similar to: invalid 'mode' of argument?

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

Canberra distance is defined in function `dist' (standard library `mva') as sum(|x_i - y_i| / |x_i + y_i|) Obviously this is undefined for cases where both x_i and y_i are zeros. Since double zeros are common in many data sets, this is a nuisance. In our field (from which the distance is coming), it is customary to remove double zeros: contribution to distance is zero when both x_i

Canberra distance is defined in function `dist' (standard library `mva') as sum(|x_i - y_i| / |x_i + y_i|) Obviously this is undefined for cases where both x_i and y_i are zeros. Since double zeros are common in many data sets, this is a nuisance. In our field (from which the distance is coming), it is customary to remove double zeros: contribution to distance is zero when both x_i

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

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-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

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

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

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

Dear R folks, One of the fantastic new tools in R is `Sweave'. I have tested it so much that I know it works and produces fine documentation, and with (GNU) Emacs/ESS it is nice to work with, too. I started to have a look at including some Swoven (is that a strong verb?) documentation with my R package, but it seems that there is no model to copy among those packages that I have installed in

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

Dear R users, Up to now, I only used precompiled packages. As I am working on vegetation ecology, I would be interested in using a package not stored by CRAN called labdsv_0.9-1.tar.gz and developped by Dave Roberts at the National Center for Ecological Analysis and Synthesis (unfortunately I did not find any corresponding .zip file). Although I tried to follow the proposed guidelines to

Hello, Can you get eigenvalues in addition to eigevectors using prcomp? If so how? I am unable to use princomp due to small sample sizes. Thank you in advance for your help! Rebecca Young -- Rebecca Young Graduate Student Ecology & Evolutionary Biology, Badyaev Lab University of Arizona 1041 E Lowell Tucson, AZ 85721-0088 Office: 425BSW rlyoung at email.arizona.edu (520) 621-4005

Dear All, It's Eszter again from Hungary. I could not solve my problem form yesterday, so I still have to ask your help. I have a binary dataset of vegetation samples and species as a comma separated file. I would like to calculate the Jaccard distance of the dataset. I have the following error message: Error in rowSums(x, prod(dn), p, na.rm) : 'x' must be numeric In addition:

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 List: I have a question regarding an MDS procedure that I am accustomed to using. I have searched around the archives a bit and the help doc and still need a little assistance. The package isoMDS is what I need to perform the non-metric scaling, but I am working with similarity matrices, not dissimilarities. The question may end up being resolved simply. Here is a bit of substantive

Good morning: I submitted a package update to CRAN and got a bounce because I had not run R CMD check with "--as-cran". I'd not heard of that before, but I'm glad to know about it now. I see it warns when my functions do use partial argument matching, and I like that advice very much. Also I see this warning * checking package subdirectories ... WARNING Found the following

There does not seem to be a RPM for Red Hat 7 of version 1.2.1. What should I do? I have a new computer with RH7. I''m willing to try to make one from the SRPM, but I''ve never done that before, and I don''t want to go to the trouble if someone else is already planning to do it soon. Likewise, I could install it from the tgz file. (I just did that on a Solaris server,