[R-sig-ME] Question on lme4 book

[Ben Bolker]

  A short and non-can-of-worms-opening answer to "how should I cite the
lme4 package"? is to use the results of citation(package="lme4").  We
are working toward a couple of submissions for the Journal of
Statistical Software, which we hope to finish soon (!) -- at which point
we will update the package citation information so that
citation(package="lme4") reports those packages ...

  cheers
    Ben Bolker

 On 13-12-09 12:56 PM, Douglas Bates wrote:
> Yesterday Taylor Russ asked
> 
> What it the proper citation for the lme4 package and the Bates' book?
> 
>  Also, can lme4 datasets (e.g., Pastes, ScotsSec, InstEval etc.) be
>  used for illustration in publications?  Can the authors grant
>  permission or is the permission from the source needed?
> 
>  Many thanks for the package and the book.  When can I hold a
> non-digital copy in my hands?
> 
> I inadvertently deleted the message and so must respond without maintaining
> the thread.
> 
> The data sets can be used in other publications.  At least my understanding
> is that the data themselves cannot be copyright (despite the "Microsoft
> Patents 1's, 0's" headline in The Onion many years ago - for those of you
> who don't know that The Onion is a satirical newspaper, that didn't really
> occur).  It is only the representation of the data, such as a table in a
> copyright publication, that can be copyright.  I suppose I should provide
> the usual caveat, "I am (thankfully) not a lawyer".
> 
> The other lme4 authors may be able to respond to the question of citing the
> lme4 package.  I regret to say that I don't know of a good way of citing
> the book and that there won't be non-digital copies.
> 
> Partly this can be attributed to my personality - I'm good at starting
> projects but not so good at finishing them.  However, finishing the book
> would involve spending time maintaining and developing the lme4 package for
> CRAN and I have completely lost my enthusiasm for doing so.
> 
> As many of you know, I am doing most of my work in the Julia language (
> www.julialang.org) now.  R is wonderful and I enjoyed most of my time
> working on R and R packages but there are inherent limitations to R,
> particularly when trying to achieve good performance on fitting complex
> models to large data sets, that make this difficult.  It would be
> attractive to have a "pure R" implementation of mixed-models but I don't
> see a way of making it run quickly and without using a lot of memory.  In
> Julia I can build a package that achieves good performance without the need
> to interface to code written in C, C++ or Fortran - in the sense that my
> package doesn't need to require compilation of code outside of that
> provided by the language itself.
> 
> It is not surprising that the design of R is starting to show its age.
>  Although R has only been around for 15-18 years, its syntax and much of
> the semantics are based on the design of "S3" which is 25-30 years old.
> 
> R packages can include code to be compiled along with the interface code
> and there are many wonderful tools to facilitate this - such as the Rcpp
> package, the devtools package and RStudio support for these packages.  I
> used these in the compiled code underlying lme4_1.0.
> 
> But even though Dirk would describe the use of Rcpp as "seamless", in my
> experience it is not, especially if you wish to have your package available
> on CRAN.
> 
> Maintaining an Rcpp-based package on CRAN these days is a case of "no good
> deed shall go unpunished" and "the flogging will continue until morale
> improves".  I am the maintainer of the RcppEigen package which apparently
> also makes me the maintainer of an Eigen port to Solaris.  When compilers
> on Solaris report errors in code from Eigen I am supposed to fix them.
>  This is difficult in that I don't have access to any computers running
> Solaris, which is a proprietary operating system as far as I can tell, and
> Eigen is a complex code base using what is called "template
> meta-programming" in C++.  Making modifications to such code can be
> difficult.  I can't claim to fully understand all the details in Eigen and
> in Rcpp.  I am a user of these code bases, not a developer. The Eigen
> authors themselves don't test their code under Solaris because they don't
> have access to Solaris systems either and they don't regard Solaris as an
> important platform for numerical computing.  The CRAN maintainers feel
> differently, which puts me in a box.
> 
> There are days when I am tempted to say, "okay, if RcppEigen is not
> suitable for CRAN then remove it" which would result in removal of all the
> packages that depend on it, including lme4.  That may seem childish of me
> but I really don't know what else to do.
> 
> So I have reached the point of saying "goodbye" to R, Rcpp and lme4 and
> switching all of my development effort to Julia.  I'm sorry but others are
> going to need to determine how to maintain lme4 to the satisfaction of the
> CRAN maintainers or whether there should be an alternative distribution
> mechanism for R packages.
> 
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