[Rcpp-devel] Question on lme4 book

Douglas Bates bates at stat.wisc.edu
Mon Dec 9 18:56:37 CET 2013

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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