similar to: The class attribute on an environment seems buggy (PR#2159)

Is there a way of calling the method of the root class directly? Here is an example explaing my question. Everything relates to S3/UseMethod classes and methods. I have an object x of class MicroarrayMatrix, which inherits from class Matrix. The "core" object of x is a simple matrix. In other words, I basically have x <- matrix(logratios, ncol=nbrOfSpots, nrow=nbrOfSlides)

>From R v1.6.0 there has been a new test added to the library() code. This test is performed when library() is ran on a "unix" system and it verifies that the "Built" platform (from the DESCRIPTION file) is "compatible" with the current platform. Here is the code extract from the local function testRversion() of library() that I am talking about: if

I am not sure if what I am asking below should be discussed under r-help or r-devel, so please feel free to move over to r-devel. This is a spin off from Gordon Smyth's question about generic functions and Robert Gentleman's reply. I have tried to raise the question before and I am sure this has been discussed by others, but never on the r-help list what I can see. My concern is that

I am not sure if what I am asking below should be discussed under r-help or r-devel, so please feel free to move over to r-devel. This is a spin off from Gordon Smyth's question about generic functions and Robert Gentleman's reply. I have tried to raise the question before and I am sure this has been discussed by others, but never on the r-help list what I can see. My concern is that

First of all, I haven't followed the discussion about the new/upcoming name space support in R so I do not know the purposes or requirements for it, neither its design, and I can only guess. I found the (initial?) notes by Luke Tierney on the Developers Page. Are there any other references? Since it seems that the current implementation (R v1.6.2) of name spaces is a "trial" version

Hi All, I'm trying to implement a quasi symmetry model for data on twin pairs. A crosstabulation of twin 1 by twin 2 (assumed symmetrical) stratified by another variable. There is a good paper on this by Phil (?) McCloud and Darroch in Biometrika (1995) which explains the method, but I've not done this before so am not clear how to code these models. Any help would be greatly

Hi, I'm using zoo because it can automatically label the months of a time series composed of daily observations. This works well for certain time series lengths, but not for others, e.g.: While: > library(zoo) > plot(zoo(runif(10), as.Date("2005-06-01") + 0:50)) Shows up the months and day of month, > plot(zoo(runif(10), as.Date("2005-06-01") + 0:380))

Hi, Can anyone explain how the standard error in arima() is calculated? Also, how can I extract it from the Arima object? I don't see it in there. > x <- rnorm(1000) > a <- arima(x, order = c(4, 0, 0)) > a Call: arima(x = x, order = c(4, 0, 0)) Coefficients: ar1 ar2 ar3 ar4 intercept -0.0451 0.0448 0.0139 -0.0688 0.0010 s.e.

Hi, I'm running R v1.9.0 on WinXP Pro. I noticed that R.exe and Rterm.exe behave differently on Ctrl-C. Starting a Windows Command prompt (cmd.exe) you get from running Rterm.exe: C:\Program Files\R>rw1090\bin\Rterm.exe --vanilla --quiet > ^C > ^C > 1+1 [1] 2 > Sys.sleep(100) # Ctrl-C after a few seconds > ^C > ^C > 1+1 [1] 2 > q() C:\Program Files\R>

I run R on MS Windows. In R2.9.0dev, I type ?base to get "R help for package base" to open. I then select ".First" from the list of contents, getting a page headed: "Initialization at Start of an R Session". About half way down there is a sentence: The command-line flag --vanilla implies --no-site-file, --no-init-file, --no-restore and --no-environ. Under

Dear R-devel, I am experiencing issues with running GAM models using mclapply, it fails to return any values if the data input becomes large. For example here the code runs fine with a df of 100 rows, but fails at 1000. library(mgcv) library(parallel) > df <- data.frame( + x = 1:100, + y = 1:100 + ) > > mclapply(1:2, function(i, df) { + fit <- gam(y ~ s(x, bs =

Hi, I'm using survreg() from the survival package for parametric survival regression (modelling inter-arrival times of patients to a waiting list as exponentially distributed, with various regressors such as queue size and season). Does anyone know which algorithm survreg() uses for this? Thanks, Gad -- Gad Abraham Department of Mathematics and Statistics The University of Melbourne

Hi Duncan, just noticed that after installing the Windows R-2.13.0 build there is no i386 directory in the R-2.13.0dev/bin directory and hence no Rgui.exe. Is this intentional with the devel version? I downloaded from http://cran.ms.unimelb.edu.au/, where it says: "This is a combined Windows 32/64 bit binary build of the 2010-11-27 r53672 development snapshot of R (which will eventually

Hi, I'm doing PCA on wide matrices and I don't understand why calling predict.prcomp on it throws an error: > x1 <- matrix(rnorm(100), 5, 20) > x2 <- matrix(rnorm(100), 5, 20) > p <- prcomp(x1) > predict(p, x2) Error in predict.prcomp(p, x2) : 'newdata' does not have the correct number of columns > dim(x2) [1] 5 20 > dim(p$rotation) [1] 20 5

Hi, I'm trying to do PCA on a n by p wide matrix (n < p), and I'd like to get more principal components than there are rows. However, svd() only returns a V matrix of with n columns (instead of p) unless the argument nv=p is set (prcomp calls svd without setting it). Moreover, the eigenvalues returned are always min(n, p) instead of p, even if nv is set: > x <-

Hi, I'm using Ubuntu Hardy i386, and the R 2.7.1 Ubuntu packages from CRAN. The CRAN r-base-dev package depends on refblas3-dev or atlas3-base-dev, but octave3.0-headers depends on libblas-dev. The two blas packages seem to conflict, so r-base-dev and octave3.0-headers can't be installed together. Is this a known issue? Thanks, Gad $ sudo apt-get install octave3.0-headers Reading

Hi, I'm using Ubuntu 9.10 amd64 with cran2deb packages (I know it's meant for Debian, it's worked fine for me for many months). Recently apt-get update has to started to complain: ... Hit http://debian.cran.r-project.org testing/ Release Get:1 http://debian.cran.r-project.org testing/ Packages [515kB] Fetched 1B in 3s (0B/s) W: Failed to fetch

Dear all, I'm writing to ask for advice as to best practice. A PhD student working with me is writing C++ code that we hope to make public as src code in our Bioconductor package edgeR. He wants to call the function fmm_spline, which is part of the source code for the stats package http://svn.r-project.org/R/trunk/src/library/stats/src/splines.c, from his C++ code. This function

Dear All, I have installed CentOS release 5.2 (Final). EMC SAN partition is mounted by using EMC Powerpath for resolving multiple paths. I was able write and read data over to SAN partition without any issues. Subsequently I have unmounted EMC SAN partition from the system and deleted LUN using Navisphere user interface. After rebooting system, I still see SAN mappings in system. Here

Hi, I have two example packages, test1 and test2, where the only code in them is: setGeneric("predict", function(object, ...) standardGeneric("predict")) (get them from http://www.cs.mu.oz.au/~gabraham/test1.tar and http://www.cs.mu.oz.au/~gabraham/test2.tar) The difference between them is that first does not have a namespace, and loads fine. The second has a namespace