search for: gchol

...don't see a mismatch. FYI, the 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{ bac...

...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 package?? The S4 structures are identical, but bdsmatrix has...

...on -g -O2 -c coxfit6b.c -o coxfit6b.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c coxfit6c.c -o coxfit6c.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c gchol.c -o gchol.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c gchol_bds.c -o gchol_bds.o gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o kinship.so agfit6b.o bdsmatrix_index1.o bdsmatrix_index2.o bdsmatrix_inde...

...ectory 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 hand", but tests/gchol2.R fails when run from R CMD check. The failure looks a lot like a method for setMethod('diag', 'gchol') is not being found. The NAMESPACE file exports diag, along with several other methods that do work. Any help would be appreciated. Terry Therneau

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

Can we do Cholesky Decompositon in R for any matrix --------------------------------- [[alternative HTML version deleted]]

The gchol function in library(kinship) does an LDL decomposition. An updated version has just recently been posted on Rforge, in the bdsmatrix library which is part of survival. > temp <- matrix(c(1,1,1,1,5,8,1,8,14), 3) > gt <- gchol(temp) > as.matrix(gt) # L [,1] [,2] [,3] [1...

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

...... .. ..@ rmat : num [1:102, 1:5] -0.00096 -0.000778 -0.000286 0.000102 -0.000688 ... .. ..@ offdiag : num 0 .. ..@ Dim : int [1:2] 102 102 .. ..@ Dimnames :List of 2 .. .. ..$ : NULL .. .. ..$ : NULL $ df : num [1:2] 6 49.3 $ hmat :Formal class 'gchol.bdsmatrix' [package "bdsmatrix"] with 6 slots .. ..@ blocksize: int [1:97] 1 1 1 1 1 1 1 1 1 1 ... .. ..@ blocks : num [1:97] 1.87 1.68 2.12 2.47 1.61 ... .. ..@ rmat : num [1:102, 1:5] -0.1885 0.0659 -0.2205 -0.0816 -0.1502 ... .. ..@ rank : int 102 .. ..@ Dim...