search for: bdsmatrix

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, ?????????????????...

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 s...

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) { fun = R_GetCCallable("bdsmatrix", "bdsmatrix_prod4"); } if (fun==NULL) {...

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, whic...

...file is below. (It is modeled on chol.Rd from the Matrix package.) Terry Therneau -------------------------------------------------- \name{backsolve} \alias{backsolve-methods} \title{Solve an Upper or Lower Triangular System} \alias{backsolve} \alias{backsolve,gchol-method} \alias{backsolve,gchol.bdsmatrix-method} \description{ Solves a system of linear equations where the coefficient matrix is upper (or \sQuote{right}, \sQuote{R}) or lower (\sQuote{left}, \sQuote{L}) triangular.\cr \code{x <- backsolve(R, b)} solves \eqn{R x = b}. } \usage{ backsolve(r, \dots) \S4method{backsolve}{g...

...kage 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 methods in the NAMESPACE file. I'd like to expose it in survival as it would make some current development easier. How do I do this without causing warning messages for anyone who loads both, e.g., anyone using the coxme p...

...)= chr [1:97] "1" "2" "3" "4" ... $ penalty : num 22.6 $ loglik : Named num [1:3] -479 -467 -435 ..- attr(*, "names")= chr [1:3] "NULL" "Integrated" "Penalized" $ variance :Formal class 'bdsmatrix' [package "bdsmatrix"] with 6 slots .. ..@ blocksize: int [1:97] 1 1 1 1 1 1 1 1 1 1 ... .. ..@ blocks : num [1:97] 0.545 0.606 0.485 0.415 0.636 ... .. ..@ rmat : num [1:102, 1:5] -0.00096 -0.000778 -0.000286 0.000102 -0.000688 ... .. ..@ offdiag : num 0 .. ..@ Dim...

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)) > mat2=bdsmatrix(rep(c(0,0,0,0,0,0,0,0,1),3),blocksize=rep(3,3),dimnames=list(ugroup,ugroup)) > group=paste(dat1$centre,dat1$treat,sep='/') > coxme(Surv(time,status) ~ as.factor(treat), data=dat1,random= ~...

...gt; On 12/29/2017 10:52 AM, William Dunlap wrote: > > 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) { > fun = R_GetCCallable("bdsmatrix", "bdsmatrix_prod4"); >...

...om(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 invisible to me) mistake. Users are very likely to use "ranef" as well. Second question. The files now declare bdsmatrix as an import rather than a depends. If one of my test files has an explicit call to a bdsmatrix function, I assume that I will need to put an explicit "require" there. Third: How should "methods" be listed? I'm getting a message from CMD check if I leave it in or leave...

...covar, uncens, centers) names(data1)<- c("y", "treat", "covar", "uncens", "centers") data1<-as.data.frame(data1)[order(centers,treat),] library(kinship) ugroup<-paste(rep(1:32, each=2), rep(0:1, 32), sep='/') #unique groups mat1<-bdsmatrix(rep(c(1,1,1), 32), blocksize=rep(2,32), dimnames=list(ugroup, ugroup)) mat2<-bdsmatrix(rep(c(0,0,0,1), 32), blocksize=rep(2,32), dimnames=list(ugroup, ugroup)) group1<-paste(data1$centers, data1$treat, sep="/") fit2<- coxme(Surv(y, uncens)~ treat + covar, data1,random=~1|group...

The package coxme depends heavily on bdsmatrix, to the point of needing access to some of its C calls. The kinship package (in progress) uses the R level functions in bdsmatrix, but not the C calls. That is, I don't want to always export the symbols. For testing I can use an explicit dyn.load('somepath/bsdmatrix.so', local=F). H...

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 directiv...

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

...nging static void (*fun)() = NULL; to DL_FUNC fun = NULL; Bill Dunlap TIBCO Software wdunlap tibco.com On Fri, Dec 29, 2017 at 5:14 AM, Therneau, Terry M., Ph.D. < therneau at mayo.edu> wrote: > 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, doubl...

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...

...> library(kinship) Loading required package: survival Loading required package: splines Loading required package: nlme Loading required package: lattice > t(temp) %*% temp `__Deferred_Default_Marker__` ----------------------------------------- Within the library is a definition of %*% for bdsmatrix objects, which is perhaps the issue. But I'm only guessing since I don't have a clear idea what the error message means. Any hints are appreciated. The new coxme/bsdmatrix packages need only a couple more functions to be a complete replacement for kinship, at which point we will deprecia...

...or stored elsewhere?) As an example, could we see the source code of "xyplot" in the following example? Thanks, > library(lattice) > xyplot function (x, data, ...) UseMethod("xyplot") <environment: namespace:lattice> > library(plm) Loading required package: bdsmatrix Attaching package: ‘bdsmatrix’ The following object(s) are masked from ‘package:base’: backsolve Loading required package: nlme Loading required package: Formula Loading required package: MASS Loading required package: sandwich Loading required package: zoo Attaching package: ‘zoo’ The fo...

...te) 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 (ismat(kmat)? ) .... (The second line is repeated multiple times for multiple arguments.? The ismat function is defined simply to save typing.) The check log contains multiple instances of the lines below: < Warning message: < In if (ismat(kma...

...kely to use "ranef" as well. Well, and you are sure that you do not want them to see the help file for ranef() ? If a user of coxme() should typically use ranef() in her own code, you should rather *depend* on lme4 than only *import* it. > Second question. The files now declare bdsmatrix as an import rather than a depends. If > one of my test files has an explicit call to a bdsmatrix function, I assume that I will > need to put an explicit "require" there. Sure. See above > Third: How should "methods" be listed? I'm getting a mess...