[R] Re: your mail

[Prof Brian D Ripley]

On Thu, 27 May 1999, Jonathan Myles wrote:

> I am currently preparing an R library to estimate 
> approximate posterior distributions for parameters in
> Generalised Linear Mixed Models by Gibbs Sampling
> which includes a lot of dynamically loaded C code.

If this is a version of your S glmm codes, we very much look forward to it.

> I'm pleased with the way in which it is working and am 
> now hammering out some documentation, but closer consideration
> of some R documentation has led me to worry that my code
> a) may not achieve certain standards of R and C programming
> and b) may not work on all systems. (I'm using 0.64.1
> on a UNIX system)
> 
> My worries are
> 
> a) That I've used calloc rather than S_alloc throughout.

Just use Calloc and Free: these are defined in S.h and (a) let R do the
error-checking and (b) on Windows ensures you get a malloc that can
actually free space.

> b) That I've used the following technique: I've
>    calls to different C programs held together in a single
>    file which looks like:
> 
>       GLM g;  /* information about the model */
>       OUTPUT o; /* information about the output *
> 
>       f1(g){ ....... }
>       f2(g,o) { ......}
> 
> 
> 
>     (GLM and OUTPUT are 
>     typedefs defined in a .h file)
> 
> 
>     with an R function that looks like :
>     {
>       <R statements>
> 
>       .C("f1",.....)
> 
>       <R statements>
>  
>       .C("f2",.....)       
> 
>        <R statements>
> 
>        ...
> 
>       }
>  
> and I rely on the fact that "g" and "o" remain the same between the successive
> calls (there's a C call at the end to free up all the memory).  is this:
> 
>       1) bad,
>       2) so bad (-;) that the R archive wouldn't really be interested in code
>          that worked in this way?

I am not clear about this.  Do you rely on g and o remaining the same
or their addresses remaining the same? And if the latter, you don't need
to pass g in again.  Garbage collection will move objects, but nothing
in R will alter them. So on my second reading of this, there is no
problem. You might want to try us on a more specific example.

> I *think* I can do it without using this technique, but it will need a lot
> of re-programming.  One way round it in S v5 uses the new .Call() 
> function---is anything similar on the agenda for future versions of R?
(It is S-PLUS 5.x or Sv4, I think.)

There is already a .External call for a very similar purpose.  I find
programming R internals a little easier than .Call().

> On another note, where in the library structure would be a good     
> place to put a LaTeX document describing the function and showing
> some examples?

Anything you put in inst gets installed, so I would suggest in  inst/doc.
By no means all R users have LaTeX, so give a .ps or a .pdf version too,
please.

Brian Ripley

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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