similar to: inheriting C symbols

R version 2.9.0 running on Centos (Red Hat linux). I have a pair of packages coxme and bdsmatrix. The latter is installed in my local library (I don't have permission for global install at work.) That is, it is in the location pointed to in R_LIBS_USER. In R, the command library(bdsmatrix) works fine. Coxme depends on bdsmatrix, in fact uses some cross-calls to it's C routines, which

I've finally narrowed down a puzzling problem: here is the short test case. tmt34% R --vanilla R version 2.10.0 (2009-10-26) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 > temp <- matrix(runif(50), ncol=2) > t(temp) %*% temp [,1] [,2] [1,] 7.916016 6.049698 [2,] 6.049698 7.650694 > library(kinship) Loading required package:

Where can I find out (and replicate) what options as-cran turns on? The issue: the following lines generate an error in R CMD check --as-cran? for coxme.? But there is no error without as-cran nor is there one when I run the code in a terminal window. ismat <- function(x)? inherits(x, "matrix") || inherits(x, "bdsmatrix") || inherits(x, "Matrix") if

And remove the cast on the return value of R_GETCCallable. And check that your function is found before using it. #include <R.h> #include <Rinternals.h> #include <R_ext/Rdynload.h> void bdsmatrix_prod4(int nrow, int nblock, int *bsize, double *bmat, double *rmat, int nfrail, double *y) { DL_FUNC fun = NULL; if (fun==NULL)

I've recently updated the coxme package, which calls internal routines from the bdsmatrix package.? (It is in fact mentioned as an example of this in the Extensions manual.) The call connections are a blocks like this, one for each of the 9 called C routines. void bdsmatrix_prod4(int nrow,??? int nblock,?? int *bsize, ??????????????????? double *bmat, double *rmat, ??????????????????? int

I'm working on the next version of coxme, one step of which is converting the bdsmatrix library from Splus to R. Actually, it is a conversion from S4 methods as first described in the Green book to S4 methods as they currently exist. Mostly it's going ok, but not entirely. 1. The biggest issue is lack of documentation. The online help pages have not been a help; they keep saying

The survival package uses a generalized cholesky decompostition throughout.? If A is a symmetric matrix A= LDL' where L is lower triangular with 1s on the diagonal, D is diagonal, and D[i,i] =0 if column i of A is redundant.? Being able to read the rank and dependencies directly off of D is very handy. The bdsmatrix package uses the same, but exposes it to the user as gchol and solve

Dear all, I am using "coxme" function in Kinship library to fit random treatment effect nested within centre. I got 3 treatments (0,1,2) and 3 centres. I used following commands, but got an error. > ugroup=paste(rep(1:3,each=3),rep(0:2,3),sep='/') > mat1=bdsmatrix(rep(c(1,1,1,1,1,1,1,1,1),3),blocksize=rep(3,3),dimnames=list(ugroup,ugroup)) >

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 current coxme code has functions that depend on bdsmatrix and others that depend on Matrix, both those pacakges define S4 methods for diag. When loaded, the message appears: replacing previous import ?diag? when loading ?Matrix? Questions: 1. Do I need to worry about this? If so, what can I do about it? I suppose I could add an importFrom directive, but it will be a pain unless there

I've converted the bdsmatrix package (used by coxme) to the newer style of S4, and uploaded it. It is in the pkg directory of survival, on r-forge. I'm stuck on something that is almost certainly a namespace issue. I've borrowed liberally from Matrix (a big help) and read the documentation, and just upgraded to 2.8.1 - but still stuck. All the tests work when I run them "by

Hi, How could I see the source code of functions in an R package? If we type ?function_name , we will see documentations of the function_name. If we type function_name, is what returns just the source code? Could we just save it in an .R file and modify as we want? However, it seems that sometimes the source code is hidden (or stored elsewhere?) As an example, could we see the source

The coxme package has a ranef() method, as does lme4. I'm having trouble getting them to play together, as shown below. (The particular model in the example isn't defensible, but uses a standard data set.) The problem is that most of the time only one of lme4 or coxme will be loaded, so each needs to define the basic ranef function as well as a method for it. But when loaded together

I get the following error from one of my Rd files in R CMD check (R 2-14.0) * checking Rd files ... WARNING Error in switch(attr(block, "Rd_tag"), TEXT = if (!grepl("^[[:space:]]* $", : EXPR must be a length 1 vector problem found in ?backsolve.Rd? This is likely something that will be glaringly obvious once it's pointed out, but without a line number I can't

I've added a "backsolve" method to the bdsmatrix library. Per the Extending manual section 7.1 I've also added the following 3 lines along with my setMethod definitions for 2 classes. backsolve <- function(r, ...) UseMethod("backsolve") backsolve.default <- base:::backsolve formals(backsolve.default) <- c(formals(backsolve.default), alist(... = )) I've

Hi, I am running the following model: fit1.full <- coxme(Surv(age_sym1, sym1) ~ sex + lifedxm*sex + (1|famid), data=bip.surv) I would like to extract the AIC from that object to calculate the AICC. However, when I look at str(fit1.full) and summary(fit1.full) (pasted below) I don't see anything that would allow me to get pull the AIC out from that object. Is there a way to retrieve the

You can legally cast a function pointer to another function pointer, where the signatures differ. (It is not legal to cast between data and function pointers.) I would make typedefs for the various signatures, as the casting syntax is more readable then. Bill Dunlap TIBCO Software wdunlap tibco.com On Fri, Dec 29, 2017 at 10:13 AM, Therneau, Terry M., Ph.D. < therneau at mayo.edu> wrote:

R-devel: I am encountering a consistency issue using socketConnection and readBin with *non-blocking* connections on Unix and Windows XP (no Vista to test). I am a bit confused by the behavior of *non-blocking* connections under Windows specifically. When calling readBin on a non-blocking connection when there is no data to read on the socket, the connection under Unix will return a vector of

Dear R users: I'm new to R and am trying to fit a mixed model Cox regression model with coxme function. I have one two-level factor (treat) and one covariate (covar) and 32 different groups (centers). I'd like to fit a random coefficients model, with treat and covar as fixed factors and a random intercept, random treat effect and random covar slope per center. I haver a couple of

I can't comment on frailtypack issues, but would like to mention that coxme will handle nested models, contrary to the statement below that "frailtypack is perhaps the only .... for nested survival data". To reprise the original post's model cgd.nfm <- coxme(Surv(Tstart, Tstop, Status) ~ Treatment + (1 | Center/ID), data=cgd.ag) And a note to the poster-- you should