similar to: rgl on Mac OS

Colleagues Running R2.2.1 on either a Linux (RedHat 9) or Mac (10.4) platform. I created a PDF document using pdf("FILENAME.pdf", bg="transparent", version="1.4"). I then imported the graphic into PowerPoint - background was set to a non-transparent color. I was hoping that the inserted graphic would be transparent - instead, it had a white background.

Hi all, I have a pretty basic question about categorical variables but I can't seem to be able to find answer so I am hoping someone here can help. I found that if the factor names are all in numbers, fitting the model in lm would return labels that are not very recognizable. # Example: let's just assume that we want to fit this model fit <- lm(height ~ age + Seed,

Hi all, I had a weird problem with xyplot and I am wondering if anyone can help me figure out what's wrong here. Basically if I call xyplot() inside a function and I call quartz() after, then the previous xyplot() does not do anything. A short demo of the issue is like this: library(lattice) plot.trends <- function() { mat <- data.frame(cbind(rnorm(100), rnorm(100))) names(mat)

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

I am attempting to install the Hmisc, rreport and Design packages, but am not able to do so. I am running R v1.9.1 on Mac OS 10.3.5. I have tried installation using both the GUI version of R and also running R from sudo in a terminal session. In the terminal I receive the following error: * Installing *source* package 'Design' ... ** libs g77 -fno-common -g -O2 -c lrmfit.f -o

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 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 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

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,

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 all, I didn't find any graphical solution in the package "mva" to plot the canonical scores from a CCA (canonical correlation analysis). Does anybody knows how to plot or has anybody already programmed : - the map of the canonical scores, - the graph of the canonical weights, - the correlation circle i.e. the canonical loadings ? Thank you for help ...

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, my attempt to install the package Hmisc v3.0-1 fails with the message: /usr/bin/ld: cannot find -lfrtbegin collect2: ld returned 1 exit status make: *** [Hmisc.so] Error 1 ERROR: compilation failed for package 'Hmisc' i'm at a loss here. any 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

Dear all, I'm trying to get a two dimensional embedding of some data using different meythods, among which princomp(), cmds(), sammon() and isoMDS(). I have a problem with sammon() because the coordinates I get are all equal to NA. What does it mean? Why the method fails in finding the coordinates? Can I do anything to get some meaningful results? Thank you very much Domenico

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 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