similar to: Error in solvet: apparently singular matrix

Hi, I'm trying to use Frank Harrell's Design:::ols function to do regression of y (numeric) on the interaction of two factors (x1 and x2), but Lapack throws an error: > library(Design) ... > load(url("http://www.csse.unimelb.edu.au/~gabraham/x")) > ols(y ~ x1 * x2, data=x) Error in chol2inv(fit$qr$qr) : 'size' cannot exceed nrow(x) = 20 > traceback()

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

Hi, I have an RData file containing a GeneSetCollection object (Bioconductor), http://www.cs.mu.oz.au/~gabraham/c2.RData. I think it uses lazy loading because packages are only loaded when I access the object (see below) in the R console. When I try the same with Rscript, it segfaults. This happens on 2.9.0 both on Linux and Mac: Rscript -e 'load("c2.RData"); c2[1]' ***

Hi, Design isn't strictly an R base package, but maybe someone can explain the following. When lrm is called within a function, it can't find the dataset dd: > library(Design) > age <- rnorm(30, 50, 10) > cholesterol <- rnorm(30, 200, 25) > ch <- cut2(cholesterol, g=5, levels.mean=TRUE) > fit <- function(ch, age) + { + d <- data.frame(ch, age) +

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 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 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

Hi, Say I have two packages, test1 and test2, that both define the generic method train (identical definition), and each has a specific train method for a different S4 object (foo and bar, resp.) I want to be able to call train(foo, x, y) and train(bar, x, y), which doesn't work since test2 masks test1, as seen below. The two solutions I can think of are to a) prefix train,

Hi, I'd like to store large covariance matrices using Matrix classes. dsyMatrix seems like the right one, but I want to specify just the upper/lower triangle and diagonal and not have to instantiate a huge n^2 vector just for the sake of having half of it ignored: Dumb example: M <- new("dsyMatrix", uplo="U", x=rnorm(1e4), Dim=as.integer(c(100, 100))) diag(M) <- 1

Hi, Say x.train is a matrix of covariates that I want to do PCA on, so I can do regression on its principal components, and x.test is a test set of the same covariates on which I want to evaluate the regression fit. I would like the covariates to be centred and scaled: p <- prcomp(x.train, center=TRUE, scale=TRUE) x.train.pc <- predict(p) Now I want to get the PCs from the test set.

Hi, Is this a bug in truehist()? > library(MASS) > x <- rep(1, 10) > truehist(x) Error in pretty(data, nbins) : invalid 'n' value Thanks, Gad > R.version platform i486-pc-linux-gnu arch i486 os linux-gnu system i486, linux-gnu status major 2 minor 4.1 year 2006 month 12 day 18 svn

Hi, Is this a bug in truehist()? > library(MASS) > x <- rep(1, 10) > truehist(x) Error in pretty(data, nbins) : invalid 'n' value Thanks, Gad > R.version platform i486-pc-linux-gnu arch i486 os linux-gnu system i486, linux-gnu status major 2 minor 4.1 year 2006 month 12 day 18 svn

Hi, If I have warnings converted to errors, and if I plot a simple plot and then resize and move the plot's window many times, I eventually get an error "Display list redraw incomplete", and after a while an endlessly repeating error "An unusual circumstance has arisen in the nesting of readline input". I cannot stop it using Ctrl-C (Ctrl-Z works though). I'm

Hello, I am unable to start an R session by double-clicking on an existing .RData file from the Windoze file explorer. A dialogue appears with the message "Fatal error: unable to restore saved data in .RData", and I notice in the R Console the last few lines are: "Loading required package: R2HTML NULL error in function () : unused argument(s) (1:43)" I tried starting

Dear list, this might be a silly question, but I am a bit lost I have bootstrapped the C-index of a logistic regression model, 500 times. > results <- boot(data=data,statistic=cindex,R=500,formula = myformula) When I plot the results I get a histogram of the bootstrapped where the Y axis is density, but it spans from 0 to about 25 > plot(results) Can anyone help me interpret

I am writing a report using Sweave with specific R output incorporated into the text using the Sexpr{} command. I have run into two specific issues: 1) If the result inside the Sexpr{} command is an integer less than 10 I would like to print the ?word? for that number ? e.g., ?seven? for 7. 2) If a p-value is ?equal to zero? to some arbitrary number of decimal places -- e.g.,

All, I'm getting the same error message as that discussed in a previous post (Feb 3, 2006). The reply to that post was to insure that the ld98 program was in the system path (as also suggested in the help on ldBands). I have done this but this does not change the result. Any advice much appreciated. David > sessionInfo() R version 2.7.2 (2008-08-25) i386-pc-mingw32 locale:

Hello useRs, I have a question regarding the function Dotplot from the Hmisc package: I want two things: 1) confidence intervals around the dots 2) some additional "annotation" points plotted in the graphic I can easily achieve (1) by constructing an appropriate object with Cbind. But for (2) when I use the panel=function argument the confidence intervals of the original plot are gone.

Hello. I am trying to load the rJava package in R-2.7.2 (Windows XP 64-bit RGui) and get the following error message even though the mentioned .dll file is located at the directory listed in the error message. I have tried to uninstall and reinstall the package but that does not resolve the problem. Then uninstallation and re-installation of R did not resolve the issue either. Any suggestions are