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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, package survival_3.2-6.tar.gz does not pass the incoming checks automatically, please see the following pre-tests: Windows:<https://win-builder.r-...

Thanks, posted to https://github.com/lme4/lme4/issues/412 for further discussion ... On Wed, Feb 22, 2017 at 10:03 AM, Therneau, Terry M., Ph.D. <therneau at mayo.edu> wrote: > I found this by accident yesterday. The program that crashes is the first > two lines of the example from the help page for nlmer. That example hasn't > changed in a long time, so I assumed that it is an R-devel issue. It could &...

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...

..., xmid = 725, scal = 350) > (nm1 <- nlmer(circumference ~ SSlogis(age, Asym, xmid, scal) ~ Asym|Tree, + Orange, start = startvec)) ==31901== Invalid write of size 4 ==31901== at 0xA13DA20: cholmod_start (cholmod_common.c:184) ==31901== by 0xD8B3065: cholmod_start (in /home/therneau/Rlib/lme4/libs/lme4.so) ==31901== by 0xD8B728D: Eigen::CholmodBase<Eigen::SparseMatrix<double, 0, int>, 1, Eigen::CholmodDecomposition<Eigen::SparseMatrix<double, 0, int>, 1> >::CholmodBase() (in /home/therneau/Rlib/lme4/libs/lme4.so) ==31901== by 0xD8B413D: Eigen::C...

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...

...contrasts. These is often a better format for tables in a publication. Yes, I can reconstruct these from the original fit, but I have a lot of variables for several models and it would be easier to have an automatic form. I suspect that there is an easy answer, but I don't see it. Terry Therneau

...brary is already loaded. I looked at the manual page for dyn.load, but don't see anything. What are we missing? Please reply via email, as I don't read this list. (But I likely will start to later this summer, when I port the newest mixed-effects Cox model code over from S). Terry Therneau Mayo Clinic therneau.terry at mayo.edu

...Ok, I know this function has to exist. I even remember that there is some sort of multi-colon secret handshake that will convince R to let you look at it, although I don't remember the form. This Nixonesque passion with hiding things is one of the reasons I still prefer Splus. Terry Therneau therneau.terry at mayo.edu

...y what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey 2016-04-15 13:58 GMT+02:00 Therneau, Terry M., Ph.D. <therneau at mayo.edu>: > I'd like to get interaction terms in a model to be in another form. > Namely, suppose I had variables age and group, the latter a factor with > levels A, B, C, with age * group in the model. What I would like are the > variables &q...

-------- 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 that everyone does CDF curves for survival data ( Kaplan-Meier = estimate of 1-CDF), but n...

Dear R-user: I am using survreg(Surv()) for fitting a Tobit model of left-censored longitudinal data. For logarithmic transformation of y data, I am trying use survreg.distributions in the following way: tfit=survreg(Surv(y, y>=-5, type="left")~x + cluster(id), dist="gaussian", data=y.data, scale=0, weights=w) my.gaussian<-survreg.distributions$gaussian

...r example: tmt1495% R --vanilla --no-environ R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) > system("printenv | grep R_LIBS") R_LIBS_SITE= R_LIBS_USER=/people/biostat2/therneau/Rlib So, per the manual R CMD check inherits the path. The question is why does it ignore it? Terry T. On 02/09/2017 02:54 AM, Martyn Plummer wrote: > On Wed, 2017-02-08 at 15:51 -0600, Therneau, Terry M., Ph.D. wrote: >> I have a local library which depends on the expm library. The...

...'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > dyn.load('survival.so') Error in dyn.load("survival.so") : unable to load shared object '/people/biostat2/therneau/research/surv/Rtest/survival.so': libR.so: cannot open shared object file: No such file or directory > q() -------------------------- Is the issue that the .so file must have been created with the R2.13 script? That's not what the error message says, however. It almost looks like...

...Other suggestions are welcome as well. At the end of the day I'd like to have a good user guide, technical reference, and solid enough code documentation that others can begin to participate as well. (Retirement in 10 years -- I don't expect to maintain this forever!) Terry Therneau therneau.terry at mayo.edu

...s * creating vignettes ... OK * checking for LF line-endings in source and make files * checking for empty or unneeded directories * looking to see if a ?data/datalist? file should be added * building ?dart_1.0-6.tar.gz? tmt-local2128% R CMD INSTALL dart_1.0-6.tar.gz * installing to library ?/home/therneau/Rlib? * installing *source* package ?dart? ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes Warning in file(con, "w") : cannot open file '/home/t...

I treat CRAN as the main repository for survival, but I have also had a github (therneau/survival) version for a couple of years.? It has a vignette2 directory, for instance, that contains extra vignettes that either take too long to run or depend on other packages.? It also gets updated more often than CRAN (though those updates mght not be as well tested yet). In any case, since...

I'm trying to plot pspline'd explanatory variables from coxph() models as per Therneau and Grambsch (Modeling Survival Data: Extending the Cox Model). They have s-plus functions for this at: http://www.mayo.edu/hsr/people/therneau/book/sfunction/gamterms.s http://www.mayo.edu/hsr/people/therneau/book/sfunction/plotterm.s I'd like to make these plots in R, but they make use of...

...(DllInfo *dll) { expm = (void (*)) R_GetCCallable("expm", "expm"); } I don't expect that this is the problem since I stole the above almost verbatim from the msm package. Terry T. On 02/09/2017 11:23 AM, Martyn Plummer wrote: > On Thu, 2017-02-09 at 09:52 -0600, Therneau, Terry M., Ph.D. wrote: >> Martin, >> I am aware of --vanilla; I use it myself for some testing. In this case R_LIBS_USER was >> set externally (part of my login) and does not involve any of the R scripts. That means >> it is inherited by any subprocess. For example: &...

Hello, I'm trying to use coxph() function to fit a very simple Cox proportional hazards regression model (only one covariate) but the parameter space is restricted to an open set (0, 1). Can I still obtain a valid estimate by using coxph function in this scenario? If yes, how? Any suggestion would be greatly appreciated. Thanks!!! [[alternative HTML version deleted]]

To enhance my understanding, and that of my students, I have a question about cox.zph in the survival package. If I have correctly gleaned the high-level point from the 1994 Biometrika paper of Grambsch and Therneau, it looks to me like cox.zph provides a mechanism to test for a simple trend in plots of a function of time, g(t) versus the scaled schoenfeld residuals and it also provides some built-in ones and the capability to provide your own. It also appears to me that different forms look at different depa...