[Rd] writing S4 documentation

2007-12-08 Thread Ben Bolker
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I am getting horribly snarled trying to write S4 documentation. What is the best existing reference? I've been looking at help("Documentation",package="methods") (which is where R-exts points to). Does http://bioinf.wehi.edu.au/limma/Rdocs.html ex

[Rd] buglet in curve?

2007-12-08 Thread Ben Bolker
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Symptoms: curve with log x axis gets the wrong x limits (in 2.6.1, I believe introduced in this version). Credit goes to Mike McCoy for detecting the problem. Demonstration: x = 1:5 plot(x,5*exp(-x),xlim=c(0.1,1000),log="x") xvec = 10^seq(-1,3

Re: [Rd] NAMESPACE choices for exporting S4 methods

2007-12-08 Thread Jay Emerson
At Brian Ripley's request, I started putting together a minimal package to illustrate the problem (see below for my original post). As usually happens, I have stumbled on the problem: our zzz.R file contained the command: .noGenerics <- TRUE which we probably copied blindly from some example. A

Re: [Rd] suggested modification to the 'mle' documentation?

2007-12-08 Thread Luke Tierney
On Sat, 8 Dec 2007, Peter Dalgaard wrote: > Luke Tierney wrote: > > [misc snippage] >>> >>> But I'd prefer to avoid the necessity for users to manipulate the >>> environment of a function. I think the pattern >>> >>> model( f, data=d ) >> >> For working at the general likelihood I think is is

Re: [Rd] suggested modification to the 'mle' documentation?

2007-12-08 Thread Luke Tierney
On Fri, 7 Dec 2007, Ben Bolker wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Luke Tierney wrote: >> On Fri, 7 Dec 2007, Duncan Murdoch wrote: >> >> >> >> For working at the general likelihood I think is is better to >> encourage the approach of definign likelihood constructor functi

Re: [Rd] NAMESPACE choices for exporting S4 methods

2007-12-08 Thread Prof Brian Ripley
On Sat, 8 Dec 2007, Jay Emerson wrote: > We are building a package, and want to create S4 methods for both head and > mean for our own BigMatrix class. Following the recommendation in "Writing > R Extensions" we use exportMethods instead of export in NAMESPACE (this is > described as being "clear

[Rd] NAMESPACE choices for exporting S4 methods

2007-12-08 Thread Jay Emerson
We are building a package, and want to create S4 methods for both head and mean for our own BigMatrix class. Following the recommendation in "Writing R Extensions" we use exportMethods instead of export in NAMESPACE (this is described as being "clearer"). This works for head, but not for mean. Ob