similar to: odd error messages coming from val.prob() {Design}

I seem to have a problem getting latex (Hmisc) to work. Any suggestions as to what I am doing wrong? Thanks library(Hmisc) aa <- data.frame(aa=1:10, bb=rnorm(10, 5, 2), cc=rnorm(10, 20, 4)) rr <- lm(cc~aa+bb, data=aa); rr latex(rr) > latex(rr) 'latex' is not recognized as an internal or external command, operable program or batch file. Warning messages: 1: In cbind(cx, cxk) :

Hi R, I wanted to know how do we access the elements of a list. In particular, v=list(c(1,2,3,4,5),c(1,2,33,4,5),c(1,2,333,4,5),c(1,2,3333,4,5)) I want to access all the thirds items of the elements of the list. i.e., I want to access the elements, 3,33,333,3333. This can be done through sapply as: sapply(v,function(x) x[3]) But I need to access this without using

Hi R-users, I have the following problem with CrossTable function within ?gmodels? package: the output of the function (format ?spss? and asresid=T) can not be stored within another object. For example: >library(gmodels) >data(infert, package = "datasets") > CrossTable(infert$education, infert$induced)->aa # the function prints everything ok on the screen > aa # works

Hi, I was trying to do cross-validation using the crossval function (bootstrap package), with the following code: --------------------------------------------------------------------------------------------------------- theta.fit <- function(x,y){ model <- svm(x,y,kernel = "linear") } theta.predict <- function(fit,x){ prediction <- predict(fit,x)

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 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()

I have tried installing the package (ROCR) with this command: Install.packages(ROCR) And with this command on the command line R CMD INSTALL ROCR_1.0-4.tar.gz But both times I get exactly the same error shown below, I don't understand what is wrong, is this an error in the package code? Thank you Philip probinson@bioinform08:/tmp/RtmpO0rFbx/downloaded_packages$ R CMD

Dear R community, I am using R version 2.4.1 GUI 1.18 on an iBook G4 with OS 10.4.10. When I try to load package 'gplots' I get the following message: > library(gplots) Loading required package: gdata Attaching package: 'gdata' The following object(s) are masked _by_ .GlobalEnv : reorder.factor Loading required package: gtools Attaching package: 'gtools'

Dear All, I recently got a 64bit machine and had netcdf-3.6.2 installed. Then I tried to install ncdf package but got the following error message when using netcdflib: gcc -std=gnu99 -I/home/ljin/share/R-2.6.1/include -I/home/ljin/share/R-2.6.1/include -I. -I/usr/local/include -fpic -g -O2 -c ncdf2.c -o ncdf2.o gcc -std=gnu99 -I/home/ljin/share/R-2.6.1/include

Dear Rlist, Using an example in box.cox.powers() help, I have the following warning message. example: library(car) >attach(Prestige) > box.cox.powers(income) Box-Cox Transformation to Normality Est.Power Std.Err. Wald(Power=0) Wald(Power=1) 0.1793 0.1108 1.6179 -7.4062 L.R. test, power = 0: 2.7103 df = 1 p = 0.0997 L.R. test, power = 1: 47.261 df = 1 p = 0

useRs, Is there a way to schedule R scripts? I would like to run certain scripts three times a day. I'm running R on Windows XP. > sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=Finnish_Finland.1252;LC_CTYPE=Finnish_Finland.1252;LC_MONETARY=Finnish_Finland.1252;LC_NUMERIC=C;LC_TIME=Finnish_Finland.1252 attached base packages: [1] splines grid stats

Dear cateGOry experts, hyperGTest documentation states that YEAST cannot be used as 'annotation' when evaluating gene ontology representation status for a given set of 'geneIds'. Because I am using a custom print I believe I need to create my own data package to use as the annotation file for 'annotation'. Can someone please describe how to make a data package that will

I know this comes up, but I didn't see my exact issue in the archives. I have variables in a dataframe that need to be recoded. Here is what I'm dealing with I have a factor called aa > class(aa) [1] "factor" > table(aa) aa * 0 1 2 3 A B C D L N T 0 0 1908 725 2089 0 0 67 0 0 2 1 6 I need to recode

This was working a few weeks ago, but perhaps the package has been updated since then. model.1 <- lrm(response ~ p_value, data=c_abl_oncogene_1_RTK) When I run the following command . . . . prediction.1 <- predict(model.1, type=c("fitted")) I get the following error message. . . . Error in predictDesign(object, ..., type = "lp", se.fit = FALSE) : could not find

Hello all, I would like to perform SVM-RFE (Guyon et al. 2002) in R and have only found one implementation of this algorithm. The function belongs to the MCRestimate package but when I try to use it I encounter a problem - the function appears to be missing a required package or other function that I simply cannot find available anywhere. Here is my session info followed by a simple example

After some struggling with the data format, non-standard in BioConductor, I have gotten cor.balance in package CORREP to work. My desire was to obtain maximum-likelihood p-values from the same data object using cor.LRtest, but it appears that this function wants something different, which I can't figure out from the documentation. Briefly, my dataset consists of 36 samples from 12

I am experiencing an OOLOCK error when attempting to update packages to my site-library. I have an identical setup on my local Linux machine, but this problem on the remote Linux machine (PPC cluster) started about 3 weeks ago and is present whether I used R-devel or R-2.6.0 or R-2.5.1. Also, of course I manually remove the 00LOCK folder after each failed attempt. Below is my error output,

Hi all - I'm playing around with an attempt to do some serial communication from within R to a microcontroller board. I open a connection: zz = file("/dev/ttyUSB0",open="a+") ## text mode ... when I execute writeLines("0",con=zz) I know the board receives the "0" because the board's serial comm LEDs light up when submit the command at the R

> mypal <- trellis.par.get('superpose.line')$col[1:2] > mycol <- mypal[1] > trellis.par.set(list(dot.symbol = list(pch = 16, cex = 1.5))) > dotplot(1:6 ~ audRating, data = txtA.ci, + scales = list(y = list(at = 1:6, labels = txtA.ci$pitchAud, col = 'black', cex = 1.1)), + ylab = '', aspect = 1.2, xlab = 'rated duration', ylim = c(0.5,

Hello, I am using the val.prob function in the Design package. I understand how the Brier quadratic error score is calculated, but I do not know how the Brier score computed on the calibrated rather than raw predicted probabilities (B cal) is calculated. My question is: how are the calibrated probabilities calculated? Any explanation of this, or references to explanations of this, would be