similar to: loading of unwanted namespace

I have a debugging environment for the survival package, perhaps unique to me, but I find it works very well. To wit, a separate directory with copies of the source code but none of the package accuements of DESCRIPTION, NAMESPACE, etc. This separate space does NOT contain a copy of src/init.c Within this I use R --vanilla, attach my .RData file, survival.so file, and away we go. That is,

When I run R CMD check on the survival package I invariably get a note: ... * checking for file ?survival/DESCRIPTION? ... OK * this is package ?survival? version ?3.2-6? * checking CRAN incoming feasibility ... NOTE Maintainer: ?Terry M Therneau <therneau.terry at mayo.edu>? ... This is sufficient for the auto-check process to return the following failure message: Dear maintainer,

I cloned therneau/survival and the installation failed since there is no definition for exported function survfit(). A file seems to be missing - there is survfit0() and survfit0.R but, compared to CRAN, no survfit.R. Georgi Boshnakov ---------------------------------------------------------------------- Message: 1 Date: Thu, 05 Sep 2019 12:53:11 -0500 From: "Therneau, Terry M.,

I've created some Splus code for a microarray problem that - needed to be in C, to take advantage of some sparse matrix properties - uses a cholesky decompostion as part of the computation For the cholesky, I used the cholesky2 routine, which is a part of the survival library. It does just what I want and I'm familiar with it (after all, I wrote it). In Splus, this all works

-------- Original Message -------- Subject: Re: How to obtain nonparametric baseline hazard estimates in the gamma frailty model? Date: Mon, 04 Nov 2013 17:27:04 -0600 From: Terry Therneau <therneau.terry at mayo.edu> To: Y <yuhanusa at gmail.com> The cumulative hazard is just -log(sfit$surv). The hazard is essentially a density estimate, and that is much harder. You'll notice

Is there a way to include the compiled version of a vignette in the doc directory but mark it to NOT be rerun by CRAN??? I think I remember that this is possible, but have forgotton how.?? (It might even be a false memory.) Terry T. Background:? Beth Atkinson and I are splitting out many of the vignettes from the survival package into a separate package survivalVignettes.? There are a few

Yes, that is exactly the problem.? The code found in the "config" script is never run.? But why doesn't it get run? On 9/6/19 5:44 AM, Georgi Boshnakov wrote: > I cloned therneau/survival and the installation failed since there is no definition for exported function survfit(). > A file seems to be missing - there is survfit0() and survfit0.R but, compared to CRAN, no

The survival package makes significant use of the "specials" argument of terms(), before calling model.frame; it is part of nearly every modeling function. The reason is that strata argments simply have to be handled differently than other things on the right hand side. Likewise for tt() and cluster(), though those are much less frequent. I now get "bug reports" from the

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 19 data sets, many of them small. The resulting file (using xz compression) is quite a bit

I have a test directory for the survival suite, and dyn.load has ceased to work in it. Below shows the log: tmt1075% R --vanilla R version 2.12.2 (2011-02-25) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain

Dear Terry, It's not surprising that different modeling functions behave differently in this respect because there's no articulated standard. Please see my response to Martin for my take on the singular.ok argument. For a highly sophisticated user like you, singular.ok=TRUE isn't problematic -- you're not going to fail to notice an NA in the coefficient vector -- but I've

A problem has been pointed out by a French user of the survival package and I'm looking for a pointer. > options(OutDec= ",") > fit <- survfit(Surv(1:6 /2) ~ 1) > fit$time [1] NA 1 NA 2 NA 3 A year or two ago some test cases that broke survfit were presented to me. The heart of the problem was numbers that were almost identical, where table(x) and unique(x) gave

I'm testing out a new version of coxme and R CMD check fails with "could not find function ranef" (or random.effects or fixef, or anything from nlme). The NAMESPACE file has the line below importFrom(nlme, ranef, random.effects, fixef, fixed.effects, VarCorr) and nlme is declared in the DESCRIPTION file as an import. I feel that I must be staring at some obvious (but

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'm converting the "Changelog" files that I have used in the survival package (since the 1980s) to the inst/NEWS.Rd format and a couple of things are not clear from the help page. 1. What should I use for the name: NEWS or survival? 2. My section headers look like \section{Changes in version 2.36-3}{ \itemize{ etc and I get "cannot extract version info from

Hi Terry, I take your question to mean how to label distinct rows of a data frame. If that is not your question please clarify. I found the row.match() function in the package prodlim that can be used to solve this. However since your request requires no additional dependencies I borrowed the relevant code from the row.match function. Here is some obfuscated code to provide your answer in one

SURVIVAL ANALYSIS IN S-PLUS by Dr Terry Therneau 14/15 May Aller?d, Denmark 16/17 May Basel, Switzerland Dr. Terry Therneau has worked in medical research statistics for over 15 years. He has written several papers on the use of residuals in the Cox model, and is the author of the survival routines found in S-PLUS, as well as the SAS routines COXREG and SURVTEST. Note: Due to his

First a statistical issue: The survfit routine will produce predicted survival curves for any requested combination of the covariates in the original model. This is not the same thing as an "adjusted" survival curve. Confusion on this is prevalent, however. True adjustment requires a population average over the confounding factors and is closely related to the standardized

>>>>> Therneau, Terry M , Ph D <therneau at mayo.edu> >>>>> on Sun, 15 Feb 2015 17:31:00 -0600 writes: > I'm testing out a new version of coxme and R CMD check fails with "could not find function > ranef" (or random.effects or fixef, or anything from nlme). The NAMESPACE file has the > line below >

It is likely a problem with survival, since 2.9 merged in a large number of changes that had occured in my source tree that had not propogated to the R tree my test suite doesn't have a test for this particular case (2 factors) and - Murphy's law applies: although almost every possible case is covered in the test suite, any new error will hit an omitted combination of