similar to: R 2.13 segfault with range()

The model.frame function has trouble with a certain type of really long formula. Here is a test: tname <- paste('var', 1:50, sep='') tmat <- matrix(rnorm(500), ncol=50, dimnames=list(NULL, tname)) tdata <- data.frame(tmat) temp1 <- paste( paste(tname, tname, sep='='), collapse=', ') temp2 <- paste("~1 + cbind(", temp1, ")")

On 06/11/2015 7:36 AM, Therneau, Terry M., Ph.D. wrote: > I am currently puzzled by a seach path behavior. I have a library of a dozen routines > getlabs(), getssn(), getecg(), ... that interface to local repositories and pull back > patient information. All have a the first 6 arguments in common, and immediately call a > second routine to do initial processing of these 6. The

> On May 1, 2018, at 6:11 AM, Therneau, Terry M., Ph.D. via R-devel <r-devel at r-project.org> wrote: > > A user sent me an example where coxph fails, and the root of the failure is a case where names(mf) is not equal to the term.labels attribute of the formula -- the latter has an extraneous newline. Here is an example that does not use the survival library. > > # first

Wolfgang, It is common to handle relative risk problems using Poisson regression. In your example you have 8 events out of 508 tries, and 0/500 in the second data set. > tdata <- data.frame(y=c(8,0), n=c(508,500), group=1:0) > fit <- glm(y ~ group + offset(log(n)), data=tdata, family=poisson) Because of the zero, the standard beta/se(beta) confidence intervals don't work.

Great catch. I'm very reluctant to use my own model.frame, since that locks me into tracking all the base R changes, potentially breaking survival in a bad way if I miss one. But, this shows me clearly what the issue is and will allow me to think about it. Another solution for the user is to use multiple ridge() calls to break it up; since he/she was using a fixed tuning parameter the

Calum had a long question about drawing survival curves after fitting a Weibull model, using pweibull, which I have not reproduced. It is easier to get survival curves using the predict function. Here is a simple example: > library(survival) > tfit <- survreg(Surv(time, status) ~ factor(ph.ecog), data=lung) > table(lung$ph.ecog) 0 1 2 3 <NA> 63 113 50 1

If save() fails because an object is not found, it should not overwrite an existing file. > a <- 1:9 > save(a, file = "a.rda") > rm(a) > load("a.rda") > a [1] 1 2 3 4 5 6 7 8 9 > rm(a) > save(a, file = "a.rda") Error in save(a, file = "a.rda") : object 'a' not found > load("a.rda") Error in

The survexp function can fail when called from another function. The "why" of this has me baffled, however. Here is a simple test case, using a very stripped down version of survexp: survexp.test <- function(formula, data, weights, subset, na.action, rmap, times, cohort=TRUE, conditional=FALSE, ratetable=survexp.us, scale=1, npoints, se.fit,

I am currently puzzled by a seach path behavior. I have a library of a dozen routines getlabs(), getssn(), getecg(), ... that interface to local repositories and pull back patient information. All have a the first 6 arguments in common, and immediately call a second routine to do initial processing of these 6. The functions "joe" and "fred" below capture the relevant

>>>>> Berry, Charles <ccberry at ucsd.edu> >>>>> on Tue, 1 May 2018 16:43:18 +0000 writes: >> On May 1, 2018, at 6:11 AM, Therneau, Terry M., Ph.D. via R-devel <r-devel at r-project.org> wrote: >> >> A user sent me an example where coxph fails, and the root of the failure is a case where names(mf) is not equal to the

Terry - your example didn't demonstrate the problem because the variable that interacted with strata (zed) was not a factor variable. But I had stated the problem incorrectly. It's not that there are too many strata terms; there are too many non-strata terms when the variable interacting with the stratification factor is a factor variable. Here is a simple example, where I have

Terry - your example didn't demonstrate the problem because the variable that interacted with strata (zed) was not a factor variable. But I had stated the problem incorrectly. It's not that there are too many strata terms; there are too many non-strata terms when the variable interacting with the stratification factor is a factor variable. Here is a simple example, where I have

Hey all, I get a warning about an unsupported file type in the data directory during R CMD check (for R 2.13.1) if I use the save function to create an Rdata, but if I save the same object to a .rda file, no warning. Section 1.1.5 (pg 11 of the pdf) of the Writing R Extensions manual (2.13.1) appears to say that .Rdata files should be fine: " Data files can have one of three types as

---------- Forwarded message ---------- From: <r-help-bounces@r-project.org> Date: Mon, May 11, 2009 at 10:24 PM Subject: The results of your email commands To: das.moumita.online@gmail.com The results of your email command are provided below. Attached is your original message. - Results: Ignoring non-text/plain MIME parts - Unprocessed: What is the function for partial

I am designing a package to analyze fire department data. I created an S4 class called CAD (short for Computer Aided Dispatch data) as part of this package that essentially extends the data.frame class. When the user initializes a CAD object, a data.frame object is broken down into seperate incident data and unit response data that are stored in separate slots. This separation is intentional

On 23/10/2020 9:25 p.m., Therneau, Terry M., Ph.D. via R-devel wrote: > I found an issue with the data() command this evening when working on the survival package. > > 1. I have a lot of data sets in the package, almost all used in at least one vignette, > help file, or test.? As a space saving measure, I have bundled many of them together, > i.e., the file data/cancer.rda contains

I would like to incorporate multiple summary plots from the rms package into a single device and to control the titles, and also to open a new device when I reach a specified number of plots. Currently I am only getting a single "plot(summary(" graph in the upper left- hand corner of each successive device. However, in the rms documention I see instances of a loop being used with

On 12/29/2017 07:34 AM, Dirk Eddelbuettel wrote: > > On 29 December 2017 at 07:23, Therneau, Terry M., Ph.D. wrote: > | The submission guide has the following cryptic (to me) sentence: > | ?? "Reasonable compression should be used for data (not just .rda files) " > | > | The survival pacakge has a fairly large number of data files --- exactly what should I be > |

Dear, When i multiply the y of a regression by 10, I would expect that the coefficient would be multiply by 10 and the z value to stay constant. Here some reproducible code to support the case. *Ex 1* library(mvtnorm) library(VGAM) set.seed(1) x=rmvnorm(1000,sigma=matrix(c(1,0.75,0.75,1),2,2))

Hi, I was wondering I'm going about this in the correct way. I need to test if there are coding sequences or exons in hg19 which match a string of 100bp "D" i.e. [A,G or T]. However I'm getting a strange result. I get a hit on chr7, using the 100bp search however when I search with 60bp sequence of "D" I don't get any hits. library("BSgenome")