similar to: class extension and documentation

I'm hoping that someone with deeper insight into S4 than I, that is to say virtually everyone reading this list, could help resolve the following problem in SparseM. We have setGeneric("backsolve", function(r, x, k = NULL, upper.tri = NULL, transpose = NULL, twice = TRUE, ...) standardGeneric("backsolve"), useAsDefault= function(r, x,

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 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 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 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

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

With 0.63.3, try test <- function(){ fn <- function(a) print("hello") print(is.function(fn)) print(names(formals("fn")))} test() if fn is not quoted in the last line of test, it works properly. test <- function(){ fn <- function() print("hello") formals(fn) <- alist(a=,b=) return(fn)} formals(test()) now try with line 3 of test changed to

Dear list, I have the following function, sugar = function(fun, id = "id"){ ff <- formals(fun) if( id %in% names(ff)) stop("id is part of args(fun)") formals(fun) <- c(unlist(ff), alist(id=)) fun } which one may use on a function foo, foo = function(x){ x } sugar(foo) # results in the extended closure, function (x, id) { x } Its limitation (other

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

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

Hi all, What's the official name for the value that represents a missing argument? e.g. formals(plot)$x str(formals(plot)$x) deparse(formals(plot)$x) is.symbol(formals(plot)$x) What's the correct way to create an object like this? (for example if you are manipulating the formals of a function to add an argument with no default value, as in http://stackoverflow.com/questions/3892580/).

Hi, I am trying to convert the following NLMIXED code to NLME, but am running into problems concerning 'Singularity in backsolve'. As I am new to R/S-Plus, I thought I may be missing something in the NLME code. NLMIXED *********** proc nlmixed data=kidney.kidney; parms delta=0.03 gamma=1.1 b1=-0.003 b2=-1.2 b3=0.09 b4=0.35 b5=-1.43 varu=0.5; eta=b1*age+b2*sex+b3*gn+b4*an+b5*pkn+u;

? Sat, 17 Feb 2024 11:15:43 -0700 "Reed A. Cartwright" <racartwright at gmail.com> ?????: > I'm wrapping a function in R and I want to record all the arguments > passed to it, including default values and missing values. This is hard if not impossible to implement for the general case because the default arguments are evaluated in the environment of the function as it

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

On Sat, Oct 15, 2016 at 2:00 AM, Martin Maechler <maechler at stat.math.ethz.ch> wrote: >>>>>> Michael Lawrence <lawrence.michael at gene.com> >>>>>> on Wed, 12 Oct 2016 15:21:13 -0700 writes: > > > Thanks, this was what I expected. There is a desire to > > eliminate the usage of pairlist from user code, which > >

Is there a way of getting the argument list of a function from within that function? For example, something like f <- function(x, y = 3) { fargs <- getFunctionArgList() print(fargs) ## Should be `alist(x, y = 3)' } Thanks, -roger

Hi, The R input/output after the following paragraph is from a session with version.string R version 2.4.0 Patched (2006-11-23 r39958). The last element, x$c, of x has no value and after the assignment of x to the formals of f, x$c does not become a formal argument of f. The second assignment does the job. It seems that x$c actually becomes the body of f after the first assignment. There is no

Dear all, I have the following problem. Given an expression object 'expr' containing a certain set of symbols (say 'a', 'b', 'c'), I would like to translate the expression object in an R function of, say, 'a', programmatically. Here an example of what I mean. Given: > expr <- expression(a+b+c) a call like: > asFunctionOf(expr, 'a',

Dear Group: I want to create a function having a ... argument and to have the default arguments evaluated, as thus: g <- function(a, b, ...) a+b formals(g) <- alist(a=,b=2+3,...=) g function (a, b = 2 + 3, ...) a + b But I want the default argument for b to be evaluated as 5. How can this be done? Note: My real need is for a more complex expression to be evaluated for the default

I need to find solutions to a tridiagonal system. By this I mean a set of linear equations Ax = d where A is a square matrix containing elements A[i,i-1], A[i,i] and A[i,i+1] for i in 1:nrow, and zero elsewhere. R is probably not the ideal way to do this, but this is part of a larger problem that requires R. In my application it is much easier (and much faster) to generate the diagonal and