[R-sig-ME] R-sig-mixed-models Digest, Vol 95, Issue 21

[Mayara Amescua]

Thank you Zuur,

I'll check it all. Everything is quite new for me.

By the way, I've been reading your book, Mixed Effect Models...(2009).
It's really nice!

Regards,
Mayara

2014-11-16 9:00 GMT-02:00 <r-sig-mixed-models-request at r-project.org>:

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> Today's Topics:
>
>    1. Re: Zero-inflated and proportional data (Highland Statistics Ltd)
>    2. Openblas and lme4 (Christian Brauner)
>    3. Re: Openblas and lme4 (Douglas Bates)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 15 Nov 2014 11:33:27 +0000
> From: Highland Statistics Ltd <highstat at highstat.com>
> To: r-sig-mixed-models at r-project.org
> Subject: Re: [R-sig-ME] Zero-inflated and proportional data
> Message-ID: <54673A07.7020105 at highstat.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
>
> Yes..it is possible. You can do this in JAGS (or OpenBUGS). You can find
> JAGS code
> for a beta GLM(M) in our 'Beginner's Guide to GLM and GLMM with R".
> Extension
> to a zero inflated beta binomial can be done via the zero trick in JAGS.
> And you
> will need to find the mean and variance of a zero inflated beta GLM.
>
>
>
> Kind regards,
>
> Alain Zuur
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 15 Nov 2014 15:09:35 +0100
> From: Christian Brauner <christianvanbrauner at gmail.com>
> To: r-sig-mixed-models at r-project.org
> Subject: [R-sig-ME] Openblas and lme4
> Message-ID: <20141115140934.GA746 at gmail.com>
> Content-Type: text/plain; charset=utf-8
>
> Hello,
>
> For testing/research purposes I compiled R from source with blas as a
> shared library. I then went on to compile openblas from source, tuned it
> to Sandybridge and linked R against. The crucial step being:
>
>     cd /usr/local/lib/R/lib \
>     && mv libRblas.so libRblas.so.old \
>     && ln -s /usr/local/lib/libopenblas_sandybridgep-r0.2.12.so
> libRblas.so
>
> It worked perfectly and I see as output from /cat/pid/status:
>     Name:   R
>     State:  S (sleeping)
>     [?]
>     Threads:        4
>     [?]
>
> Tests with the Matrix library confirm that threading works and the
> increase in speed is significant for linear algebra operations such as
> solve(), chol() etc.
>
> I was wondering if lmer can make any use of this? I couldn't find a lot
> on the internet. Just some posts from R-bloggers vaguely referencing
> lme4 and some comments by Doug but I couldn't come to a conclusion
> whether lme4 will see improvements in speed at least for larger models.
> So far all my calls to lmer() on R with openblas run on a single core.
> To pinpoint whether I did something wrong during compilation or if lme4
> cannot reall profit from openblas I thought asking here might be a good
> idea.
>
> Best,
> Christian
>
>
>
>
> (For the sake of completeness: The exact compilation instructions I used
> can also be found here
>
> https://github.com/brauner/dockR/blob/master/r-patched-ivy-openblas/Dockerfile
> .
> Someone who runs an ivy- or sandybridge cpu and uses docker can also
> pull a docker image with "docker pull brauner/rblas" and check for
> himself if I did something wrong.)
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 15 Nov 2014 16:12:20 +0000
> From: Douglas Bates <bates at stat.wisc.edu>
> To: Christian Brauner <christianvanbrauner at gmail.com>,
>         r-sig-mixed-models at r-project.org
> Subject: Re: [R-sig-ME] Openblas and lme4
> Message-ID:
>         <
> CAO7JsnQ_PaT7HZbUr4A_ASuk2xWA5sTUeoqSw0V9+2FPt-r_dA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> The bulk of the linear algebra calculations in lme4 are done using the
> Eigen C++ library which does not rely on the BLAS.  Thus a multi-threaded
> BLAS will not affect lme4 speed to any great extent.  I believe that Eigen
> has its own multi-thread capabilities but it has been a while since I
> checked.
>
> On Sat Nov 15 2014 at 8:05:00 AM Christian Brauner <
> christianvanbrauner at gmail.com> wrote:
>
> > Hello,
> >
> > For testing/research purposes I compiled R from source with blas as a
> > shared library. I then went on to compile openblas from source, tuned it
> > to Sandybridge and linked R against. The crucial step being:
> >
> >     cd /usr/local/lib/R/lib \
> >     && mv libRblas.so libRblas.so.old \
> >     && ln -s /usr/local/lib/libopenblas_sandybridgep-r0.2.12.so
> > libRblas.so
> >
> > It worked perfectly and I see as output from /cat/pid/status:
> >     Name:   R
> >     State:  S (sleeping)
> >     [?]
> >     Threads:        4
> >     [?]
> >
> > Tests with the Matrix library confirm that threading works and the
> > increase in speed is significant for linear algebra operations such as
> > solve(), chol() etc.
> >
> > I was wondering if lmer can make any use of this? I couldn't find a lot
> > on the internet. Just some posts from R-bloggers vaguely referencing
> > lme4 and some comments by Doug but I couldn't come to a conclusion
> > whether lme4 will see improvements in speed at least for larger models.
> > So far all my calls to lmer() on R with openblas run on a single core.
> > To pinpoint whether I did something wrong during compilation or if lme4
> > cannot reall profit from openblas I thought asking here might be a good
> > idea.
> >
> > Best,
> > Christian
> >
> >
> >
> >
> > (For the sake of completeness: The exact compilation instructions I used
> > can also be found here
> > https://github.com/brauner/dockR/blob/master/r-patched-
> > ivy-openblas/Dockerfile.
> > Someone who runs an ivy- or sandybridge cpu and uses docker can also
> > pull a docker image with "docker pull brauner/rblas" and check for
> > himself if I did something wrong.)
> >
> > _______________________________________________
> > R-sig-mixed-models at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >
> >
>
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>
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