If you are generalizing this, the saving of the RNG information to
reproduce normally distribution random number also needs to save the
normal generator information. (This looks like an omission in
simulate.lm.) You might want to consider adding the simple functions
setRNG and getRNG from my setRNG package. Roughly, the functions make
the first ten lines of simulate.lm or Ben's code into a function call,
which may not be so important other than the missing normal information,
but having a standardized object with all the information seems to be
useful.
The package also has documentation and tests, which can be helpful for
other package builders that define simulate methods. It has been around
for a long time so has been pretty well tested.
Paul Gilbert
Martin Maechler wrote:
Thanks a lot, Heather,
"HT" == Heather Turner <heather.tur...@warwick.ac.uk>
on Fri, 13 Feb 2009 11:49:06 +0000 writes:
HT> Dear Martin,
HT> I think a simulate.glm method ought to be able to work for gnm objects
HT> too. David Firth and I started to work on this a long time ago, but
HT> stopped part-way through when simulate.lm was introduced, thinking that
HT> simulate.glm was probably in the pipeline and we were duplicating
HT> effort. Obviously we have let this slip when a contribution might have
HT> been useful. We developed a prototype for poisson, binomial, gaussian,
HT> gamma and inverse gaussian models which might be usefully merged with
HT> Ben's proposed simulate.glm. What's the best way to go about this? I
HT> would also like to test the proposed simulate.glm to check whether it
HT> will work with gnm objects or whether a simulate.gnm will be necessary.
In the mean time, private e-mail communications have started on
the subject, and yes, we are very insterested in finding
``the best'' possible way, probably making use of
Heather+David's code together with Ben's.
One alternative (not mentioned yet on R-devel), we've been
considering is to use simulate.lm() to also deal with "glm" (and
possibly "gnm") objects ``in one place''.
Martin
HT> Martin Maechler wrote:
>>>>>>> "BB" == Ben Bolker <bol...@ufl.edu>
>>>>>>> on Thu, 12 Feb 2009 11:29:14 -0500 writes:
>>
BB> I have found the "simulate" method (incorporated
BB> in some packages) very handy. As far as I can tell the
BB> only class for which simulate is actually implemented
BB> in base R is lm ... this is actually a little dangerous
BB> for a naive user who might be tempted to try
BB> simulate(X) where X is a glm fit instead, because
BB> it defaults to simulate.lm (since glm inherits from
BB> the lm class), and the answers make no sense ...
>>
BB> Here is my simulate.glm(), which is modeled on
BB> simulate.lm . It implements simulation for poisson
BB> and binomial (binary or non-binary) models, should
BB> be easy to implement others if that seems necessary.
>>
BB> I hereby request comments and suggest that it wouldn't
BB> hurt to incorporate it into base R ... (I will write
BB> docs for it if necessary, perhaps by modifying ?simulate --
BB> there is no specific documentation for simulate.lm)
>>
BB> cheers
BB> Ben Bolker
>>
>> [...............]
>>
>> Hi Ben,
>> thank you for your proposals.
>>
>> I agree that simulate.glm() has been in missing in some way,
>> till now, in particular, as, as you note, "glm" objects extend
>> "lm" ones and hence simulate(<glm>, ...) currently dispatches to
>> calling simulate.lm(....) which is only correct in the case of
>> the gaussian family.
>>
>> I have looked at your proposal a bit, already "improved" the
>> code slightly (e.g. re-include the comment you lost when you
>> ``copied'' simulate.lm(): In such cases, please work from the
>> source, not from what you get by print()ing
>> stats:::simulate.lm --- the source is either a recent tarball,
>> or the SVN repository, in this case, file
>> https://svn.r-project.org/R/trunk/src/library/stats/R/lm.R ]
>> and am planning to look at your and some own examples;
>> all with the goal to indeed include this in the R standard
>> 'stats' package in R-devel [to become R 2.9.0 in the future].
>>
>> About the help page: At the moment, I think that only a few
>> words would need to be added to the simulate help page,
>> i.e., https://svn.r-project.org/R/trunk/src/library/stats/man/simulate.Rd
>> and will be happy to receive a patch against this file.
>>
>> Thank you again, and best regards,
>> Martin Maechler, ETH Zurich
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