[R-sig-ME] rpt.remlLMM(y, groups) causes R to crash

[Ben Bolker]

On 14-06-08 04:30 PM, AvianResearchDivision wrote:
> Hi Ben,
> 
> Thank you again for the response and I apologize for my delay getting
> back to you.  I tried running the example data from 'rptR' and got my
> computer to crash by increasing npermut and nboot a bit, so it doesn't
> seem it's necessarily an issue with my data, other than the fact that my
> data might make it happen quicker.  I ran my data using rpt.anova and
> mcmc instead of remlLMM and those run fine, so who knows what is going on.
> 
> I suppose I don't know what you mean by "Do you have the same kinds of
> problems if you run from a batch file rather than from the Windows
> GUI?"  I'm not overly competent in R, so I apologize for my lack of
> understanding.
> 
> 
> Jacob

  You should be able to run a batch file by saving all of your commands
to a self-contained .R file; opening a terminal/command window and
making sure that Rscript.exe is in your path for executable files; and
then running (something like) Rscript.exe -e filename.R

http://stackoverflow.com/questions/3412911/r-exe-rcmd-exe-rscript-exe-and-rterm-exe-whats-the-difference
> 
> 
> 
> On Fri, Jun 6, 2014 at 2:00 PM, Ben Bolker <bbolker at gmail.com
> <mailto:bbolker at gmail.com>> wrote:
> 
>     On 14-06-06 12:28 PM, AvianResearchDivision wrote:
>     > Hi Ben,
>     >
>     > Thanks for the response.  I'm sorry I didn't give you the heads up
>     about
>     > r-forge.  I messed around with 'nboot' and 'npermut' by decreasing
>     from
>     > their defaults of 1000 to 10 and that allowed me to run it just
>     fine.  In
>     > general, what is the harm in straying away from these default
>     parameters?
>     >
>     > Jacob
> 
>          I don't think you've actually solved your problem this way, but you
>     have demonstrated that it's something having to do with a
>     computationally intensive workload, and not something intrinsic about
>     the code. That is, there's not something about running a single
>     bootstrap or permutation that will make your computer crash.  (The other
>     thing to try is using small values of nboot/npermut, but re-running the
>     command many times to see if you can trigger a crash.) On the other
>     hand, computer-crashing bugs are usually *not* deterministic in this way
>     -- they often depend on some haphazard or not-easily-repeatable sequence
>     of interactions with the operating system ...)
> 
>        My more basic question is whether you can make R crash by using the
>     examples with large values of nboot/npermut (in which case this is a
>     general issue) or not (in which case it seems like an interaction
>     between some quirk of your data and the software).  I haven't looked
>     into what npermut/nboot are doing, but they're presuming computing some
>     sort of simulation-based p-values/confidence intervals; if you only run
>     a small number of replicates, then your estimates will be very coarse.
>     I'm guessing that the small values of nboot/npermut in the examples are
>     there so that people aren't accidentally running long/slow jobs when
>     they try out the examples, not that these values are really recommended
>     for production use. It *might* be possible to get the same answers by
>     running a large number of commands that each run a small number of
>     permutation/bootstrap samples and then assembling them, but that's
>     likely to be tricky.
> 
>       Do you have the same kinds of problems if you run from a batch file
>     rather than from the Windows GUI?
> 
>       I *was* going to say that we do know of a few memory-access issues
>     with lme4, but now that I remember that rpt.remlLMM uses lme and not
>     lmer, I can't see why that would matter ...
> 
>       cheers
>         Ben Bolker
> 
>     >
>     >
>     > On Fri, Jun 6, 2014 at 10:54 AM, Ben Bolker <bbolker at gmail.com
>     <mailto:bbolker at gmail.com>> wrote:
>     >
>     >> On 14-06-06 10:31 AM, AvianResearchDivision wrote:
>     >>> Hi all,
>     >>>
>     >>> After running mixed models using 'lme4', I have moved on to
>     calculating
>     >>> repeatabilities using the package 'rptR' on my data set.  I have 879
>     >>> observations over 59 individuals.  I am using the calll
>     >>> rpt.remlLMM(y,groups) to obtain repeatabilities, but after about 15
>     >> seconds
>     >>> I get a error stating:
>     >>>
>     >>>  R for Windows GUI front-end has stopped working
>     >>>
>     >>> A problem caused the program to stop working correctly.  Windows
>     will
>     >> close
>     >>> the program and notify you if a solution is available.
>     >>>
>     >>>
>     >>> I am running Windows 7 with a i3 processor and 4 gb of memory so I
>     >> wouldn't
>     >>> expect this error to be computer performance related.
>     >>>
>     >>> I should note that I can run the rpt.aov(y,groups) call just
>     fine.  When
>     >>> running the following mixed model, I don't have any convergence
>     issues:
>     >>>
>     >>> lmer(Response~Predictor+(Predictor|Individual))
>     >>>
>     >>>
>     >>> Has anyone come across this issue or have any suggestions?
>     >>>
>     >>>
>     >>> Best,
>     >>> Jacob
>     >>>
>     >>
>     >>   (It would help to specify that rptR is available from r-forge:
>     it took
>     >> me a few extra minutes to dig around and find it.)
>     >>
>     >>   For what it's worth, rpt.remlLMM appears to use nlme::lme (not
>     >> lme4::lmer) internally.   There doesn't seem to be anything
>     particularly
>     >> scary in the guts of the function (e.g. no calls to compiled
>     code), so I
>     >> really haven't much of a clue.  A reproducible example would
>     probably be
>     >> helpful.  (Probably worth checking with the package maintainer as
>     well:
>     >>  maintainer("rptR")).
>     >>
>     >>   Can you run the examples in ?rpt.remlLMM successfully?  What if you
>     >> take those examples and bump up the number of permutation/bootstrap
>     >> replicates?
>     >>
>     >>   Ben Bolker
>     >>
>     >>
>     >>
>     >>
>     >>
>     >
> 
>