similar to: Rd error message

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

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

>>>>> "JonR" == Jonathan Rougier <J.C.Rougier@durham.ac.uk> writes: JonR> ... By the way, I have `solve' JonR> methods for triangular matrices and variance matrices -- would JonR> you be interested? { Jonathan, I hope it's okay if I CC this to R-devel; this must be of a wider interest } Ye.e..s; for triangular ones,

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

Hi I'm trying to use ouch's hansen and brown functions but I get the error: > brown(logflatnodes,archotreeouch) Error in backsolve(l, x, k = k, upper.tri = upper.tri, transpose = transpose) : NA/NaN/Inf in foreign function call (arg 1) and with hansen also: Error in optim(par = c(sqrt.alpha, sigma), fn = function(par) { : function cannot be evaluated at initial parameters

Hello, Here's an example that renders correctly using Rd2txt / Rd2latex / R CMD Rd2pdf, but has problems under Rd2HTML: \name{foo} \title{foo} \section{foo}{ This should be on a separate paragraph This should be on a separate paragraph This should be on a separate paragraph \Sexpr[stage=render,results=rd]{ paste( rep('Sexpr: This should be on a separate

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

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,] 1 0.00 0 [2,] 1 1.00 0 [3,] 1 1.75 1 > diag(gt) # D [1]

This issue ties loosely into other recent S4 topics on this board. The methods package defines a number of implicit generics for linear algebra related functions (rcond, norm, backsolve) that, when used, interfere with base package operations. Here is the cut-and-paste version of the code the illustrates the problem: # rcond x1 <- cbind(1, 1:10) rcond(x1) setGeneric("rcond")

For example, if I call "library(spam)", I would get messages like this Package 'spam' is loaded. Spam version 0.27-0 (2011-08-17). Type demo( spam) for some demos, help( Spam) for an overview of this package. Help for individual functions is optained by adding the suffix '.spam' to the function name, e.g. 'help(chol.spam)'. Attaching package: ?spam? The

I'm trying to read data a program produces in matrixmarket array format into R and its giving me fits. I've tried read.MM (below) and readMM (from the Matrix package) but neither works. One of them says array format isn't supported, the other reports something indecipherable about Fortran. Here's the file contents. Can't get much simpler than that! %%MatrixMarket matrix array

I am getting the above warning following loading of Geneland 3.1.5 on unix , while a simple plot sends output to the pdf file ( see attached code) no output results from Geneland functions, resulting in empty pdf files > library (Geneland) Loading required package: RandomFields Loading required package: fields Loading required package: spam Package 'spam' is loaded. Spam version

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

I am receiving the above error ( full r session output below) the script runs OK in windows. and "genotypes" and "ploidy" are both correct arguments any suggestions would be most welcome Nevil Amos MERG/ACB Monash University School of Biological Sciences > library(Geneland) Loading required package: RandomFields Loading required package: fields Loading required

I cleaned up my old benchmarking code and added checks for missing data to compare various ways of finding OLS regression coefficients. I thought I would share this for others. the long and short of it is that I would recommend ols.crossprod = function (y, x) { x <- as.matrix(x) ok <- (!is.na(y))&(!is.na(rowSums(x))) y <- y[ok]; x

Hi, this is perhaps not so much an issue, but as you are currently working on the Rd parser anyway... When you want to document specific S4 methods for an S4 generic by \S4method{} within a \usage{} environment, and the second (signature_list) argument is "long", be it because you use multiple dispatch, be it because you use long class-names, (or both), one would probably like to be

Hello, I am using R 2.11.0. I have a curious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped

Hello, I am using R 2.11.0. I have a curious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped

Dear developers, We want to use "\S4method" to document new S4-methods for "[" and "[<-". We use this for other functions/methods and it works without any problem, but in case of "[" and "[<-" we didn't manage to bring this to work. The problem occurs in the development version of our package "distrSim" which can be found

Given S4 methods [ and [<-, how do I write the Rd-file usage clause for the latter one? What I have now is: \S4method{[}{TimeSeries,TimeDate,missing}(x, i, j, ..., drop) \S4method{[<-}{TimeSeries,TimeDate,missing,ANY}(x, i, j, ..., value) which results in the following output: ## S4 method for signature 'TimeSeries, TimeDate, missing': x[i, j, ..., drop]