gentleman introduced their R. cheers, jari oksanen On 21 Apr 2004, at 15:57, Hanke, Alex wrote: Dear R-Help Does The R Package for Multivariate and Spatial Analysis Version 4.0 (Casgrain

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

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 PLEASE do read the posting guide! http://www.R-project.org

Re: [R] quadratic form

.) 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] error in rowSums:'x' must be numeric

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, Univ Oulu, 90014 Oulu, Finland email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa/ __ R-help

Re: [R] voronoi

, jari oksanen 2005/11/13, Robert [EMAIL PROTECTED]: Is there any pure r code to do delaunay or voronoi diagrams? Thanks! - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list

Re: [R] open source and 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 __ R-help@stat.math.ethz.ch

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

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

Re: [R] suppress tick labels

? 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 -- Jari Oksanen, Oulu

Re: [R] question about capscale (vegan)

: permutest.cca(object, step, ...) 2: anova.cca(my.cap) 1: anova(my.cap) ), but anova.cca doesn't seem to handle situations where there isn't an unconstrained component. I've CC'd Jari Oksanen, the author of vegan to insure he sees this. Dear y'all, I agree with this analysis: you have no residual

[R] isoMDS - high stress value and strange configuration

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 (assuming they use the same stress). cheers, jari oksanen -- Jari Oksanen

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

' 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 used isoMDS quite a lot, and I have had good experience. Cheers, Jari Oksanen

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

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 (see isoMDS help). Cheers, Jari Oksanen

Re: [R] something missing in summary()

, 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-help

[R] RDA and trend surface regression

, 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 polynomial constraints is an Extremely Bad Idea(TM). cheers, Jari Oksanen __ R-help@stat.math.ethz.ch mailing

Re: [R] RDA and trend surface regression

polynomial conditions (partial out polynomial effects in Canoco language). In that case it may make sense to use quadratic (or polynomial) constraints or conditions. cheers, Jari Oksanen __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch

[R] distance metrics

- function(dist, i, j) { dist[idx(i, j, attr(dist, Size))] } which can be used with fewer bracket types: getidx(dist, 2417, 1105). cheers, jari oksanen __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] about hcluster

. 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 and provide commented, minimal, self-contained, reproducible code.

Re: [R] Abundance data ordination in R

something like handling zeros as missing values of various degrees(!), but my decency prohibits me to write about these methods. cheers, jari oksanen __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] Help about princomp

, 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/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting

Re: [R] dist label names

, rownames(mod$points)) I hope this helps. However, it is new to me that Euclidean distance is an appropritae metric for governance indicators (but none of my business). Cheers, jari oksanen __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch

[R] step in Sweave

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 PLEASE do read the posting guide http://www.R-project.org

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

. 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 and provide commented, minimal, self-contained, reproducible code.

Re: [R] biplot package

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 time. It would be nice to be able to have this kind of interface for your enhanced code, too. cheers, jari oksanen

Re: [R] correspondence analysis

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 between programs. I hope this helps, Jari Oksanen __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch

Re: [R] Error using mgcv package

. There may be other problems, but this probably fixes tha one you reported above. cheers, jari oksanen And after deleting df's model.gam - gam(formula = RES ~ CAT01+s(NUM01)+CAT02+CAT03+s(NUM02)+CAT04+ + CAT05+s(NUM03)+CAT06+CAT07+s(NUM04)+CAT08+s(NUM05)+CAT09+ + CAT10+s(NUM06)+CAT11+NUM07+CAT12

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

, 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 directly (although the author was not reading email in July). Best wishes, Jari Oksanen

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

of years ago, mainly to identify unstable points with alternative locations, but that produced 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

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