[R-sig-ME] predict.merMod

[Ben Bolker]

On Wed, Sep 17, 2014 at 3:22 PM, Alex Whitworth <whitworth.alex at gmail.com>
wrote:

> Dr Bolker,
>
> I tried installing the development / github version of lme4 today and ran
> into an error. R system messages copied below. Any help would be
> appreciated.
>

  I'm cc'ing this to r-sig-mixed-models in case anyone has an idea.
  In the meantime,
* I'm also posting a Windows binary of the latest development version
(today's github version), as built by CRAN's win-builder, to
http://lme4.r-forge.r-project.org/repos/ ; it will take up to 24 hours to
show up there
* I've also put a version at
http://ms.mcmaster.ca/~bolker/R/bin/windows/contrib/3.1/ , available
immediately

  You can install this under R 3.1.* with an appropriate
install.packages(...,repos=...) incantation, or download the .zip file and
install it locally.


>
> On a second note, I'm still working on my "hacked" version of the predict
> function predict.merMod2() . I've solved one of the issues I was running
> into but am still working on an issue related to the random effects for
> grouping variables that are of type factor.
>

  (What other kinds of grouping variables are there ...  ?)



> I hope to be able to solve this / put the solution on stackoverflow in the
> near-ish future.
>

  I'm hoping that the predict.merMod in the development version will solve
all your problems, or that if it doesn't you can create a small
reproducible example and I can fix it centrally.  Provide that you're not
trying to do something really weird/baroque, it makes more sense to have
the package Just Work than to have a proliferation of individual
fixes/workarounds.


>
>
>
> -------------------------------------------------------------------------------------------------------------------
> Restarting R session...
>
> > devtools::install_github("lme4","lme4")
> Installing github repo lme4/master from lme4
> Downloading master.zip from
> https://github.com/lme4/lme4/archive/master.zip
> Installing package from
> C:\Users\alewit\AppData\Local\Temp\RtmpYHOfgM/master.zip
> Installing lme4
> "C:/PROGRA~1/R/R-31~1.1/bin/x64/R" --vanilla CMD build  \
>
> "C:\Users\alewit\AppData\Local\Temp\RtmpYHOfgM\devtools138845a711f6\lme4-master"
> --no-manual  \
>   --no-resave-data
>
> * checking for file
> 'C:\Users\alewit\AppData\Local\Temp\RtmpYHOfgM\devtools138845a711f6\lme4-master/DESCRIPTION'
> ... OK
> * preparing 'lme4':
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> Warning in cleanup_pkg(pkgdir, Log) :
>   unable to run 'make clean' in 'src'
> * installing the package to build vignettes
> Warning: running command '"C:/PROGRA~1/R/R-31~1.1/bin/x64/Rcmd.exe"
> INSTALL -l "C:\Users\alewit\AppData\Local\Temp\Rtmp2ppmfo\Rinst13c46423bb3"
> --no-multiarch
> "C:/Users/alewit/AppData/Local/Temp/Rtmp2ppmfo/Rbuild13c45c0e2b4e/lme4"'
> had status 1
>       -----------------------------------
> * installing *source* package 'lme4' ...
> ** libs
> Warning: running command 'make -f "Makevars.win" -f
> "C:/PROGRA~1/R/R-31~1.1/etc/x64/Makeconf" -f
> "C:/PROGRA~1/R/R-31~1.1/share/make/winshlib.mk"
> SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)'
> SHLIB="lme4.dll" WIN=64 TCLBIN=64 OBJECTS="external.o glmFamily.o
> mcmcsamp.o optimizer.o predModule.o respModule.o"' had status 127
> ERROR: compilation failed for package 'lme4'
> * removing
> 'C:/Users/alewit/AppData/Local/Temp/Rtmp2ppmfo/Rinst13c46423bb3/lme4'
>       -----------------------------------
> ERROR: package installation failed
> Error: Command failed (1)
>

  I'm not  sure what's going on here.  Googling for "status 127" suggests
that it's a pretty generic error code, so it doesn't give a lot of clues.
Is it possible you're having permissions errors (hinted at by "unable to
run 'make clean' in 'src'"?  What happens if you try disabling vignette
building using build_vignettes=FALSE in your install_github() ?

  Are you able to install other packages from github?


> Alex Whitworth
> whitworth.alex at gmail.com
> (c) 828.429.7478
>
> On Thu, Aug 28, 2014 at 4:13 PM, Ben Bolker <bbolker at gmail.com> wrote:
>
>> On 14-08-28 06:46 PM, Alex Whitworth wrote:
>> > Dr. Bolker,
>> >
>> > Could you please take a look at the function I have posted on
>> > StackOverflow
>> > <
>> http://stackoverflow.com/questions/25538199/design-matrix-for-mlm-from-librarylme4-with-fixed-and-random-effects
>> >?
>> > I believe that it is working correctly and would appreciate your review.
>> >
>> > Thanks,
>> >
>> > Alex Whitworth
>> > whitworth.alex at gmail.com <mailto:whitworth.alex at gmail.com>
>> >
>>
>>   I saw that.  I will look at it if I have a chance.  I am
>> simultaneously impressed by your incentive and ability to solve your own
>> problems and a little bit frustrated at our inability to communicate
>> very effectively: I think your problems could probably be fixed by a
>> fairly minor adjustment to predict.merMod , which is likely better
>> tested and handles a wider range of cases.  On the other hand, if you
>> needed the solution right away ...  ( a workaround that occurred to me
>> would be to make predictions on an augmented set of new data that
>> included all of the factor levels, then throw away the ones you don't
>> want).
>>
>>   If you want to test your function thoroughly, you can try the tests
>> outlined in
>>
>> https://github.com/lme4/lme4/blob/master/tests/predsim.R
>> https://github.com/lme4/lme4/blob/master/inst/tests/test-methods.R
>> (search in this one for context("predict"))
>>
>>  By the way, getting standard errors of predictions that account
>> properly for uncertainty in the random-effects parameters is (alas) a
>> considerably harder problem ...
>>
>>   cheers
>>     Ben Bolker
>>
>>
>

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