[R] Mac/PC differences in lmer results

Wed Jun 5 14:19:26 CEST 2019

To check whether the data are being read in appropriately, what happens
when you plot the distribution of each of the independent variables on
the respective systems?

-A

On Wed, 5 Jun 2019 12:32:28 +0200
Olivier Crouzet <olivier.crouzet using univ-nantes.fr> wrote:

> Hi,
> 
> 32bit vs. 64bit systems? 
> 
> Another thing I would look at would be how the windows machine will
> read the data file. Though issues should probably only arise with
> respect to text data, I've often experienced problems with reading
> unicode csv files on windows computers compared with unix-based
> computers. No guarantee though, just suggestions...
> 
> Olivier.
> 
> On Wed, 5 Jun 2019 12:15:53 +0200
> Nicolas Schuck <nico.schuck using gmail.com> wrote:
> 
> > bert: you are right, sorry for not cc-ing the list. thanks also for
> > the hint. 
> > 
> > I wanted to bring this up here again, emphasising that we do find in
> > at least one case *a very large difference* in the p value, using
> > the same scripts and data on a windows versus mac machine (see
> > reproducible example in the gitlab link posted below). I have now
> > come across several instances in which results of (g)lmer models
> > don’t agree on windows vs unix-based machines, which I find a bit
> > disturbing. any ideas where non-negligible differences could come
> > from? 
> > 
> > thanks, 
> > nico 
> > 
> >   
> > > On 30. May 2019, at 16:58, Bert Gunter <bgunter.4567 using gmail.com>
> > > wrote:
> > > 
> > > 
> > > Unless there us good reason not to, always cc the list. I have
> > > done so here.
> > > 
> > > The R Installation manual has some info on how to use different
> > > BLASes I believe, but someone with expertise (I have none) needs
> > > to respond to your queries.
> > > 
> > > On Thu, May 30, 2019 at 7:50 AM Nicolas Schuck
> > > <nico.schuck using gmail.com <mailto:nico.schuck using gmail.com>> wrote: I
> > > know that it is in use on the Mac, see sessionInfo below. I have
> > > to check on the Win system. Why would that make such a difference
> > > and how could I make the Win get the same results as the Unix
> > > Systems? 
> > > 
> > > R version 3.6.0 (2019-04-26) 
> > > Platform: x86_64-apple-darwin15.6.0 (64-bit) 
> > > Running under: macOS Mojave 10.14.5 
> > > Matrix products: default 
> > > BLAS:  /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib 
> > > LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib 
> > > Random number generation: 
> > > RNG:  Mersenne-Twister 
> > > Normal:  Inversion Sample:  Rounding 
> > > locale: [1]
> > > en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> > > attached base packages: [1] stats  graphics  grDevices utils
> > > datasets  methods  base Thanks, Nico On 30. May 2019, at 16:34,
> > > Bert Gunter <bgunter.4567 using gmail.com
> > > <mailto:bgunter.4567 using gmail.com>> wrote:
> > >   
> > >> The BLAS in use on each?
> > >> 
> > >> Bert Gunter
> > >> 
> > >> "The trouble with having an open mind is that people keep coming
> > >> along and sticking things into it."
> > >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip
> > >> )
> > >> 
> > >> 
> > >> On Thu, May 30, 2019 at 5:27 AM Nicolas Schuck
> > >> <nico.schuck using gmail.com <mailto:nico.schuck using gmail.com>> wrote:
> > >> Dear fellow R coders, 
> > >> 
> > >> I am observing differences in results obtained using glmer when
> > >> using a Mac or Linux computer versus a PC. Specifically, I am
> > >> talking about a relatively complex glmer model with a nested
> > >> random effects structure. The model is set up in the following
> > >> way: gcctrl = glmerControl(optimizer=c('nloptwrap'), optCtrl =
> > >> list (maxfun = 500000), calc.derivs = FALSE)
> > >> 
> > >> glmer_pre_instr1 = glmer(
> > >>       formula = cbind(FREQ, NSAMP-FREQ) ~ FDIST_minz + poly
> > >> (RFREQ,2) + ROI + (1 + FDIST_minz + RFREQ + ROI|ID/COL), data =
> > >> cdf_pre_instr, family = binomial, 
> > >>       control = gcctrl)
> > >> 
> > >> Code and data of an example for which I find reproducible,
> > >> non-negligible differences between Mac/Win can be found here:
> > >> https://gitlab.com/nschuck/glmer_sandbox/tree/master
> > >> <https://gitlab.com/nschuck/glmer_sandbox/tree/master>
> > >> <https://gitlab.com/nschuck/glmer_sandbox/tree/master
> > >> <https://gitlab.com/nschuck/glmer_sandbox/tree/master>> The
> > >> differences between the fitted models seem to be most pronounced
> > >> regarding the estimated correlation structure of the random
> > >> effects terms. Mac and Linux yield very similar results, but
> > >> Windows deviates quite a bit in some cases. This has a large
> > >> impact on p values obtained when performing model comparisons. I
> > >> have tried this on Mac OS 10.14, Windows 10 and Ubuntu and
> > >> Debian. All systems I have tried are using lme 1.1.21 and R
> > >> 3.5+. 
> > >> 
> > >> Does anyone have an idea what the underlying cause might be? 
> > >> 
> > >> Thanks, 
> > >> Nico 
> > >> 
> > >> 
> > >> 
> > >> 
> > >>         [[alternative HTML version deleted]]
> > >> 
> > >> ______________________________________________
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> > >> posting guide http://www.R-project.org/posting-guide.html
> > >> <http://www.r-project.org/posting-guide.html> and provide
> > >> commented, minimal, self-contained, reproducible code.  
> > 
> > 
> > 	[[alternative HTML version deleted]]
> > 
> > ______________________________________________
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> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html and provide commented,
> > minimal, self-contained, reproducible code.  
> 
> 