similar to: segmentation fault: formula() with long variable names (PR#3680)

R version: 1.7.1 OS: Red Hat Linux 7.2 When "covmat" is supplied in princomp(), the output value "center" is all NA's, even though the input matrix was indeed centered. I haven't read anything about this in the help file for princomp(). See code below for an example: pc2$center is all NA's. Jerome Asselin x <- rnorm(6) y <- rnorm(6) X <- cbind(x,y)

I am confused on how the log-likelihood is calculated in a parametric survival problem with frailty. I see a contradiction in the frailty() help file vs. the source code of frailty.gamma(), frailty.gaussian() and frailty.t(). The function frailty.gaussian() appears to calculate the penalty as the negative log-density of independent Gaussian variables, as one would expect: >

I would like to document my findings (with a potential FIX) regarding the issue of calculation of the degrees of freedom with nlme(). The program given at the bottom of this email generates and fit 20 data sets with a mixed-effects LINEAR model, but using the function nlme() instead of lme(). In each case, the correct number of degrees of freedom for the intercept parameter is 12. However, in

The problem occurs when the sample odds ratio is Inf, such as in the following example. Given the fact that both upper bounds of the two 95% confidence intervals are Inf, I would have expected that the two lower bounds be equal, but they aren't. x <- matrix(c(9,4,0,2),2,2) x # [,1] [,2] #[1,] 9 0 #[2,] 4 2 rbind("two.sided.95CI"=fisher.test(x)$conf.int,

Hi there, I want to justify to right the text of my legend. Consider this short reproducable example. x <- 1:5 y1 <- 1/x y2 <- 2/x plot(rep(x,2),c(y1,y2),type="n",xlab="x",ylab="y") lines(x,y1) lines(x,y2,lty=2) legend(5,2,c("1,000","1,000,000"),lty=1:2,xjust=1,yjust=1)

I am trying to fit a lognormal distribution on interval-censored data. Some of my intervals have a lower bound of zero. Unfortunately, it seems like survreg() cannot deal with lower bounds of zero, despite the fact that plnorm(0)==0 and pnorm(-Inf)==0 are well defined. Below is a short example to reproduce the problem. Does anyone know why survreg() must behave that way? Is there an alternate

Hi, I would like to recommend a minor modification in axis() which I believe can simplify the making of plots for publications. I am trying to define default values for par() in order to make labels bigger and lines thicker, so that the resulting plots look good when resized for publication purposes. I ran into the following problem... axis() does not use par() values as default for

R version: 1.7.1 OS: Red Hat Linux 7.2 Hi all, The formula object in model.frame() is not retrieved properly when model.frame() is called from within a function and the "subset" argument is supplied. foo <- function(formula,data,subset=NULL) { cat("\n*****Does formula[-3] == ~y ?**** TRUE *****\n") print(formula[-3] == ~y) cat("\n*****Result of model.frame()

Full_Name: Jerome Asselin Version: 1.6.2 OS: RedHat Linux 7.2 Submission from: (NULL) (142.103.173.179) Should be an easy fix... Consider the examble below: plot(0,0) legend(0,0,c("Hello!","Hi!"),pch=1:2,lty=1:2,trace=T) It gives the following trace: > plot(0,0) > legend(0,0,c("Hello!","Hi!"),pch=1:2,lty=1:2,trace=T) xchar= 0.05178 ;

Is there a simpler way then the solution to the one that was posted here? I'm not very proficient with legend, and I don't understand this solution. All I have is two or more lines on one plot that I want to put a legend on and I can't figure out how to do it from the examples. Can you give a very simple example? It does not have to be fancy!! I have never worked with a

Hi, Are there some packages which can generate multi-normal, multi-t, etc multivariate sampling? thanks! Best wishes, Peng ******************************* Peng Zhang Department of Biostatistics Harvard School of Public Health 655 Huntington Avenue Boston, Massachusetts 02115 ******************************* I believe I can fly I believe I can touch the sky

I'm doing prediction of the survival cases using gene expression profiles(Affymetrix chips). Can somebody tell me how to use the Cox PH model to select genes and make a prediction of survival? Thanks. Guangchun

I have a data file where each entry is indexed by the time in seconds since epoch (e.g. 1046315697). Is there an easy way to convert this time value into a more friendly time (such as Month-Year) when plotting it? I searched through the manual, mailing lists, and functions like as.POSIXct and strptime, but didn't find what I need. Thanks, Sharad.

Hello, does R have functions for setting and testing bit values? I want to conserve memory for storing presence/absence data for large multiple arrays within a single array, using element values like present[x,y] <- ntharray[x,y]*(2^n) where presence is 1, non-presence is 0 and n is the nth array e.g. 1*(2^0) + 0*(2^1) + 0*(2^2) + 1*(2^3) + 0(2^4) for storing the value 9 for presence in

Hi, I'm trying to construct a legend which has four lines of text and associated symbols. The first two symbols need to be normal lines which vary only in colour. The second two symbols should have filled boxes. How do I suppress the fill boxes in the first two lines? J.

Full_Name: Jerome Asselin Version: 1.7.1 OS: Red Hat Linux 7.2 Submission from: (NULL) (24.77.125.119) Setting the parameter na.action=na.omit should remove incomplete records in princomp. However this does not seem to work as expected. See example below. Sincerely, Jerome Asselin data(USArrests) princomp(USArrests, cor = TRUE) #THIS WORKS USArrests[1,3] <- NA princomp(USArrests, cor =

Full_Name: Jerome Asselin Version: 1.8.0 OS: RedHat Linux 7.2 Submission from: (NULL) (142.103.177.13) I would not expect a segmentation fault; perhaps an error message. > .Call("log") Segmentation fault This is always reproducable for me. Sincerely, Jerome Asselin

Hello, I have a beginner's Q: if i want to know all the functions provided by a package, what is command for that? in another word, Is there a command to list all the commands available in a packege? thanks a lot, yan

Hi, I'm facing this problem quite a lot, so it seems worthwhile to check to see what the most efficient solution is. I've two vectors x (values ordered) and y. I've ranges x < x0, x0 <= x < x1, x1 <= x < x2, x2 <= x < x3, x > xn and want to construct a subvector yprime of y which consists of the first/last value of y whose x values are in the range. For

Full_Name: Jerome Asselin Version: 1.6.1 OS: RedHat Linux 7.2 Submission from: (NULL) (142.103.173.179) Hello, I get a segmentation fault when I run the following code. I wouldn't expect meaningful results because my response variable contains only missing values. However, I would expect something like a regular error (not a segmentation fault). library(survival) data <-