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Hello I will be applying MDS (actually Isomap) to make a psychological "concept map" of the similarities between N concepts. I would like to scale to a large number of concepts, however, the resulting N*(N-1) pairwise similarities is prohibitive for a user survey. I'm thinking of giving people random subsets of the pairwise similarities. Does anyone have recommendations for this

...definitely prefer to use R whenever feasible (both for research and teaching). Thanks for developing a superb computing/programming environment. Kenneth Nordstr?m ...................................................................... Kenneth Nordstr?m Kenneth.Nordstrom at oulu.fi Professor of Statistics Head of Statistics Division Dept of Math Sciences Tel: +358-8-553 1829 Univ of Oulu +358-8-553 1820 (secr) P.O. Box 3000 Fax: +358-8-553 1848 FIN-90014 Univ of Oulu FINLAND...

...t;nc ; j++) { if(R_FINITE(x[i1]) && R_FINITE(x[i2])) { - dist += fabs(x[i1] - x[i2])/fabs(x[i1] + x[i2]); + sum = fabs(x[i1] + x[i2]); + if (sum > 0.0) + dist += fabs(x[i1] - x[i2])/sum; count++; } Best wishes, Jari Oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland Ph. +358 8 5531526 (job), mobile +358 40 5136529 email jari.oksanen at oulu.fi, homepage http://cc.oulu.fi/~jarioksa/ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Sen...

...t;nc ; j++) { if(R_FINITE(x[i1]) && R_FINITE(x[i2])) { - dist += fabs(x[i1] - x[i2])/fabs(x[i1] + x[i2]); + sum = fabs(x[i1] + x[i2]); + if (sum > 0.0) + dist += fabs(x[i1] - x[i2])/sum; count++; } Best wishes, Jari Oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland Ph. +358 8 5531526 (job), mobile +358 40 5136529 email jari.oksanen at oulu.fi, homepage http://cc.oulu.fi/~jarioksa/ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Sen...

...on is that those binaries are tied to that particular build of R, > and will not work with a general build on MacOS X. > > I would expect this to work from the command-line in the GUI console, and > had believed it had been tested there. > > > On Tue, 3 May 2005 jari.oksanen@oulu.fi wrote: > > > Full_Name: Jari Oksanen > > Version: R 2.1.0 > > OS: MacOS 10.3.9 > > Submission from: (NULL) (130.231.102.145) > > > > > > For various reasons (which need not be expanded here) I have tried to update my > > long neglected R in Mac...

Dear R-help, I'm trying to create a simple R package that contains 3 string functions, but I have run into some problems: what are the correct permission for the files in the package directory? Yours faitfully, Rasmus * checking for file `stringfun/DESCRIPTION' ... OK * checking package directory ... OK * checking for sufficient/correct file permissions ... WARNING * Found the

Hi After trying a simple decorana analysis (from the vegan package) on a simple data frame which contains no NA's the following error was returned: > tt_decorana(covN) Error in decorana(covN) : NA/NaN/Inf in foreign function call (arg 1) Have any vegan users come across this error and know what can be done about it? Cheers, J

Hi, I'd like to perform Dufrene-Legendre Indicator Species Analysis for a multivariate regression tree. However I have problems with arguments of duleg(veg,class,numitr=1000)function. How to obtain a vector of numeric class memberships for samples, or a classification object returned from mvpart? thanks in advance -- Best regards, Agnieszka Strzelczak

Dear Colleagues, As a novice I was trying to calculate Shannon diversity index using diversity function in vegan package and kept having same error message. Error in sum(..., na.rm = na.rm) : invalid 'mode' of argument My dataset is from microarray and have abundant missing values, so I tried labeling them as NA and 0, but still same error message. Shannon index is negative

Hi, It seems like a number of people on this list can install rgl but have problem loading it. I found myself in the same situation too. I have tried the workaround of removing /usr/X11R6/lib from DYLD_LIBRARY_PATH, but it doesn't seem to work for me, I am still getting the same error (that everyone else seems to get). Can anyone give me some ideas on what else to try? I have Mac OS 10.3.5,

Dear R-users: Im trying (using gam package) to develop a stepwise analysis. My gam object contains five pedictor variables (a,b,c,d,e,f). I define the step.gam: step.gam(gamobject, scope=list("a"= ~s(a,4), "b"= ~s(b,4), "c"= ~s(c,4), "d"= ~s(d,4), "e"= ~s(e,4), "f"= ~s(f,4))) However, the result shows a formula containing the whole

...ome (working at ~5KB file transfer speed in practice) I am really concerned with this aspect as well (it doesn't concern me at all when at work). Is the assumption that users won't have tools to build a pdf from the Sweave source? 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 jari.oksanen at oulu.fi, homepage http://cc.oulu.fi/~jarioksa/ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R...

...to be modest and shy in suggestions so that it would be up to the user to get those extra packages needed without requiring them in R CMD check? I stumbled on this with earlier versions of R, and then my solution was to suggest nothing. 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 jari.oksanen at oulu.fi, homepage http://cc.oulu.fi/~jarioksa/

...t. * I replaced reference to a non-existent function ~~fun~~ with a reference to function help. I'm sorry for the formatting of the diff file: my emacs/ESS is cleverer than I and changes indentation and line breaks against my will. 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 jari.oksanen at oulu.fi, homepage http://cc.oulu.fi/~jarioksa/

Dear All I am trying to do a partial canonical analysis of principal coordinates using Bray-Curtis distances. The capscale addin to R appears to be the only way of doing it, however, when I try and calculate a Bray-Curtis distance matrix either using Capscale or Vegedist (capscale I understand uses Vegedist anyway to calculate its distance matrix), R uses up all available memory on the computer,

I have been trying to use the rbeta() function to generate random beta variates with a particular mean and standard deviaiton for some simulation problems I am working on, however I am unsure of the relationship between the parameters shape1 and shape2 and the mean and standard deviation of the beta distribution. I am guessing that there is a formula for this, but I am unsure what it is. Can

...to R in Linux (RH7.1, gcc "2.96" g77), but one friend of mine told it crashes R when linked to Windows R. I don't have Windows R with building tools anywhere I know, so I am not sure if this is the cause of the failure. 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 jari.oksanen at oulu.fi, homepage http://cc.oulu.fi/~jarioksa/ ------- End of Forwarded Message -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read h...

Hi: The y axis on the hist function seems to set its limits oddly. sometimes, it covers the full range of the data and sometimes it stops one major tick short. I have had this behavior with a variety of data sets, and it can easily be reproduced by just running the following several times: hist(rnorm(100000)) I have tried explicitly setting ylim to the range of values produced by rnorm

I am trying to install labDSV from http://labdsv.nr.usu.edu/ into R-Windows 1.5.0. It only comes as a TAR file which extracts into folders that seem to match those for other libraries DATA, MAN, R and SRC. I have manually copied these folders into a folder called labDSV under the Library directory under R. However when I load the library I get a message that the library contains no R code.

Dear Help List, My name is Matt Oliver. I have been using R for about a year and find it very helpful. However, I have a need for a function that I cannot find. I am not very good at programming so I thought I would ask the group. I have an irregular grid of data (x = Longitude, y = Latitude). Each pair of my x,y has a categorical value. Obviously linear or any other numerically based